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Sample records for proteins kinetic studies

  1. Kinetics and Thermodynamics of Membrane Protein Folding

    Directory of Open Access Journals (Sweden)

    Ernesto A. Roman

    2014-03-01

    Full Text Available Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

  2. Quantification of protein interaction kinetics in a micro droplet

    Energy Technology Data Exchange (ETDEWEB)

    Yin, L. L. [Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 (United States); College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044 (China); Wang, S. P., E-mail: shaopeng.wang@asu.edu, E-mail: njtao@asu.edu; Shan, X. N.; Tao, N. J., E-mail: shaopeng.wang@asu.edu, E-mail: njtao@asu.edu [Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 (United States); Zhang, S. T. [College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044 (China)

    2015-11-15

    Characterization of protein interactions is essential to the discovery of disease biomarkers, the development of diagnostic assays, and the screening for therapeutic drugs. Conventional flow-through kinetic measurements need relative large amount of sample that is not feasible for precious protein samples. We report a novel method to measure protein interaction kinetics in a single droplet with sub microliter or less volume. A droplet in a humidity-controlled environmental chamber is replacing the microfluidic channels as the reactor for the protein interaction. The binding process is monitored by a surface plasmon resonance imaging (SPRi) system. Association curves are obtained from the average SPR image intensity in the center area of the droplet. The washing step required by conventional flow-through SPR method is eliminated in the droplet method. The association and dissociation rate constants and binding affinity of an antigen-antibody interaction are obtained by global fitting of association curves at different concentrations. The result obtained by this method is accurate as validated by conventional flow-through SPR system. This droplet-based method not only allows kinetic studies for proteins with limited supply but also opens the door for high-throughput protein interaction study in a droplet-based microarray format that enables measurement of many to many interactions on a single chip.

  3. Periodic and stochastic thermal modulation of protein folding kinetics.

    Science.gov (United States)

    Platkov, Max; Gruebele, Martin

    2014-07-21

    Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude.

  4. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and ... optimization; dimerization kinetics; sensitivity analysis; stochastic simulation ... tion in large molecules and clusters, or the design ..... An unbiased strategy of allocating.

  5. Kinetics of fibrilar aggregation of food proteins

    NARCIS (Netherlands)

    Arnaudov, L.N.

    2005-01-01

    In this thesis we study the kinetics of fibrilar aggregation of two model proteins widely used in the food industry -b-lactoglobulin (b-lg) and hen

  6. Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion.

    Science.gov (United States)

    Pan, Yanbo; Cheng, Kai; Mao, Jiawei; Liu, Fangjie; Liu, Jing; Ye, Mingliang; Zou, Hanfa

    2014-10-01

    Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins.

  7. Advanced path sampling of the kinetic network of small proteins

    NARCIS (Netherlands)

    Du, W.

    2014-01-01

    This thesis is focused on developing advanced path sampling simulation methods to study protein folding and unfolding, and to build kinetic equilibrium networks describing these processes. In Chapter 1 the basic knowledge of protein structure and folding theories were introduced and a brief overview

  8. Kinetics of protein unfolding at interfaces

    International Nuclear Information System (INIS)

    Yano, Yohko F

    2012-01-01

    The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces. (topical review)

  9. Proteomic analyses for profiling regulated proteins/enzymes by Fucus vesiculosus fucoidan in B16 melanoma cells: A combination of enzyme kinetics functional study.

    Science.gov (United States)

    Wang, Zhi-Jiang; Zheng, Li; Yang, Jun-Mo; Kang, Yani; Park, Yong-Doo

    2018-06-01

    Fucoidans are complex sulfated polysaccharides that have a wide range of biological activities. Previously, we reported the various effects of Fucus vesiculosus fucoidan on tyrosinase and B16 melanoma cells. In this study, to identify fucoidan-targeted proteins in B16 melanoma cells, we performed a proteomics study and integrated enzyme kinetics. We detected 19 candidate proteins dysregulated by fucoidan treatment. Among the probed proteins, the enzyme kinetics of two candidate enzymes, namely lactate dehydrogenase (LDH) as an upregulated protein and superoxide dismutase (SOD) as a downregulated enzyme, were determined. The enzyme kinetics results showed that Fucus vesiculosus fucoidan significantly inhibited LDH catalytic function while it did not affect SOD activity even at a high dose, while only slightly decreased activity (up to 10%) at a low dose. Based on our previous and present observations, fucoidan could inhibit B16 melanoma cells growth via regulating proteins/enzymes expression levels such as LDH and SOD known as cell survival biomarkers. Interestingly, both expression level and enzyme catalytic activity of LDH were regulated by fucoidan, which could directly induce the apoptotic effect on B16 melanoma cells along with SOD downregulation. This study highlights how combining proteomics with enzyme kinetics can yield valuable insights into fucoidan targets. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. The kinetics of removal of heat-induced excess nuclear protein

    International Nuclear Information System (INIS)

    Roti, J.L.R.; Uygur, N.; Higashikubo, R.

    1984-01-01

    To investigate the role of protein content, temperature and heating time in the removal of heat-induced excess protein associated with the isolated nucleus, the kinetics of protein removal was monitored for 6 to 8 hours following exposure to 7 hyperthermic protocols. Four of these (47 0 C-7.5 min., 46 0 C-15 min., 45 0 C-30 min., and 44 0 C-60 min.) resulted in a nuclear protein content approximately twice that of nuclei from unheated cells (2.05 +- .14) following heat exposure. Three protocols (45 0 C-15 min., 44 0 C-30 min. and 43 0 C-60 min.) resulted in a nuclear protein content approximately 1.6 times normal (1.63 +- .12). If nuclear protein content were the only determinant in the recovery rate, then the same half time for nuclear protein removal would be expected within each group of protocols. Rate constants for nuclear protein removal were obtained by regression analysis. The half-time for nuclear protein removal increased with decreasing temperature and increasing heating time for the same nuclear protein content. This result suggests that the heating time and temperature are more of a determinant in the removal kinetics than protein content alone. Extended kinetics of recovery (to 36 hours) showed incomplete recovery and a secondary increase in protein associated with the isolated nucleus. These results were due to cell-cycle rearrangement (G/sub 2/ block) and unbalanced growth

  11. Amyloid protein unfolding and insertion kinetics on neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

    2010-03-01

    Atomistic details of beta-amyloid (Aβ ) protein unfolding and lipid interaction kinetics mediated by the neuronal membrane surface are important for developing new therapeutic strategies to prevent and cure Alzheimer's disease. Using all-atom MD simulations, we explored the early unfolding and insertion kinetics of 40 and 42 residue long Aβ in binary lipid mixtures with and without cholesterol that mimic the cholesterol-depleted and cholesterol-enriched lipid nanodomains of neurons. The protein conformational transition kinetics was evaluated from the secondary structure profile versus simulation time plot. The extent of membrane disruption was examined by the calculated order parameters of lipid acyl chains and cholesterol fused rings as well as the density profiles of water and lipid headgroups at defined regions across the lipid bilayer from our simulations. Our results revealed that both the cholesterol content and the length of the protein affect the protein-insertion and membrane stability in our model lipid bilayer systems.

  12. Kinetics of protein adsorption/desorption mediated by pH-responsive polymer layer

    International Nuclear Information System (INIS)

    Su Xiao-Hang; Lei Qun-Li; Ren Chun-Lai

    2015-01-01

    We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the theoretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetics of protein adsorption are verified to be well controlled by the solution pH. The kinetics and the amount of adsorbed proteins at equilibrium are greatly increased when the solution environment changes from acid to neutral. The reason is that the increased pH promotes the dissociation of the weak polyelectrolyte, resulting in more charged monomers and more stretched chains. Thus the steric repulsion within the polymer layer is weakened, which effectively lowers the barrier felt by the protein during the process of adsorption. Interestingly, we also find that the kinetics of protein desorption is almost unchanged with the variation of pH. It is because although the barrier formed by the polymer layer changes along with the change of pH, the potential at contact with the surface varies equally. Our results may provide useful insights into controllable protein adsorption/desorption in practical applications. (paper)

  13. Microphase Separation Controlled beta-Sheet Crystallization Kinetics in Fibrous Proteins

    International Nuclear Information System (INIS)

    Hu, X.; Lu, Q.; Kaplan, D.; Cebe, P.

    2009-01-01

    Silk is a naturally occurring fibrous protein with a multiblock chain architecture. As such, it has many similarities with synthetic block copolymers, including the possibility for e-sheet crystallization restricted within the crystallizable blocks. The mechanism of isothermal crystallization kinetics of e-sheet crystals in silk multiblock fibrous proteins is reported in this study. Kinetics theories, such as Avrami analysis which was established for studies of synthetic polymer crystal growth, are for the first time extended to investigate protein self-assembly in e-sheet rich Bombyx mori silk fibroin samples, using time-resolved Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and synchrotron real-time wide-angle X-ray scattering (WAXS). The Avrami exponent, n, was close to 2 for all methods and crystallization temperatures, indicating formation of e-sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in synthetic polymers. Observations by scanning electron microscopy support the view that the protein structures vary during the different stages of crystal growth, and show a microphase separation pattern after chymotrypsin enzyme biodegradation. We present a model to explain the crystallization of the multiblock silk fibroin protein, by analogy to block copolymers: crystallization of e-sheets occurs under conditions of geometrical restriction caused by phase separation of the crystallizable and uncrystallizable blocks. This crystallization model could be widely applicable in other proteins with multiblock (i.e., crystallizable and noncrystallizable) domains.

  14. Physical principles of filamentous protein self-assembly kinetics

    Science.gov (United States)

    Michaels, Thomas C. T.; Liu, Lucie X.; Meisl, Georg; Knowles, Tuomas P. J.

    2017-04-01

    The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer’s and Parkinson’s diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.

  15. Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

    Science.gov (United States)

    Finkelstein, A. V.

    1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

  16. Kinetics of protein adsorption/desorption mediated by pH-responsive polymer layer

    Science.gov (United States)

    Su, Xiao-Hang; Lei, Qun-Li; Ren, Chun-Lai

    2015-11-01

    We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the theoretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetics of protein adsorption are verified to be well controlled by the solution pH. The kinetics and the amount of adsorbed proteins at equilibrium are greatly increased when the solution environment changes from acid to neutral. The reason is that the increased pH promotes the dissociation of the weak polyelectrolyte, resulting in more charged monomers and more stretched chains. Thus the steric repulsion within the polymer layer is weakened, which effectively lowers the barrier felt by the protein during the process of adsorption. Interestingly, we also find that the kinetics of protein desorption is almost unchanged with the variation of pH. It is because although the barrier formed by the polymer layer changes along with the change of pH, the potential at contact with the surface varies equally. Our results may provide useful insights into controllable protein adsorption/desorption in practical applications. Project supported by the National Natural Science Foundation of China (Grant Nos. 21274062, 11474155, and 91027040).

  17. Enzyme kinetic characterization of protein tyrosine phosphatases

    DEFF Research Database (Denmark)

    Peters, Günther H.J.; Branner, S.; Møller, K. B.

    2003-01-01

    Protein tyrosine phosphatases (PTPs) play a central role in cellular signaling processes, resulting in an increased interest in modulating the activities of PTPs. We therefore decided to undertake a detailed enzyme kinetic evaluation of various transmembrane and cytosolic PTPs (PTPalpha, PTPbeta...

  18. Physical principles of filamentous protein self-assembly kinetics

    International Nuclear Information System (INIS)

    Michaels, Thomas C T; Liu, Lucie X; Meisl, Georg; Knowles, Tuomas P J

    2017-01-01

    The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer’s and Parkinson’s diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes. (topical review)

  19. Ligand-promoted protein folding by biased kinetic partitioning.

    Science.gov (United States)

    Hingorani, Karan S; Metcalf, Matthew C; Deming, Derrick T; Garman, Scott C; Powers, Evan T; Gierasch, Lila M

    2017-04-01

    Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems.

  20. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    Science.gov (United States)

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  1. Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles

    Science.gov (United States)

    Sreeja, K. K.; Sunil Kumar, P. B.

    2018-04-01

    The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten their aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein interactions can result in large protein clusters indicating a route to lipid mediated signal amplification. At high protein concentrations, the domains form buds similar to that seen in lipid-lipid interaction induced phase separation. Protein interaction induced domain budding is suppressed when proteins act as anisotropic inclusions and exhibit nematic orientational order. The kinetics of protein clustering and resulting conformational changes are shown to be significantly different for the isotropic and anisotropic curvature inducing proteins.

  2. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-12-15

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

  3. Kinetic variation of protein metabolism in pregnant rats

    International Nuclear Information System (INIS)

    Kubo, Katsuharu

    1980-01-01

    Kinetic variation of nitrogen metabolism in the skeletal muscle and liver of rats during the course of pregnancy was studied by the use of 15 N-amino nitrogen during acclimatization on a protein-free diet. 15 N from 15 N-glycine given on day 1 of pregnancy decreased from the 1st to 2nd trimester in the liver, suggesting contribution to the N metabolic pool. In the muscle, the rate of 15 N showed a marked decrease in the 2nd trimester, indicating, along with an increased accumulation of the total muscular N content, N accumulation in muscle protein in the 2nd trimester and promoted decomposition of mobiler muscular protein in the 2nd trimester. The marked decrease in the muscle 15 N content from the 2nd trimester and the decrease in the total N content in the 3rd trimester support the serious involvement of muscular N in fetal growth. The level of 15 N from 15 N-ammonium during the course of pregnancy was significantly high in the 2nd trimester and low in the 3rd. The 2nd trimester showed amino N accumulation in the muscle, and the 3rd, a decrease in N accumulation and amino N release. In regard to the kinetics of 15 N-lysine in the cell fraction, the muscular microsomes showed a high 15 N accumulation in the 2nd trimester and a voluminous release in the 3rd trimester. In contrast, the liver microsomes showed a linear decrease of 15 N up to 2nd trimester, followed by no change. (Chiba, N.)

  4. THE SURFACE-MEDIATED UNFOLDING KINETICS OF GLOBULAR PROTEINS IS DEPENDENT ON MOLECULAR WEIGHT AND TEMPERATURE

    Energy Technology Data Exchange (ETDEWEB)

    Patananan, A.N.; Goheen, S.C.

    2008-01-01

    The adsorption and unfolding pathways of proteins on rigid surfaces are essential in numerous complex processes associated with biomedical engineering, nanotechnology, and chromatography. It is now well accepted that the kinetics of unfolding are characterized by chemical and physical interactions dependent on protein deformability and structure, as well as environmental pH, temperature, and surface chemistry. Although this fundamental process has broad implications in medicine and industry, little is known about the mechanism because of the atomic lengths and rapid time scales involved. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the globular proteins to non-porous cationic polymer beads. The protein fractions were adsorbed at different residence times (0, 9, 10, 20, and 30 min) at near-physiological conditions using a gradient elution system similar to that in high-performance liquid chromatography. The elution profi les and retention times were obtained by ultraviolet/visible spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to irreversible protein unfolding on the non-porous surfaces. These data, and those of previous studies, fi t a positively increasing linear trend between percent unfolding after a fi xed (9 min) residence time (71.8%, 31.1%, and 32.1% of myoglobin, β-glucosidase, and ovalbumin, respectively) and molecular weight. Of all the proteins examined so far, only myoglobin deviated from this trend with higher than predicted unfolding rates. Myoglobin also exhibited an increase in retention time over a wide temperature range (0°C and 55°C, 4.39 min and 5.74 min, respectively) whereas ovalbumin and β-glucosidase did not. Further studies using a larger set of proteins are required to better understand the physiological and physiochemical implications of protein unfolding kinetics. This study confi rms that surface

  5. Is automated kinetic measurement superior to end-point for advanced oxidation protein product?

    Science.gov (United States)

    Oguz, Osman; Inal, Berrin Bercik; Emre, Turker; Ozcan, Oguzhan; Altunoglu, Esma; Oguz, Gokce; Topkaya, Cigdem; Guvenen, Guvenc

    2014-01-01

    Advanced oxidation protein product (AOPP) was first described as an oxidative protein marker in chronic uremic patients and measured with a semi-automatic end-point method. Subsequently, the kinetic method was introduced for AOPP assay. We aimed to compare these two methods by adapting them to a chemistry analyzer and to investigate the correlation between AOPP and fibrinogen, the key molecule responsible for human plasma AOPP reactivity, microalbumin, and HbA1c in patients with type II diabetes mellitus (DM II). The effects of EDTA and citrate-anticogulated tubes on these two methods were incorporated into the study. This study included 93 DM II patients (36 women, 57 men) with HbA1c levels > or = 7%, who were admitted to the diabetes and nephrology clinics. The samples were collected in EDTA and in citrate-anticoagulated tubes. Both methods were adapted to a chemistry analyzer and the samples were studied in parallel. In both types of samples, we found a moderate correlation between the kinetic and the endpoint methods (r = 0.611 for citrate-anticoagulated, r = 0.636 for EDTA-anticoagulated, p = 0.0001 for both). We found a moderate correlation between fibrinogen-AOPP and microalbumin-AOPP levels only in the kinetic method (r = 0.644 and 0.520 for citrate-anticoagulated; r = 0.581 and 0.490 for EDTA-anticoagulated, p = 0.0001). We conclude that adaptation of the end-point method to automation is more difficult and it has higher between-run CV% while application of the kinetic method is easier and it may be used in oxidative stress studies.

  6. Kinetic parameters of protein metabolism in rats during protein-free feeding

    International Nuclear Information System (INIS)

    Krawielitzki, K.; Schadereit, R.; Wuensche, J.

    1987-01-01

    16 male rats of 100 g live weight were given 50 mg of a mixture containing 15 N-labelled amino acids as a single dose within a protein-free feeding period. Following this the 15 N excretion in feces and urine as well as the development of the 15 N excess in different organs and tissues were estimated over 3 days by slaughtering the animals within given 7 time intervals. Using a 3 pool model and the computer program for the interpretation of 15 N tracer experiments by Toewe et al. (1984), kinetic parameters such as the rate of protein synthesis, protein breakdown and the rate of reutilization were calculated. Despite a negative N balance (- 41.8 mg N/d) under protein-free conditions the protein metabolism of the rat shows high dynamics characterized by a high flux rate (225 mg N/d) and a high rate of body protein synthesis (181 mg/d). The reutilization was 85 %. Depending on time the 15 N excess in the tested organs and tissues showed significant differences and seems to demonstrate that under these conditions protein synthesis mainly takes place in the most important organs (e.g. intestinal tract, liver). Under protein-free feeding conditions protein synthesis and protein breakdown of the whole body seems to be slightly increased in comparison to N balanced feeding conditions. (author)

  7. Protein Exposed Hydrophobicity Reduces the Kinetic Barrier for Adsorption of Ovalbumin to the Air-Water Interface

    NARCIS (Netherlands)

    Wierenga, P.A.; Meinders, M.B.J.; Egmond, M.R.; Voragen, F.A.G.J.; Jongh, H.H.J. de

    2003-01-01

    Using native and caprylated ovalbumin, the role of exposed hydrophobicity on the kinetics of protein adsorption to the air - water interface is studied. First, changes in the chemical properties of the protein upon caprylation were characterized followed by measurement of the changes in adsorption

  8. Protein exposed hydrophobicity reduces the kinetic barrier for adsoption of ovalbumin to the air-water interface.

    NARCIS (Netherlands)

    Wierenga, P.A.; Meinders, M.B.J.; Egmond, M.R.; Voragen, A.G.J.

    2003-01-01

    Using native and caprylated ovalbumin, the role of exposed hydrophobicity on the kinetics of protein adsorption to the air-water interface is studied. First, changes in the chemical properties of the protein upon caprylation were characterized followed by measurement of the changes in adsorption

  9. Kinetic Stability of Proteins in Beans and Peas: Implications for Protein Digestibility, Seed Germination, and Plant Adaptation.

    Science.gov (United States)

    Xia, Ke; Pittelli, Sandy; Church, Jennifer; Colón, Wilfredo

    2016-10-12

    Kinetically stable proteins (KSPs) are resistant to the denaturing detergent sodium dodecyl sulfate (SDS). Such resilience makes KSPs resistant to proteolytic degradation and may have arisen in nature as a mechanism for organismal adaptation and survival against harsh conditions. Legumes are well-known for possessing degradation-resistant proteins that often diminish their nutritional value. Here we applied diagonal two-dimensional (D2D) SDS-polyacrylamide gel electrophoresis (PAGE), a method that allows for the proteomics-level identification of KSPs, to a group of 12 legumes (mostly beans and peas) of agricultural and nutritional importance. Our proteomics results show beans that are more difficult to digest, such as soybean, lima beans, and various common beans, have high contents of KSPs. In contrast, mung bean, red lentil, and various peas that are highly digestible contain low amounts of KSPs. Identified proteins with high kinetic stability are associated with warm-season beans, which germinate at higher temperatures. In contrast, peas and red lentil, which are cool-season legumes, contain low levels of KSPs. Thus, our results show protein kinetic stability is an important factor in the digestibility of legume proteins and may relate to nutrition efficiency, timing of seed germination, and legume resistance to biotic stressors. Furthermore, we show D2D SDS-PAGE is a powerful method that could be applied for determining the abundance and identity of KSPs in engineered and wild legumes and for advancing basic research and associated applications.

  10. Effective computation of stochastic protein kinetic equation by reducing stiffness via variable transformation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lijin, E-mail: ljwang@ucas.ac.cn [School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049 (China)

    2016-06-08

    The stochastic protein kinetic equations can be stiff for certain parameters, which makes their numerical simulation rely on very small time step sizes, resulting in large computational cost and accumulated round-off errors. For such situation, we provide a method of reducing stiffness of the stochastic protein kinetic equation by means of a kind of variable transformation. Theoretical and numerical analysis show effectiveness of this method. Its generalization to a more general class of stochastic differential equation models is also discussed.

  11. Energy and Protein Supplementation Does Not Affect Protein and Amino Acid Kinetics or Pregnancy Outcomes in Underweight Indian Women.

    Science.gov (United States)

    Dwarkanath, Pratibha; Hsu, Jean W; Tang, Grace J; Anand, Pauline; Thomas, Tinku; Thomas, Annamma; Sheela, C N; Kurpad, Anura V; Jahoor, Farook

    2016-02-01

    In India, the prevalence of low birth weight is high in women with a low body mass index (BMI), suggesting that underweight women are not capable of providing adequate energy and protein for fetal growth. Furthermore, as pregnancy progresses, there is increased need to provide methyl groups for methylation reactions associated with the synthesis of new proteins and, unlike normal-BMI American women, low-BMI Indian women are unable to increase methionine transmethylation and remethylation rates as pregnancy progresses from trimester 1 to 3. This also negatively influences birth weight. The aim was to determine the effect of dietary supplementation with energy and protein from 12 ± 1 wk of gestation to time of delivery compared with no supplement on pregnancy outcomes, protein kinetics, and the fluxes of the methyl group donors serine and glycine. Protein kinetics and serine and glycine fluxes were measured by using standard stable isotope tracer methods in the fasting and postprandial states in 24 pregnant women aged 22.9 ± 0.7 y with low BMIs [BMI (in kg/m(2)) ≤18.5] at 12 ± 1 wk (trimester 1) and 30 ± 1 wk (trimester 3) of gestation. After the first measurement, subjects were randomly assigned to either receive the supplement (300 kcal/d, 15 g protein/d) or no supplement. Supplementation had no significant effect on any variable of pregnancy outcome, and except for fasting state decreases in leucine flux (125 ± 7.14 compared with 113 ± 5.06 μmol ⋅ kg(-1) ⋅ h(-1); P = 0.04) and nonoxidative disposal (110 ± 6.97 compared with 101 ± 3.69 μmol ⋅ kg(-1) ⋅ h(-1); P = 0.02) from trimesters 1 to 3, it had no effect on any other leucine kinetic variable or urea, glycine, and serine fluxes. We conclude that in Indian women with a low BMI, supplementation with energy and protein from week 12 of pregnancy to time of delivery does not improve pregnancy outcome, whole-body protein kinetics, or serine and glycine fluxes. © 2016 American Society for Nutrition.

  12. Kinetic studies of the yeast His-Asp phosphorelay signaling pathway

    Science.gov (United States)

    Kaserer, Alla O.; Andi, Babak; Cook, Paul F.; West, Ann H.

    2010-01-01

    For both prokaryotic and eukaryotic His-Asp phosphorelay signaling pathways, the rates of protein phosphorylation and dephosphorylation determine the stimulus-to-response time frame. Thus, kinetic studies of phosphoryl group transfer between signaling partners are important for gaining a full understanding of how the system is regulated. In many cases, the phosphotransfer reactions are too fast for rates to be determined by manual experimentation. Rapid quench flow techniques thus provide a powerful method for studying rapid reactions that occur in the millisecond time frame. In this chapter, we describe experimental design and procedures for kinetic characterization of the yeast SLN1-YPD1-SSK1 osmoregulatory phosphorelay system using a rapid quench flow kinetic instrument. PMID:20946842

  13. Equilibrium amide hydrogen exchange and protein folding kinetics

    International Nuclear Information System (INIS)

    Bai Yawen

    1999-01-01

    The classical Linderstrom-Lang hydrogen exchange (HX) model is extended to describe the relationship between the HX behaviors (EX1 and EX2) and protein folding kinetics for the amide protons that can only exchange by global unfolding in a three-state system including native (N), intermediate (I), and unfolded (U) states. For these slowly exchanging amide protons, it is shown that the existence of an intermediate (I) has no effect on the HX behavior in an off-pathway three-state system (I↔U↔N). On the other hand, in an on-pathway three-state system (U↔I↔N), the existence of a stable folding intermediate has profound effect on the HX behavior. It is shown that fast refolding from the unfolded state to the stable intermediate state alone does not guarantee EX2 behavior. The rate of refolding from the intermediate state to the native state also plays a crucial role in determining whether EX1 or EX2 behavior should occur. This is mainly due to the fact that only amide protons in the native state are observed in the hydrogen exchange experiment. These new concepts suggest that caution needs to be taken if one tries to derive the kinetic events of protein folding from equilibrium hydrogen exchange experiments

  14. Low thermodynamic but high kinetic stability of an antifreeze protein from Rhagium mordax

    DEFF Research Database (Denmark)

    Friis, Dennis Steven; Johnsen, Johannes Lørup; Kristiansen, Erlend

    2014-01-01

    The equilibrium heat stability and the kinetic heat tolerance of a recombinant antifreeze protein (AFP) from the beetle Rhagium mordax (RmAFP1) are studied through differential scanning calorimetry and circular dichroism spectroscopy. In contrast to other insect AFPs studied with this respect......, the RmAFP1 has only one disulfide bridge. The melting temperature, Tm, of the protein is determined to be 28.5°C (pH 7.4), which is much lower than most of those reported for AFPs or globular proteins in general. Despite its low melting temperature, both biophysical and activity measurements show...

  15. Kinetic catalytic studies of scorpion's hemocyanin

    International Nuclear Information System (INIS)

    Queinnec, E.; Vuillaume, M.; Gardes-Albert, M.; Ferradini, C.; Ducancel, F.

    1991-01-01

    Hemocyanins are copper proteins which function as oxygen carriers in the haemolymph of Molluscs and Arthropods. They possess enzymatic properties: peroxidatic and catalatic activities, although they have neither iron nor porphyrin ring at the active site. The kinetics of the catalytic reaction is described. The reaction of superoxide anion with hemocyanin has been studied using pulse radiolysis at pH 9. The catalytic rate constant is 3.5 X 10 7 mol -1 .l.s -1 [fr

  16. Lipo-Protein Emulsion Structure in the Diet Affects Protein Digestion Kinetics, Intestinal Mucosa Parameters and Microbiota Composition.

    Science.gov (United States)

    Oberli, Marion; Douard, Véronique; Beaumont, Martin; Jaoui, Daphné; Devime, Fabienne; Laurent, Sandy; Chaumontet, Catherine; Mat, Damien; Le Feunteun, Steven; Michon, Camille; Davila, Anne-Marie; Fromentin, Gilles; Tomé, Daniel; Souchon, Isabelle; Leclerc, Marion; Gaudichon, Claire; Blachier, François

    2018-01-01

    Food structure is a key factor controlling digestion and nutrient absorption. We test the hypothesis that protein emulsion structure in the diet may affect digestive and absorptive processes. Rats (n = 40) are fed for 3 weeks with two diets chemically identical but based on lipid-protein liquid-fine (LFE) or gelled-coarse (GCE) emulsions that differ at the macro- and microstructure levels. After an overnight fasting, they ingest a 15 N-labeled LFE or GCE test meal and are euthanized 0, 15 min, 1 h, and 5 h later. 15 N enrichment in intestinal contents and blood are measured. Gastric emptying, protein digestion kinetics, 15 N absorption, and incorporation in blood protein and urea are faster with LFE than GCE. At 15 min time point, LFE group shows higher increase in GIP portal levels than GCE. Three weeks of dietary adaptation leads to higher expression of cationic amino acid transporters in ileum of LFE compared to GCE. LFE diet raises cecal butyrate and isovalerate proportion relative to GCE, suggesting increased protein fermentation. LFE diet increases fecal Parabacteroides relative abundance but decreases Bifidobacterium, Sutterella, Parasutterella genera, and Clostridium cluster XIV abundance. Protein emulsion structure regulates digestion kinetics and gastrointestinal physiology, and could be targeted to improve food health value. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Biomarker kinetics in the prediction of VAP diagnosis: results from the BioVAP study

    NARCIS (Netherlands)

    Póvoa, Pedro; Martin-Loeches, Ignacio; Ramirez, Paula; Bos, Lieuwe D.; Esperatti, Mariano; Silvestre, Joana; Gili, Gisela; Goma, Gema; Berlanga, Eugenio; Espasa, Mateu; Gonçalves, Elsa; Torres, Antoni; Artigas, Antonio

    2016-01-01

    Prediction of diagnosis of ventilator-associated pneumonia (VAP) remains difficult. Our aim was to assess the value of biomarker kinetics in VAP prediction. We performed a prospective, multicenter, observational study to evaluate predictive accuracy of biomarker kinetics, namely C-reactive protein

  18. An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates

    International Nuclear Information System (INIS)

    Gal, Maayan; Kern, Thomas; Schanda, Paul; Frydman, Lucio; Brutscher, Bernhard

    2009-01-01

    Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1 H- 15 N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds

  19. Real-time Kinetics of High-mobility Group Box 1 (HMGB1) Oxidation in Extracellular Fluids Studied by in Situ Protein NMR Spectroscopy*

    Science.gov (United States)

    Zandarashvili, Levani; Sahu, Debashish; Lee, Kwanbok; Lee, Yong Sun; Singh, Pomila; Rajarathnam, Krishna; Iwahara, Junji

    2013-01-01

    Some extracellular proteins are initially secreted in reduced forms via a non-canonical pathway bypassing the endoplasmic reticulum and become oxidized in the extracellular space. One such protein is HMGB1 (high-mobility group box 1). Extracellular HMGB1 has different redox states that play distinct roles in inflammation. Using a unique NMR-based approach, we have investigated the kinetics of HMGB1 oxidation and the half-lives of all-thiol and disulfide HMGB1 species in serum, saliva, and cell culture medium. In this approach, salt-free lyophilized 15N-labeled all-thiol HMGB1 was dissolved in actual extracellular fluids, and the oxidation and clearance kinetics were monitored in situ by recording a series of heteronuclear 1H-15N correlation spectra. We found that the half-life depends significantly on the extracellular environment. For example, the half-life of all-thiol HMGB1 ranged from ∼17 min (in human serum and saliva) to 3 h (in prostate cancer cell culture medium). Furthermore, the binding of ligands (glycyrrhizin and heparin) to HMGB1 significantly modulated the oxidation kinetics. Thus, the balance between the roles of all-thiol and disulfide HMGB1 proteins depends significantly on the extracellular environment and can also be artificially modulated by ligands. This is important because extracellular HMGB1 has been suggested as a therapeutic target for inflammatory diseases and cancer. Our work demonstrates that the in situ protein NMR approach is powerful for investigating the behavior of proteins in actual extracellular fluids containing an enormous number of different molecules. PMID:23447529

  20. A KINETIC MODEL FOR MONO-LAYER GLOBULAR PROTEIN ADSORPTION ON SOLID/LIQUID INTERFACES

    Directory of Open Access Journals (Sweden)

    Kamal I. M. Al-Malah

    2012-12-01

    Full Text Available A kinetic model was derived for globular protein adsorption. The model takes into account the three possible scenarios of a protein molecule in solution, being exposed to an interface: adsorption step from the solution to the interface; the possible desorption back into the solution; and the surface-induced unfolding or spreading of the protein unto the substrate surface. A globular protein molecule is visualized as a sphere with radius D. In addition to the general case of protein adsorption, which portrays either the surface coverage (Theta or surface concentration (� as a function of the adsorption time, special cases, like equilibrium condition, lowsurface coverage, irreversible, and Langmuirian were also presented and treated in light of the derived model. The general model was simplified for each of the subset cases. The irreversibility versus reversibility of protein adsorption was discussed. The substrate surface energetics or effects are accounted for via the proposition of the percent relative change in D/V ratio for the adsorbing protein, called (D/VPRC parameter. (D/VPRC is calculated with respect to the monolayer surface concentration of protein, where the latter is given by D/Vratio. This can be used as a landmark to protein adsorption isotherms or even kinetics. This is visualized as an indicator for solid substrate effects on the adsorbing proteins. (D/VPRC can be zero (fresh monolayer, negative (aged monolayer, or positive (multi-layer. The reference surface concentration is reported for some selected proteins.

  1. Effect of burn and first-pass splanchnic leucine extraction on protein kinetics in rats

    International Nuclear Information System (INIS)

    Karlstad, M.D.; DeMichele, S.J.; Istfan, N.; Blackburn, G.L.; Bistrian, B.R.

    1988-01-01

    The effects of burn and first-pass splanchnic leucine extraction (FPE) on protein kinetics and energy expenditure were assessed by measuring O 2 consumption, CO 2 production, nitrogen balance, leucine kinetics, and tissue fractional protein synthetic rates (FSR-%/day) in enterally fed rats. Anesthetized male rats (200 g) were scalded on their dorsum with boiling water (25-30% body surface area) and enterally fed isovolemic diets that provided 60 kcal/day and 2.4 g of amino acids/day for 3 days. Controls were not burned. An intravenous or intragastric infusion of L-[1- 14 C]leucine was used to assess protein kinetics on day 3. FPE was taken as the ratio of intragastric to intravenous plasma leucine specific activity. There was a 69% reduction in cumulative nitrogen balance (P less than 0.001) and a 17-19% increase in leucine oxidation (P less than 0.05) and total energy expenditure (P less than 0.01) in burned rats. A 15% decrease in plasma leucine clearance (P less than 0.05) was accompanied by a 20% increase in plasma [leucine] (P less than 0.01) in burned rats. Burn decreased rectus muscle FSR from 5.0 +/- 0.4 to 3.5 +/- 0.5 (P less than 0.05) and increased liver FSR from 19.0 +/- 0.5 to 39.2 +/- 3.4 (P less than 0.01). First pass extraction of dietary leucine by the splanchnic bed was 8% in controls and 26% in burned rats. Leucine kinetics corrected for FPE showed increased protein degradation with burn that was not evident without FPE correction. This hypermetabolic burn model can be useful in the design of enteral diets that optimize rates of protein synthesis and degradation

  2. A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction.

    Science.gov (United States)

    Li, Ying; Xu, Fei; Liu, Chao; Xu, Youzhi; Feng, Xiaojun; Liu, Bi-Feng

    2013-08-21

    Kinetic measurement of biomacromolecular interaction plays a significant role in revealing the underlying mechanisms of cellular activities. Due to the small diffusion coefficient of biomacromolecules, it is difficult to resolve the rapid kinetic process with traditional analytical methods such as stopped-flow or laminar mixers. Here, we demonstrated a unique continuous-flow laminar mixer based on microfluidic dual-hydrodynamic focusing to characterize the kinetics of DNA-protein interactions. The time window of this mixer for kinetics observation could cover from sub-milliseconds to seconds, which made it possible to capture the folding process with a wide dynamic range. Moreover, the sample consumption was remarkably reduced to <0.55 μL min⁻¹, over 1000-fold saving in comparison to those reported previously. We further interrogated the interaction kinetics of G-quadruplex and the single-stranded DNA binding protein, indicating that this novel micromixer would be a useful approach for analyzing the interaction kinetics of biomacromolecules.

  3. Metabolic Turnover of Synaptic Proteins: Kinetics, Interdependencies and Implications for Synaptic Maintenance

    Science.gov (United States)

    Cohen, Laurie D.; Zuchman, Rina; Sorokina, Oksana; Müller, Anke; Dieterich, Daniela C.; Armstrong, J. Douglas; Ziv, Tamar; Ziv, Noam E.

    2013-01-01

    Chemical synapses contain multitudes of proteins, which in common with all proteins, have finite lifetimes and therefore need to be continuously replaced. Given the huge numbers of synaptic connections typical neurons form, the demand to maintain the protein contents of these connections might be expected to place considerable metabolic demands on each neuron. Moreover, synaptic proteostasis might differ according to distance from global protein synthesis sites, the availability of distributed protein synthesis facilities, trafficking rates and synaptic protein dynamics. To date, the turnover kinetics of synaptic proteins have not been studied or analyzed systematically, and thus metabolic demands or the aforementioned relationships remain largely unknown. In the current study we used dynamic Stable Isotope Labeling with Amino acids in Cell culture (SILAC), mass spectrometry (MS), Fluorescent Non–Canonical Amino acid Tagging (FUNCAT), quantitative immunohistochemistry and bioinformatics to systematically measure the metabolic half-lives of hundreds of synaptic proteins, examine how these depend on their pre/postsynaptic affiliation or their association with particular molecular complexes, and assess the metabolic load of synaptic proteostasis. We found that nearly all synaptic proteins identified here exhibited half-lifetimes in the range of 2–5 days. Unexpectedly, metabolic turnover rates were not significantly different for presynaptic and postsynaptic proteins, or for proteins for which mRNAs are consistently found in dendrites. Some functionally or structurally related proteins exhibited very similar turnover rates, indicating that their biogenesis and degradation might be coupled, a possibility further supported by bioinformatics-based analyses. The relatively low turnover rates measured here (∼0.7% of synaptic protein content per hour) are in good agreement with imaging-based studies of synaptic protein trafficking, yet indicate that the metabolic load

  4. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

    Science.gov (United States)

    Rajabi, Khadijeh

    2015-01-01

    A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

  5. Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

    Science.gov (United States)

    Bandyopadhyay, Pradipta; Kuntz, Irwin D

    2009-01-01

    The determination of protein structure using distance constraints is a new and promising field of study. One implementation involves attaching residues of a protein using a cross-linking agent, followed by protease digestion, analysis of the resulting peptides by mass spectroscopy, and finally sequence threading to detect the protein folds. In the present work, we carry out computational modeling of the kinetics of cross-linking reactions in proteins using the master equation approach. The rate constants of the cross-linking reactions are estimated using the pKas and the solvent-accessible surface areas of the residues involved. This model is tested with fibroblast growth factor (FGF) and cytochrome C. It is consistent with the initial experimental rate data for individual lysine residues for cytochrome C. Our model captures all observed cross-links for FGF and almost 90% of the observed cross-links for cytochrome C, although it also predicts cross-links that were not observed experimentally (false positives). However, the analysis of the false positive results is complicated by the fact that experimental detection of cross-links can be difficult and may depend on specific experimental conditions such as pH, ionic strength. Receiver operator characteristic plots showed that our model does a good job in predicting the observed cross-links. Molecular dynamics simulations showed that for cytochrome C, in general, the two lysines come closer for the observed cross-links as compared to the false positive ones. For FGF, no such clear pattern exists. The kinetic model and MD simulation can be used to study proposed cross-linking protocols.

  6. Structure–kinetic relationship study of CDK8/CycC specific compounds

    Science.gov (United States)

    Schneider, Elisabeth V.; Böttcher, Jark; Huber, Robert; Maskos, Klaus; Neumann, Lars

    2013-01-01

    In contrast with the very well explored concept of structure–activity relationship, similar studies are missing for the dependency between binding kinetics and compound structure of a protein ligand complex, the structure–kinetic relationship. Here, we present a structure–kinetic relationship study of the cyclin-dependent kinase 8 (CDK8)/cyclin C (CycC) complex. The scaffold moiety of the compounds is anchored in the kinase deep pocket and extended with diverse functional groups toward the hinge region and the front pocket. These variations can cause the compounds to change from fast to slow binding kinetics, resulting in an improved residence time. The flip of the DFG motif (“DMG” in CDK8) to the inactive DFG-out conformation appears to have relatively little influence on the velocity of binding. Hydrogen bonding with the kinase hinge region contributes to the residence time but has less impact than hydrophobic complementarities within the kinase front pocket. PMID:23630251

  7. Glutamic Acid as Enhancer of Protein Synthesis Kinetics in Hepatocytes from Old Rats.

    Science.gov (United States)

    Brodsky, V Y; Malchenko, L A; Butorina, N N; Lazarev Konchenko, D S; Zvezdina, N D; Dubovaya, T K

    2017-08-01

    Dense cultures of hepatocytes from old rats (~2 years old, body weight 530-610 g) are different from similar cultures of hepatocytes from young rats by the low amplitude of protein synthesis rhythm. Addition of glutamic acid (0.2, 0.4, or 0.6 mg/ml) into the culture medium with hepatocytes of old rats resulted in increase in the oscillation amplitudes of the protein synthesis rhythm to the level of young rats. A similar action of glutamic acid on the protein synthesis kinetics was observed in vivo after feeding old rats with glutamic acid. Inhibition of metabotropic receptors of glutamic acid with α-methyl-4-carboxyphenylglycine (0.01 mg/ml) abolished the effect of glutamic acid. The amplitude of oscillation of the protein synthesis rhythm in a cell population characterizes synchronization of individual oscillations caused by direct cell-cell communications. Hence, glutamic acid, acting as a receptor-dependent transmitter, enhanced direct cell-cell communications of hepatocytes that were decreased with aging. As differentiated from other known membrane signaling factors (gangliosides, norepinephrine, serotonin, dopamine), glutamic acid can penetrate into the brain and thus influence the communications and protein synthesis kinetics that are disturbed with aging not only in hepatocytes, but also in neurons.

  8. Heparin kinetics

    International Nuclear Information System (INIS)

    Swart, C.A.M. de.

    1983-01-01

    The author has studied the kinetics of heparin and heparin fractions after intravenous administration in humans and in this thesis the results of this study are reported. Basic knowledge about the physico-chemical properties of heparin and its interactions with proteins resulting in anticoagulant and lipolytic effects are discussed in a review (chapter II), which also comprises some clinical aspects of heparin therapy. In chapter III the kinetics of the anticoagulant effect are described after intravenous administration of five commercial heparin preparations. A mathematical model is presented that fits best to these kinetics. The kinetics of the anticoagulant and lipolytic effects after intravenous injection of various 35 S-radiolabelled heparin fractions and their relationship with the disappearance of the radiolabel are described in chapter IV. Chapter V gives a description of the kinetics of two radiolabels after injection of in vitro formed complexes consisting of purified, 125 I-radiolabelled antithrombin III and various 35 S-radiolabelled heparin fractions. (Auth.)

  9. A calorimetric study of solute effects on the kinetic stability of a-amylase

    DEFF Research Database (Denmark)

    Olsen, Søren Nymand; Andersen, Kim Bruno; Øgendal, Lars Holm

    2009-01-01

    In this study we evaluated the applications of isothermal titration calorimetry (ITC) to Study solute effects on the kinetics of irreversible protein denaturation. More specifically, denaturation of Bacillus Halmapalus alpha-amylase (BHA) was initiated by addition of EDTA to the calorimetric cell...

  10. A study of whole body protein kinetics in malnourished children with persistent diarrhea: A double blind trial of zinc supplementation

    International Nuclear Information System (INIS)

    Bhutta, Z.A.; Nizami, S.Q.; Hardy, S.; Hendricks, K.

    1996-01-01

    Persistent diarrhoea (PD) is globally recognized as a major cause of childhood morbidity and mortality. PD is closely associated with malnutrition and nutrition rehabilitation especially domiciliary dietary therapy posses a therapeutic challenge. While there has been success in managing such children with locally home available traditional diets, there has been concern with the potential of associated micronutrient especially zinc deficiency. We are evaluating the impact of zinc supplementation of a traditional rice-lentil (khitchri) and yogurt diet in malnourished children with PD in randomized double blind study. In addition to the impact on weight gain, stool output and body composition, we will evaluate whole body protein kinetics using the modified CRP protocol [employing 15 N-glycine, H 13 Co 3 and 1- 13 C leucine]. We will also estimate the effect of coexisting illnesses, especially febrile episodes on nutritional recovery and protein metabolism. (author). 20 refs, 5 figs, 1 tab

  11. Estimation of lymphatic conductance. A model based on protein-kinetic studies and haemodynamic measurements in patients with cirrhosis of the liver and in pigs

    DEFF Research Database (Denmark)

    Henriksen, Jens Henrik Sahl

    1985-01-01

    A model of lymphatic conductivity (i.e. flow rate per unit pressure difference = conductance) based on protein-kinetic and haemodynamic measurements is described. The model is applied to data from patients with cirrhosis and from pigs with different haemodynamic abnormalities in the hepatosplanch......A model of lymphatic conductivity (i.e. flow rate per unit pressure difference = conductance) based on protein-kinetic and haemodynamic measurements is described. The model is applied to data from patients with cirrhosis and from pigs with different haemodynamic abnormalities...... compatible with increased sinusoidal wall tightening and fibrosis in the interstitial space of the liver. The model presented supports the so-called 'lymph-imbalance' theory of ascites formation according to which a relatively insufficient lymph drainage is important in the pathogenesis of hepatic ascites....

  12. Ingestion of Casein in a Milk Matrix Modulates Dietary Protein Digestion and Absorption Kinetics but Does Not Modulate Postprandial Muscle Protein Synthesis in Older Men.

    Science.gov (United States)

    Churchward-Venne, Tyler A; Snijders, Tim; Linkens, Armand M A; Hamer, Henrike M; van Kranenburg, Janneau; van Loon, Luc J C

    2015-07-01

    The slow digestion and amino acid absorption kinetics of isolated micellar casein have been held responsible for its relatively lower postprandial muscle protein synthetic response compared with rapidly digested proteins such as isolated whey. However, casein is normally consumed within a milk matrix. We hypothesized that protein digestion and absorption kinetics and the subsequent muscle protein synthetic response after micellar casein ingestion are modulated by the milk matrix. The aim of this study was to determine the impact of a milk matrix on casein protein digestion and absorption kinetics and postprandial muscle protein synthesis in older men. In a parallel-group design, 32 healthy older men (aged 71 ± 1 y) received a primed continuous infusion of L-[ring-(2)H5]-phenylalanine, L-[ring-3,5-(2)H2]-tyrosine, and L-[1-(13)C]-leucine, and ingested 25 g intrinsically L-[1-(13)C]-phenylalanine and L-[1-(13)C]-leucine labeled casein dissolved in bovine milk serum (Cas+Serum) or water (Cas). Plasma samples and muscle biopsies were collected in the postabsorptive state and for 300 min in the postprandial period to examine whole-body and skeletal muscle protein metabolism. Casein ingestion increased plasma leucine and phenylalanine concentrations and L-[1-(13)C]-phenylalanine enrichments, with a more rapid rise after Cas vs. Cas+Serum. Nonetheless, dietary protein-derived phenylalanine availability did not differ between Cas+Serum (47 ± 2%, mean ± SEM) and Cas (46 ± 3%) when assessed over the 300-min postprandial period (P = 0.80). The milk matrix did not modulate postprandial myofibrillar protein synthesis rates from 0 to 120 min (0.038 ± 0.005 vs. 0.031 ± 0.007%/h) or from 120 to 300 min (0.052 ± 0.004 vs. 0.067 ± 0.005%/h) after Cas+Serum vs. Cas. Similarly, no treatment differences in muscle protein-bound L-[1-(13)C]-phenylalanine enrichments were observed at 120 min (0.003 ± 0.001 vs. 0.002 ± 0.001) or 300 min (0.015 ± 0.002 vs. 0.016 ± 0.002 mole

  13. Recruitment kinetics of DNA repair proteins Mdc1 and Rad52 but not 53BP1 depend on damage complexity.

    Directory of Open Access Journals (Sweden)

    Volker Hable

    Full Text Available The recruitment kinetics of double-strand break (DSB signaling and repair proteins Mdc1, 53BP1 and Rad52 into radiation-induced foci was studied by live-cell fluorescence microscopy after ion microirradiation. To investigate the influence of damage density and complexity on recruitment kinetics, which cannot be done by UV laser irradiation used in former studies, we utilized 43 MeV carbon ions with high linear energy transfer per ion (LET = 370 keV/µm to create a large fraction of clustered DSBs, thus forming complex DNA damage, and 20 MeV protons with low LET (LET = 2.6 keV/µm to create mainly isolated DSBs. Kinetics for all three proteins was characterized by a time lag period T(0 after irradiation, during which no foci are formed. Subsequently, the proteins accumulate into foci with characteristic mean recruitment times τ(1. Mdc1 accumulates faster (T(0 = 17 ± 2 s, τ(1 = 98 ± 11 s than 53BP1 (T(0 = 77 ± 7 s, τ(1 = 310 ± 60 s after high LET irradiation. However, recruitment of Mdc1 slows down (T(0 = 73 ± 16 s, τ(1 = 1050 ± 270 s after low LET irradiation. The recruitment kinetics of Rad52 is slower than that of Mdc1, but exhibits the same dependence on LET. In contrast, the mean recruitment time τ(1 of 53BP1 remains almost constant when varying LET. Comparison to literature data on Mdc1 recruitment after UV laser irradiation shows that this rather resembles recruitment after high than low LET ionizing radiation. So this work shows that damage quality has a large influence on repair processes and has to be considered when comparing different studies.

  14. Structural and kinetic analysis of the unnatural fusion protein 4-coumaroyl-CoA ligase::stilbene synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yechun; Yi, Hankuil; Wang, Melissa; Yu, Oliver; Jez, Joseph M. (WU); (Danforth)

    2012-10-24

    To increase the biochemical efficiency of biosynthetic systems, metabolic engineers have explored different approaches for organizing enzymes, including the generation of unnatural fusion proteins. Previous work aimed at improving the biosynthesis of resveratrol, a stilbene associated a range of health-promoting activities, in yeast used an unnatural engineered fusion protein of Arabidopsis thaliana (thale cress) 4-coumaroyl-CoA ligase (At4CL1) and Vitis vinifera (grape) stilbene synthase (VvSTS) to increase resveratrol levels 15-fold relative to yeast expressing the individual enzymes. Here we present the crystallographic and biochemical analysis of the 4CL::STS fusion protein. Determination of the X-ray crystal structure of 4CL::STS provides the first molecular view of an artificial didomain adenylation/ketosynthase fusion protein. Comparison of the steady-state kinetic properties of At4CL1, VvSTS, and 4CL::STS demonstrates that the fusion protein improves catalytic efficiency of either reaction less than 3-fold. Structural and kinetic analysis suggests that colocalization of the two enzyme active sites within 70 {angstrom} of each other provides the basis for enhanced in vivo synthesis of resveratrol.

  15. Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.

    Science.gov (United States)

    Bernstein, Rachel; Schmidt, Kierstin L; Harbury, Pehr B; Marqusee, Susan

    2011-06-28

    Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.

  16. Effects of Polymer Hydrophobicity on Protein Structure and Aggregation Kinetics in Crowded Milieu.

    Science.gov (United States)

    Breydo, Leonid; Sales, Amanda E; Frege, Telma; Howell, Mark C; Zaslavsky, Boris Y; Uversky, Vladimir N

    2015-05-19

    We examined the effects of water-soluble polymers of various degrees of hydrophobicity on the folding and aggregation of proteins. The polymers we chose were polyethylene glycol (PEG) and UCON (1:1 copolymer of ethylene glycol and propylene glycol). The presence of additional methyl groups in UCON makes it more hydrophobic than PEG. Our earlier analysis revealed that similarly sized PEG and UCON produced different changes in the solvent properties of water in their solutions and induced morphologically different α-synuclein aggregates [Ferreira, L. A., et al. (2015) Role of solvent properties of aqueous media in macromolecular crowding effects. J. Biomol. Struct. Dyn., in press]. To improve our understanding of molecular mechanisms defining behavior of proteins in a crowded environment, we tested the effects of these polymers on secondary and tertiary structure and aromatic residue solvent accessibility of 10 proteins [five folded proteins, two hybrid proteins; i.e., protein containing ordered and disordered domains, and three intrinsically disordered proteins (IDPs)] and on the aggregation kinetics of insulin and α-synuclein. We found that effects of both polymers on secondary and tertiary structures of folded and hybrid proteins were rather limited with slight unfolding observed in some cases. Solvent accessibility of aromatic residues was significantly increased for the majority of the studied proteins in the presence of UCON but not PEG. PEG also accelerated the aggregation of protein into amyloid fibrils, whereas UCON promoted aggregation to amyloid oligomers instead. These results indicate that even a relatively small change in polymer structure leads to a significant change in the effect of this polymer on protein folding and aggregation. This is an indication that protein folding and especially aggregation are highly sensitive to the presence of other macromolecules, and an excluded volume effect is insufficient to describe their effect.

  17. Spatiotemporal kinetics of γ-H2AX protein on charged particles induced DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Niu, H., E-mail: hniu@mx.nthu.edu.tw [Nuclear Science and Technology Development Center, National Tsing Hua University, Hsinchu, Taiwan (China); Chang, H.C. [Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan (China); Cho, I.C. [Institute for Radiological Research, Chang Gung University and Chang Gung Memorial Hospital, Taoyuan, Taiwan (China); Chen, C.H. [Nuclear Science and Technology Development Center, National Tsing Hua University, Hsinchu, Taiwan (China); Liu, C.S. [Cancer Center of Taipei Veterans General Hospital, Taipei, Taiwan (China); Chou, W.T. [Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan (China)

    2014-08-15

    Highlights: • Charged particles can induce more complex DNA damages, and these complex damages have higher ability to cause the cell death or cell carcinogenesis. • In this study, we used γ-H2AX protein to investigate the spatiotemporal kinetics of DNA double strand breaks in particle irradiated HeLa cells. • The HeLa cells were irradiated by 400 keV alpha-particles in four different dosages. • The result shows that a good linear relationship can be observed between foci number and radiation dose. • The data shows that the dissolution rate of γ-H2AX foci agree with the two components DNA repairing model, and it was decreasing as the radiation dose increased. • These results suggest that charged particles can induce more complex DNA damages and causing the retardation of DNA repair. - Abstract: In several researches, it has been demonstrated that charged particles can induce more complex DNA damages. These complex damages have higher ability to cause the cell death or cell carcinogenesis. For this reason, clarifying the DNA repair mechanism after charged particle irradiation plays an important role in the development of charged particle therapy and space exploration. Unfortunately, the detail spatiotemporal kinetic of DNA damage repair is still unclear. In this study, we used γ-H2AX protein to investigate the spatiotemporal kinetics of DNA double strand breaks in alpha-particle irradiated HeLa cells. The result shows that the intensity of γ-H2AX foci increased gradually, and reached to its maximum at 30 min after irradiation. A good linear relationship can be observed between foci intensity and radiation dose. After 30 min, the γ-H2AX foci intensity was decreased with time passed, but remained a large portion (∼50%) at 48 h passed. The data show that the dissolution rate of γ-H2AX foci agreed with two components DNA repairing model. These results suggest that charged particles can induce more complex DNA damages and causing the retardation of DNA

  18. Characteristics of selective fluoride adsorption by biocarbon-Mg/Al layered double hydroxides composites from protein solutions: kinetics and equilibrium isotherms study.

    Science.gov (United States)

    Ma, Wei; Lv, Tengfei; Song, Xiaoyan; Cheng, Zihong; Duan, Shibo; Xin, Gang; Liu, Fujun; Pan, Decong

    2014-03-15

    In the study, two novel applied biocarbon-Mg/Al layered double hydroxides composites (CPLDH and CPLDH-Ca) were successfully prepared and characterized by TEM, ICP-AES, XFS, EDS, FTIR, XRD, BET and pHpzc. The fluoride removal efficiency (RF) and protein recovery ratio (RP) of the adsorbents were studied in protein systems of lysozyme (LSZ) and bovine serum albumin (BSA). The results showed that the CPLDH-Ca presented remarkable performance for selective fluoride removal from protein solution. It reached the maximum RF of 92.1% and 94.8% at the CPLDH-Ca dose of 2.0g/L in LSZ and BSA system, respectively. The RP in both systems of LSZ and BSA were more than 90%. Additionally, the RP of CPLDH-Ca increased with the increase of ionic strengths, and it almost can be 100% with more than 93% RF. Fluoride adsorption by the CPLDH-Ca with different initial fluoride concentrations was found to obey the mixed surface reaction and diffusion controlled adsorption kinetic model, and the overall reaction rate is probably controlled by intra-particle diffusion, boundary layer diffusion and reaction process. The adsorption isotherms of fluoride in BSA system fit the Langmuir-Freundlich model well. The BSA has synergistic effect on fluoride adsorption and the degree increased with the increase of the initial BSA concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride.

    Science.gov (United States)

    Jha, Santosh Kumar; Marqusee, Susan

    2014-04-01

    Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).

  20. Study on a hidden protein-DNA binding in salmon sperm DNA sample by dynamic kinetic capillary isoelectric focusing

    International Nuclear Information System (INIS)

    Liang Liang; Dou Peng; Dong Mingming; Ke Xiaokang; Bian Ningsheng; Liu Zhen

    2009-01-01

    Nuclease P1 is an important enzyme that hydrolyzes RNA or single-stranded DNA into nucleotides, and complete digestion is an essential basis for assays based on this enzyme. To digest a doubled-stranded DNA, the enzyme is usually combined with heat denaturing, which breaks doubled-stranded DNA into single strands. This paper presents an un-expected phenomenon that nuclease P1, in combination with heat denaturing, fails to completely digest a DNA sample extracted from salmon sperm. Under the experimental conditions used, at which nuclease P1 can completely digest calf thymus DNA, the digestion yield of salmon sperm DNA was only 89.5%. Spectrometric measurement indicated that a total protein of 4.7% is present in the DNA sample. To explain the reason for this phenomenon, the dynamic kinetic capillary isoelectric focusing (DK-CIEF) approach proposed previously, which allows for the discrimination of different types of protein-DNA interactions and the measurement of the individual dissociation rate constants, was modified and applied to examine possible protein-DNA interactions involved. It was found that a non-specific DNA-protein binding occurs in the sample, the dissociation rate constant for which was measured to be 7.05 ± 0.83 x 10 -3 s -1 . The formation of DNA-protein complex was suggested to be the main reason for the incomplete digestion of the DNA sample. The modified DK-CIEF approach can be applied as general DNA samples, with the advantages of fast speed and low sample consumption.

  1. Effects of grain source, grain processing, and protein degradability on rumen kinetics and microbial protein synthesis in Boer kids.

    Science.gov (United States)

    Brassard, M-E; Chouinard, P Y; Berthiaume, R; Tremblay, G F; Gervais, R; Martineau, R; Cinq-Mars, D

    2015-11-01

    Microbial protein synthesis in the rumen would be optimized when dietary carbohydrates and proteins have synchronized rates and extent of degradation. The aim of this study was to evaluate the effect of varying ruminal degradation rate of energy and nitrogen sources on intake, nitrogen balance, microbial protein yield, and kinetics of nutrients in the rumen of growing kids. Eight Boer goats (38.2 ± 3.0 kg) were used. The treatments were arranged in a split-plot Latin square design with grain sources (barley or corn) forming the main plots (squares). Grain processing methods and levels of protein degradability formed the subplots in a 2 × 2 factorial arrangement for a total of 8 dietary treatments. The grain processing method was rolling for barley and cracking for corn. Levels of protein degradability were obtained by feeding untreated soybean meal (SBM) or heat-treated soybean meal (HSBM). Each experimental period lasted 21 d, consisting of a 10-d adaptation period, a 7-d digestibility determination period, and a 4-d rumen evacuation and sampling period. Kids fed with corn had higher purine derivatives (PD) excretion when coupled with SBM compared with HSBM and the opposite occurred with barley-fed kids ( ≤ 0.01). Unprocessed grain offered with SBM led to higher PD excretion than with HSBM whereas protein degradability had no effect when processed grain was fed ( ≤ 0.03). Results of the current experiment with high-concentrate diets showed that microbial N synthesis could be maximized in goat kids by combining slowly fermented grains (corn or unprocessed grains) with a highly degradable protein supplement (SBM). With barley, a more rapidly fermented grain, a greater microbial N synthesis was observed when supplementing a low-degradable protein (HSBM).

  2. How changing the particle structure can speed up protein mass transfer kinetics in liquid chromatography.

    Science.gov (United States)

    Gritti, Fabrice; Horvath, Krisztian; Guiochon, Georges

    2012-11-09

    The mass transfer kinetics of a few compounds (uracil, 112 Da), insulin (5.5 kDa), lysozyme (13.4 kDa), and bovine serum albumin (BSA, 67 kDa) in columns packed with several types of spherical particles was investigated under non-retained conditions, in order to eliminate the poorly known contribution of surface diffusion to overall sample diffusivity across the porous particles in RPLC. Diffusivity across particles is then minimum. Based on the porosity of the particles accessible to analytes, it was accurately estimated from the elution times, the internal obstruction factor (using Pismen correlation), and the hindrance diffusion factor (using Renkin correlation). The columns used were packed with fully porous particles 2.5 μm Luna-C(18) 100 Å, core-shell particles 2.6 μm Kinetex-C(18) 100 Å, 3.6 μm Aeris Widepore-C(18) 200 Å, and prototype 2.7 μm core-shell particles (made of two concentric porous shells with 100 and 300 Å average pore size, respectively), and with 3.3 μm non-porous silica particles. The results demonstrate that the porous particle structure and the solid-liquid mass transfer resistance have practically no effect on the column efficiency for small molecules. For them, the column performance depends principally on eddy dispersion (packing homogeneity), to a lesser degree on longitudinal diffusion (effective sample diffusivity along the packed bed), and only slightly on the solid-liquid mass transfer resistance (sample diffusivity across the particle). In contrast, for proteins, this third HETP contribution, hence the porous particle structure, together with eddy dispersion govern the kinetic performance of columns. Mass transfer kinetics of proteins was observed to be fastest for columns packed with core-shell particles having either a large core-to-particle ratio or having a second, external, shell made of a thin porous layer with large mesopores (200-300 Å) and a high porosity (~/=0.5-0.7). The structure of this external shell seems

  3. Drainage and Stratification Kinetics of Foam Films

    Science.gov (United States)

    Zhang, Yiran; Sharma, Vivek

    2014-03-01

    Baking bread, brewing cappuccino, pouring beer, washing dishes, shaving, shampooing, whipping eggs and blowing bubbles all involve creation of aqueous foam films. Foam lifetime, drainage kinetics and stability are strongly influenced by surfactant type (ionic vs non-ionic), and added proteins, particles or polymers modify typical responses. The rate at which fluid drains out from a foam film, i.e. drainage kinetics, is determined in the last stages primarily by molecular interactions and capillarity. Interestingly, for certain low molecular weight surfactants, colloids and polyelectrolyte-surfactant mixtures, a layered ordering of molecules, micelles or particles inside the foam films leads to a stepwise thinning phenomena called stratification. Though stratification is observed in many confined systems including foam films containing particles or polyelectrolytes, films containing globular proteins seem not to show this behavior. Using a Scheludko-type cell, we experimentally study the drainage and stratification kinetics of horizontal foam films formed by protein-surfactant mixtures, and carefully determine how the presence of proteins influences the hydrodynamics and thermodynamics of foam films.

  4. Quantification of Protein-Induced Membrane Remodeling Kinetics In Vitro with Lipid Multilayer Gratings

    Science.gov (United States)

    Lowry, Troy W.; Hariri, Hanaa; Prommapan, Plengchart; Kusi-Appiah, Aubrey; Vafai, Nicholas; Bienkiewicz, Ewa A.; Van Winkle, David H.; Stagg, Scott M.

    2016-01-01

    The dynamic self-organization of lipids in biological systems is a highly regulated process that enables the compartmentalization of living systems at micro- and nanoscopic scales. Consequently, quantitative methods for assaying the kinetics of supramolecular remodeling such as vesicle formation from planar lipid bilayers or multilayers are needed to understand cellular self-organization. Here, a new nanotechnology-based method for quantitative measurements of lipid–protein interactions is presented and its suitability for quantifying the membrane binding, inflation, and budding activity of the membrane-remodeling protein Sar1 is demonstrated. Lipid multilayer gratings are printed onto surfaces using nanointaglio and exposed to Sar1, resulting in the inflation of lipid multilayers into unilamellar structures, which can be observed in a label-free manner by monitoring the diffracted light. Local variations in lipid multilayer volume on the surface is used to vary substrate availability in a microarray format. A quantitative model is developed that allows quantification of binding affinity (KD) and kinetics (kon and koff). Importantly, this assay is uniquely capable of quantifying membrane remodeling. Upon Sar1-induced inflation of single bilayers from surface supported multilayers, the semicylindrical grating lines are observed to remodel into semispherical buds when a critical radius of curvature is reached. PMID:26649649

  5. Kinetics of microstructure formation of high-pressure induced gel from a whey protein isolate

    Science.gov (United States)

    He, Jin-Song; Yang, Hongwei; Zhu, Wanpeng; Mu, Tai-Hua

    2010-03-01

    The kinetic process of pressure-induced gelation of whey protein isolate (WPI) solutions was studied using in situ light scattering. The relationship of the logarithm of scattered light intensity (I) versus time (t) was linear after the induced time and could be described by the Cahn-Hilliard linear theory. With increasing time, the scattered intensity deviated from the exponential relationship, and the time evolution of the scattered light intensity maximum Im and the corresponding wavenumber qm could be described in terms of the power-law relationship as Im~fβ and qm~f-α, respectively. These results indicated that phase separation occurred during the gelation of WPI solutions under high pressure.

  6. Calmodulin-lanthanide ion exchange kinetics

    International Nuclear Information System (INIS)

    Buccigross, J.; O'Donnell, C.; Nelson, D.

    1985-01-01

    A flow dialysis apparatus suitable for the study of high affinity metal binding proteins has been utilized to study calmodulin-metal exchange kinetics. Calmodulin labeled with Eu-155 and Gd-153 was dialyzed against buffer containing various competing metal ions. The rate of metal exchange was monitored by a gamma-ray scintillation detector. The kinetics of exchange are first order, and the rates fall into two categories: Ca (II) and CD (II) in one, and the lanthanides Eu (III), Gd (III), and La (III) in the other

  7. Glucose and protein kinetics in patients undergoing colorectal surgery: perioperative amino acid versus hypocaloric dextrose infusion.

    Science.gov (United States)

    Lugli, Andrea Kopp; Schricker, Thomas; Wykes, Linda; Lattermann, Ralph; Carli, Franco

    2010-11-01

    Surgical injury provokes a stress response that leads to a catabolic state and, when prolonged, interferes with the postoperative recovery process. This study tests the impact of 2 nutrition support regimens on protein and glucose metabolism as part of an integrated approach in the perioperative period incorporating epidural analgesia in 18 nondiabetic patients undergoing colorectal surgery. To test the hypothesis that parenteral amino acid infusion (amino acid group, n = 9) maintains glucose homeostasis while maintaining normoglycemia and reduces proteolysis compared with infusion of dextrose alone (DEX group, n = 9), glucose and protein kinetics were measured before and on the second day after surgery using a stable isotope tracer technique. Postoperatively, the rate of appearance of glucose was higher (P dextrose alone. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. Fiber digestion kinetics and protein degradability characteristics of stockpiled Tifton 85 bermudagrass.

    Science.gov (United States)

    Sechler, S R; Mullenix, M K; Holland, C M; Muntifering, R B

    2017-09-01

    A 2-yr study was conducted to determine effects of N fertilization level on fiber digestion kinetics and protein degradability characteristics of stockpiled Tifton 85 bermudagrass (T85). Six 0.76-ha pastures of stockpiled T85 were cut to a 10-cm stubble height on August 1 of each yr and fertilized with 56 (56N), 112 (112N), or 168 (168N) kg N/ha (2 pastures/treatment). Fiber digestion kinetics included the 72-hr potential extent of NDF digestion (PED), rate of NDF digestion, and lag time. In yr 1 and 2, PED decreased over the stockpile season. Rates of NDF digestion did not differ ( > 0.05) among N fertilization treatments in either yr. In yr 1, rate of NDF digestion was greatest ( digestion decreased ( digestion rates were similar for November and January 21 sampling dates. Lag time was greater ( digestion ( = -0.60 and -0.25 in yr 1 and 2, respectively) was observed. There was a trend ( = 0.06) for lignin concentration to be positively correlated with lag time ( = 0.39) in yr 1, and a strong relationship was observed in yr 2 ( = 0.91; digestion in stockpiled T85 were influenced more by temporal changes over the stockpile season than by N fertilization level. Supplement formulations based on kinetic parameters of fiber digestion may require periodic adjustment to insure that energy-yielding components of NDF are sufficient to meet animal requirements throughout the stockpile season. The CP fraction in stockpiled T85 contains sufficient RDP to support fibrolytic activity and growth of ruminal microorganisms throughout the stockpile season. Toward the latter end of the season, supplementation with sources of digestible fiber and RDP could be expected to increase MP supply to the host animal.

  9. Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies.

    Science.gov (United States)

    Deganutti, Giuseppe; Moro, Stefano

    2017-04-01

    Kinetic and thermodynamic ligand-protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand-protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand-protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand-protein binding.

  10. Liquefaction chemistry and kinetics: Hydrogen utilization studies

    Energy Technology Data Exchange (ETDEWEB)

    Rothenberger, K.S.; Warzinski, R.P.; Cugini, A.V. [Pittsburgh Energy Technology Center, PA (United States)] [and others

    1995-12-31

    The objectives of this project are to investigate the chemistry and kinetics that occur in the initial stages of coal liquefaction and to determine the effects of hydrogen pressure, catalyst activity, and solvent type on the quantity and quality of the products produced. The project comprises three tasks: (1) preconversion chemistry and kinetics, (2) hydrogen utilization studies, and (3) assessment of kinetic models for liquefaction. The hydrogen utilization studies work will be the main topic of this report. However, the other tasks are briefly described.

  11. Kinetics of microstructure formation of high-pressure induced gel from a whey protein isolate

    International Nuclear Information System (INIS)

    He Jinsong; Yang Hongwei; Zhu Wanpeng; Mu Taihua

    2010-01-01

    The kinetic process of pressure-induced gelation of whey protein isolate (WPI) solutions was studied using in situ light scattering. The relationship of the logarithm of scattered light intensity (I) versus time (t) was linear after the induced time and could be described by the Cahn-Hilliard linear theory. With increasing time, the scattered intensity deviated from the exponential relationship, and the time evolution of the scattered light intensity maximum I m and the corresponding wavenumber q m could be described in terms of the power-law relationship as I m ∼f β and q m ∼f -α , respectively. These results indicated that phase separation occurred during the gelation of WPI solutions under high pressure.

  12. Kinetic studies of elementary chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Durant, J.L. Jr. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

  13. 15N tracer kinetic studies on the validity of various 15N tracer substances for determining whole-body protein parameters in very small preterm infants

    International Nuclear Information System (INIS)

    Plath, C.; Heine, W.; Wutzke, K.D.; Krienke, L.; Toewe, J.M.; Massute, G.; Windischmann, C.

    1987-01-01

    Reliable 15 N tracer substances for tracer kinetic determination of whole-body protein parameters in very small preterm infants are still a matter of intensive research, especially after some doubts have been raised about the validity of [ 15 N]glycine, a commonly used 15 N tracer. Protein turnover, synthesis, breakdown, and further protein metabolism data were determined by a paired comparison in four preterm infants. Their post-conceptual age was 32.2 +/- 0.8 weeks, and their body weight was 1670 +/- 181 g. Tracer substances applied in this study were a [ 15 N]amino acid mixture (Ia) and [ 15 N]glycine (Ib). In a second group of three infants with a post conceptual age of 15 N-labeled 32.0 +/- 1.0 weeks and a body weight of 1,907 +/- 137 g, yeast protein hydrolysate (II) was used as a tracer substance. A three-pool model was employed for the analysis of the data. This model takes into account renal and fecal 15 N losses after a single 15 N pulse. Protein turnovers were as follows: 11.9 +/- 3.1 g kg-1 d-1 (Ia), 16.2 +/- 2.5 g kg-1 d-1 (Ib), and 10.8 +/- 3.0 g kg-1 d-1 (II). We were able to demonstrate an overestimation of the protein turnover when Ib was used. There was an expected correspondence in the results obtained from Ia and II. The 15 N-labeled yeast protein hydrolysate is a relatively cheap tracer that allows reliable determination of whole-body protein parameters in very small preterm infants

  14. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

    Science.gov (United States)

    Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

    2015-09-01

    Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

  15. Kinetic Titration Series with Biolayer Interferometry

    Science.gov (United States)

    Frenzel, Daniel; Willbold, Dieter

    2014-01-01

    Biolayer interferometry is a method to analyze protein interactions in real-time. In this study, we illustrate the usefulness to quantitatively analyze high affinity protein ligand interactions employing a kinetic titration series for characterizing the interactions between two pairs of interaction patterns, in particular immunoglobulin G and protein G B1 as well as scFv IC16 and amyloid beta (1–42). Kinetic titration series are commonly used in surface plasmon resonance and involve sequential injections of analyte over a desired concentration range on a single ligand coated sensor chip without waiting for complete dissociation between the injections. We show that applying this method to biolayer interferometry is straightforward and i) circumvents problems in data evaluation caused by unavoidable sensor differences, ii) saves resources and iii) increases throughput if screening a multitude of different analyte/ligand combinations. PMID:25229647

  16. Kinetics and thermodynamics studies on the BMP-2 adsorption onto hydroxyapatite surface with different multi-morphological features

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Zhiwei; Huangfu, Changxin; Wang, Yanying; Ge, Hongwei; Yao, Yao; Zou, Ping; Wang, Guangtu [College of Science, Sichuan Agricultural University, Ya' an 625014 (China); He, Hua [Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Wenjiang, Sichuan 611130 (China); Rao, Hanbing, E-mail: rhbscu@gmail.com [College of Science, Sichuan Agricultural University, Ya' an 625014 (China)

    2015-07-01

    The effect of the surface topography on protein adsorption process is of great significance for designing hydroxyapatite (HA) ceramic material surfaces. In this work, three different topographies of HA materials HA-sheet, HA-rod, and HA-whisker were synthesized and testified by X-ray diffraction (XRD), Fourier transform infrared (FT-IR), Brunauer–Emmett–Teller (BET) and a field emission scanning electron microscopy (FE-SEM). We have systematically investigated the adsorption kinetics and thermodynamics of bone morphogenetic proteins (BMP-2) on the three different topography surfaces of HA, respectively. The results showed that the maximum adsorption capacities of HA-sheet, HA-rod and HA-whisker were (219.96 ± 10.18), (247.13 ± 12.35), and (354.67 ± 17.73) μg · g{sup −1}, respectively. Kinetic parameters, rate constants, equilibrium adsorption capacities and related correlation coefficients, for each kinetic model were calculated as well as discussed. It demonstrated that the adsorption of BMP-2 onto HA could be described by the pseudo second-order equation. Adsorption of BMP-2 onto HA followed the Langmuir isotherm. It confirmed that compared with other samples HA-whisker had more adsorption sites for its high specific surface area which could provide more opportunities for protein molecules. The adsorption processes were endothermic (ΔH > 0), spontaneous (ΔG < 0) and entropy increasing (ΔS > 0). A possible adsorption mechanism has been proposed. In addition, the BMP-2 could be adsorbed to the surface which existed slight conformational changes by FT-IR. - Highlights: • A novel protein adsorption studies based on sheet, rod and whisker of HA were designed. • Kinetic and thermodynamics parameters of BMP-2 and HA bonded materials were evaluated. • Surface topographies of the HA effect BMP-2 adsorption • The HA-whisker material had excellent adsorption performance for protein enrichment. • The electrostatic interaction is responsible for the

  17. Kinetics and thermodynamics studies on the BMP-2 adsorption onto hydroxyapatite surface with different multi-morphological features

    International Nuclear Information System (INIS)

    Lu, Zhiwei; Huangfu, Changxin; Wang, Yanying; Ge, Hongwei; Yao, Yao; Zou, Ping; Wang, Guangtu; He, Hua; Rao, Hanbing

    2015-01-01

    The effect of the surface topography on protein adsorption process is of great significance for designing hydroxyapatite (HA) ceramic material surfaces. In this work, three different topographies of HA materials HA-sheet, HA-rod, and HA-whisker were synthesized and testified by X-ray diffraction (XRD), Fourier transform infrared (FT-IR), Brunauer–Emmett–Teller (BET) and a field emission scanning electron microscopy (FE-SEM). We have systematically investigated the adsorption kinetics and thermodynamics of bone morphogenetic proteins (BMP-2) on the three different topography surfaces of HA, respectively. The results showed that the maximum adsorption capacities of HA-sheet, HA-rod and HA-whisker were (219.96 ± 10.18), (247.13 ± 12.35), and (354.67 ± 17.73) μg · g −1 , respectively. Kinetic parameters, rate constants, equilibrium adsorption capacities and related correlation coefficients, for each kinetic model were calculated as well as discussed. It demonstrated that the adsorption of BMP-2 onto HA could be described by the pseudo second-order equation. Adsorption of BMP-2 onto HA followed the Langmuir isotherm. It confirmed that compared with other samples HA-whisker had more adsorption sites for its high specific surface area which could provide more opportunities for protein molecules. The adsorption processes were endothermic (ΔH > 0), spontaneous (ΔG < 0) and entropy increasing (ΔS > 0). A possible adsorption mechanism has been proposed. In addition, the BMP-2 could be adsorbed to the surface which existed slight conformational changes by FT-IR. - Highlights: • A novel protein adsorption studies based on sheet, rod and whisker of HA were designed. • Kinetic and thermodynamics parameters of BMP-2 and HA bonded materials were evaluated. • Surface topographies of the HA effect BMP-2 adsorption • The HA-whisker material had excellent adsorption performance for protein enrichment. • The electrostatic interaction is responsible for the BMP-2

  18. Analysis of residuals from enzyme kinetic and protein folding experiments in the presence of correlated experimental noise.

    Science.gov (United States)

    Kuzmic, Petr; Lorenz, Thorsten; Reinstein, Jochen

    2009-12-01

    Experimental data from continuous enzyme assays or protein folding experiments often contain hundreds, or even thousands, of densely spaced data points. When the sampling interval is extremely short, the experimental data points might not be statistically independent. The resulting neighborhood correlation invalidates important theoretical assumptions of nonlinear regression analysis. As a consequence, certain goodness-of-fit criteria, such as the runs-of-signs test and the autocorrelation function, might indicate a systematic lack of fit even if the experiment does agree very well with the underlying theoretical model. A solution to this problem is to analyze only a subset of the residuals of fit, such that any excessive neighborhood correlation is eliminated. Substrate kinetics of the HIV protease and the unfolding kinetics of UMP/CMP kinase, a globular protein from Dictyostelium discoideum, serve as two illustrative examples. A suitable data-reduction algorithm has been incorporated into software DYNAFIT [P. Kuzmic, Anal. Biochem. 237 (1996) 260-273], freely available to all academic researchers from http://www.biokin.com.

  19. A single cysteine post-translational oxidation suffices to compromise globular proteins kinetic stability and promote amyloid formation

    Directory of Open Access Journals (Sweden)

    Patrizia Marinelli

    2018-04-01

    Full Text Available Oxidatively modified forms of proteins accumulate during aging. Oxidized protein conformers might act as intermediates in the formation of amyloids in age-related disorders. However, it is not known whether this amyloidogenic conversion requires an extensive protein oxidative damage or it can be promoted just by a discrete, localized post-translational modification of certain residues. Here, we demonstrate that the irreversible oxidation of a single free Cys suffices to severely perturb the folding energy landscape of a stable globular protein, compromise its kinetic stability, and lead to the formation of amyloids under physiological conditions. Experiments and simulations converge to indicate that this specific oxidation-promoted protein aggregation requires only local unfolding. Indeed, a large scale analysis indicates that many cellular proteins are at risk of undergoing this kind of deleterious transition; explaining how oxidative stress can impact cell proteostasis and subsequently lead to the onset of pathological states. Keywords: Protein oxidation, Protein misfolding, Protein aggregation, Oxidative stress, Post-translational modification

  20. The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids

    Science.gov (United States)

    Newton, Arthur C.; Kools, Ramses; Swenson, David W. H.; Bolhuis, Peter G.

    2017-10-01

    The association and dissociation of particles via specific anisotropic interactions is a fundamental process, both in biology (proteins) and in soft matter (colloidal patchy particles). The presence of alternative binding sites can lead to multiple productive states and also to non-productive "decoy" or intermediate states. Besides anisotropic interactions, particles can experience non-specific isotropic interactions. We employ single replica transition interface sampling to investigate how adding a non-productive binding site or a nonspecific isotropic interaction alters the dimerization kinetics of a generic patchy particle model. The addition of a decoy binding site reduces the association rate constant, independent of the site's position, while adding an isotropic interaction increases it due to an increased rebinding probability. Surprisingly, the association kinetics becomes non-monotonic for a tetramer complex formed by multivalent patchy particles. While seemingly identical to two-particle binding with a decoy state, the cooperativity of binding multiple particles leads to a kinetic optimum. Our results are relevant for the understanding and modeling of biochemical networks and self-assembly processes.

  1. A simple theory of motor protein kinetics and energetics. II.

    Science.gov (United States)

    Qian, H

    2000-01-10

    A three-state stochastic model of motor protein [Qian, Biophys. Chem. 67 (1997) pp. 263-267] is further developed to illustrate the relationship between the external load on an individual motor protein in aqueous solution with various ATP concentrations and its steady-state velocity. A wide variety of dynamic motor behavior are obtained from this simple model. For the particular case of free-load translocation being the most unfavorable step within the hydrolysis cycle, the load-velocity curve is quasi-linear, V/Vmax = (cF/Fmax-c)/(1-c), in contrast to the hyperbolic relationship proposed by A.V. Hill for macroscopic muscle. Significant deviation from the linearity is expected when the velocity is less than 10% of its maximal (free-load) value--a situation under which the processivity of motor diminishes and experimental observations are less certain. We then investigate the dependence of load-velocity curve on ATP (ADP) concentration. It is shown that the free load Vmax exhibits a Michaelis-Menten like behavior, and the isometric Fmax increases linearly with ln([ATP]/[ADP]). However, the quasi-linear region is independent of the ATP concentration, yielding an apparently ATP-independent maximal force below the true isometric force. Finally, the heat production as a function of ATP concentration and external load are calculated. In simple terms and solved with elementary algebra, the present model provides an integrated picture of biochemical kinetics and mechanical energetics of motor proteins.

  2. Kinetics of microstructure formation of high-pressure induced gel from a whey protein isolate

    Energy Technology Data Exchange (ETDEWEB)

    He Jinsong; Yang Hongwei; Zhu Wanpeng [Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084 (China); Mu Taihua, E-mail: mutaihuacaas@126.co [Institute of Agro-Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100094 (China)

    2010-03-01

    The kinetic process of pressure-induced gelation of whey protein isolate (WPI) solutions was studied using in situ light scattering. The relationship of the logarithm of scattered light intensity (I) versus time (t) was linear after the induced time and could be described by the Cahn-Hilliard linear theory. With increasing time, the scattered intensity deviated from the exponential relationship, and the time evolution of the scattered light intensity maximum I{sub m} and the corresponding wavenumber q{sub m} could be described in terms of the power-law relationship as I{sub m}{approx}f{sup {beta}} and q{sub m}{approx}f{sup -}{alpha}, respectively. These results indicated that phase separation occurred during the gelation of WPI solutions under high pressure.

  3. Measuring kinetic drivers of pneumolysin pore structure.

    Science.gov (United States)

    Gilbert, Robert J C; Sonnen, Andreas F-P

    2016-05-01

    Most membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins are thought to form pores in target membranes by assembling into pre-pore oligomers before undergoing a pre-pore to pore transition. Assembly during pore formation is into both full rings of subunits and incomplete rings (arcs). The balance between arcs and full rings is determined by a mechanism dependent on protein concentration in which arc pores arise due to kinetic trapping of the pre-pore forms by the depletion of free protein subunits during oligomerization. Here we describe the use of a kinetic assay to study pore formation in red blood cells by the MACPF/CDC pneumolysin from Streptococcus pneumoniae. We show that cell lysis displays two kinds of dependence on protein concentration. At lower concentrations, it is dependent on the pre-pore to pore transition of arc oligomers, which we show to be a cooperative process. At higher concentrations, it is dependent on the amount of pneumolysin bound to the membrane and reflects the affinity of the protein for its receptor, cholesterol. A lag occurs before cell lysis begins; this is dependent on oligomerization of pneumolysin. Kinetic dissection of cell lysis by pneumolysin demonstrates the capacity of MACPF/CDCs to generate pore-forming oligomeric structures of variable size with, most likely, different functional roles in biology.

  4. Kinetics of inclusion body formation and its correlation with the characteristics of protein aggregates in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Arun K Upadhyay

    Full Text Available The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2-3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies.

  5. Kinetics of Inclusion Body Formation and Its Correlation with the Characteristics of Protein Aggregates in Escherichia coli

    Science.gov (United States)

    Upadhyay, Arun K.; Murmu, Aruna; Singh, Anupam; Panda, Amulya K.

    2012-01-01

    The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH) and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm) and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2–3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies. PMID:22479486

  6. Kinetic Study of Curcumin on Modal Fabric

    Directory of Open Access Journals (Sweden)

    Abu Naser Md. Ahsanul Haque

    2018-03-01

    Full Text Available A kinetic study of curcumin on modal fabric was carried out using an initial dye concentration of 1 g/L at three different temperatures, 70 °C, 85 °C and 100 °C, at pH 7 and an material to liquor ratio of 1:20. Pseudo first-order and pseudo second-order kinetics were applied, and it was found that the adsorption kinetics of curcumin on modal fabric matched the pseudo second-order kinetic model. The activation energy was found to be equal to 71.14 kJ/mol, while the enthalpy and entropy of activation were 68.16 kJ/mol and –66.02 J/molK respectively.

  7. The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies

    Science.gov (United States)

    Pant, Kiran; Anderson, Brian; Perdana, Hendrik; Malinowski, Matthew A.; Win, Aye T.; Williams, Mark C.

    2018-01-01

    The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292–296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes. PMID:29634784

  8. Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons

    International Nuclear Information System (INIS)

    Roder, H.; Wuethrich, K.

    1986-01-01

    A method to be used for experimental studies of protein folding introduced by Schmid and Baldwin, which is based on the competition between amide hydrogen exchange and protein refolding, was extended by using rapid mixing techniques and 1 H NMR to provide site-resolved kinetic information on the early phases of protein structure acquisition. In this method, a protonated solution of the unfolded protein is rapidly mixed with a deuterated buffer solution at conditions assuring protein refolding in the mixture. This simultaneously initiates the exchange of unprotected amide protons with solvent deuterium and the refolding of protein segments which can protect amide groups from further exchange. After variable reaction times the amide proton exchange is quenched while folding to the native form continues to completion. By using 1 H NMR, the extent of exchange at individual amide sites is then measured in the refolded protein. Competition experiments at variable reaction times or variable pH indicate the time at which each amide group is protected in the refolding process. This technique was applied to the basic pancreatic trypsin inhibitor, for which sequence-specific assignments of the amide proton NMR lines had previously been obtained. For eight individual amide protons located in the beta-sheet and the C-terminal alpha-helix of this protein, apparent refolding rates in the range from 15 s-1 to 60 s-1 were observed. These rates are on the time scale of the fast folding phase observed with optical probes

  9. Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions.

    Science.gov (United States)

    Götz, Markus; Wortmann, Philipp; Schmid, Sonja; Hugel, Thorsten

    2018-01-30

    Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM). Therefore, multi-color smFRET is a versatile tool for studying biomolecular complexes in a quantitative manner and in a previously unachievable detail. Here, we demonstrate how to overcome the special challenges of multi-color smFRET experiments on proteins. We present detailed protocols for obtaining the data and for extracting kinetic information. This includes trace selection criteria, state separation, and the recovery of state trajectories from the noisy data using a 3D ensemble Hidden Markov Model (HMM). Compared to other methods, the kinetic information is not recovered from dwell time histograms but directly from the HMM. The maximum likelihood framework allows us to critically evaluate the kinetic model and to provide meaningful uncertainties for the rates. By applying our method to the heat shock protein 90 (Hsp90), we are able to disentangle the nucleotide binding and the global conformational changes of the protein. This allows us to directly observe the cooperativity between the two nucleotide binding pockets of the Hsp90 dimer.

  10. Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series

    NARCIS (Netherlands)

    Roelofsen, Johan; Alvarez Llamas, Gloria; Dijkstra, Martijn; Breitling, Rainer; Havenga, Klaas; Bijzet, Johannes; Zandbergen, Wouter; de Vries, Marcel; Ploeg, Rutger J.; Vonk, Roel J.

    Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series.Roelofsen H, Alvarez-Llamas G, Dijkstra M, Breitling R, Havenga K, Bijzet J, Zandbergen W, de Vries MP, Ploeg RJ, Vonk RJ. Centre for Medical Biomics, University Medical Centre

  11. Kinetic studies of acid inactivation of alpha-amylase from Aspergillus oryzae

    DEFF Research Database (Denmark)

    Carlsen, Morten; Nielsen, Jens Bredal; Villadsen, John

    1996-01-01

    The stability of alpha-amylase from Aspergillus oryzae has been studied at different pH. The enzyme is extremely stable at neutral pH (pH 5-8), whereas outside this pH-range a substantial loss of activity is observed. The acid-inactivation of alpha-amylase from A. oryzae was monitored on...... regains part of its activity, and the reactivation process also follows first-order kinetics. The irreversible loss of activity is found not to result from a protease contamination of the protein samples. A proposed model, where irreversibly inactivated a-amylase is formed both directly from the active...

  12. AFM study of adsorption of protein A on a poly(dimethylsiloxane) surface

    International Nuclear Information System (INIS)

    Yu Ling; Lu Zhisong; Gan Ye; Liu Yingshuai; Li, C M

    2009-01-01

    In this paper, the morphology and kinetics of adsorption of protein A on a PDMS surface is studied by AFM. The results of effects of pH, protein concentration and contact time of the adsorption reveal that the morphology of adsorbed protein A is significantly affected by pH and adsorbed surface concentration, in which the pH away from the isoelectric point (IEP) of protein A could produce electrical repulsion to change the protein conformation, while the high adsorbed surface protein volume results in molecular networks. Protein A can form an adsorbed protein film on PDMS with a maximum volume of 2.45 x 10 -3 μm 3 . This work enhances our fundamental understanding of protein A adsorption on PDMS, a frequently used substrate component in miniaturized immunoassay devices.

  13. Identifiability study of the proteins degradation model, based on ADM1, using simultaneous batch experiments

    DEFF Research Database (Denmark)

    Flotats, X.; Palatsi, J.; Ahring, Birgitte Kiær

    2006-01-01

    are not inhibiting the hydrolysis process. The ADM1 model adequately expressed the consecutive steps of hydrolysis and acidogenesis, with estimated kinetic values corresponding to a fast acidogenesis and slower hydrolysis. The hydrolysis was found to be the rate limiting step of anaerobic degradation. Estimation...... of yield coefficients based on the relative initial slopes of VFA profiles obtained in a simple batch experiment produced satisfactory results. From the identification study, it was concluded that it is possible to determine univocally the related kinetic parameter values for protein degradation...... if the evolution of amino acids is measured in simultaneous batch experiments, with different initial protein and amino acids concentrations....

  14. Kinetic Uptake Studies of Powdered Materials in Solution

    Directory of Open Access Journals (Sweden)

    Mohamed H. Mohamed

    2015-06-01

    Full Text Available Challenges exist for the study of time dependent sorption processes for heterogeneous systems, especially in the case of dispersed nanomaterials in solvents or solutions because they are not well suited to conventional batch kinetic experiments. In this study, a comparison of batch versus a one-pot setup in two variable configurations was evaluated for the study of uptake kinetics in heterogeneous (solid/solution systems: (i conventional batch method; (ii one-pot system with dispersed adsorbent in solution with a semi-permeable barrier (filter paper or dialysis tubing for in situ sampling; and (iii one-pot system with an adsorbent confined in a semi-permeable barrier (dialysis tubing or filter paper barrier with ex situ sampling. The sorbent systems evaluated herein include several cyclodextrin-based polyurethane materials with two types of phenolic dyes: p-nitrophenol and phenolphthalein. The one-pot kinetics method with in situ (Method ii or ex situ (Method iii sampling described herein offers significant advantages for the study of heterogeneous sorption kinetics of highly dispersed sorbent materials with particles sizes across a range of dimensions from the micron to nanometer scale. The method described herein will contribute positively to the development of advanced studies for heterogeneous sorption processes where an assessment of the relative uptake properties is required at different experimental conditions. The results of this study will be advantageous for the study of nanomaterials with significant benefits over batch kinetic studies for a wide range of heterogeneous sorption processes.

  15. Synthetic peptides and ribosomal proteins as substrate for 60S ribosomal protein kinase from yeast cells

    DEFF Research Database (Denmark)

    Grankowski, N; Gasior, E; Issinger, O G

    1993-01-01

    Kinetic studies on the 60S protein kinase were conducted with synthetic peptides and ribosomal proteins as substrate. Peptide RRREEESDDD proved to be the best synthetic substrate for this enzyme. The peptide has a sequence of amino acids which most closely resembles the structure of potential...... phosphorylation sites in natural substrates, i.e., acidic ribosomal proteins. The superiority of certain kinetic parameters for 60S kinase obtained with the native whole 80S ribosomes over those of the isolated fraction of acidic ribosomal proteins indicates that the affinity of 60S kinase to the specific protein...

  16. Protein conformational transitions at the liquid-gas interface as studied by dilational surface rheology.

    Science.gov (United States)

    Noskov, Boris A

    2014-04-01

    Experimental results on the dynamic dilational surface elasticity of protein solutions are analyzed and compared. Short reviews of the protein behavior at the liquid-gas interface and the dilational surface rheology precede the main sections of this work. The kinetic dependencies of the surface elasticity differ strongly for the solutions of globular and non-globular proteins. In the latter case these dependencies are similar to those for solutions of non-ionic amphiphilic polymers and have local maxima corresponding to the formation of the distal region of the surface layer (type I). In the former case the dynamic surface elasticity is much higher (>60 mN/m) and the kinetic dependencies are monotonical and similar to the data for aqueous dispersions of solid nanoparticles (type II). The addition of strong denaturants to solutions of bovine serum albumin and β-lactoglobulin results in an abrupt transition from the type II to type I dependencies if the denaturant concentration exceeds a certain critical value. These results give a strong argument in favor of the preservation of the protein globular structure in the course of adsorption without any denaturants. The addition of cationic surfactants also can lead to the non-monotonical kinetic dependencies of the dynamic surface elasticity indicating destruction of the protein tertiary and secondary structures. The addition of anionic surfactants gives similar results only for the protein solutions of high ionic strength. The influence of cationic surfactants on the local maxima of the kinetic dependencies of the dynamic surface elasticity for solutions of a non-globular protein (β-casein) differs from the influence of anionic surfactants due to the heterogeneity of the charge distribution along the protein chain. In this case one can use small admixtures of ionic surfactants as probes of the adsorption mechanism. The effect of polyelectrolytes on the kinetic dependencies of the dynamic surface elasticity of protein

  17. Study of internal oxidation kinetics of molybdenum base alloys

    International Nuclear Information System (INIS)

    Krushinskij, Yu.Yu.; Belyakov, B.G.; Belomyttsev, M.Yu.

    1989-01-01

    Metallographic and microdurometric method as well as new technique were used to study kinetics of internal oxidation (IO). It is shown that study of IO kinetics on the base of metallographic measurements of layers depth is not correct because it is related with insufficient sensitivity of the method. IO kinetics under conditions of formation of molybdenum oxide layer on saturated material surface as well as IO of alloy with high carbon content were investigated. Oxide film formation does not affect the IO kinetics; decarburization observed along with oxidation increases the apparent activation energy and K exponent on time dependence of diffusion layer depth

  18. Kinetic Properties of α-Galactosidase and the Localization of Total Proteins in Erwinia chrysanthemi

    Directory of Open Access Journals (Sweden)

    John Morgan Brand

    2004-01-01

    Full Text Available Erwinia chrysanthemi is an enterobacterium that causes soft-rot in plants in general, resulting in enormous economic losses annually. For the pathogen to survive in the host plant, it has to use the readily assimilable compounds from the host fluids and degrade the host tissue. To accomplish this, E. chrysanthemi produces several extracellular and intracellular enzymes. Among the intracellular enzymes there is a special digestive class, the galactosidases, which can be either periplasmic or cytoplasmic. α-Galactosidase is known to degrade melibiose and raffinose into glucose and galactose, and into galactose and sucrose respectively. The aim of the present study was to investigate the kinetic properties of α-galactosidase in E. chrysanthemi, and the localization of total proteins, after culturing it in the presence of raffinose and melibiose. The α-galactosidase that degrades melibiose seems to be the same enzyme that is also responsible for the breakdown of raffinose in E. chrysanthemi. It is localized mainly in the cytoplasm with a fraction of between 2.4 and 5.4 % localized in the periplasm. The majority of E. chrysanthemi proteins have cytoplasmic localization.

  19. Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study

    International Nuclear Information System (INIS)

    Das, Biswajit; Gangopadhyay, Gautam

    2012-01-01

    Graphical abstract: Stochastic theory of interfacial enzyme kinetics is formulated. Numerical results of macroscopic phenomenon of lag-burst kinetics is obtained by using a kinetic Monte Carlo approach to single enzyme activity. Highlights: ► An enzyme is attached with the fluid state phospholipid molecules on the Langmuir monolayer. ► Through the diffusion, the enzyme molecule reaches the gel–fluid interface. ► After hydrolysing a phospholipid molecule it predominantly leaves the surface in the lag phase. ► The enzyme is strictly attached to the surface with scooting mode of motion and the burst phase appears. - Abstract: In the spirit of Gillespie’s stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.

  20. Tracer kinetics: Modelling of tracer behaviour in nonlinear and nonsteady state systems exemplified by the evaluation of protein turnover in plant organs

    International Nuclear Information System (INIS)

    Winkler, E.

    1991-01-01

    If nonlinear biological processes are investigated by means of tracer experiments they can be modelled with linear kinetic equations (compartment equations) as long as the total system is in a stationary state. But if nonstationary behaviour is included considerations on the kinetics of the individual processes are necessary. Within the range of biological and agricultural investigations especially first order reactions (constant fraction processes), zero order reactions (constant amount process) and saturation reactions (Michaelis-Menten-kinetics) are to be taken into account. A rigorous treatment of data based on system theory can be preceeded by graphic-algebraic procedure which may be more or less uncertain in its results but which can easily be handled. An example is given of methodological considerations concerning the combination of evaluation procedures and the discrimination between different reaction mechanisms. It treats protein turnover in 2 different parts of growing wheat plants investigated by means of an 15 N-tracer experiment. Whereas in a stationary system (upper stalk section) linear tracer equations were sufficient irrespective of the true reaction mechanism, for protein synthesis in the upper leaf as a nonstationary system it was necessary to decide between the hypotheses of a zero order and a first order reaction. In accordance with statements in the literature the unambiguous result was a combination of protein synthesis as a zero order process and of protein degradation as a first order process. (orig.) [de

  1. Kinetics of ethylcyclohexane pyrolysis and oxidation: An experimental and detailed kinetic modeling study

    KAUST Repository

    Wang, Zhandong

    2015-07-01

    Ethylcyclohexane (ECH) is a model compound for cycloalkanes with long alkyl side-chains. A preliminary investigation on ECH (Wang et al., Proc. Combust. Inst., 35, 2015, 367-375) revealed that an accurate ECH kinetic model with detailed fuel consumption mechanism and aromatic growth pathways, as well as additional ECH pyrolysis and oxidation data with detailed species concentration covering a wide pressure and temperature range are required to understand the ECH combustion kinetics. In this work, the flow reactor pyrolysis of ECH at various pressures (30, 150 and 760Torr) was studied using synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (PIMS) and gas chromatography (GC). The mole fraction profiles of numerous major and minor species were evaluated, and good agreement was observed between the PIMS and GC data sets. Furthermore, a fuel-rich burner-stabilized laminar premixed ECH/O2/Ar flame at 30Torr was studied using synchrotron VUV PIMS. A detailed kinetic model for ECH high temperature pyrolysis and oxidation was developed and validated against the pyrolysis and flame data performed in this work. Further validation of the kinetic model is presented against literature data including species concentrations in jet-stirred reactor oxidation, ignition delay times in a shock tube, and laminar flame speeds at various pressures and equivalence ratios. The model well predicts the consumption of ECH, the growth of aromatics, and the global combustion properties. Reaction flux and sensitivity analysis were utilized to elucidate chemical kinetic features of ECH combustion under various reaction conditions. © 2015 The Combustion Institute.

  2. A simple three-dimensional-focusing, continuous-flow mixer for the study of fast protein dynamics.

    Science.gov (United States)

    Burke, Kelly S; Parul, Dzmitry; Reddish, Michael J; Dyer, R Brian

    2013-08-07

    We present a simple, yet flexible microfluidic mixer with a demonstrated mixing time as short as 80 μs that is widely accessible because it is made of commercially available parts. To simplify the study of fast protein dynamics, we have developed an inexpensive continuous-flow microfluidic mixer, requiring no specialized equipment or techniques. The mixer uses three-dimensional, hydrodynamic focusing of a protein sample stream by a surrounding sheath solution to achieve rapid diffusional mixing between the sample and sheath. Mixing initiates the reaction of interest. Reactions can be spatially observed by fluorescence or absorbance spectroscopy. We characterized the pixel-to-time calibration and diffusional mixing experimentally. We achieved a mixing time as short as 80 μs. We studied the kinetics of horse apomyoglobin (apoMb) unfolding from the intermediate (I) state to its completely unfolded (U) state, induced by a pH jump from the initial pH of 4.5 in the sample stream to a final pH of 2.0 in the sheath solution. The reaction time was probed using the fluorescence of 1-anilinonaphthalene-8-sulfonate (1,8-ANS) bound to the folded protein. We observed unfolding of apoMb within 760 μs, without populating additional intermediate states under these conditions. We also studied the reaction kinetics of the conversion of pyruvate to lactate catalyzed by lactate dehydrogenase using the intrinsic tryptophan emission of the enzyme. We observe sub-millisecond kinetics that we attribute to Michaelis complex formation and loop domain closure. These results demonstrate the utility of the three-dimensional focusing mixer for biophysical studies of protein dynamics.

  3. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    International Nuclear Information System (INIS)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein's amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate

  4. Kinetic Basis of Nucleotide Selection Employed by a Protein Template-Dependent DNA Polymerase†

    Science.gov (United States)

    Brown, Jessica A.; Fowler, Jason D.; Suo, Zucai

    2010-01-01

    Rev1, a Y-family DNA polymerase, contributes to spontaneous and DNA damage-induced mutagenic events. In this paper, we have employed pre-steady state kinetic methodology to establish a kinetic basis for nucleotide selection by human Rev1, a unique nucleotidyl transferase that uses a protein template-directed mechanism to preferentially instruct dCTP incorporation. This work demonstrated that the high incorporation efficiency of dCTP is dependent on both substrates: an incoming dCTP and a templating base dG. The extremely low base substitution fidelity of human Rev1 (100 to 10-5) was due to the preferred misincorporation of dCTP with templating bases dA, dT, and dC over correct dNTPs. Using non-natural nucleotide analogs, we showed that hydrogen bonding interactions between residue R357 of human Rev1 and an incoming dNTP are not essential for DNA synthesis. Lastly, human Rev1 discriminates between ribonucleotides and deoxyribonucleotides mainly by reducing the rate of incorporation, and the sugar selectivity of human Rev1 is sensitive to both the size and orientation of the 2′-substituent of a ribonucleotide. PMID:20518555

  5. Modeling of kinetics of the inducible protein complexes of the SOS system in bacteria E. coli which realize TLS process

    International Nuclear Information System (INIS)

    Belov, O.V.

    2008-01-01

    The mathematical model describing kinetics of the inducible genes of the protein complexes, formed during SOS response in bacteria Escherichia coli is developed. Within the bounds of developed approaches the auxiliary mathematical model describing changes in concentrations of the dimers, which are the components of final protein complexes, is developed. The solutions of both models are based on the experimental data concerning expression of the basic genes of the SOS system in bacteria Escherichia coli

  6. Cell-Free Protein Synthesis Enhancement from Real-Time NMR Metabolite Kinetics: Redirecting Energy Fluxes in Hybrid RRL Systems.

    Science.gov (United States)

    Panthu, Baptiste; Ohlmann, Théophile; Perrier, Johan; Schlattner, Uwe; Jalinot, Pierre; Elena-Herrmann, Bénédicte; Rautureau, Gilles J P

    2018-01-19

    A counterintuitive cell-free protein synthesis (CFPS) strategy, based on reducing the ribosomal fraction in rabbit reticulocyte lysate (RRL), triggers the development of hybrid systems composed of RRL ribosome-free supernatant complemented with ribosomes from different mammalian cell-types. Hybrid RRL systems maintain translational properties of the original ribosome cell types, and deliver protein expression levels similar to RRL. Here, we show that persistent ribosome-associated metabolic activity consuming ATP is a major obstacle for maximal protein yield. We provide a detailed picture of hybrid CFPS systems energetic metabolism based on real-time nuclear magnetic resonance (NMR) investigation of metabolites kinetics. We demonstrate that protein synthesis capacity has an upper limit at native ribosome concentration and that lower amounts of the ribosomal fraction optimize energy fluxes toward protein translation, consequently increasing CFPS yield. These results provide a rationalized strategy for further mammalian CFPS developments and reveal the potential of real-time NMR metabolism phenotyping for optimization of cell-free protein expression systems.

  7. Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis.

    Science.gov (United States)

    Honda, Ryo

    2018-02-27

    Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP Sc . Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Whole body creatine and protein kinetics in healthy men and women: effects of creatine and amino acid supplementation.

    Science.gov (United States)

    Kalhan, Satish C; Gruca, Lourdes; Marczewski, Susan; Bennett, Carole; Kummitha, China

    2016-03-01

    Creatine kinetics were measured in young healthy subjects, eight males and seven females, age 20-30 years, after an overnight fast on creatine-free diet. Whole body turnover of glycine and its appearance in creatine was quantified using [1-(13)C] glycine and the rate of protein turnover was quantified using L-ring [(2)H5] phenylalanine. The creatine pool size was estimated by the dilution of a bolus [C(2)H3] creatine. Studies were repeated following a five days supplement creatine 21 g.day(-1) and following supplement amino acids 14.3 g day(-1). Creatine caused a ten-fold increase in the plasma concentration of creatine and a 50 % decrease in the concentration of guanidinoacetic acid. Plasma amino acids profile showed a significant decrease in glycine, glutamine, and taurine and a significant increase in citrulline, valine, lysine, and cysteine. There was a significant decrease in the rate of appearance of glycine, suggesting a decrease in de-novo synthesis (p = 0.006). The fractional and absolute rate of synthesis of creatine was significantly decreased by supplemental creatine. Amino acid supplement had no impact on any of the parameters. This is the first detailed analysis of creatine kinetics and the effects of creatine supplement in healthy young men and women. These methods can be applied for the analysis of creatine kinetics in different physiological states.

  9. The Kinetics of Crystallization of Colloids and Proteins: A Light Scattering Study

    Science.gov (United States)

    McClymer, Jim

    2002-01-01

    Hard-sphere colloidal systems serve as model systems for aggregation, nucleation, crystallization and gelation as well as interesting systems in their own right.There is strong current interest in using colloidal systems to form photonic crystals. A major scientific thrust of NASA's microgravity research is the crystallization of proteins for structural determination. The crystallization of proteins is a complicated process that requires a great deal of trial and error experimentation. In spite of a great deal of work, "better" protein crystals cannot always be grown in microgravity and conditions for crystallization are not well understood. Crystallization of colloidal systems interacting as hard spheres and with an attractive potential induced by entropic forces have been studied in a series of static light scattering experiments. Additionally, aggregation of a protein as a function of pH has been studied using dynamic light scattering. For our experiments we used PMMA (polymethylacrylate) spherical particles interacting as hard spheres, with no attractive potential. These particles have a radius of 304 nanometers, a density of 1.22 gm/ml and an index of refraction of 1.52. A PMMA colloidal sample at a volume fraction of approximately 54% was index matched in a solution of cycloheptyl bromide (CHB) and cis-decalin. The sample is in a glass cylindrical vial that is placed in an ALV static and dynamic light scattering goniometer system. The vial is immersed in a toluene bath for index matching to minimize flair. Vigorous shaking melts any colloidal crystals initially present. The sample is illuminated with diverging laser light (632.8 nanometers) from a 4x microscope objective placed so that the beam is approximately 1 cm in diameter at the sample location. The sample is rotated about its long axis at approximately 3.5 revolutions per minute (highest speed) as the colloidal crystal system is non-ergodic. The scattered light is detected at various angles using the

  10. Study of the interactions between riboflavin and protein

    International Nuclear Information System (INIS)

    Zhao Hongwei; Zhang Zhaoxia; Zhu Hongping; Ge Min; Miao Jinling; Wang Wenfeng; Yao Side

    2006-01-01

    Riboflavin (VB 2 ), a vitamin that is a natural constituent of living organisms, plays an important role in the process of metabolism and it is essential for normal cellular functions and growth. As an endogenous photosensitizer, riboflavin induces photooxidation damages to cells of skin and eye, causing inflammation, accelerated aging and mutation. The photodynamic actions of riboflavin on DNA have been studied extensively, however, its photodynamic actions on protein and enzyme are less studied due to the complex types and structures of proteins, and less attentions have been paid to photosensitive protein damages than DNA. In our lab, the interactions between riboflavin and serum albumin and lysozyme have been carried out by using transient absorption spectrometry, emission spectrometer analysis and electrophoresis techniques. It was found that stable state products and transient process of photosensitive damage to proteins were closely relative to concentration of riboflavin, time of irradiation and the atmosphere of the solutions. The results indicates that proteins can be photosensitive damaged by riboflavin irradiated by UV lights. Riboflavin can quench the intrinsic fluorescence of protein. Both dynamic and static quenching are simultaneous involved. The binding constants, the kinetics and spectroscopic properties of riboflavin interaction with albumin and lysozyme have also been investigated. Mechanisms of the photosensitive damages to proteins were discussed. The experiments also indicated that antioxidants such as melatonin and chlorogenic acid can reduce the damage of lysozyme effectively. (authors)

  11. Kinetic modelling of the Maillard reaction between proteins and sugars

    NARCIS (Netherlands)

    Brands, C.M.J.

    2002-01-01

    Keywords: Maillard reaction, sugar isomerisation, kinetics, multiresponse modelling, brown colour formation, lysine damage, mutagenicity, casein, monosaccharides, disaccharides, aldoses, ketoses

    The aim of this thesis was to determine the kinetics of the Maillard reaction between

  12. Solvent Effects on Protein Folding/Unfolding

    Science.gov (United States)

    García, A. E.; Hillson, N.; Onuchic, J. N.

    Pressure effects on the hydrophobic potential of mean force led Hummer et al. to postulate a model for pressure denaturation of proteins in which denaturation occurs by means of water penetration into the protein interior, rather than by exposing the protein hydrophobic core to the solvent --- commonly used to describe temperature denaturation. We study the effects of pressure in protein folding/unfolding kinetics in an off-lattice minimalist model of a protein in which pressure effects have been incorporated by means of the pair-wise potential of mean force of hydrophobic groups in water. We show that pressure slows down the kinetics of folding by decreasing the reconfigurational diffusion coefficient and moves the location of the folding transition state.

  13. Interaction between bacterial outer membrane proteins and periplasmic quality control factors: a kinetic partitioning mechanism.

    Science.gov (United States)

    Wu, Si; Ge, Xi; Lv, Zhixin; Zhi, Zeyong; Chang, Zengyi; Zhao, Xin Sheng

    2011-09-15

    The OMPs (outer membrane proteins) of Gram-negative bacteria have to be translocated through the periplasmic space before reaching their final destination. The aqueous environment of the periplasmic space and high permeability of the outer membrane engender such a translocation process inevitably challenging. In Escherichia coli, although SurA, Skp and DegP have been identified to function in translocating OMPs across the periplasm, their precise roles and their relationship remain to be elucidated. In the present paper, by using fluorescence resonance energy transfer and single-molecule detection, we have studied the interaction between the OMP OmpC and these periplasmic quality control factors. The results of the present study reveal that the binding rate of OmpC to SurA or Skp is much faster than that to DegP, which may lead to sequential interaction between OMPs and different quality control factors. Such a kinetic partitioning mechanism for the chaperone-substrate interaction may be essential for the quality control of the biogenesis of OMPs.

  14. Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro.

    Directory of Open Access Journals (Sweden)

    Sophia Rudorf

    2014-10-01

    Full Text Available The molecular machinery of life relies on complex multistep processes that involve numerous individual transitions, such as molecular association and dissociation steps, chemical reactions, and mechanical movements. The corresponding transition rates can be typically measured in vitro but not in vivo. Here, we develop a general method to deduce the in-vivo rates from their in-vitro values. The method has two basic components. First, we introduce the kinetic distance, a new concept by which we can quantitatively compare the kinetics of a multistep process in different environments. The kinetic distance depends logarithmically on the transition rates and can be interpreted in terms of the underlying free energy barriers. Second, we minimize the kinetic distance between the in-vitro and the in-vivo process, imposing the constraint that the deduced rates reproduce a known global property such as the overall in-vivo speed. In order to demonstrate the predictive power of our method, we apply it to protein synthesis by ribosomes, a key process of gene expression. We describe the latter process by a codon-specific Markov model with three reaction pathways, corresponding to the initial binding of cognate, near-cognate, and non-cognate tRNA, for which we determine all individual transition rates in vitro. We then predict the in-vivo rates by the constrained minimization procedure and validate these rates by three independent sets of in-vivo data, obtained for codon-dependent translation speeds, codon-specific translation dynamics, and missense error frequencies. In all cases, we find good agreement between theory and experiment without adjusting any fit parameter. The deduced in-vivo rates lead to smaller error frequencies than the known in-vitro rates, primarily by an improved initial selection of tRNA. The method introduced here is relatively simple from a computational point of view and can be applied to any biomolecular process, for which we have

  15. Compartmental Modeling and Dosimetry of in Vivo Metabolic Studies of Leucine and Three Secretory Proteins in Humans Using Radioactive Tracers

    Science.gov (United States)

    Venkatakrishnan, Vaidehi

    1995-01-01

    Physical and mathematical models provide a systematic means of looking at biological systems. Radioactive tracer kinetic studies open a unique window to study complex tracee systems such as protein metabolism in humans. This research deals with compartmental modeling of tracer kinetic data on leucine and apolipoprotein metabolism obtained using an endogenous tritiated leucine tracer administered as a bolus, and application of compartmental modeling techniques for dosimetric evaluation of metabolic studies of radioiodinated apolipoproteins. Dr. Waldo R. Fisher, Department of Medicine, was the coordinating research supervisor and the work was carried out in his laboratory. A compartmental model for leucine kinetics in humans has been developed that emphasizes its recycling pathways which were examined over two weeks. This model builds on a previously published model of Cobelli et al, that analyzed leucine kinetic data up to only eight hours. The proposed model includes different routes for re-entry of leucine from protein breakdown into plasma accounting for proteins which turn over at different rates. This new model successfully incorporates published models of three secretory proteins: albumin, apoA-I, and VLDL apoB, in toto thus increasing its validity and utility. The published model of apoA-I, based on an exogenous radioiodinated tracer, was examined with data obtained using an endogenous leucine tracer using compartmental techniques. The analysis concludes that the major portion of apoA-I enters plasma by a fast pathway but the major fraction of apoA-I in plasma resides with a second slow pathway; further the study is suggestive of a precursor-product relationship between the two plasma apoA-I pools. The possible relevance of the latter suggestion to the aberrant kinetics of apoA-I in Tangier disease is discussed. The analysis of apoA-II data resulted in similar conclusions. A methodology for evaluating the dosimetry of radioiodinated apolipoproteins by

  16. Analytical techniques for the study of polyphenol-protein interactions.

    Science.gov (United States)

    Poklar Ulrih, Nataša

    2017-07-03

    This mini review focuses on advances in biophysical techniques to study polyphenol interactions with proteins. Polyphenols have many beneficial pharmacological properties, as a result of which they have been the subject of intensive studies. The most conventional techniques described here can be divided into three groups: (i) methods used for screening (in-situ methods); (ii) methods used to gain insight into the mechanisms of polyphenol-protein interactions; and (iii) methods used to study protein aggregation and precipitation. All of these methods used to study polyphenol-protein interactions are based on modifications to the physicochemical properties of the polyphenols or proteins after binding/complex formation in solution. To date, numerous review articles have been published in the field of polyphenols. This review will give a brief insight in computational methods and biosensors and cell-based methods, spectroscopic methods including fluorescence emission, UV-vis adsorption, circular dichroism, Fourier transform infrared and mass spectrometry, nuclear magnetic resonance, X-ray diffraction, and light scattering techniques including small-angle X-ray scattering and small-angle neutron scattering, and calorimetric techniques (isothermal titration calorimetry and differential scanning calorimetry), microscopy, the techniques which have been successfully used for polyphenol-protein interactions. At the end the new methods based on single molecule detection with high potential to study polyphenol-protein interactions will be presented. The advantages and disadvantages of each technique will be discussed as well as the thermodynamic, kinetic or structural parameters, which can be obtained. The other relevant biophysical experimental techniques that have proven to be valuable, such electrochemical methods, hydrodynamic techniques and chromatographic techniques will not be described here.

  17. Kinetic study of UV-irradiated amorphous sulfur by EPR spectroscopy

    International Nuclear Information System (INIS)

    El Mkami, H.; Smith, G.M.

    2005-01-01

    Electron paramagnetic resonance (EPR) spectroscopy is used to investigate UV-irradiation damage in amorphous sulfur by examining post-irradiation kinetics as a function of UV-exposure time. The kinetic study is described by first-order concurrent reactions where the sulfur, as reactant, undergoes two parallel processes leading to the formation of two distinct defects called S 1 * and S 2 *. The temperature dependence of the EPR intensities of the signals, related to these defects, is used in the kinetic study

  18. Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies.

    Science.gov (United States)

    Noguchi, Hiroki; Mylemans, Bram; De Zitter, Elke; Van Meervelt, Luc; Tame, Jeremy R H; Voet, Arnout

    2018-03-18

    β-propeller proteins are highly symmetrical, being composed of a repeated motif with four anti-parallel β-sheets arranged around a central axis. Recently we designed the first completely symmetrical β-propeller protein, Pizza6, consisting of six identical tandem repeats. Pizza6 is expected to prove a useful building block for bionanotechnology, and also a tool to investigate the folding and evolution of β-propeller proteins. Folding studies are made difficult by the high stability and the lack of buried Trp residues to act as monitor fluorophores, so we have designed and characterized several Trp-containing Pizza6 derivatives. In total four proteins were designed, of which three could be purified and characterized. Crystal structures confirm these mutant proteins maintain the expected structure, and a clear redshift of Trp fluorescence emission could be observed upon denaturation. Among the derivative proteins, Pizza6-AYW appears to be the most suitable model protein for future folding/unfolding kinetics studies as it has a comparable stability as natural β-propeller proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Analysis of the kinetic mechanism of recombinant human isoprenylcysteine carboxylmethyltransferase (Icmt

    Directory of Open Access Journals (Sweden)

    Baron Rudi A

    2004-12-01

    Full Text Available Abstract Background Isoprenylcysteine carboxyl methyltransferase (Icmt is the third of three enzymes that posttranslationally modify proteins that contain C-terminal CaaX motifs. The processing of CaaX proteins through this so-called prenylation pathway via a route initiated by addition of an isoprenoid lipid is required for both membrane targeting and function of the proteins. The involvement of many CaaX proteins such as Ras GTPases in oncogenesis and other aberrant proliferative disorders has led to the targeting of the enzymes involved in their processing for therapeutic development, necessitating a detailed understanding of the mechanisms of the enzymes. Results In this study, we have investigated the kinetic mechanism of recombinant human Icmt. In the reaction catalyzed by Icmt, S-adenosyl-L-methionine (AdoMet provides the methyl group that is transferred to the second substrate, the C-terminal isoprenylated cysteine residue of a CaaX protein, thereby generating a C-terminal prenylcysteine methyl ester on the protein. To facilitate the kinetic analysis of Icmt, we synthesized a new small molecule substrate of the enzyme, biotin-S-farnesyl-L-cysteine (BFC. Initial kinetic analysis of Icmt suggested a sequential mechanism for the enzyme that was further analyzed using a dead end competitive inhibitor, S-farnesylthioacetic acid (FTA. Inhibition by FTA was competitive with respect to BFC and uncompetitive with respect to AdoMet, indicating an ordered mechanism with SAM binding first. To investigate the order of product dissociation, product inhibition studies were undertaken with S-adenosyl-L-homocysteine (AdoHcy and the N-acetyl-S-farnesyl-L-cysteine methylester (AFCME. This analysis indicated that AdoHcy is a competitive inhibitor with respect to AdoMet, while AFCME shows a noncompetitive inhibition with respect to BFC and a mixed-type inhibition with respect to AdoMet. These studies established that AdoHcy is the final product released, and

  20. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

    Science.gov (United States)

    Kouza, Maksim; Co, Nguyen Truong; Li, Mai Suan; Kmiecik, Sebastian; Kolinski, Andrzej; Kloczkowski, Andrzej; Buhimschi, Irina Alexandra

    2018-06-01

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40 and Aβ42 and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics.

  1. Kinetic-energy functionals studied by surface calculations

    DEFF Research Database (Denmark)

    Vitos, Levente; Skriver, Hans Lomholt; Kollár, J.

    1998-01-01

    The self-consistent jellium model of metal surfaces is used to study the accuracy of a number of semilocal kinetic-energy functionals for independent particles. It is shown that the poor accuracy exhibited by the gradient expansion approximation and most of the semiempirical functionals in the lo...... density, high gradient limit may be subtantially improved by including locally a von Weizsacker term. Based on this, we propose a simple one-parameter Pade's approximation, which reproduces the exact Kohn-Sham surface kinetic energy over the entire range of metallic densities....

  2. Hydrogen exchange kinetics in a membrane protein determined by 15N NMR spectroscopy: Use of the INEPT [insensitive nucleus enhancement by polarization transfer] experiment to follow individual amides in detergent-solubilized M13 coat protein

    International Nuclear Information System (INIS)

    Henry, G.D.; Sykes, B.D.

    1990-01-01

    The coat protein of the filamentous coliphage M13 is a 50-residue polypeptide which spans the inner membrane of the Escherichia coli host upon infection. Amide hydrogen exchange kinetics have been used to probe the structure and dynamics of M13 coat protein which has been solubilized in sodium dodecyl sulfate (SDS) micelles. In a previous 1 H nuclear magnetic resonance (NMR) study, multiple exponential analysis of the unresolved amide proton envelope revealed the existence of two slow kinetic sets containing a total of about 30 protons. The slower set (15-20 amides) originates from the hydrophobic membrane-spanning region and exchanges at least 10 5 -fold slower than the unstructured, non-H-bonded model polypeptide poly(DL-alanine). Herein the authors use 15 N NMR spectroscopy of biosynthetically labeled coat protein to follow individual, assigned, slowly exchanging amides in or near the hydrophobic segment. The INEPT (insensitive nucleus enhancement by polarization transfer) experiments can be used to transfer magnetization to the 15 N nucleus from a coupled proton; when 15 N-labeled protonated protein is dissolved in 2 H 2 O, the INEPT signal disappears with time as the amide protons are replaced by solvent deuterons. Amide hydrogen exchange is catalyzed by both H + and OH - ions. The time-dependent exchange-out experiment is suitable for slow exchange rates (k ex ). The INEPT experiment was also adapted to measure some of the more rapidly exchanging amides in the coat protein using either saturation transfer from water or exchange effects on the polarization transfer step itself. The results of all of these experiments are consistent with previous models of the coat protein in which a stable segment extends from the hydrophobic membrane-spanning region through to the C-terminus, whereas the N-terminal region is undergoing more extensive dynamic fluctuations

  3. Characterization of CobB kinetics and inhibition by nicotinamide.

    Directory of Open Access Journals (Sweden)

    Julia Gallego-Jara

    Full Text Available Lysine acetylation has emerged as a global protein regulation system in all domains of life. Sirtuins, or Sir2-like enzymes, are a family of histone deacetylases characterized by their employing NAD+ as a co-substrate. Sirtuins can deacetylate several acetylated proteins, but a consensus substrate recognition sequence has not yet been established. Product inhibition of many eukaryotic sirtuins by nicotinamide and its analogues has been studied in vitro due to their potential role as anticancer agents. In this work, the kinetics of CobB, the main Escherichia coli deacetylase, have been characterized. To our knowledge, this is the first kinetic characterization of a sirtuin employing a fully acetylated and natively folded protein as a substrate. CobB deacetylated several acetyl-CoA synthetase acetylated lysines with a single kinetic rate. In addition, in vitro nicotinamide inhibition of CobB has been characterized, and the intracellular nicotinamide concentrations have been determined under different growth conditions. The results suggest that nicotinamide can act as a CobB regulator in vivo. A nicotinamidase deletion strain was thus phenotypically characterized, and it behaved similarly to the ΔcobB strain. The results of this work demonstrate the potential regulatory role of the nicotinamide metabolite in vivo.

  4. Characterization of CobB kinetics and inhibition by nicotinamide.

    Science.gov (United States)

    Gallego-Jara, Julia; Écija Conesa, Ana; de Diego Puente, Teresa; Lozano Terol, Gema; Cánovas Díaz, Manuel

    2017-01-01

    Lysine acetylation has emerged as a global protein regulation system in all domains of life. Sirtuins, or Sir2-like enzymes, are a family of histone deacetylases characterized by their employing NAD+ as a co-substrate. Sirtuins can deacetylate several acetylated proteins, but a consensus substrate recognition sequence has not yet been established. Product inhibition of many eukaryotic sirtuins by nicotinamide and its analogues has been studied in vitro due to their potential role as anticancer agents. In this work, the kinetics of CobB, the main Escherichia coli deacetylase, have been characterized. To our knowledge, this is the first kinetic characterization of a sirtuin employing a fully acetylated and natively folded protein as a substrate. CobB deacetylated several acetyl-CoA synthetase acetylated lysines with a single kinetic rate. In addition, in vitro nicotinamide inhibition of CobB has been characterized, and the intracellular nicotinamide concentrations have been determined under different growth conditions. The results suggest that nicotinamide can act as a CobB regulator in vivo. A nicotinamidase deletion strain was thus phenotypically characterized, and it behaved similarly to the ΔcobB strain. The results of this work demonstrate the potential regulatory role of the nicotinamide metabolite in vivo.

  5. Fluorescent Protein Voltage Probes Derived from ArcLight that Respond to Membrane Voltage Changes with Fast Kinetics

    Science.gov (United States)

    Han, Zhou; Jin, Lei; Platisa, Jelena; Cohen, Lawrence B.; Baker, Bradley J.; Pieribone, Vincent A.

    2013-01-01

    We previously reported the discovery of a fluorescent protein voltage probe, ArcLight, and its derivatives that exhibit large changes in fluorescence intensity in response to changes of plasma membrane voltage. ArcLight allows the reliable detection of single action potentials and sub-threshold activities in individual neurons and dendrites. The response kinetics of ArcLight (τ1-on ~10 ms, τ2-on ~ 50 ms) are comparable with most published genetically-encoded voltage probes. However, probes using voltage-sensing domains other than that from the Ciona intestinalis voltage sensitive phosphatase exhibit faster kinetics. Here we report new versions of ArcLight, in which the Ciona voltage-sensing domain was replaced with those from chicken, zebrafish, frog, mouse or human. We found that the chicken and zebrafish-based ArcLight exhibit faster kinetics, with a time constant (τ) less than 6ms for a 100 mV depolarization. Although the response amplitude of these two probes (8-9%) is not as large as the Ciona-based ArcLight (~35%), they are better at reporting action potentials from cultured neurons at higher frequency. In contrast, probes based on frog, mouse and human voltage sensing domains were either slower than the Ciona-based ArcLight or had very small signals. PMID:24312287

  6. Fluorescent protein voltage probes derived from ArcLight that respond to membrane voltage changes with fast kinetics.

    Directory of Open Access Journals (Sweden)

    Zhou Han

    Full Text Available We previously reported the discovery of a fluorescent protein voltage probe, ArcLight, and its derivatives that exhibit large changes in fluorescence intensity in response to changes of plasma membrane voltage. ArcLight allows the reliable detection of single action potentials and sub-threshold activities in individual neurons and dendrites. The response kinetics of ArcLight (τ1-on ~10 ms, τ2-on ~ 50 ms are comparable with most published genetically-encoded voltage probes. However, probes using voltage-sensing domains other than that from the Ciona intestinalis voltage sensitive phosphatase exhibit faster kinetics. Here we report new versions of ArcLight, in which the Ciona voltage-sensing domain was replaced with those from chicken, zebrafish, frog, mouse or human. We found that the chicken and zebrafish-based ArcLight exhibit faster kinetics, with a time constant (τ less than 6 ms for a 100 mV depolarization. Although the response amplitude of these two probes (8-9% is not as large as the Ciona-based ArcLight (~35%, they are better at reporting action potentials from cultured neurons at higher frequency. In contrast, probes based on frog, mouse and human voltage sensing domains were either slower than the Ciona-based ArcLight or had very small signals.

  7. Kinetic Study on Pyrolysis of Oil Palm Frond

    International Nuclear Information System (INIS)

    Soon, V S Y; Chin, B L F; Lim, A C R

    2016-01-01

    The pyrolysis of oil palm frond is studied using thermogravimetric analysis (TGA) equipment. The present study investigates the thermal degradation behaviour and determination of the kinetic parameters such as the activation energy (E A ) and pre-exponential factor (A) values of oil palm frond under pyrolysis condition. The kinetic data is produced based on first order rate of reaction. In this study, the experiments are conducted at different heating rates of 10, 20, 30, 40 and 50 K/min in the temperature range of 323-1173 K under non-isothermal condition. Argon gas is used as an inert gas to remove any entrapment of gases in the TGA equipment. (paper)

  8. Kinetic study of ozonation of molasses fermentation wastewater

    International Nuclear Information System (INIS)

    Coca, M.; Pena, M.; Gonzalez, G.

    2007-01-01

    A kinetic study of molasses wastewater ozonation was carried out in a stirred tank reactor to obtain the rate constants for the decolorization reaction and the regime through which ozone is absorbed. First, fundamental mass transfer parameters such as ozone solubility, volumetric mass transfer coefficients and ozone decomposition kinetics were determined from semi-batch experiments in organic-free solutions with an ionic composition similar that of industrial wastewater. The influence of operating variables such as the stirring rate and gas flow rate on the kinetic and mass transfer parameters was also studied. The application of film theory allows to establish that the reactions between ozone and colored compounds in wastewater take place in the fast and pseudo-first-order regime, within the liquid film. The decolorization rate constants were evaluated at pH 8.7 and 25 deg. C, varying from 0.6 x 10 7 to 3.8 x 10 7 L mol -1 s -1 , depending on the stirring rate and the inlet gas flow

  9. Kinetic study on Iranian furfural extract hydrocracking

    Energy Technology Data Exchange (ETDEWEB)

    Zarkesh, J.; Akbarnejad, M. M. [NIOC Research Institute of Petroleum Industry, Tehran (Iran, Islamic Republic of); Khorasheh, F. [Sharif Univ. of Technology, Tehran (Iran, Islamic Republic of); Badakhshan, A. [Calgary Univ., AB (Canada)

    1998-05-01

    Upgrading heavy crude oil to light crude oil is one of the most important refining processes. Familiarity with the kinetics and related kinetic models is one of the important aspects of developing expertise in this field. This joint study between the NIOC Institute of Research of the Petroleum Industry and Sharif University was undertaken to determine the most appropriate upgrading process for Iranian heavy feed stock and to predict the conversion and product distribution in commercial hydrocracking units. The study involved the evaluation of stoichiometry of the hydrocracking process, focusing on the catalytic hydrocracking of furfural extract (a by-product of the lubricating oil plant) of the Tehran refinery. A pilot plant reactor was used. Good correspondence between model predictions and theoretical values was obtained.

  10. Kinetics of the association of dengue virus capsid protein with the granular component of nucleolus.

    Science.gov (United States)

    Tiwary, Ashish Kumar; Cecilia, D

    2017-02-01

    Dengue virus (DENV) replicates in the cytoplasm but translocation of the capsid protein (C) to the nucleoli of infected cells has been shown to facilitate virus multiplication for DENV-2. This study demonstrates that the nucleolar localization of C occurs with all four serotypes of DENV. The interaction of C with the nucleolus was found to be dynamic with a mobile fraction of 66% by FRAP. That the C shuttled between the nucleus and cytoplasm was suggested by FLIP and translation inhibition experiments. Colocalization with B23 indicated that DENV C targeted the granular component (GC) of the nucleolus. Presence of DENV C in the nucleolus affected the recovery kinetics of B23 in infected and transfected cells. Sub-nucleolar localization of DENV C of all serotypes to the GC, its mobility in and out of the nucleolus and its affect on the dynamics of B23 is being shown for the first time. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. In-Situ Optical Studies of Oxidation/Reduction Kinetics on SOFC Cermet Anodes

    Science.gov (United States)

    2010-12-28

    DATES COVERED (From - To) 1/29/10-9/30/10 4. TITLE AND SUBTITLE In situ optical studies of oxidation/reduction kinetics on SOFC cermet anodes 5a...0572 In-situ Optical Studies of Oxidation/Reduction Kinetics on SOFC Cermet Anodes Department of Chemistry and Biochemistry Montana State University...of Research In-situ Optical Studies of Oxidation/Reduction Kinetics on SOFC Cermet Anodes Principal Investigator Robert Walker Organization

  12. A Critical Appraisal of Quantitative Studies of Protein Degradation in the Framework of Cellular Proteostasis

    Directory of Open Access Journals (Sweden)

    Beatriz Alvarez-Castelao

    2012-01-01

    Full Text Available Protein homeostasis, proteostasis, is essential to understand cell function. Protein degradation is a crucial component of the proteostatic mechanisms of the cell. Experiments on protein degradation are nowadays present in many investigations in the field of molecular and cell biology. In the present paper, we focus on the different experimental approaches to study protein degradation and present a critical appraisal of the results derived from steady-state and kinetic experiments using detection of unlabelled and labelled protein methodologies with a proteostatic perspective. This perspective allows pinpointing the limitations in interpretation of results and the need of further experiments and/or controls to establish “definitive evidence” for the role of protein degradation in the proteostasis of a given protein or the entire proteome. We also provide a spreadsheet for simple calculations of mRNA and protein decays for mimicking different experimental conditions and a checklist for the analysis of experiments dealing with protein degradation studies that may be useful for researchers interested in the area of protein turnover.

  13. c-SRC mediates neurite outgrowth through recruitment of Crk to the scaffolding protein Sin/Efs without altering the kinetics of ERK activation

    DEFF Research Database (Denmark)

    Yang, Liang-Tung; Alexandropoulos, Konstantina; Sap, Jan

    2002-01-01

    moderate activation of endogenous SRC by receptor-protein-tyrosine phosphatase alpha (a physiological SRC activator). We show that such a qualitative change in the response to EGF is not accompanied by changes in the extent or kinetics of ERK induction in response to this factor. Instead, the pathway...

  14. Studying protein assembly with reversible Brownian dynamics of patchy particles

    International Nuclear Information System (INIS)

    Klein, Heinrich C. R.; Schwarz, Ulrich S.

    2014-01-01

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly

  15. Studying protein assembly with reversible Brownian dynamics of patchy particles

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: ulrich.schwarz@bioquant.uni-heidelberg.de [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)

    2014-05-14

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.

  16. Adsorption of a small protein to a methyl-terminated hydrophobic surfaces

    DEFF Research Database (Denmark)

    Otzen, Daniel; Oliveberg, M.; Höök, F.

    2003-01-01

    We have studied the adsorption kinetics of a small monomeric protein S6 using the quartz crystal microbalance with dissipation monitoring (QCM-D) technique. Competitive adsorption from various proportions of native (Nat) and denatured (Den) protein in the bulk phase was carried out using a range...... of chemical denaturant concentrations. The ratio between Nat and Den in bulk has a profound affect on the adsorption behavior, most obvious from a significant (one order of magnitude) increase in the rate of a lag– and consolidation–adsorption phase when Nat is the major species present in bulk, signaling...... that these adsorption phases originates from the Den fraction of proteins in the bulk. To determine whether the kinetics of protein unfolding in the bulk phase are rate-limiting for adsorption of Nat, the adsorption kinetics of wildtype S6 with the mutant VA85 (whose unfolding kinetics are around 30 times more rapid...

  17. Load-dependent surface diffusion model for analyzing the kinetics of protein adsorption onto mesoporous materials.

    Science.gov (United States)

    Marbán, Gregorio; Ramírez-Montoya, Luis A; García, Héctor; Menéndez, J Ángel; Arenillas, Ana; Montes-Morán, Miguel A

    2018-02-01

    The adsorption of cytochrome c in water onto organic and carbon xerogels with narrow pore size distributions has been studied by carrying out transient and equilibrium batch adsorption experiments. It was found that equilibrium adsorption exhibits a quasi-Langmuirian behavior (a g coefficient in the Redlich-Peterson isotherms of over 0.95) involving the formation of a monolayer of cyt c with a depth of ∼4nm on the surface of all xerogels for a packing density of the protein inside the pores of 0.29gcm -3 . A load-dependent surface diffusion model (LDSDM) has been developed and numerically solved to fit the experimental kinetic adsorption curves. The results of the LDSDM show better fittings than the standard homogeneous surface diffusion model. The value of the external mass transfer coefficient obtained by numerical optimization confirms that the process is controlled by the intraparticle surface diffusion of cyt c. The surface diffusion coefficients decrease with increasing protein load down to zero for the maximum possible load. The decrease is steeper in the case of the xerogels with the smallest average pore diameter (∼15nm), the limit at which the zero-load diffusion coefficient of cyt c also begins to be negatively affected by interactions with the opposite wall of the pore. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life.

    Directory of Open Access Journals (Sweden)

    M Luisa Romero-Romero

    Full Text Available The relationship between the denaturation temperatures of proteins (Tm values and the living temperatures of their host organisms (environmental temperatures: TENV values is poorly understood. Since different proteins in the same organism may show widely different Tm's, no simple universal relationship between Tm and TENV should hold, other than Tm≥TENV. Yet, when analyzing a set of homologous proteins from different hosts, Tm's are oftentimes found to correlate with TENV's but this correlation is shifted upward on the Tm axis. Supporting this trend, we recently reported Tm's for resurrected Precambrian thioredoxins that mirror a proposed environmental cooling over long geological time, while remaining a shocking ~50°C above the proposed ancestral ocean temperatures. Here, we show that natural selection for protein kinetic stability (denaturation rate can produce a Tm↔TENV correlation with a large upward shift in Tm. A model for protein stability evolution suggests a link between the Tm shift and the in vivo lifetime of a protein and, more specifically, allows us to estimate ancestral environmental temperatures from experimental denaturation rates for resurrected Precambrian thioredoxins. The TENV values thus obtained match the proposed ancestral ocean cooling, support comparatively high Archaean temperatures, and are consistent with a recent proposal for the environmental temperature (above 75°C that hosted the last universal common ancestor. More generally, this work provides a framework for understanding how features of protein stability reflect the environmental temperatures of the host organisms.

  19. Novel swirl-flow reactor for kinetic studies of semiconductor photocatalysis

    NARCIS (Netherlands)

    Ray, A.K; Beenackers, A.A C M

    1997-01-01

    A new two-phase swirl-flow monolithic-type reactor was designed to study the kinetics of heterogeneous photocatalytic processes on immobilized semiconductor catalysts. True kinetic rate constants for destruction of a textile dye were measured as a function of wavelength of light intensity and angle

  20. Kinetic study of enzymatic hydrolysis of potato starch

    Directory of Open Access Journals (Sweden)

    Óscar Fernando Castellanos Domínguez

    2004-01-01

    Full Text Available This article describes the kinetic study of potato starch enzymatic hydrolysis using soluble enzymes (Novo Nordisk. Different assays divided into four groups were used: reaction time (with which it was possible to reduce the 48-72 hour duration reported in the literature to 16 hours with comparable productivity levels; selecting the set of enzymes to be used (different types were evaluated - BAN and Termamyl as alfa-amylases during dextrinisation stage, and AMG, Promozyme and Fungamyl for sacarification reaction- identifying those presenting the best performance during hydrolysis.Reaction conditions were optimised for the process's two stages (destrinisation and sacarification. Enzyme dose, calcium cofactor concentration, pH, temperature and agitation speed were studied for the first stage. Enzyme ratio, pH and agitation speed were studied for sacarification; the latter parameter reported values having no antecedents in the literature (60 rpm and 30 rpm for first and second reactions, respectively. Michaelis Menten kinetics were calculated once conditions had been optimised, varying substrate from 10-50% P/V, obtaining km and Vmax kinetic parameters for each reaction. A kinetic model was found according to local working conditions which was able to explain potato starch conversion to glucose syrup, achieving 96 dextrose equivalents by the end of the reaction, being well within the maximum range reported in the literature (94-98.Laboratory equipment was constructed prior to carrying out assays which was able to reproduce and improve the conditions reported in the literature, making it a useful, reliable tool for use in assays returning good results.

  1. Kinetics of ethylcyclohexane pyrolysis and oxidation: An experimental and detailed kinetic modeling study

    KAUST Repository

    Wang, Zhandong; Zhao, Long; Wang, Yu; Bian, Huiting; Zhang, Lidong; Zhang, Feng; Li, Yuyang; Sarathy, Mani; Qi, Fei

    2015-01-01

    species were evaluated, and good agreement was observed between the PIMS and GC data sets. Furthermore, a fuel-rich burner-stabilized laminar premixed ECH/O2/Ar flame at 30Torr was studied using synchrotron VUV PIMS. A detailed kinetic model for ECH high

  2. Energetics and Kinetics of trans-SNARE Zippering

    Science.gov (United States)

    Rebane, Aleksander A.; Shu, Tong; Krishnakumar, Shyam; Rothman, James E.; Zhang, Yongli

    Synaptic exocytosis relies on assembly of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins into a four-helix bundle to drive membrane fusion. Complementary SNAREs anchored to the synaptic vesicle (v-SNARE) and the plasma membrane (t-SNARE) associate from their N-termini, transiting a half-assembled intermediate (trans-SNARE), and ending at their C-termini with a rapid power stroke that leads to membrane fusion. Although cytosolic SNARE assembly has been characterized, it remains unknown how membranes modulate the energetics and kinetics of SNARE assembly. Here, we present optical tweezers measurements on folding of single membrane proteins in phospholipid bilayers. To our knowledge, this is the first such report. We measured the energetics, kinetics, and assembly intermediates of trans-SNAREs formed between a t-SNARE inserted into a bead-supported bilayer and a v-SNARE in a nanodisc. We found that the repulsive force of the apposed membranes increases the lifetime of the half-assembled intermediate. Our findings provide a single-molecule platform to study the regulation of trans-SNARE assembly by proteins that act on the half-assembled state, and thus reveal the mechanistic basis of the speed and high fidelity of synaptic transmission. This work was supported by US National Institutes of Health Grants F31 GM119312-01 (to A.A.R) and R01 GM093341 (to Y.Z.).

  3. Effect of resistance training and protein intake pattern on myofibrillar protein synthesis and proteome kinetics in older men in energy restriction.

    Science.gov (United States)

    Murphy, Caoileann H; Shankaran, Mahalakshmi; Churchward-Venne, Tyler A; Mitchell, Cameron J; Kolar, Nathan M; Burke, Louise M; Hawley, John A; Kassis, Amira; Karagounis, Leonidas G; Li, Kelvin; King, Chelsea; Hellerstein, Marc; Phillips, Stuart M

    2018-06-01

    Strategies to enhance the loss of fat while preserving muscle mass during energy restriction are of great importance to prevent sarcopenia in overweight older adults. We show for the first time that the integrated rate of synthesis of numerous individual contractile, cytosolic and mitochondrial skeletal muscle proteins was increased by resistance training (RT) and unaffected by dietary protein intake pattern during energy restriction in free-living, obese older men. We observed a correlation between the synthetic rates of skeletal muscle-derived proteins obtained in serum (creatine kinase M-type, carbonic anhydrase 3) and the synthetic rates of proteins obtained via muscle sampling; and that the synthesis rates of these proteins in serum revealed the stimulatory effects of RT. These results have ramifications for understanding the influence of RT on skeletal muscle and are consistent with the role of RT in maintaining muscle protein synthesis and potentially supporting muscle mass preservation during weight loss. We determined how the pattern of protein intake and resistance training (RT) influenced longer-term (2 weeks) integrated myofibrillar protein synthesis (MyoPS) during energy restriction (ER). MyoPS and proteome kinetics were measured during 2 weeks of ER alone and 2 weeks of ER plus RT (ER + RT) in overweight/obese older men. Participants were randomized to consume dietary protein in a balanced (BAL: 25% daily protein per meal × 4 meals) or skewed (SKEW: 7:17:72:4% daily protein per meal) pattern (n = 10 per group). Participants ingested deuterated water during the consecutive 2-week periods, and skeletal muscle biopsies and serum were obtained at the beginning and conclusion of ER and ER + RT. Bulk MyoPS (i.e. synthesis of the myofibrillar protein sub-fraction) and the synthetic rates of numerous individual skeletal muscle proteins were quantified. Bulk MyoPS was not affected by protein distribution during ER or ER + RT (ER: BAL = 1.24

  4. Microsecond time-scale kinetics of transient biochemical reactions

    NARCIS (Netherlands)

    Mitic, S.; Strampraad, M.J.F.; Hagen, W.R.; de Vries, S.

    2017-01-01

    To afford mechanistic studies in enzyme kinetics and protein folding in the microsecond time domain we have developed a continuous-flow microsecond time-scale mixing instrument with an unprecedented dead-time of 3.8 ± 0.3 μs. The instrument employs a micro-mixer with a mixing time of 2.7 μs

  5. Kinetic and Related Determinants of Plasma Triglyceride Concentration in Abdominal Obesity: Multicenter Tracer Kinetic Study.

    Science.gov (United States)

    Borén, Jan; Watts, Gerald F; Adiels, Martin; Söderlund, Sanni; Chan, Dick C; Hakkarainen, Antti; Lundbom, Nina; Matikainen, Niina; Kahri, Juhani; Vergès, Bruno; Barrett, P Hugh R; Taskinen, Marja-Riitta

    2015-10-01

    Patients with obesity and diabetes mellitus have increased risk of cardiovascular disease. A major cause is an atherogenic dyslipidemia related primarily to elevated plasma concentrations of triglyceride-rich lipoproteins. The aim of this study was to clarify determinants of plasma triglyceride concentration. We focused on factors that predict the kinetics of very-low density lipoprotein 1 (VLDL1) triglycerides. A multicenter study using dual stable isotopes (deuterated leucine and glycerol) and multicompartmental modeling was performed to elucidate the kinetics of triglycerides and apoB in VLDL1 in 46 subjects with abdominal obesity and additional cardiometabolic risk factors. Results showed that plasma triglyceride concentrations were dependent on both the secretion rate (r=0.44, Ptriglycerides and VLDL1-apoB. Liver fat mass was independently and directly associated with secretion rates of VLDL1-triglycerides (r=0.56, Ptriglycerides (r=0.48, Ptriglyceride concentrations in abdominal obesity are determined by the kinetics of VLDL1 subspecies, catabolism being mainly dependent on apoC-III concentration and secretion on liver fat content. Reduction in liver fat and targeting apoC-III may be an effective approach for correcting triglyceride metabolism atherogenic dyslipidemia in obesity. © 2015 American Heart Association, Inc.

  6. Flow-Based Systems for Rapid and High-Precision Enzyme Kinetics Studies

    Directory of Open Access Journals (Sweden)

    Supaporn Kradtap Hartwell

    2012-01-01

    Full Text Available Enzyme kinetics studies normally focus on the initial rate of enzymatic reaction. However, the manual operation of steps of the conventional enzyme kinetics method has some drawbacks. Errors can result from the imprecise time control and time necessary for manual changing the reaction cuvettes into and out of the detector. By using the automatic flow-based analytical systems, enzyme kinetics studies can be carried out at real-time initial rate avoiding the potential errors inherent in manual operation. Flow-based systems have been developed to provide rapid, low-volume, and high-precision analyses that effectively replace the many tedious and high volume requirements of conventional wet chemistry analyses. This article presents various arrangements of flow-based techniques and their potential use in future enzyme kinetics applications.

  7. Equilibrium, kinetic and thermodynamic studies of uranium biosorption by calcium alginate beads

    International Nuclear Information System (INIS)

    Bai, Jing; Fan, Fangli; Wu, Xiaolei; Tian, Wei; Zhao, Liang; Yin, Xiaojie; Fan, Fuyou; Li, Zhan; Tian, Longlong; Wang, Yang; Qin, Zhi; Guo, Junsheng

    2013-01-01

    Calcium alginate beads are potential biosorbent for radionuclides removal as they contain carboxyl groups. However, until now limited information is available concerning the uptake behavior of uranium by this polymer gel, especially when sorption equilibrium, kinetics and thermodynamics are concerned. In present work, batch experiments were carried out to study the equilibrium, kinetics and thermodynamics of uranium sorption by calcium alginate beads. The effects of initial solution pH, sorbent amount, initial uranium concentration and temperature on uranium sorption were also investigated. The determined optimal conditions were: initial solution pH of 3.0, added sorbent amount of 40 mg, and uranium sorption capacity increased with increasing initial uranium concentration and temperature. Equilibrium data obtained under different temperatures were fitted better with Langmuir model than Freundlich model, uranium sorption was dominated by a monolayer way. The kinetic data can be well depicted by the pseudo-second-order kinetic model. The activation energy derived from Arrhenius equation was 30.0 kJ/mol and the sorption process had a chemical nature. Thermodynamic constants such as ΔH 0 , ΔS 0 and ΔG 0 were also evaluated, results of thermodynamic study showed that the sorption process was endothermic and spontaneous. -- Highlights: • Equilibrium, kinetics and thermodynamics of uranium sorption by CaAlg were studied. • Equilibrium studies show that Langmuir isotherm better fit with experimental data. • Pseudo-second-order kinetics model is found to be well depicting the kinetic data. • Thermodynamic study shows that the sorption process is endothermic and spontaneous

  8. Periodic protein adsorption at the gold/biotin aqueous solution interface: evidence of kinetics with time delay

    Science.gov (United States)

    Neff, H.; Laborde, H. M.; Lima, A. M. N.

    2016-11-01

    An oscillatory molecular adsorption pattern of the protein neutravidin from aqueous solution onto gold, in presence of a pre-deposited self assembled mono-molecular biotin film, is reported. Real time surface Plasmon resonance sensing was utilized for evaluation of the adsorption kinetics. Two different fractions were identified: in the initial phase, protein molecules attach irreversibly onto the Biotin ligands beneath towards the jamming limit, forming a neutravidin-biotin fraction. Afterwards, the growth rate exhibits distinct, albeit damped adsorption-desorption oscillations over an extended time span, assigned to a quasi reversibly bound fraction. These findings agree with, and firstly confirm a previously published model, proposing macro-molecular adsorption with time delay. The non-linear dynamic model is applicable to and also resembles non-damped oscillatory binding features of the hetero-catalytic oxidation of carbon monoxide molecules on platinum in the gas phase. An associated surface residence time can be linked to the dynamics and time scale required for self-organization.

  9. Mixtures of rubber tyre and plastic wastes pyrolysis: A kinetic study

    International Nuclear Information System (INIS)

    Miranda, Miguel; Cabrita, I.; Pinto, Filomena; Gulyurtlu, I.

    2013-01-01

    The study performed aimed at analysing possible routes for pyrolysis reaction mechanisms of polymeric materials namely RT (rubber tyre) and plastic wastes (PE (polyethylene), PP (polypropylene) and PS (polystyrene)). Consequently, and seeking sustainable transformation of waste streams into valuable chemicals and renewable liquid fuels, mixture of 30% RT, 20% PE, 30% PP and 20% PS was subjected to pyrolysis. Different kinetic models were studied using experimental data. None of the mechanisms found in literature led to a numerical adjustment and different pathways were investigated. Kinetic studies were performed aiming to evaluate direct conversions into new solid, liquid and gaseous products and if parallel reactions and/or reversible elementary steps should be included. Experiments were performed in batch system at different temperatures and reaction times. Kinetic models were evaluated and reaction pathways were proposed. Models reasonably fit experimental data, allow explaining wastes thermal degradation. Kinetic parameters were estimated for all temperatures and dependence of Ea and pre-exponential factor on temperature was evaluated. The rate constant of some reactions exhibited nonlinear temperature dependence on the logarithmic form of Arrhenius law. This fact strongly suggests that temperature has a significant effect on reaction mechanism of pyrolysis of mixtures of rubber tyre and plastic wastes. - Highlights: • Kinetic study of rubber tyre (RT) and different plastic wastes (PE, PP and PS) was performed in batch reactor. • Definition of possible pathways taken into account for the formation of final products. • Kinetic parameters were estimated. • The effect of reaction temperature and reaction time on liquid composition was performed

  10. Pyrolysis of Waste Castor Seed Cake: A Thermo-Kinetics Study

    Directory of Open Access Journals (Sweden)

    Abdullahi Muhammad Sokoto

    2018-03-01

    Full Text Available Biomass pyrolysis is a thermo-chemical conversion process that is of both industrial and ecological importance. The efficient chemical transformation of waste biomass to numerous products via pyrolysis reactions depends on process kinetic rates; hence the need for kinetic models to best design and operate the pyrolysis. Also, for an efficient design of an environmentally sustainable pyrolysis process of a specific lignocellulosic waste, a proper understanding of its thermo-kinetic behavior is imperative. Thus, pyrolysis kinetics of castor seed de-oiled cake (Ricinus communis using thermogravimetric technique was studied. The decomposition of the cake was carried out in a nitrogen atmosphere with a flow rate of 100mL min-1 from ambient temperature to 900 °C. The results of the thermal profile showed moisture removal and devolatilization stages, and maximum decomposition of the cake occurred at a temperature of 200-400 °C. The kinetic parameters such as apparent activation energy, pre-exponential factor, and order of reaction were determined using Friedman (FD, Kissinger-Akahira-Sunose (KAS, and Flynn-Wall-Ozawa (FWO kinetic models. The average apparent activation energy values of 124.61, 126.95 and 129.80 kJmol-1 were calculated from the slopes of the respective models. The apparent activation energy values obtained depends on conversion, which is an evidence of multi-step kinetic process during the pyrolytic decomposition of the cake. The kinetic data would be of immense benefit to model, design and develop a suitable thermo-chemical system for the conversion of waste de-oil cake to energy carrier.

  11. Effect of feeding aflatoxin on nitrogen kinetics in crossbred and buffalo calves fed different levels of protein

    International Nuclear Information System (INIS)

    Dass, R.S.; Arora, S.P.

    1989-01-01

    The studies were conducted to elucidate the effect of feeding aflatoxin on nitrogen kinetics in rumen fistulated calves. One calf each in groups 1, 2, 5 and 6 and one bufffalo calf each, in groups 3, 4, 7 and 8 were alloted. Calves of groups 5 to 8 were provided optimum protein (OP) while those in groups 1 to 4 were given 42.5 per cent more protein (HP) in their diets. In addition, animals in groups 2, 4, 6 and 8 were given an oral dose of aflatoxin at the rate of 1.0 ppm of drymatter intake. Subsequent to digestibility trial, 2 hourly feeding was practised for 10 days, after which 15 N-ammonium sulphate and 51 Cr-EDTA were infused intra-ruminally. Results indicated that there was no effect of feeding aflatoxin on the digestibility of nutrients except crude protein. Nitrogen balances were better with groups fed OP diets as compared to HP diets, more in crossbreds than the buffalo. The estimated rumen volume ranged from 37.70 to 56.00 litres and rumen fluid outflow rates varied from 87.34 to 123.70 litres per day. Ruminal ammonia pool size, ruminal ammonia entry rates and irreversible loss rates were higher in HP fed groups without showing any effect of afflatoxins. Ruminal ammonia-N was better utilized for incorporation into bacterial protein and for transfer to plasma urea-N with OP fed groups, again without showing aflatoxin toxicity effect. Ruminal ammonia-N excretion pattern through urine was greater as a result of aflatoxin toxicity, more in crossbreds as compared to buffalo. (author). 19 refs. 5 tabs

  12. Kinetics of oxidation of bilirubin and its protein complex by hydrogen peroxide in aqueous solutions

    Science.gov (United States)

    Solomonov, A. V.; Rumyantsev, E. V.; Antina, E. V.

    2010-12-01

    A comparative study of oxidation reactions of bilirubin and its complex with albumin was carried out in aqueous solutions under the action of hydrogen peroxide and molecular oxygen at different pH values. Free radical oxidation of the pigment in both free and bound forms at pH 7.4 was shown not to lead to the formation of biliverdin, but to be associated with the decomposition of the tetrapyrrole chromophore into monopyrrolic products. The effective and true rate constants of the reactions under study were determined. It was assumed that one possible mechanism of the oxidation reaction is associated with the interaction of peroxyl radicals and protons of the NH groups of bilirubin molecules at the limiting stage with the formation of a highly reactive radical intermediate. The binding of bilirubin with albumin was found to result in a considerable reduction in the rate of the oxidation reaction associated with the kinetic manifestation of the protein protection effect. It was found that the autoxidation of bilirubin by molecular oxygen with the formation of biliverdin at the intermediate stage can be observed with an increase in the pH of solutions.

  13. Kinetics and thermodynamics studies on the BMP-2 adsorption onto hydroxyapatite surface with different multi-morphological features.

    Science.gov (United States)

    Lu, Zhiwei; Huangfu, Changxin; Wang, Yanying; Ge, Hongwei; Yao, Yao; Zou, Ping; Wang, Guangtu; He, Hua; Rao, Hanbing

    2015-01-01

    The effect of the surface topography on protein adsorption process is of great significance for designing hydroxyapatite (HA) ceramic material surfaces. In this work, three different topographies of HA materials HA-sheet, HA-rod, and HA-whisker were synthesized and testified by X-ray diffraction (XRD), Fourier transform infrared (FT-IR), Brunauer-Emmett-Teller (BET) and a field emission scanning electron microscopy (FE-SEM). We have systematically investigated the adsorption kinetics and thermodynamics of bone morphogenetic proteins (BMP-2) on the three different topography surfaces of HA, respectively. The results showed that the maximum adsorption capacities of HA-sheet, HA-rod and HA-whisker were (219.96 ± 10.18), (247.13 ± 12.35), and (354.67 ± 17.73) μg · g(-1), respectively. Kinetic parameters, rate constants, equilibrium adsorption capacities and related correlation coefficients, for each kinetic model were calculated as well as discussed. It demonstrated that the adsorption of BMP-2 onto HA could be described by the pseudo second-order equation. Adsorption of BMP-2 onto HA followed the Langmuir isotherm. It confirmed that compared with other samples HA-whisker had more adsorption sites for its high specific surface area which could provide more opportunities for protein molecules. The adsorption processes were endothermic (ΔH > 0), spontaneous (ΔG 0). A possible adsorption mechanism has been proposed. In addition, the BMP-2 could be adsorbed to the surface which existed slight conformational changes by FT-IR. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Kinetic study of solid-state processes

    International Nuclear Information System (INIS)

    Malek, Jiri; Mitsuhashi, Takefumi

    2003-01-01

    A simple method for kinetic analysis of solid-state processes has been developed and the criteria capable of classifying different processes are explored. They provide a useful tool for the determination of the most suitable kinetic model. The method has been applied to the analysis of calorimetric data corresponding to the crystallization processes in amorphous ZrO 2 . It is found that the crystallization kinetics of amorphous powder sample exhibits a complex behavior under non-isothermal conditions. A two-parameter model provides a satisfactory description of the crystallization process for isothermal and non-isothermal conditions. This enables better control of crystallization extent in fine ZrO 2 powders that is important for preparation of zirconia ceramics with defined properties. (author)

  15. Kinetic study on UV-absorber photodegradation under different conditions

    Energy Technology Data Exchange (ETDEWEB)

    Bubev, Emil, E-mail: ebubev@my.uctm.edu [University of Chemical Technology and Metallurgy, Department of Physical Chemistry (Bulgaria); Georgiev, Anton [University of Chemical Technology and Metallurgy, Department of Organic Chemistry (Bulgaria); Machkova, Maria [University of Chemical Technology and Metallurgy, Department of Physical Chemistry (Bulgaria)

    2016-09-12

    The photodegradation kinetics of two benzophenone derivative UV-absorbers (UVAs)-BP-4 (benzophenone-4) and 4-HBP (4-hydroxybenzophenone), as additives in polyvinyl acetate (PVAc) films, were studied. Solution-processed PVAc films were irradiated in different environments in order to study oxygen and atmospheric humidity influence on UVA photodegradation. Photodegradation was traced by absorption intensity loss via UV–vis spectroscopy. Both UVAs exhibited excellent photostability in an inert atmosphere. Rate constants showed that BP-4 has better permanence in absence of oxygen. Both film types experienced rapid absorption loss, when irradiated in an oxygen containing atmosphere. UVA degradation was treated as a two-stage process. The photodegradation kinetics in the first stage agreed with the adopted complex rate law, but the second stage was best described by pseudo-first order kinetics. BP-4 exhibited better stability. Oxygen was established as the main accelerating factor for photodegradation of benzophenone derivatives UV-absorbers in thin PVAc films.

  16. Lithium hydride hydrolysis: experimental and kinetic study

    International Nuclear Information System (INIS)

    Charton, S.; Maupoix, C.; Brevet, A.; Delaunay, F.; Heintz, O.; Saviot, L.

    2006-01-01

    In this work has been studied the contribution of various analyses techniques in the framework, on the one hand of revealing the mechanisms implied in lithium hydride hydrolysis, and on the other hand of studying the kinetics of hydrogen production. Among the methods recently investigated, Raman spectroscopy, XPS and SIMS seem to be particularly attractive. (O.M.)

  17. Formation of protein/surfactant adsorption layer at the air/water interface as studied by dilational surface rheology.

    Science.gov (United States)

    Mikhailovskaya, A A; Noskov, B A; Lin, S-Y; Loglio, G; Miller, R

    2011-08-25

    The dynamic dilatational surface elasticity of mixed solutions of globular proteins (β-lactoglobulin (BLG) and bovine serum albumin (BSA)) with cationic (dodecyltrimethylammonium bromide (DTAB)) and anionic (sodium dodecyl sulfate (SDS)) surfactants was measured as a function of the surfactant concentration and surface age. If the cationic surfactant concentration exceeds a certain critical value, the kinetic dependencies of the dynamic surface elasticity of BLG/DTAB and BSA/DTAB solutions become nonmonotonous and resemble those of mixed solutions of proteins with guanidine hydrochloride. This result indicates not only the destruction of the protein tertiary structure in the surface layer of mixed solution but also a strong perturbation of the secondary structure. The corresponding kinetic dependencies for protein solutions with added anionic surfactants are always monotonous, thereby revealing a different mechanism of the adsorption layer formation. One can assume that the secondary structure is destroyed to a lesser extent in the latter case and hinders the formation of loops and tails at the interface. The increase of the solution's ionic strength by the addition of sodium chloride results in stronger changes of the protein conformations in the surface layer and the appearance of a local maximum in the kinetic dependencies of the dynamic surface elasticity in a relatively narrow range of SDS concentration. © 2011 American Chemical Society

  18. Kinetic memory based on the enzyme-limited competition.

    Science.gov (United States)

    Hatakeyama, Tetsuhiro S; Kaneko, Kunihiko

    2014-08-01

    Cellular memory, which allows cells to retain information from their environment, is important for a variety of cellular functions, such as adaptation to external stimuli, cell differentiation, and synaptic plasticity. Although posttranslational modifications have received much attention as a source of cellular memory, the mechanisms directing such alterations have not been fully uncovered. It may be possible to embed memory in multiple stable states in dynamical systems governing modifications. However, several experiments on modifications of proteins suggest long-term relaxation depending on experienced external conditions, without explicit switches over multi-stable states. As an alternative to a multistability memory scheme, we propose "kinetic memory" for epigenetic cellular memory, in which memory is stored as a slow-relaxation process far from a stable fixed state. Information from previous environmental exposure is retained as the long-term maintenance of a cellular state, rather than switches over fixed states. To demonstrate this kinetic memory, we study several models in which multimeric proteins undergo catalytic modifications (e.g., phosphorylation and methylation), and find that a slow relaxation process of the modification state, logarithmic in time, appears when the concentration of a catalyst (enzyme) involved in the modification reactions is lower than that of the substrates. Sharp transitions from a normal fast-relaxation phase into this slow-relaxation phase are revealed, and explained by enzyme-limited competition among modification reactions. The slow-relaxation process is confirmed by simulations of several models of catalytic reactions of protein modifications, and it enables the memorization of external stimuli, as its time course depends crucially on the history of the stimuli. This kinetic memory provides novel insight into a broad class of cellular memory and functions. In particular, applications for long-term potentiation are discussed

  19. Characterization of redox proteins using electrochemical methods

    OpenAIRE

    Verhagen, M.

    1995-01-01

    The use of electrochemical techniques in combination with proteins started approximately a decade ago and has since then developed into a powerfull technique for the study of small redox proteins. In addition to the determination of redox potentials, electrochemistry can be used to obtain information about the kinetics of electron transfer between proteins and about the dynamic behaviour of redox cofactors in proteins. This thesis describes the results of a study, initiated to get a ...

  20. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations.

    Science.gov (United States)

    Ozgur, Beytullah; Ozdemir, E Sila; Gursoy, Attila; Keskin, Ozlem

    2017-04-20

    Intrinsic fluctuations of a protein enable it to sample a large repertoire of conformers including the open and closed forms. These distinct forms of the protein called conformational substates pre-exist together in equilibrium as an ensemble independent from its ligands. The role of ligand might be simply to alter the equilibrium toward the most appropriate form for binding. Normal mode analysis is proved to be useful in identifying the directions of conformational changes between substates. In this study, we demonstrate that the ratios of normalized weights of a few normal modes driving the protein between its substates can give insights about the ratios of kinetic conversion rates of the substates, although a direct relation between the eigenvalues and kinetic conversion rates or populations of each substate could not be observed. The correlation between the normalized mode weight ratios and the kinetic rate ratios is around 83% on a set of 11 non-enzyme proteins and around 59% on a set of 17 enzymes. The results are suggestive that mode motions carry intrinsic relations with thermodynamics and kinetics of the proteins.

  1. Kinetics of Internal-Loop Formation in Polypeptide Chains: A Simulation Study

    Science.gov (United States)

    Doucet, Dana; Roitberg, Adrian; Hagen, Stephen J.

    2007-01-01

    The speed of simple diffusional motions, such as the formation of loops in the polypeptide chain, places one physical limit on the speed of protein folding. Many experimental studies have explored the kinetics of formation of end-to-end loops in polypeptide chains; however, protein folding more often requires the formation of contacts between interior points on the chain. One expects that, for loops of fixed contour length, interior loops will form more slowly than end-to-end loops, owing to the additional excluded volume associated with the “tails”. We estimate the magnitude of this effect by generating ensembles of randomly coiled, freely jointed chains, and then using the theory of Szabo, Schulten, and Schulten to calculate the corresponding contact formation rates for these ensembles. Adding just a few residues, to convert an end-to-end loop to an internal loop, sharply decreases the contact rate. Surprisingly, the relative change in rate increases for a longer loop; sufficiently long tails, however, actually reverse the effect and accelerate loop formation slightly. Our results show that excluded volume effects in real, full-length polypeptides may cause the rates of loop formation during folding to depart significantly from the values derived from recent loop-formation experiments on short peptides. PMID:17208979

  2. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Carson M Andorf

    Full Text Available Protein-protein interactions are critical to elucidating the role played by individual proteins in important biological pathways. Of particular interest are hub proteins that can interact with large numbers of partners and often play essential roles in cellular control. Depending on the number of binding sites, protein hubs can be classified at a structural level as singlish-interface hubs (SIH with one or two binding sites, or multiple-interface hubs (MIH with three or more binding sites. In terms of kinetics, hub proteins can be classified as date hubs (i.e., interact with different partners at different times or locations or party hubs (i.e., simultaneously interact with multiple partners.Our approach works in 3 phases: Phase I classifies if a protein is likely to bind with another protein. Phase II determines if a protein-binding (PB protein is a hub. Phase III classifies PB proteins as singlish-interface versus multiple-interface hubs and date versus party hubs. At each stage, we use sequence-based predictors trained using several standard machine learning techniques.Our method is able to predict whether a protein is a protein-binding protein with an accuracy of 94% and a correlation coefficient of 0.87; identify hubs from non-hubs with 100% accuracy for 30% of the data; distinguish date hubs/party hubs with 69% accuracy and area under ROC curve of 0.68; and SIH/MIH with 89% accuracy and area under ROC curve of 0.84. Because our method is based on sequence information alone, it can be used even in settings where reliable protein-protein interaction data or structures of protein-protein complexes are unavailable to obtain useful insights into the functional and evolutionary characteristics of proteins and their interactions.We provide a web server for our three-phase approach: http://hybsvm.gdcb.iastate.edu.

  3. Two states or not two states: Single-molecule folding studies of protein L

    Science.gov (United States)

    Aviram, Haim Yuval; Pirchi, Menahem; Barak, Yoav; Riven, Inbal; Haran, Gilad

    2018-03-01

    Experimental tools of increasing sophistication have been employed in recent years to study protein folding and misfolding. Folding is considered a complex process, and one way to address it is by studying small proteins, which seemingly possess a simple energy landscape with essentially only two stable states, either folded or unfolded. The B1-IgG binding domain of protein L (PL) is considered a model two-state folder, based on measurements using a wide range of experimental techniques. We applied single-molecule fluorescence resonance energy transfer (FRET) spectroscopy in conjunction with a hidden Markov model analysis to fully characterize the energy landscape of PL and to extract the kinetic properties of individual molecules of the protein. Surprisingly, our studies revealed the existence of a third state, hidden under the two-state behavior of PL due to its small population, ˜7%. We propose that this minority intermediate involves partial unfolding of the two C-terminal β strands of PL. Our work demonstrates that single-molecule FRET spectroscopy can be a powerful tool for a comprehensive description of the folding dynamics of proteins, capable of detecting and characterizing relatively rare metastable states that are difficult to observe in ensemble studies.

  4. Measurements of Protein Crystal Face Growth Rates

    Science.gov (United States)

    Gorti, S.

    2014-01-01

    Protein crystal growth rates will be determined for several hyperthermophile proteins.; The growth rates will be assessed using available theoretical models, including kinetic roughening.; If/when kinetic roughening supersaturations are established, determinations of protein crystal quality over a range of supersaturations will also be assessed.; The results of our ground based effort may well address the existence of a correlation between fundamental growth mechanisms and protein crystal quality.

  5. Kinetic Modeling of Methionine Oxidation in Monoclonal Antibodies from Hydrogen Peroxide Spiking Studies.

    Science.gov (United States)

    Hui, Ada; Lam, Xanthe M; Kuehl, Christopher; Grauschopf, Ulla; Wang, Y John

    2015-01-01

    When isolator technology is applied to biotechnology drug product fill-finish process, hydrogen peroxide (H2O2) spiking studies for the determination of the sensitivity of protein to residual peroxide in the isolator can be useful for assessing a maximum vapor phase hydrogen peroxide (VPHP) level. When monoclonal antibody (mAb) drug products were spiked with H2O2, an increase in methionine (Met 252 and Met 428) oxidation in the Fc region of the mAbs with a decrease in H2O2 concentration was observed for various levels of spiked-in peroxide. The reaction between Fc-Met and H2O2 was stoichiometric (i.e., 1:1 molar ratio), and the reaction rate was dependent on the concentrations of mAb and H2O2. The consumption of H2O2 by Fc-Met oxidation in the mAb followed pseudo first-order kinetics, and the rate was proportional to mAb concentration. The extent of Met 428 oxidation was half of that of Met 252, supporting that Met 252 is twice as reactive as Met 428. Similar results were observed for free L-methionine when spiked with H2O2. However, mAb formulation excipients may affect the rate of H2O2 consumption. mAb formulations containing trehalose or sucrose had faster H2O2 consumption rates than formulations without the sugars, which could be the result of impurities (e.g., metal ions) present in the excipients that may act as catalysts. Based on the H2O2 spiking study results, we can predict the amount Fc-Met oxidation for a given protein concentration and H2O2 level. Our kinetic modeling of the reaction between Fc-Met oxidation and H2O2 provides an outline to design a H2O2 spiking study to support the use of VPHP isolator for antibody drug product manufacture. Isolator technology is increasing used in drug product manufacturing of biotherapeutics. In order to understand the impact of residual vapor phase hydrogen peroxide (VPHP) levels on protein product quality, hydrogen peroxide (H2O2) spiking studies may be performed to determine the sensitivity of monoclonal antibody

  6. Modeling capsid kinetics assembly from the steady state distribution of multi-sizes aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Hozé, Nathanaël; Holcman, David

    2014-01-24

    The kinetics of aggregation for particles of various sizes depends on their diffusive arrival and fusion at a specific nucleation site. We present here a mean-field approximation and a stochastic jump model for aggregates at equilibrium. This approach is an alternative to the classical Smoluchowski equations that do not have a close form and are not solvable in general. We analyze these mean-field equations and obtain the kinetics of a cluster formation. Our approach provides a simplified theoretical framework to study the kinetics of viral capsid formation, such as HIV from the self-assembly of the structural proteins Gag.

  7. Study on the agglomeration kinetics of uranium peroxide

    International Nuclear Information System (INIS)

    Bertrand, M.; Mojica Rodriguez, L.A.; Muhr, H.; Plasari, E.; Auger, F.

    2016-01-01

    Considering the previous study dealing with thermodynamic and kinetic phenomena (nucleation and crystal growth) during the uranium peroxide precipitation, this work focuses on the agglomeration mechanism. It provides the results obtained from the experiments carried out in a mixed suspension - mixed product removal (MSMPR) mixer operating at steady state. The influence of the operating parameters on the uranium peroxide agglomerates was studied in order to identify the agglomeration kernel. The method is based on the resolution of the population balance equation using the method of moments and the experimental particle size distributions. The results lead to a size-independent kernel directly proportional to the crystal growth rate. Under the stirring conditions studied, the agglomeration appears to be significantly reduced by mixing which results in a kernel inversely proportional to the average shear rate. The agglomeration kinetic law obtained in this study will be used for the process modelling in a further study. (authors)

  8. Study on the agglomeration kinetics of uranium peroxide

    Energy Technology Data Exchange (ETDEWEB)

    Bertrand, M.; Mojica Rodriguez, L.A. [CEA, Centre de Marcoule, Nuclear Energy Division, RadioChemistry and Process Department, 17171, Bagnols-sur-Ceze 30207 (France); Muhr, H.; Plasari, E. [Reaction and Process Engineering Laboratory, CNRS, University of Lorraine. 1 rue Grandville, BP 20451, Nancy 54001 (France); Auger, F. [Areva Mines/SEPA. 2 route de Lavaugrasse, Bessines-sur-Gartempe 87250 (France)

    2016-07-01

    Considering the previous study dealing with thermodynamic and kinetic phenomena (nucleation and crystal growth) during the uranium peroxide precipitation, this work focuses on the agglomeration mechanism. It provides the results obtained from the experiments carried out in a mixed suspension - mixed product removal (MSMPR) mixer operating at steady state. The influence of the operating parameters on the uranium peroxide agglomerates was studied in order to identify the agglomeration kernel. The method is based on the resolution of the population balance equation using the method of moments and the experimental particle size distributions. The results lead to a size-independent kernel directly proportional to the crystal growth rate. Under the stirring conditions studied, the agglomeration appears to be significantly reduced by mixing which results in a kernel inversely proportional to the average shear rate. The agglomeration kinetic law obtained in this study will be used for the process modelling in a further study. (authors)

  9. Phenylalanine kinetics in human adipose tissue.

    OpenAIRE

    Coppack, S W; Persson, M; Miles, J M

    1996-01-01

    Very little is known about the regulation of protein metabolism in adipose tissue. In this study systemic, adipose tissue, and forearm phenylalanine kinetics were determined in healthy postabsorptive volunteers before and during a 2-h glucose infusion (7 mg.kg-1.min-1). [3H]Phenylalanine was infused and blood was sampled from a radial artery, a subcutaneous abdominal vein, and a deep forearm vein. Adipose tissue and forearm blood flow were measured with 133Xe and plethysmography, respectively...

  10. Kinetics of the H 2O 2-dependent ligninase-catalyzed oxidation of veratryl alcohol in the presence of cationic surfactant studied by spectrophotometric technique

    Science.gov (United States)

    Liu, Airong; Huang, Xirong; Song, Shaofang; Wang, Dan; Lu, Xuemei; Qu, Yinbo; Gao, Peiji

    2003-09-01

    The kinetics of ligninase-catalyzed oxidation of veratryl alcohol (VA) by H 2O 2 in the aqueous medium containing cationic surfactant cetyltrimethylammonium bromide (CTAB) has been investigated using spectrophotometric technique. Steady-state kinetic studies at different concentrations of CTAB indicate that the reaction follows a ping pong mechanism and the mechanism always holds but the kinetic parameters vary with CTAB concentrations. CTAB is a weak inhibitor for ligninase; it lowers the maximum initial velocity. CTAB also causes the Michaelis constant of H 2O 2 to decrease dramatically and that of VA to increase markedly. Based on the changes in kinetic parameters of the enzyme-catalyzed reaction at different CTAB concentrations (lower than, near to and larger than its critical micelle concentration) and the effects of the CTAB monomer and the micelles on the spectra of VA and its corresponding aldehyde, a conclusion could be made that modification of the enzymatic protein by the surfactant monomer should be responsible for the above-mentioned results.

  11. Statistical inference in single molecule measurements of protein adsorption

    Science.gov (United States)

    Armstrong, Megan J.; Tsitkov, Stanislav; Hess, Henry

    2018-02-01

    Significant effort has been invested into understanding the dynamics of protein adsorption on surfaces, in particular to predict protein behavior at the specialized surfaces of biomedical technologies like hydrogels, nanoparticles, and biosensors. Recently, the application of fluorescent single molecule imaging to this field has permitted the tracking of individual proteins and their stochastic contribution to the aggregate dynamics of adsorption. However, the interpretation of these results is complicated by (1) the finite time available to observe effectively infinite adsorption timescales and (2) the contribution of photobleaching kinetics to adsorption kinetics. Here, we perform a protein adsorption simulation to introduce specific survival analysis methods that overcome the first complication. Additionally, we collect single molecule residence time data from the adsorption of fibrinogen to glass and use survival analysis to distinguish photobleaching kinetics from protein adsorption kinetics.

  12. Kinetic Studies of Catalytic Oxidation of Cyclohexene Using ...

    African Journals Online (AJOL)

    acer

    Kinetic Studies of Catalytic Oxidation of Cyclohexene Using Chromium VI Oxide in. Acetic Acid ... respect to the oxidant using pseudo-order approximation method. .... making the concentration of the cyclohexene in ..... on Titanium Silicate.

  13. Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

    Directory of Open Access Journals (Sweden)

    David S. Kliger

    2009-04-01

    Full Text Available Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t £ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-ms conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 ms timescale to a compact intermediate IC containing some native-like secondary structure. Although the existence and nature of IC as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of IC as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that IC may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

  14. Linear and nonlinear kinetic-stability studies in tokamaks

    International Nuclear Information System (INIS)

    Tang, W.M.; Chance, M.S.; Chen, L.; Krommes, J.A.; Lee, W.W.; Rewoldt, G.

    1982-09-01

    This paper presents results of theoretical investigations on important linear kinetic properties of low frequency instabilities in toroidal systems and on nonlinear processes which could significantly influence their impact on anomalous transport. Analytical and numerical methods and also particle simulations have been employed to carry out these studies. In particular, the following subjects are considered: (1) linear stability analysis of kinetic instabilities for realistic tokamak equilibria and the application of such calculations to the PDX and PLT tokamak experiments including the influence of a hot beam-ion component; (2) determination of nonlinearly saturated, statistically steady states of three interacting drift modes; and (3) gyrokinetic particle simulation of drift instabilities

  15. Thermogravimetric kinetic study of agricultural residue biomass pyrolysis based on combined kinetics.

    Science.gov (United States)

    Wang, Xun; Hu, Mian; Hu, Wanyong; Chen, Zhihua; Liu, Shiming; Hu, Zhiquan; Xiao, Bo

    2016-11-01

    Pyrolytic kinetic of an agricultural residue (AR) feedstock, a mixture of plants (cotton, wheat, rich, corn) stems, was investigated based on combined kinetics. The most suitable mechanism for AR one-step pyrolysis was f(α)=(1-α)(1.1816)α(-1.8428) with kinetic parameters of: apparent activation energy 221.7kJ/mol, pre-exponential factor 4.17E16s(-1). Pyrolysis of AR feedstock could not be described by one-step reaction attributes to heterogeneous features of pyrolysis processes. Combined kinetics three-parallel-reaction (CK-TPR) model fitted the pyrolysis experimental data very well. Reaction mechanisms for pseudo hemicelluloses, cellulose, lignin in CK-TPR model was f(α)=(1-α)(1.6244)α(-0.3371)[-ln(1-α)](-0.0515), f(α)=(1-α)(1.0597)α(-0.6909)[-ln(1-α)](0.9026) and f(α)=(1-α)(2.9577)α(-4.7719), respectively. Apparent activation energy of three pseudo components followed the order of Elignin(197.3kJ/mol)>Ecellulose(176.3kJ/mol)>Ehemicelluloses (151.1kJ/mol). Mechanism of hemicelluloses pyrolysis could be further expressed as f(α)=(1-α)(1.4). The pyrolytic mechanism of cellulose met the Nucleation well. However, mechanism of lignin pyrolysis was complex, which possibly was the combined effects of Nucleation, Diffusion, Geometrical contraction, and Power law. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. A Dansyl Fluorescence-Based Assay for Monitoring Kinetics of Lipid Extraction and Transfer

    Science.gov (United States)

    Ran, Yong

    2008-01-01

    Lipid transfer proteins (LTPs) play important roles in cellular biology, and fluorescence spectroscopy has found wide range use as a facile means for time-resolved monitoring of protein-lipid interactions[1]. Here, we show how the fluorescence emission properties of dansyl-DHPE can be exploited to characterize lipid extraction and lipid transfer kinetics. The GM2 activator protein serves as an example LTP where the ability to independently characterize lipid extraction from donor vesicles, formation of a protein:lipid complex in solution, and release of lipid from the complex to acceptor liposomes is crucial for full kinetic characterization of lipid transfer. PMID:18694718

  17. Kinetic and equilibrium study for the sorption of Pb(II) ions from ...

    African Journals Online (AJOL)

    Kinetic and equilibrium study for the sorption of Pb(II) ions from aqueous phase by water hyacinth ( Eichhornia crassipes ) ... Bulletin of the Chemical Society of Ethiopia ... Abstract. This paper reports the kinetic and equilibrium studies of Eichhornia crassipes root biomass as a biosorbent for Pb(II) ions from aqueous system.

  18. Cardiovascular Small Heat Shock Protein HSPB7 Is a Kinetically Privileged Reactive Electrophilic Species (RES) Sensor.

    Science.gov (United States)

    Surya, Sanjna L; Long, Marcus J C; Urul, Daniel A; Zhao, Yi; Mercer, Emily J; EIsaid, Islam M; Evans, Todd; Aye, Yimon

    2018-02-08

    Small heat shock protein (sHSP)-B7 (HSPB7) is a muscle-specific member of the non-ATP-dependent sHSPs. The precise role of HSPB7 is enigmatic. Here, we disclose that zebrafish Hspb7 is a kinetically privileged sensor that is able to react rapidly with native reactive electrophilic species (RES), when only substoichiometric amounts of RES are available in proximity to Hspb7 expressed in living cells. Among the two Hspb7-cysteines, this RES sensing is fulfilled by a single cysteine (C117). Purification and characterizations in vitro reveal that the rate for RES adduction is among the most efficient reported for protein-cysteines with native carbonyl-based RES. Covalent-ligand binding is accompanied by structural changes (increase in β-sheet-content), based on circular dichroism analysis. Among the two cysteines, only C117 is conserved across vertebrates; we show that the human ortholog is also capable of RES sensing in cells. Furthermore, a cancer-relevant missense mutation reduces this RES-sensing property. This evolutionarily conserved cysteine-biosensor may play a redox-regulatory role in cardioprotection.

  19. Kinetics of lipid-nanoparticle-mediated intracellular mRNA delivery and function

    Science.gov (United States)

    Zhdanov, Vladimir P.

    2017-10-01

    mRNA delivery into cells forms the basis for one of the new and promising ways to treat various diseases. Among suitable carriers, lipid nanoparticles (LNPs) with a size of about 100 nm are now often employed. Despite high current interest in this area, the understanding of the basic details of LNP-mediated mRNA delivery and function is limited. To clarify the kinetics of mRNA release from LNPs, the author uses three generic models implying (i) exponential, (ii) diffusion-controlled, and (iii) detachment-controlled kinetic regimes, respectively. Despite the distinct differences in these kinetics, the associated transient kinetics of mRNA translation to the corresponding protein and its degradation are shown to be not too sensitive to the details of the mRNA delivery by LNPs (or other nanocarriers). In addition, the author illustrates how this protein may temporarily influence the expression of one gene or a few equivalent genes. The analysis includes positive or negative regulation of the gene transcription via the attachment of the protein without or with positive or negative feedback in the gene expression. Stable, bistable, and oscillatory schemes have been scrutinized in this context.

  20. Derivation of kinetic coefficients by atomistic methods for studying defect behavior in Mo

    International Nuclear Information System (INIS)

    Insepov, Z.; Rest, J.; Yacout, A.M.; Kuksin, A.Yu.; Norman, G.E.; Stegailov, V.V.; Starikov, S.V.; Yanilkin, A.V.

    2012-01-01

    Highlights: ► A multiscale concept couples molecular dynamics (MD) with ab initio and kinetic rate theory. ► Evolution of a system of self-interstitial atoms and vacancies in Mo is studied by MD. ► Formation of di-SIA clusters and SIA–vacancy recombination is analyzed. ► 1D diffusion of self-interstitials at various temperature and defect concentrations were studied. ► This paper provides a powerful predictive tool for simulating irradiation of nuclear materials. - Abstract: A multiscale concept for irradiated materials simulation is formulated based on coupling molecular dynamics simulations (MD) where the potential was obtained from ab initio data of energies of the basic defect structures, with kinetic mesoscale models. The evolution of a system containing self-interstitial atoms (SIAs) and vacancies in crystalline molybdenum is investigated by means of MD. The kinetics of formation of di-SIA clusters and SIA–vacancy recombination is analyzed via approaches used in the kinetic theory of radiation ageing. The effects of 1D diffusion of SIAs, temperature, and defect concentrations on the reaction rates are also studied. This approach can validate both the kinetic mechanisms and the appropriate kinetic coefficients, offering the potential to significantly reduce the uncertainty of the kinetic methodology and providing a powerful predictive tool for simulating irradiation behavior of nuclear materials.

  1. A comparison of pine and spruce in recovery from winter stress; changes in recovery kinetics, and the abundance and phosphorylation status of photosynthetic proteins during winter.

    Science.gov (United States)

    Merry, Ryan; Jerrard, Jacob; Frebault, Julia; Verhoeven, Amy

    2017-09-01

    During winter evergreens maintain a sustained form of thermal energy dissipation that results in reduced photochemical efficiency measured using the chlorophyll fluorescence parameter Fv/Fm. Eastern white pine (Pinus strobus L.) and white spruce [Picea glauca (Moench) Voss] have been shown to differ in their rate of recovery of Fv/Fm from winter stress. The goal of this study was to monitor changes in photosynthetic protein abundance and phosphorylation status during winter recovery that accompany these functional changes. An additional goal was to determine whether light-dependent changes in light harvesting complex II (LHCII) phosphorylation occur during winter conditions. We used a combination of field measurements and recovery experiments to monitor chlorophyll fluorescence and photosynthetic protein content and phosphorylation status. We found that pine recovered three times more slowly than spruce, and that the kinetics of recovery in spruce included a rapid and slow component, while in pine there was only a rapid component to recovery. Both species retained relatively high amounts of the light harvesting protein Lhcb5 (CP26) and the PsbS protein during winter, suggesting a role for these proteins in sustained thermal dissipation. Both species maintained high phosphorylation of LHCII and the D1 protein in darkness during winter. Pine and spruce differed in the kinetics of the dephosphorylation of LHCII and D1 upon warming, suggesting the rate of dephosphorylation of LHCII and D1 may be important in the rapid component of recovery from winter stress. Finally, we demonstrated that light-dependent changes in LHII phosphorylation do not continue to occur on subzero winter days and that needles are maintained in a phosphorylation pattern consistent with the high light conditions to which those needles are exposed. Our results suggest a role for retained phosphorylation of both LHCII and D1 in maintenance of the photosynthetic machinery in a winter conformation

  2. Autophagosome Proteins LC3A, LC3B and LC3C Have Distinct Subcellular Distribution Kinetics and Expression in Cancer Cell Lines.

    Directory of Open Access Journals (Sweden)

    Michael I Koukourakis

    Full Text Available LC3s (MAP1-LC3A, B and C are structural proteins of autophagosomal membranes, widely used as biomarkers of autophagy. Whether these three LC3 proteins have a similar biological role in autophagy remains obscure. We examine in parallel the subcellular expression patterns of the three LC3 proteins in a panel of human cancer cell lines, as well as in normal MRC5 fibroblasts and HUVEC, using confocal microscopy and western blot analysis of cell fractions. In the cytoplasm, there was a minimal co-localization between LC3A, B and C staining, suggesting that the relevant autophagosomes are formed by only one out of the three LC3 proteins. LC3A showed a perinuclear and nuclear localization, while LC3B was equally distributed throughout the cytoplasm and localized in the nucleolar regions. LC3C was located in the cytoplasm and strongly in the nuclei (excluding nucleoli, where it extensively co-localized with the LC3A and the Beclin-1 autophagy initiating protein. Beclin 1 is known to contain a nuclear trafficking signal. Blocking nuclear export function by Leptomycin B resulted in nuclear accumulation of all LC3 and Beclin-1 proteins, while Ivermectin that blocks nuclear import showed reduction of accumulation, but not in all cell lines. Since endogenous LC3 proteins are used as major markers of autophagy in clinical studies and cell lines, it is essential to check the specificity of the antibodies used, as the kinetics of these molecules are not identical and may have distinct biological roles. The distinct subcellular expression patterns of LC3s provide a basis for further studies.

  3. Tolrestat kinetics

    International Nuclear Information System (INIS)

    Hicks, D.R.; Kraml, M.; Cayen, M.N.; Dubuc, J.; Ryder, S.; Dvornik, D.

    1984-01-01

    The kinetics of tolrestat, a potent inhibitor of aldose reductase, were examined. Serum concentrations of tolrestat and of total 14 C were measured after dosing normal subjects and subjects with diabetes with 14 C-labeled tolrestat. In normal subjects, tolrestat was rapidly absorbed and disappearance from serum was biphasic. Distribution and elimination t 1/2s were approximately 2 and 10 to 12 hr, respectively, after single and multiple doses. Unchanged tolrestat accounted for the major portion of 14 C in serum. Radioactivity was rapidly and completely excreted in urine and feces in an approximate ratio of 2:1. Findings were much the same in subjects with diabetes. In normal subjects, the kinetics of oral tolrestat were independent of dose in the 10 to 800 mg range. Repetitive dosing did not result in unexpected cumulation. Tolrestat was more than 99% bound to serum protein; it did not compete with warfarin for binding sites but was displaced to some extent by high concentrations of tolbutamide or salicylate

  4. Laboratory studies on the adsorption kinetics of 137Cs in sediment

    International Nuclear Information System (INIS)

    Jaison, T.J.; Patra, A.K.; Ravi, P.M.; Sarkar, P.K.

    2012-01-01

    During the operation of a nuclear reactor, extreme care is taken to minimize the release of radionuclides to the environment. Low level radioactive liquid waste generated is treated and released to the nearest water body after monitoring to ensure that the activity levels are well within the regulatory limits. Environmental Survey Laboratories (ESL) attached to power plants carry out a systematic environmental monitoring and impact assessment to ensure that the dose to the member of public is well within the limits. This paper presents the results of a systematic laboratory study carried out at ESL, Kakrapar Atomic Power Station (KAPS) on the adsorption kinetics of 137 Cs in sediment. The study is to evaluate the sorption kinetics of 137 Cs + onto site specific sediment. Sets of adsorption experiments were conducted at specific time intervals for two different 137 Cs + concentrations, keeping other experimental conditions same. The kinetics of 137 Cs + adsorption on sediment is analyzed using pseudo first order, pseudo second order, and intra-particle diffusion kinetic models. The pseudo-second order kinetic model is better correlated with the kinetics data compared with the pseudo first-order model. This indicates 137 Cs + ions can be involved in chemical bonding during the adsorption process to the analysed sediment. This chemi-sorption processes show a good compliance with the pseudo-second order kinetic model. It is also evident that lower concentration exhibits greater adsorption rate (k 2 value is 1.85 x 10 -5 Bq g -1 min -1 for 1245 Bq sets and 1.05 x 10 -5 Bq g -1 min -1 for 2456 Bq sets) from the pseudo second order model. Intra-particle diffusion rate constants (K id ) were also obtained by two different models for both the concentrations and found to be higher for higher concentration. (author)

  5. How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction.

    Science.gov (United States)

    Jeffery, Kathleen A; Pelaez, Nancy; Anderson, Trevor R

    2018-01-01

    To keep biochemistry instruction current and relevant, it is crucial to expose students to cutting-edge scientific research and how experts reason about processes governed by thermodynamics and kinetics such as protein folding and dynamics. This study focuses on how experts explain their research into this topic with the intention of informing instruction. Previous research has modeled how expert biologists incorporate research methods, social or biological context, and analogies when they talk about their research on mechanisms. We used this model as a guiding framework to collect and analyze interview data from four experts. The similarities and differences that emerged from analysis indicate that all experts integrated theoretical knowledge with their research context, methods, and analogies when they explained how phenomena operate, in particular by mapping phenomena to mathematical models; they explored different processes depending on their explanatory aims, but readily transitioned between different perspectives and explanatory models; and they explained thermodynamic and kinetic concepts of relevance to protein folding in different ways that aligned with their particular research methods. We discuss how these findings have important implications for teaching and future educational research. © 2018 K. A. Jeffery et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  6. Insilico study of the A(2A)R-D (2)R kinetics and interfacial contact surface for heteromerization.

    Science.gov (United States)

    Prakash, Amresh; Luthra, Pratibha Mehta

    2012-10-01

    G-protein-coupled receptors (GPCRs) are cell surface receptors. The dynamic property of receptor-receptor interactions in GPCRs modulates the kinetics of G-protein signaling and stability. In the present work, the structural and dynamic study of A(2A)R-D(2)R interactions was carried to acquire the understanding of the A(2A)R-D(2)R receptor activation and deactivation process, facilitating the design of novel drugs and therapeutic target for Parkinson's disease. The structure-based features (Alpha, Beta, SurfAlpha, and SurfBeta; GapIndex, Leakiness and Gap Volume) and slow mode model (ENM) facilitated the prediction of kinetics (K (off), K (on), and K (d)) of A(2A)R-D(2)R interactions. The results demonstrated the correlation coefficient 0.294 for K (d) and K (on) and the correlation coefficient 0.635 for K (d) and K (off), and indicated stable interfacial contacts in the formation of heterodimer. The coulombic interaction involving the C-terminal tails of the A(2A)R and intracellular loops (ICLs) of D(2)R led to the formation of interfacial contacts between A(2A)R-D(2)R. The properties of structural dynamics, ENM and KFC server-based hot-spot analysis illustrated the stoichiometry of A(2A)R-D(2)R contact interfaces as dimer. The propensity of amino acid residues involved in A(2A)R-D(2)R interaction revealed the presence of positively (R, H and K) and negatively (E and D) charged structural motif of TMs and ICL3 of A(2A)R and D(2)R at interface of dimer contact. Essentially, in silico structural and dynamic study of A(2A)R-D(2)R interactions will provide the basic understanding of the A(2A)R-D(2)R interfacial contact surface for activation and deactivation processes, and could be used as constructive model to recognize the protein-protein interactions in receptor assimilations.

  7. Oxidation of L-cystine by chromium(VI) - a kinetic study | Kumar ...

    African Journals Online (AJOL)

    The kinetics of the title reaction was studied spectrophotometrically in HClO4 medium at 380 nm. The data suggested that the order with respect to cystine is fractional, whereas chromium(VI) follows first order kinetics. The reaction was second order in [H+]. Cysteic acid was found to be the main product of oxidation.

  8. Study of kinetics of extraction of actinides in processes of reprocessing of nuclear fuels

    International Nuclear Information System (INIS)

    Lamotte, Claude

    1978-01-01

    This research thesis reports a bibliographical study on extraction kinetics. After some generalities on solvent-based extraction, and on the chemistry of actinides in solution, on the methods of kinetics study which are generally used and their mathematical treatments, the author compares the published results for the extraction kinetics of nitric acid, uranium VI, uranium IV, neptunium IV and plutonium IV [fr

  9. Kinetic intermediates en route to the final serpin-protease complex: studies of complexes of α1-protease inhibitor with trypsin.

    Science.gov (United States)

    Maddur, Ashoka A; Swanson, Richard; Izaguirre, Gonzalo; Gettins, Peter G W; Olson, Steven T

    2013-11-01

    Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-Å translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, α1-protease inhibitor (α1PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled α1PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism.

  10. Experimental and Chemical Kinetic Modeling Study of Dimethylcyclohexane Oxidation and Pyrolysis

    KAUST Repository

    Eldeeb, Mazen A.

    2016-08-30

    A combined experimental and chemical kinetic modeling study of the high-temperature ignition and pyrolysis of 1,3-dimethylcyclohexane (13DMCH) is presented. Ignition delay times are measured behind reflected shock waves over a temperature range of 1049–1544 K and pressures of 3.0–12 atm. Pyrolysis is investigated at average pressures of 4.0 atm at temperatures of 1238, 1302, and 1406 K. By means of mid-infrared direct laser absorption at 3.39 μm, fuel concentration time histories are measured under ignition and pyrolytic conditions. A detailed chemical kinetic model for 13DMCH combustion is developed. Ignition measurements show that the ignition delay times of 13DMCH are longer than those of its isomer, ethylcyclohexane. The proposed chemical kinetic model predicts reasonably well the effects of equivalence ratio and pressure, with overall good agreement between predicted and measured ignition delay times, except at low dilution levels and high pressures. Simulated fuel concentration profiles agree reasonably well with the measured profiles, and both highlight the influence of pyrolysis on the overall ignition kinetics at high temperatures. Sensitivity and reaction pathway analyses provide further insight into the kinetic processes controlling ignition and pyrolysis. The work contributes toward improved understanding and modeling of the oxidation and pyrolysis kinetics of cycloalkanes.

  11. Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways.

    Science.gov (United States)

    Nagy, Péter

    2013-05-01

    Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. This review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.

  12. Effects of solute-solute interactions on protein stability studied using various counterions and dendrimers.

    Directory of Open Access Journals (Sweden)

    Curtiss P Schneider

    Full Text Available Much work has been performed on understanding the effects of additives on protein thermodynamics and degradation kinetics, in particular addressing the Hofmeister series and other broad empirical phenomena. Little attention, however, has been paid to the effect of additive-additive interactions on proteins. Our group and others have recently shown that such interactions can actually govern protein events, such as aggregation. Here we use dendrimers, which have the advantage that both size and surface chemical groups can be changed and therein studied independently. Dendrimers are a relatively new and broad class of materials which have been demonstrated useful in biological and therapeutic applications, such as drug delivery, perturbing amyloid formation, etc. Guanidinium modified dendrimers pose an interesting case given that guanidinium can form multiple attractive hydrogen bonds with either a protein surface or other components in solution, such as hydrogen bond accepting counterions. Here we present a study which shows that the behavior of such macromolecule species (modified PAMAM dendrimers is governed by intra-solvent interactions. Attractive guanidinium-anion interactions seem to cause clustering in solution, which inhibits cooperative binding to the protein surface but at the same time, significantly suppresses nonnative aggregation.

  13. The kinetics of multi-compartmentalized systems, studied by radioactive tracers

    International Nuclear Information System (INIS)

    Gouveia, A.S. de.

    1978-01-01

    The use of compartmental models to investigate kinetic problems is presented. This use is restricted, however, to linear models. As an application of different methods, the kinetic behaviour of haemaccel labelled with iodine 131 is studied, the interval of the physically viable solutions being established. The existence of a class of solutions is explained as a result of lack of knowledge of a complete data set. The possibility of obtaining a single solution is also discussed. The formalism of the program SAAM (Simulation, Analysis and modelling) now judged very important for the study of multi-compartimental analysis is presented. (I.C.R) [pt

  14. Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

    A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

  15. Protein digestion kinetics in pigs and poultry

    NARCIS (Netherlands)

    Chen, Hsuan

    2017-01-01

    Increasing the protein efficiency is considered a main strategy for sustainable feeding of pigs and poultry. In practice, protein in pig and poultry diets originates from different ingredients, selected in diet formulation based on their nutritional value and cost. Currently, the nutritional

  16. Studying pressure denaturation of a protein by molecular dynamics simulations.

    Science.gov (United States)

    Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar

    2010-05-15

    Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties

  17. Studies of combustion kinetics and mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Gutman, D. [Catholic Univ. of America, Washington, DC (United States)

    1993-12-01

    The objective of the current research is to gain new quantitative knowledge of the kinetics and mechanisms of polyatomic free radicals which are important in hydrocarbon combustion processes. The special facility designed and built for these (which includes a heatable tubular reactor coupled to a photoionization mass spectrometer) is continually being improved. Where possible, these experimental studies are coupled with theoretical ones, sometimes conducted in collaboration with others, to obtain an improved understanding of the factors determining reactivity. The decomposition of acetyl radicals, isopropyl radicals, and n-propyl radicals have been studied as well as the oxidation of methylpropargyl radicals.

  18. Isothermal, kinetic and thermodynamic studies on basic dye sorption ...

    African Journals Online (AJOL)

    Isothermal, kinetic and thermodynamic studies on basic dye sorption onto tartaric acid esterified wheat straw. ... African Journal of Biotechnology ... esterified wheat straw (EWS), was originally prepared by solid phase thermochemistry method.

  19. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  20. In-cell thermodynamics and a new role for protein surfaces.

    Science.gov (United States)

    Smith, Austin E; Zhou, Larry Z; Gorensek, Annelise H; Senske, Michael; Pielak, Gary J

    2016-02-16

    There is abundant, physiologically relevant knowledge about protein cores; they are hydrophobic, exquisitely well packed, and nearly all hydrogen bonds are satisfied. An equivalent understanding of protein surfaces has remained elusive because proteins are almost exclusively studied in vitro in simple aqueous solutions. Here, we establish the essential physiological roles played by protein surfaces by measuring the equilibrium thermodynamics and kinetics of protein folding in the complex environment of living Escherichia coli cells, and under physiologically relevant in vitro conditions. Fluorine NMR data on the 7-kDa globular N-terminal SH3 domain of Drosophila signal transduction protein drk (SH3) show that charge-charge interactions are fundamental to protein stability and folding kinetics in cells. Our results contradict predictions from accepted theories of macromolecular crowding and show that cosolutes commonly used to mimic the cellular interior do not yield physiologically relevant information. As such, we provide the foundation for a complete picture of protein chemistry in cells.

  1. Kinetics of the Adsorption of Bovine Serum Albumin of White Wine ...

    African Journals Online (AJOL)

    This study investigates the kinetics of adsorption of bovine serum albumin, BSA, in white wine model solutions onto activated carbon, AC, and alumina, AL. Pseudo-first order and pseudo-second order models were applied to determine the rate and mechanism of adsorption of the white wine protein during the haze removal ...

  2. Quantitative analysis of protein-ligand interactions by NMR.

    Science.gov (United States)

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  3. Kinetic studies on the hafnium nad deuterium

    International Nuclear Information System (INIS)

    Bing Wenzeng; Long Xinggui; Zhu Zuliang

    2009-04-01

    Through the method of reaction rate analysis in a constant volume reactor, the time dependence of the pressure drop of the hafnium deuteride formation are studied over a temperature range 573-873 K on a metal hydride thermodynamic and kinetic parameters measuring apparatus. The rate constants of the hafnium deuteride formation, which are 0.0530 s -1 , 0.0452 s -1 , 0.0319 s -1 , 0.0261 s -1 , are calculated at a serial temperatures of 573 K, 673 K, 773 K, 873 K and the initial pressure of 13 kPa. The activation energy of the reaction is (-10.1±1.5) kJ·mol -1 . Comparing the above results with those of titanium deuteride formation on the same measuring apparatus, the kinetic mechanism of the deuteride formation of hafnium and titanium is considered different. It is concluded that the reaction rate of hafnium absorbing deuterium may be controlled by phase transformation and surface oxidation. (authors)

  4. Kinetic Analysis of the Multivalent Ligand Binding Interaction between Protein A/G and IgG: A Standard System Setting.

    Science.gov (United States)

    Reader, Peter P; Shaw, Andrew M

    2017-09-28

    Recombinant protein A/G (PAG) has a sequence coding for eight IgG binding sites and has enhanced interspecies affinity. High-frequency sampling of a PAG titration with IgG produces concentration profiles that are sensitive to the kinetic availability of the binding sites. The full kinetic model developed here for IgG binding sequentially to PAG shows only two distinct kinetic processes, describing an initial rapid association of two antibodies to PAG with a rate constant k-fast = (1.86 ± 0.08) × 10 6 M -1 s -1 and a slower antibody binding process to all remaining sites, k-slow = (1.24 ± 0.05) × 10 4 M -1 s -1 . At equilibrium (after 1 h), the maximum IgG occupancy of PAG is 2.8 ± 0.5, conflicting with the genetic evidence of eight binding sites and suggesting significant steric hindrance of the neighboring IgG binding sites. The phosphate-buffered saline (PBS) solution defines a standard system setting, and this may be compared with other settings. The mean association rate of PAG-IgG n in the standard setting is 282 ± 20% higher than when PAG is tethered to a surface. A systems biology approach requires that a model parameter set that defines a system in a standard setting should be transferable to another system. The transfer of parameters between settings may be performed using activity coefficients characterizing an effective concentration of species in a system, a i = γ i c i . The activity correction, γ, for the eight-site occupancy is γ = 0.35 ± 0.06, and mapping from the standard setting to the solution setting suggests γ PAG-IgG = 0.4 ± 0.03. The role of activity coefficients and transferability of kinetic parameters between system settings is discussed.

  5. Activation gating kinetics of GIRK channels are mediated by cytoplasmic residues adjacent to transmembrane domains.

    Science.gov (United States)

    Sadja, Rona; Reuveny, Eitan

    2009-01-01

    G-protein-coupled inwardly rectifying potassium channels (GIRK/Kir3.x) are involved in neurotransmission-mediated reduction of excitability. The gating mechanism following G protein activation of these channels likely proceeds from movement of inner transmembrane helices to allow K(+) ions movement through the pore of the channel. There is limited understanding of how the binding of G-protein betagamma subunits to cytoplasmic regions of the channel transduces the signal to the transmembrane regions. In this study, we examined the molecular basis that governs the activation kinetics of these channels, using a chimeric approach. We identified two regions as being important in determining the kinetics of activation. One region is the bottom of the outer transmembrane helix (TM1) and the cytoplasmic domain immediately adjacent (the slide helix); and the second region is the bottom of the inner transmembrane helix (TM2) and the cytoplasmic domain immediately adjacent. Interestingly, both of these regions are sufficient in mediating the kinetics of fast activation gating. This result suggests that there is a cooperative movement of either one of these domains to allow fast and efficient activation gating of GIRK channels.

  6. A comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded LH2 light-harvesting complexes.

    Science.gov (United States)

    Freiberg, Arvi; Rätsep, Margus; Timpmann, Kõu

    2012-08-01

    Integral membrane proteins constitute more than third of the total number of proteins present in organisms. Solubilization with mild detergents is a common technique to study the structure, dynamics, and catalytic activity of these proteins in purified form. However beneficial the use of detergents may be for protein extraction, the membrane proteins are often denatured by detergent solubilization as a result of native lipid membrane interactions having been modified. Versatile investigations of the properties of membrane-embedded and detergent-isolated proteins are, therefore, required to evaluate the consequences of the solubilization procedure. Herein, the spectroscopic and kinetic fingerprints have been established that distinguish excitons in individual detergent-solubilized LH2 light-harvesting pigment-protein complexes from them in the membrane-embedded complexes of purple photosynthetic bacteria Rhodobacter sphaeroides. A wide arsenal of spectroscopic techniques in visible optical range that include conventional broadband absorption-fluorescence, fluorescence anisotropy excitation, spectrally selective hole burning and fluorescence line-narrowing, and transient absorption-fluorescence have been applied over broad temperature range between physiological and liquid He temperatures. Significant changes in energetics and dynamics of the antenna excitons upon self-assembly of the proteins into intracytoplasmic membranes are observed, analyzed, and discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. Copyright © 2011. Published by Elsevier B.V.

  7. Development of simple kinetic models and parameter estimation for ...

    African Journals Online (AJOL)

    In order to describe and predict the growth and expression of recombinant proteins by using a genetically modified Pichia pastoris, we developed a number of unstructured models based on growth kinetic equation, fed-batch mass balance and the assumptions of constant cell and protein yields. The growth of P. pastoris on ...

  8. Ruminal degradation kinetics of protein foods by in vitro gas production technique

    Directory of Open Access Journals (Sweden)

    Ivone Yurika Mizubuti

    2014-02-01

    Full Text Available Chemical analysis of carbohydrates and nitrogen fractions, as well as, determination their carbohydrates digestion rates in soyben meal (SM, crambe meal (CM, radish meal (RM, wet brewery residue (WBR and dehydrated silkworm chrysalis (SCD were accomplished. The kinetics parameters of non-fibrous carbohydrates (NFC and B2 fraction were estimated using cumulative gas production technique. Among the foods studied there was considerable variation in chemical composition. The crambe meal was the only food that did not present synchronism between carbohydrate and nitrogen fractions. In this food there was predominance of A+B1 carbohydrates fractions and B1+B2 nitrogen compounds fraction, and for the other predominated B2 carbohydrate fraction and B1+ B2 nitrogen compounds fraction. There were differences among the digestive kinetic parameters for all foods. The greater participation in gas production due to non-fibrous carbohydrates was found in the crambe meal and oilseed radish meal. The fermentation of fibrous carbohydrates provided higher gas volume in the wet brewery residue and in the soybean meal, however, the soybean meal was food with higher total gas volume. Non fibrous carbohydrates degradation rates of wet brewery residue and dehydrated silkworm chrysalis were far below the limits of degradation of this fraction. Due to the parameters obtained by the cumulative gas production, the soybean meal was the best food, however, all others have potential for use in animal nutrition. The cumulative gas production technique allows the estimative of degradation rates and provides further information about the ruminal fermentation kinetics of foods.

  9. Protein folding simulations: from coarse-grained model to all-atom model.

    Science.gov (United States)

    Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei

    2009-06-01

    Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL

  10. Kinetic Studies of Catalytic Oxidation of Cyclohexene Using ...

    African Journals Online (AJOL)

    Cyclohexene was oxidized using chromium (VI) oxide (CrO3) in pure acetic acid medium. The products of oxidation were analysed using simple qualitative analysis, IR spectroscopy and Gas chromatography-Mass spectrometry (GC/MS). Kinetics studies were carried out to determine the order of reaction, rate constant and ...

  11. A kinetic study of textile dyeing wastewater degradation by Penicillium chrysogenum.

    Science.gov (United States)

    Durruty, Ignacio; Fasce, Diana; González, Jorge Froilán; Wolski, Erika Alejandra

    2015-06-01

    The potential of Penicillium chrysogenum to decolorize azo dyes and a real industrial textile wastewater was studied. P. chrysogenum was able to decolorize and degrade three azo dyes (200 mg L(-1)), either independently or in a mixture of them, using glucose as a carbon source. A kinetic model for degradation was developed and it allowed predicting the degradation kinetics of the mixture of the three azo dyes. In addition, P. chrysogenum was able to decolorize real industrial wastewater. The kinetic model proposed was also able to predict the decolorization of the real wastewater. The calibration of the proposed model makes it a useful tool for future wastewater facilities' design and for practical applications.

  12. Kinetics of leptin binding to the Q223R leptin receptor.

    Directory of Open Access Journals (Sweden)

    Hans Verkerke

    Full Text Available Studies in human populations and mouse models of disease have linked the common leptin receptor Q223R mutation to obesity, multiple forms of cancer, adverse drug reactions, and susceptibility to enteric and respiratory infections. Contradictory results cast doubt on the phenotypic consequences of this variant. We set out to determine whether the Q223R substitution affects leptin binding kinetics using surface plasmon resonance (SPR, a technique that allows sensitive real-time monitoring of protein-protein interactions. We measured the binding and dissociation rate constants for leptin to the extracellular domain of WT and Q223R murine leptin receptors expressed as Fc-fusion proteins and found that the mutant receptor does not significantly differ in kinetics of leptin binding from the WT leptin receptor. (WT: ka 1.76×106±0.193×106 M-1 s-1, kd 1.21×10-4±0.707×10-4 s-1, KD 6.47×10-11±3.30×10-11 M; Q223R: ka 1.75×106±0.0245×106 M-1 s-1, kd 1.47×10-4±0.0505×10-4 s-1, KD 8.43×10-11±0.407×10-11 M. Our results support earlier findings that differences in affinity and kinetics of leptin binding are unlikely to explain mechanistically the phenotypes that have been linked to this common genetic variant. Future studies will seek to elucidate the mechanism by which this mutation influences susceptibility to metabolic, infectious, and malignant pathologies.

  13. Developmental block and programmed cell death in Bos indicus embryos: effects of protein supplementation source and developmental kinetics.

    Directory of Open Access Journals (Sweden)

    Sheila Merlo Garcia

    Full Text Available The aims of this study were to determine if the protein source of the medium influences zebu embryo development and if developmental kinetics, developmental block and programmed cell death are related. The culture medium was supplemented with either fetal calf serum or bovine serum albumin. The embryos were classified as Fast (n = 1,235 or Slow (n = 485 based on the time required to reach the fourth cell cycle (48 h and 90 h post insemination - hpi -, respectively. The Slow group was further separated into two groups: those presenting exactly 4 cells at 48 hpi (Slow/4 cells and those that reached the fourth cell cycle at 90 hpi (Slow. Blastocyst quality, DNA fragmentation, mitochondrial membrane potential and signs of apoptosis or necrosis were evaluated. The Slow group had higher incidence of developmental block than the Fast group. The embryos supplemented with fetal calf serum had lower quality. DNA fragmentation and mitochondrial membrane potential were absent in embryos at 48 hpi but present at 90 hpi. Early signs of apoptosis were more frequent in the Slow and Slow/4 cell groups than in the Fast group. We concluded that fetal calf serum reduces blastocyst development and quality, but the mechanism appears to be independent of DNA fragmentation. The apoptotic cells detected at 48 hpi reveal a possible mechanism of programmed cell death activation prior to genome activation. The apoptotic cells observed in the slow-developing embryos suggested a relationship between programmed cell death and embryonic developmental kinetics in zebu in vitro-produced embryos.

  14. Kinetic models of gene expression including non-coding RNAs

    Energy Technology Data Exchange (ETDEWEB)

    Zhdanov, Vladimir P., E-mail: zhdanov@catalysis.r

    2011-03-15

    In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

  15. Studies of U(4) oxidation kinetics in nitric acid and TBP phases

    International Nuclear Information System (INIS)

    Taylor, R.J.; Denniss, I.S.; Koltunov, V.S.; Marchenko, V.I.; Dvoeglazov, K.N.; Savilova, O.A.; Broan, C.J.

    2000-01-01

    U(IV) is an important reagent in current reprocessing plants since it is used to reduce Pu(IV) to Pu(III), therefore, allowing the efficient separation of U and Pu in multi-stage counter-current solvent extraction contactors. The benefits of U(IV) are that it is a kinetically fast reductant and it is a salt free reagent, since U(IV) is oxidised to U(VI) and so does not add to the aqueous waste volumes. Many kinetic reactions of U(IV) have been studied in the past and these are used by BNFL to model the behaviour of U(IV) in process flowsheets. However, some reactions have either not been studied or have been studied many times without conclusive resolution. Therefore, to expand our understanding of U(IV) in the process and to generate data that underpins process models, we are studying a series of U(IV) reactions, and this paper will summarize the results of our kinetic and mechanistic studies. (authors)

  16. Kinetic Studies on Ni-YSZ Composite Electrodes

    DEFF Research Database (Denmark)

    Njodzefon, Jean-Claude; Sudireddy, Bhaskar Reddy; Hjelm, Johan

    2015-01-01

    AC and DC techniques were applied to investigate the electrochemical reaction kinetics of porous composite Ni/8-mol% yttria-stabilized zirconia (Ni/8YSZ) solid oxide cell (SOC) electrodes using a novel pseudo-3-electrode cell geometry. From OCV impedance spectra an activation energy Ea of 1.13 e......V, prefactor yan of 3.7·105·T, hydrogen and steam partial pressure dependencies a and b respectively of -0.07 and 0.22 were determined. DC current density vs. overpotential curves compared with those predicted using the determined kinetic parameters. Apparent Butler-Volmer charge transfer coefficients α were...... branch and the need for different α values for each branch suggests that a simple BV model of the measured electrode kinetics is insufficient and/or different reaction mechanisms might be occurring in anodic vs cathodic polarization....

  17. Kinetic study and thermal decomposition behavior of viscoelastic memory foam

    International Nuclear Information System (INIS)

    Garrido, María A.; Font, Rafael; Conesa, Juan A.

    2016-01-01

    Highlights: • The thermal degradation has been studied under three different atmospheres. • Pyrolysis and combustion kinetic models have been proposed. • Evolved products under different atmospheres have been analyzed by TG-FTIR and TG-MS. - Abstract: A systematic investigation of the thermal decomposition of viscoelastic memory foam (VMF) was performed using thermogravimetric analysis (TGA) to obtain the kinetic parameters, and thermogravimetric analysis coupled to Fourier Transformed Infrared Spectrometry (TGA-FTIR) and thermogravimetric analysis coupled to Mass Spectrometry (TGA-MS) to obtain detailed information of evolved products on pyrolysis and oxidative degradations. Two consecutive nth-order reactions were employed to correlate the experimental data from dynamic and isothermal runs performed at three different heating rates (5, 10 and 20 K/min) under an inert atmosphere. On the other hand, for the kinetic study of the oxidative decomposition, the data from combustion (synthetic air) and poor oxygen combustion (N_2:O_2 = 9:1) runs, at three heating rates and under dynamic and isothermal conditions, were correlated simultaneously. A kinetic model consisting of three consecutive reactions presented a really good correlation in all runs. TGA-FTIR analysis showed that the main gases released during the pyrolysis of VMF were determined as ether and aliphatic hydrocarbons, whereas in combustion apart from the previous gases, aldehydes, amines and CO_2 have also been detected as the main gases. These results were confirmed by the TGA-MS.

  18. Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

    Science.gov (United States)

    Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

    2010-06-22

    The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

  19. Bench-scale Kinetics Study of Mercury Reactions in FGD Liquors

    Energy Technology Data Exchange (ETDEWEB)

    Gary Blythe; John Currie; David DeBerry

    2008-03-31

    This document is the final report for Cooperative Agreement DE-FC26-04NT42314, 'Kinetics Study of Mercury Reactions in FGD Liquors'. The project was co-funded by the U.S. DOE National Energy Technology Laboratory and EPRI. The objective of the project has been to determine the mechanisms and kinetics of the aqueous reactions of mercury absorbed by wet flue gas desulfurization (FGD) systems, and develop a kinetics model to predict mercury reactions in wet FGD systems. The model may be used to determine optimum wet FGD design and operating conditions to maximize mercury capture in wet FGD systems. Initially, a series of bench-top, liquid-phase reactor tests were conducted and mercury species concentrations were measured by UV/visible light spectroscopy to determine reactant and byproduct concentrations over time. Other measurement methods, such as atomic absorption, were used to measure concentrations of vapor-phase elemental mercury, that cannot be measured by UV/visible light spectroscopy. Next, a series of bench-scale wet FGD simulation tests were conducted. Because of the significant effects of sulfite concentration on mercury re-emission rates, new methods were developed for operating and controlling the bench-scale FGD experiments. Approximately 140 bench-scale wet FGD tests were conducted and several unusual and pertinent effects of process chemistry on mercury re-emissions were identified and characterized. These data have been used to develop an empirically adjusted, theoretically based kinetics model to predict mercury species reactions in wet FGD systems. The model has been verified in tests conducted with the bench-scale wet FGD system, where both gas-phase and liquid-phase mercury concentrations were measured to determine if the model accurately predicts the tendency for mercury re-emissions. This report presents and discusses results from the initial laboratory kinetics measurements, the bench-scale wet FGD tests, and the kinetics modeling

  20. Bumetanide kinetics in renal failure

    International Nuclear Information System (INIS)

    Pentikaeinen, P.J.P.; Pasternack, A.; Lampainen, E.; Neuvonen, P.J.; Penttilae, A.

    1985-01-01

    To study the effects of renal failure on bumetanide kinetics, the authors administered single intravenous doses of 1.0 mg/3.08 microCi 14 C-bumetanide to six healthy subjects and 22 patients with variable degrees of renal failure. The kinetics of 14 C-bumetanide and total 14 C were adequately described by a two-compartment open model in the control subjects and in the patients. The volume of the central compartment and the distribution t1/2 were of the same order in both groups, whereas the mean (+/- SE) volume at steady state was larger (22.1 +/- 1.6 and 16.9 +/- 1.0 L) and the elimination t1/2 was longer (1.9 +/- 0.2 and 1.4 +/- 0.1 hours) in patients with renal failure than in healthy controls. Bumetanide renal clearance was lower (10 +/- 3 and 90 +/- 13 ml/min) in patients than in subjects and correlated with creatinine clearance (r = 0.784) and log serum creatinine level (r = -0.843), whereas nonrenal clearance was significantly higher in the patients (153 +/- 14 and 99 +/- 6 ml/min). Bumetanide total plasma clearance did not significantly change. The non-protein-bound, free fraction of bumetanide was higher in patients and correlated with plasma albumin levels (r = -0.777). The kinetics of total 14 C showed similar but greater changes than those of 14C-bumetanide. Thus the most important changes in bumetanide kinetics in patients with renal failure are low renal clearance and a high free fraction, with a consequent increase in nonrenal clearance, volume of distribution, and elimination t1/2

  1. Whey Protein Supplementation Enhances Whole Body Protein Metabolism and Performance Recovery after Resistance Exercise: A Double-Blind Crossover Study.

    Science.gov (United States)

    West, Daniel W D; Abou Sawan, Sidney; Mazzulla, Michael; Williamson, Eric; Moore, Daniel R

    2017-07-11

    No study has concurrently measured changes in free-living whole body protein metabolism and exercise performance during recovery from an acute bout of resistance exercise. We aimed to determine if whey protein ingestion enhances whole body net protein balance and recovery of exercise performance during overnight (10 h) and 24 h recovery after whole body resistance exercise in trained men. In a double-blind crossover design, 12 trained men (76 ± 8 kg, 24 ± 4 years old, 14% ± 5% body fat; means ± standard deviation (SD)) performed resistance exercise in the evening prior to consuming either 25 g of whey protein (PRO; MuscleTech 100% Whey) or an energy-matched placebo (CHO) immediately post-exercise (0 h), and again the following morning (~10 h of recovery). A third randomized trial, completed by the same participants, involving no exercise and no supplement served as a rested control trial (Rest). Participants ingested [ 15 N]glycine to determine whole body protein kinetics and net protein balance over 10 and 24 h of recovery. Performance was assessed pre-exercise and at 0, 10, and 24 h of recovery using a battery of tests. Net protein balance tended to improve in PRO ( P = 0.064; effect size (ES) = 0.61, PRO vs. CHO) during overnight recovery. Over 24 h, net balance was enhanced in PRO ( P = 0.036) but not in CHO ( P = 0.84; ES = 0.69, PRO vs. CHO), which was mediated primarily by a reduction in protein breakdown (PRO protein supplementation improved MVC (ES = 0.76), REP (ES = 0.44), and peak power (ES = 0.55). In conclusion, whey protein supplementation enhances whole body anabolism, and may improve acute recovery of exercise performance after a strenuous bout of resistance exercise.

  2. The Study of a Simple Redox Reaction as an Experimental Approach to Chemical Kinetics.

    Science.gov (United States)

    Elias, Horst; Zipp, Arden P.

    1988-01-01

    Recommends using iodide ions and peroxodisulfate ions for studying rate laws instead of the standard iodine clock for kinetic study. Presents the methodology and a discussion of the kinetics involved for a laboratory experiment for a high school or introductory college course. (ML)

  3. ENZYMATIC KINETIC STUDY HYDROLASE FROM CITRUS

    Directory of Open Access Journals (Sweden)

    Israel Hernández

    2015-09-01

    Full Text Available In this paper the degrading activity of enzymes derived from orange peels (Citrus x sinensis, grapefruit (Citrus paradise and pineapple (Ananas comosus on the organic matter in wastewater is evaluated. This activity is measured indirectly by quantifying the biochemical oxygen demand (COD before and after degradation process based on a period of time using the HACH DR / 2010, and then the kinetic study was performed by the differential method and integral with the experimental data, obtaining a reaction order of 1 to pectinase (orange, and order 2 for bromelain (pineapple.

  4. The Mechanisms of Aberrant Protein Aggregation

    Science.gov (United States)

    Cohen, Samuel; Vendruscolo, Michele; Dobson, Chris; Knowles, Tuomas

    2012-02-01

    We discuss the development of a kinetic theory for understanding the aberrant loss of solubility of proteins. The failure to maintain protein solubility results often in the assembly of organized linear structures, commonly known as amyloid fibrils, the formation of which is associated with over 50 clinical disorders including Alzheimer's and Parkinson's diseases. A true microscopic understanding of the mechanisms that drive these aggregation processes has proved difficult to achieve. To address this challenge, we apply the methodologies of chemical kinetics to the biomolecular self-assembly pathways related to protein aggregation. We discuss the relevant master equation and analytical approaches to studying it. In particular, we derive the underlying rate laws in closed-form using a self-consistent solution scheme; the solutions that we obtain reveal scaling behaviors that are very generally present in systems of growing linear aggregates, and, moreover, provide a general route through which to relate experimental measurements to mechanistic information. We conclude by outlining a study of the aggregation of the Alzheimer's amyloid-beta peptide. The study identifies the dominant microscopic mechanism of aggregation and reveals previously unidentified therapeutic strategies.

  5. A kinetic study of the electrochemical hydrogenation of ethylene

    International Nuclear Information System (INIS)

    Sedighi, S.; Gardner, C.L.

    2010-01-01

    In this study, we have examined the kinetics of the electrochemical hydrogenation of ethylene in a PEM reactor. While in itself this reaction is of little industrial interest, this reaction can be looked upon as a model reaction for many of the important hydrogenation processes including the refining of heavy oils and the hydrogenation of vegetable oils. To study the electrochemical hydrogenation of ethylene, several experimental techniques have been used including polarization measurements, measurement of the composition of the exit gases and potential step, transient measurements. The results show that the hydrogenation reaction proceeds rapidly and essentially to completion. By fitting the experimental transient data to the results from a zero-dimensional mathematical model of the process, a set of kinetic parameters for the reactions has been obtained that give generally good agreement with the experimental results. It seems probable that similar experimental techniques could be used to study the electrochemical hydrogenation of other unsaturated organic molecules of more industrial significance.

  6. Characteristics and kinetic studies of Hydrilla verticillata pyrolysis via thermogravimetric analysis.

    Science.gov (United States)

    Hu, Zhiquan; Chen, Zhihua; Li, Genbao; Chen, Xiaojuan; Hu, Mian; Laghari, Mahmood; Wang, Xun; Guo, Dabin

    2015-10-01

    The pyrolysis characteristics and kinetic of Hydrilla verticillata (HV) have been investigated using non-isothermal thermogravimetric analysis. The results showed that the pyrolysis behavior of HV can be divided into two independent stages. The kinetics of Stage I was investigated using a distributed activation energy model (DAEM) with discrete 99 first-order reactions. Stage II was an independent stage which corresponds to the decomposition of calcium oxalate, whose kinetics was studied using iso-conversional method together with compensation effect and master-plots method. The activation energies ranged from 92.39 to 506.17 and 190.42 to 222.48 kJ/mol for the first and second stages respectively. Calculated data gave very good fit to the experimental data. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  8. A Study on the Kinetic Characteristics of Transmutation Process Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Chang Hyun; You, Young Woo; Cho, Jae seon; Huh, Chang Wook; Kim, Doh Hyung [Seoul National University, Seoul (Korea, Republic of)

    1997-07-01

    The purpose of this study is to examine the transient heat transfer characteristics of liquid mental as the coolant used in accelerator-driven transmutation process reactor which is related the disposal of high-level radioactive nuclide. At current stage, the accelerator-driven transmutation process is investigated as the most appropriate method among many transmutation process methods. In this study, previous research works are investigated especially about the thermal hydraulics and kinetic behavior of coolant material including heat transfer of coolant in transmutation process reactor. A study on the heat transfer characteristics of liquid metal is performed based on the thermal hydraulic kinetic characteristics of liquid metal reactor which uses liquid metal coolant. Based on this study, the most appropriate material for the coolant of transmutation reactor will be recommended. 53 refs., 15 tabs., 33 figs. (author)

  9. Effects of varying ruminally undegradable protein supplementation on forage digestion, nitrogen metabolism, and urea kinetics in Nellore cattle fed low-quality tropical forage.

    Science.gov (United States)

    Batista, E D; Detmann, E; Titgemeyer, E C; Valadares Filho, S C; Valadares, R F D; Prates, L L; Rennó, L N; Paulino, M F

    2016-01-01

    Effects of supplemental RDP and RUP on nutrient digestion, N metabolism, urea kinetics, and muscle protein degradation were evaluated in Nellore heifers () consuming low-quality signal grass hay (5% CP and 80% NDF, DM basis). Five ruminally and abomasally cannulated Nellore heifers (248 ± 9 kg) were used in a 5 × 5 Latin square. Treatments were the control (no supplement) and RDP supplementation to meet 100% of the RDP requirement plus RUP provision to supply 0, 50, 100, or 150% of the RUP requirement. Supplemental RDP (casein plus NPN) was ruminally dosed twice daily, and RUP supply (casein) was continuously infused abomasally. Jugular infusion of [NN]-urea with measurement of enrichment in urine was used to evaluate urea kinetics. The ratio of urinary 3-methylhistidine to creatinine was used to estimate skeletal muscle protein degradation. Forage NDF intake (2.48 kg/d) was not affected ( ≥ 0.37) by supplementation, but supplementation did increase ruminal NDF digestion ( Urea entry rate and gastrointestinal entry rate of urea were increased by supplementation ( urea entry rate and tended ( = 0.07) to linearly increase gastrointestinal entry rate of urea. Urea use for anabolic purposes tended ( = 0.07) to be increased by supplementation, and RUP provision also tended ( = 0.08) to linearly increase the amount of urea used for anabolism. The fraction of recycled urea N incorporated into microbial N was greater ( urea from the renal tubule than did supplemented heifers. Overall, unsupplemented heifers had greater mobilization of AA from myofibrillar protein, which provided N for urea synthesis and subsequent recycling. Supplemental RUP, when RDP was supplied, not only increased N retention but also supported increased urea N recycling and increased ruminal microbial protein synthesis.

  10. Mechanism, kinetics and application studies on enhanced activated sludge by interior microelectrolysis.

    Science.gov (United States)

    Yang, Xiaoyi; Xue, Yu; Wang, Wenna

    2009-01-01

    Enhanced activated sludge by interior microelectrolysis (EAIM) was studied to treat textile wastewater, kinetics, mechanism and application of which were also discussed in comparison with traditional activated sludge and interior microelectrolysis, respectively. The results of kinetics study indicated three different processes all followed first-order kinetics well. In EAIM, three impact factors take effects on COD removal, which are flocculation, activated sludge and electrophoresis and redox. In terms of assumption of no interaction among three COD removal mechanisms, 49.6% of the total COD removal is ascribed to flocculation, 30.1% to activated sludge and 20.3% to electrophoresis and redox. EAIM showed its advantages in COD removal efficiency, extensive adaptability to complex composition and wide range of pH. EAIM-aerobic process provided an efficient and economic performance for dealing with textile wastewater.

  11. Kinetic studies on the oxidation of oxyhemoglobin by biologically active iron thiosemicarbazone complexes: relevance to iron-chelator-induced methemoglobinemia.

    Science.gov (United States)

    Basha, Maram T; Rodríguez, Carlos; Richardson, Des R; Martínez, Manuel; Bernhardt, Paul V

    2014-03-01

    The oxidation of oxyhemoglobin to methemoglobin has been found to be facilitated by low molecular weight iron(III) thiosemicarbazone complexes. This deleterious reaction, which produces hemoglobin protein units unable to bind dioxygen and occurs during the administration of iron chelators such as the well-known 3-aminopyridine-2-pyridinecarbaldehyde thiosemicarbazone (3-AP; Triapine), has been observed in the reaction with Fe(III) complexes of some members of the 3-AP structurally-related thiosemicarbazone ligands derived from di-2-pyridyl ketone (HDpxxT series). We have studied the kinetics of this oxidation reaction in vitro using human hemoglobin and found that the reaction proceeds with two distinct time-resolved steps. These have been associated with sequential oxidation of the two different oxyheme cofactors in the α and β protein chains. Unexpected steric and hydrogen-bonding effects on the Fe(III) complexes appear to be the responsible for the observed differences in the reaction rate across the series of HDpxxT ligand complexes used in this study.

  12. Discrete kinetic models from funneled energy landscape simulations.

    Directory of Open Access Journals (Sweden)

    Nicholas P Schafer

    Full Text Available A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK. In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.

  13. Kinetic Study of Acetone-Butanol-Ethanol Fermentation in Continuous Culture

    Science.gov (United States)

    Buehler, Edward A.; Mesbah, Ali

    2016-01-01

    Acetone-butanol-ethanol (ABE) fermentation by clostridia has shown promise for industrial-scale production of biobutanol. However, the continuous ABE fermentation suffers from low product yield, titer, and productivity. Systems analysis of the continuous ABE fermentation will offer insights into its metabolic pathway as well as into optimal fermentation design and operation. For the ABE fermentation in continuous Clostridium acetobutylicum culture, this paper presents a kinetic model that includes the effects of key metabolic intermediates and enzymes as well as culture pH, product inhibition, and glucose inhibition. The kinetic model is used for elucidating the behavior of the ABE fermentation under the conditions that are most relevant to continuous cultures. To this end, dynamic sensitivity analysis is performed to systematically investigate the effects of culture conditions, reaction kinetics, and enzymes on the dynamics of the ABE production pathway. The analysis provides guidance for future metabolic engineering and fermentation optimization studies. PMID:27486663

  14. Kinetics and Mechanisms of Thiol–Disulfide Exchange Covering Direct Substitution and Thiol Oxidation-Mediated Pathways

    Science.gov (United States)

    2013-01-01

    Abstract Significance: Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol–disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. Critical Issues: This review is focused on the kinetics and mechanisms of thiol–disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Recent Advances and Future Directions: Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery. Antioxid. Redox Signal. 18, 1623–1641. PMID:23075118

  15. A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

    A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

  16. Kinetic analysis of the reactions of hypobromous acid with protein components

    DEFF Research Database (Denmark)

    Pattison, David I; Davies, Michael Jonathan

    2004-01-01

    available for HOBr. In this study, rate constants for reaction of HOBr with protein components have been determined. The second-order rate constants (22 degrees C, pH 7.4) for reaction with protein sites vary by 8 orders of magnitude and decrease in the order Cys > Trp approximately Met approximately His...

  17. In vitro studies of ante-mortem proliferation kinetics

    International Nuclear Information System (INIS)

    McBride, W.H.; Withers, H.R.

    1986-01-01

    Using K562 human erythroblastoid cells, it was concluded that dose fractionation has no discrepant effect on the ante-mortem proliferation kinetics of doomed cells as opposed to clonogenic cell survival and that effects on ante-mortem proliferation kinetics cannot be solely responsible for the differences in fractionation response between early and late responding tissues. (UK)

  18. Kinetic studies on leucite precursors

    Czech Academy of Sciences Publication Activity Database

    Mrázová, M.; Kloužková, A.; Kohoutková, Martina

    2009-01-01

    Roč. 7, č. 2 (2009), s. 205-210 ISSN 1895-1066 R&D Projects: GA MPO 2A-1TP1/063 Institutional research plan: CEZ:AV0Z40320502 Keywords : leucite * crystallization kinetics * hydrothermal Subject RIV: JH - Ceramics, Fire-Resistant Materials and Glass Impact factor: 1.065, year: 2009

  19. Estimating kinetic mechanisms with prior knowledge I: Linear parameter constraints.

    Science.gov (United States)

    Salari, Autoosa; Navarro, Marco A; Milescu, Mirela; Milescu, Lorin S

    2018-02-05

    To understand how ion channels and other proteins function at the molecular and cellular levels, one must decrypt their kinetic mechanisms. Sophisticated algorithms have been developed that can be used to extract kinetic parameters from a variety of experimental data types. However, formulating models that not only explain new data, but are also consistent with existing knowledge, remains a challenge. Here, we present a two-part study describing a mathematical and computational formalism that can be used to enforce prior knowledge into the model using constraints. In this first part, we focus on constraints that enforce explicit linear relationships involving rate constants or other model parameters. We develop a simple, linear algebra-based transformation that can be applied to enforce many types of model properties and assumptions, such as microscopic reversibility, allosteric gating, and equality and inequality parameter relationships. This transformation converts the set of linearly interdependent model parameters into a reduced set of independent parameters, which can be passed to an automated search engine for model optimization. In the companion article, we introduce a complementary method that can be used to enforce arbitrary parameter relationships and any constraints that quantify the behavior of the model under certain conditions. The procedures described in this study can, in principle, be coupled to any of the existing methods for solving molecular kinetics for ion channels or other proteins. These concepts can be used not only to enforce existing knowledge but also to formulate and test new hypotheses. © 2018 Salari et al.

  20. Shock wave, fluid instability and implosion studies with a kinetic particle approach

    Science.gov (United States)

    Sagert, Irina; Even, Wesley P.; Strother, Terrance T.

    2016-10-01

    Many problems in laboratory plasma physics are subject to flows that move between the continuum and the kinetic regime. The correct description of these flows is crucial in order to capture their impact on the system's dynamical evolution. Examples are capsule implosions in inertial confinement fusion (ICF). Although their dynamics is predominantly shaped by shock waves and fluid instabilities, non-equilibrium flows in form of deuterium/tritium ions have been shown to play a significant role. We present recent studies with our Monte Carlo kinetic particle code that is designed to capture continuum and kinetic flows in large physical systems with possible applications in ICF studies. Discussed results will include standard shock wave and fluid instability tests and simulations that are adapted towards future ICF studies with comparisons to hydrodynamic simulations. This work used the Wolf TriLAB Capacity Cluster at LANL. I.S. acknowledges support through a Director's fellowship (20150741PRD3) from Los Alamos National Laboratory.

  1. Adsorption kinetics of c-Fos and c-Jun to air-water interfaces.

    Science.gov (United States)

    Del Boca, Maximiliano; Nobre, Thatyane Morimoto; Zaniquelli, Maria Elisabete Darbello; Maggio, Bruno; Borioli, Graciela A

    2007-11-01

    The kinetics of adsorption to air-water interfaces of the biomembrane active transcription factors c-Fos, c-Jun and their mixtures is investigated. The adsorption process shows three distinct stages: a lag time, a fast pseudo zero-order stage, and a halting stage. The initial stage determines the course of the process, which is concentration dependent until the end of the fast stage. We show that c-Fos has faster adsorption kinetics than c-Jun over all three stages and that the interaction between both proteins is apparent in the adsorption profiles of the mixtures. Protein molecular reorganization at the interface determines the transition to the final adsorption stage of the pure proteins as well as that of the mixtures.

  2. Inactivation disinfection property of Moringa Oleifera seed extract: optimization and kinetic studies

    Science.gov (United States)

    Idris, M. A.; Jami, M. S.; Hammed, A. M.

    2017-05-01

    This paper presents the statistical optimization study of disinfection inactivation parameters of defatted Moringa oleifera seed extract on Pseudomonas aeruginosa bacterial cells. Three level factorial design was used to estimate the optimum range and the kinetics of the inactivation process was also carried. The inactivation process involved comparing different disinfection models of Chicks-Watson, Collins-Selleck and Homs models. The results from analysis of variance (ANOVA) of the statistical optimization process revealed that only contact time was significant. The optimum disinfection range of the seed extract was 125 mg/L, 30 minutes and 120rpm agitation. At the optimum dose, the inactivation kinetics followed the Collin-Selleck model with coefficient of determination (R2) of 0.6320. This study is the first of its kind in determining the inactivation kinetics of pseudomonas aeruginosa using the defatted seed extract.

  3. Kinetic properties of ATP sulfurylase and APS kinase from Thiobacillus denitrificans.

    Science.gov (United States)

    Gay, Sean C; Fribourgh, Jennifer L; Donohoue, Paul D; Segel, Irwin H; Fisher, Andrew J

    2009-09-01

    The Thiobacillus denitrificans genome contains two sequences corresponding to ATP sulfurylase (Tbd_0210 and Tbd_0874). Both genes were cloned and expressed protein characterized. The larger protein (Tbd_0210; 544 residues) possesses an N-terminal ATP sulfurylase domain and a C-terminal APS kinase domain and was therefore annotated as a bifunctional enzyme. But, the protein was not bifunctional because it lacked ATP sulfurylase activity. However, the enzyme did possess APS kinase activity and displayed substrate inhibition by APS. Truncated protein missing the N-terminal domain had APS kinase activity suggesting the function of the inactive sulfurylase domain is to promote the oligomerization of the APS kinase domains. The smaller gene product (Tbd_0874; 402 residues) possessed strong ATP sulfurylase activity with kinetic properties that appear to be kinetically optimized for the direction of APS utilization and ATP+sulfate production, which is consistent with an enzyme that functions physiologically to produce inorganic sulfate.

  4. Convergent synthesis of proteins by kinetically controlled ligation

    Science.gov (United States)

    Kent, Stephen; Pentelute, Brad; Bang, Duhee; Johnson, Erik; Durek, Thomas

    2010-03-09

    The present invention concerns methods and compositions for synthesizing a polypeptide using kinetically controlled reactions involving fragments of the polypeptide for a fully convergent process. In more specific embodiments, a ligation involves reacting a first peptide having a protected cysteyl group at its N-terminal and a phenylthioester at its C-terminal with a second peptide having a cysteine residue at its N-termini and a thioester at its C-termini to form a ligation product. Subsequent reactions may involve deprotecting the cysteyl group of the resulting ligation product and/or converting the thioester into a thiophenylester.

  5. Kinetics of Glycoxidation of Bovine Serum Albumin by Glucose, Fructose and Ribose and Its Prevention by Food Components

    Directory of Open Access Journals (Sweden)

    Izabela Sadowska-Bartosz

    2014-11-01

    Full Text Available The aim of this study was to compare the kinetics of the glycoxidation of bovine serum albumin (BSA as a model protein by three sugars: glucose, fructose and ribose, using fluorometric measurements of the content of advanced glycation end products (AGEs, protein-bound fructosamine, dityrosine, N'-formylkynurenine, kynurenine, tryptophan, the content of advanced oxidation protein products (AOPP, protein carbonyl groups, as well as thiol groups. Moreover, the levels of glycoalbumin and AGEs were determined by using an enzyme-linked immunosorbent assay. Based on the kinetic results, the optimal incubation time for studies of the modification of the glycoxidation rate by additives was chosen, and the effects of 25 compounds of natural origin on the glycoxidation of BSA induced by various sugars were examined. The same compounds were found to have different effects on glycoxidation induced by various sugars, which suggests caution in extrapolation from experiments based on one sugar to other sugars. From among the compounds tested, the most effective inhibitors of glycoxidation were: polyphenols, pyridoxine and 1-cyano-4-hydroxycinnamic acid.

  6. Adsorption of saturated fatty acid in urea complexation: Kinetics and equilibrium studies

    Science.gov (United States)

    Setyawardhani, Dwi Ardiana; Sulistyo, Hary; Sediawan, Wahyudi Budi; Fahrurrozi, Mohammad

    2018-02-01

    Urea complexation is fractionation process for concentrating poly-unsaturated fatty acids (PUFAs) from vegetable oil or animal fats. For process design and optimization in commercial industries, it is necessary to provide kinetics and equilibrium data. Urea inclusion compounds (UICs) as the product is a unique complex form which one molecule (guest) is enclosed within another molecule (host). In urea complexation, the guest-host bonding exists between saturated fatty acids (SFAs) and crystalline urea. This research studied the complexation is analogous to an adsorption process. The Batch adsorption process was developed to obtain the experimental data. The ethanolic urea solution was mixed with SFA in certain compositions and adsorption times. The mixture was heated until it formed homogenous and clear solution, then it cooled very slowly until the first numerous crystal appeared. Adsorption times for the kinetic data were determined since the crystal formed. The temperature was maintained constant at room temperature. Experimental sets of data were observed with adsorption kinetics and equilibrium models. High concentration of saturated fatty acid (SFA) was used to represent adsorption kinetics and equilibrium parameters. Kinetic data were examined with pseudo first-order, pseudo second-order and intra particle diffusion models. Linier, Freundlich and Langmuir isotherm were used to study the equilibrium model of this adsorption. The experimental data showed that SFA adsorption in urea crystal followed pseudo second-order model. The compatibility of the data with Langmuir isotherm showed that urea complexation was a monolayer adsorption.

  7. Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

    Science.gov (United States)

    Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

    2017-12-21

    In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

  8. Kinetic study of the reaction of chlorine atoms with hydroxyacetone in gas-phase

    Science.gov (United States)

    Stoeffler, Clara; Joly, Lilian; Durry, Georges; Cousin, Julien; Dumelié, Nicolas; Bruyant, Aurélien; Roth, Estelle; Chakir, Abdelkhaleq

    2013-12-01

    In this letter the kinetics of the reaction of hydroxyacetone CH3C(O)CH2OH with Cl atoms is investigated using the relative rate technique. Experiments are carried out in a 65 L multipass photoreactor in the temperature range of 281-350 K. A mid-infrared spectrometer based on a quantum cascade laser in external cavity emitting at 9.5 μm is used to analyze the reactants. The determined rate coefficient for the investigated reaction is (1.7 ± 0.3) × 10-11exp(381.5 ± 57.3/T). The results are presented and discussed in terms of precision and compared with those obtained previously. The impact of Cl atoms on the atmospheric life time of hydroxyacetone is also discussed. Developing analytical techniques to quantify this compound in the atmosphere. Several methods of measurement have been used including the technique of proton transfer mass spectrometry (PTR-MS) [2] and derivatization with a chemical agent such as dinitrophenylhydrazine (DNPH) [3,4] followed by GC/MS or HPLC analyses. The HA amount in the troposphere was found to be in the order of a few hundred parts per trillion by volume [4], Performing laboratory experiments in order to study the HA reactivity with atmospheric oxidants. The first study on the kinetic of the reaction between OH radicals and HA was made by Dagault et al. [5] whose work was performed at room temperature by flash photolysis-resonance fluorescence. The determined rate constant implies a lifetime of a few days for HA relative to oxidation by OH radicals. Orlando et al. performed mechanistic and kinetics studies of the reaction of HA with OH radicals and Cl atoms at room temperature using a relative method [6]. Products detection was performed using FTIR spectroscopy. Moreover, these authors studied the photolysis of HA to determine its quantum yield and UV absorption spectrum. These studies showed that HA is principally removed from the atmosphere by reaction with OH radicals. Kinetic studies of the reaction of OH radicals with HA as a

  9. Insulin-like growth factors and leucine kinetics during exercise training in children with cystic fibrosis

    NARCIS (Netherlands)

    Gulmans, [No Value; van der Laag, J; Wattimena, D; van Doorn, J; Oostveen, D; Berger, R; van de Meer, K

    Background: Little is known about the metabolic effects of exercise training in children with cystic fibrosis. The hypothesis for the current study was that in patients with declining clinical status, exercise increases circulating insulin-like growth factors (IGFs) and improves protein kinetics.

  10. Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

    International Nuclear Information System (INIS)

    Różycki, Bartosz; Cieplak, Marek

    2014-01-01

    We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme

  11. Photoaggregation of crystallins (main proteins of eye lens) under the effect of XeCl laser radiation

    Science.gov (United States)

    Soustov, Lev V.; Chelnokov, Evgeny V.; Bityurin, Nikita M.; Kiselev, A. L.; Nemov, V. V.; Sergeev, Yu. V.; Ostrovsky, Michail A.

    2004-07-01

    UV light is one of primary factors associated with cataract formation in the eye lens. α-, β-, γ-Crystallins maintain lens transparency, and damage to these proteins plays a major role in cataract formation. The effect of XeCl laser radiation (308 nm) on βL-crystallin solution is studied. The strong dependence of protein aggregation kinetics on both laser fluence (w) and repetition rate (F) is investigated. The kinetics features are similar to those of carbonic anhydrase photoaggregation studied previously.

  12. Construction of a biodynamic model for Cry protein production studies.

    Science.gov (United States)

    Navarro-Mtz, Ana Karin; Pérez-Guevara, Fermín

    2014-12-01

    Mathematical models have been used from growth kinetic simulation to gen regulatory networks prediction for B. thuringiensis culture. However, this culture is a time dependent dynamic process where cells physiology suffers several changes depending on the changes in the cell environment. Therefore, through its culture, B. thuringiensis presents three phases related with the predominance of three major metabolic pathways: vegetative growth (Embded-Meyerhof-Parnas pathway), transition (γ-aminobutiric cycle) and sporulation (tricarboxylic acid cycle). There is not available a mathematical model that relates the different stages of cultivation with the metabolic pathway active on each one of them. Therefore, in the present study, and based on published data, a biodynamic model was generated to describe the dynamic of the three different phases based on their major metabolic pathways. The biodynamic model is used to study the interrelation between the different culture phases and their relationship with the Cry protein production. The model consists of three interconnected modules where each module represents one culture phase and its principal metabolic pathway. For model validation four new fermentations were done showing that the model constructed describes reasonably well the dynamic of the three phases. The main results of this model imply that poly-β-hydroxybutyrate is crucial for endospore and Cry protein production. According to the yields of dipicolinic acid and Cry from poly-β-hydroxybutyrate, calculated with the model, the endospore and Cry protein production are not just simultaneous and parallel processes they are also competitive processes.

  13. Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion.

    Science.gov (United States)

    Zhao, Chunhui; Mu, Hui; Zhao, Yuxiao; Wang, Liguo; Zuo, Bin

    2018-02-01

    This study firstly evaluated the microbial role when choosing the acclimated anaerobic granular sludge (AGS) and waste activated sludge (WAS) as microbial and nutritional regulators to improve the biomethanation of fruit and vegetable wastes (FVW). Results showed that the enriched hydrogenotrophic methanogens, and Firmicutes and Spirochaeta in the AGS were responsible for the enhanced methane yield. A synthetic waste representing the mixture of WAS and FVW was then used to investigate the influences of different substrate composition on methane generations. The optimal mass ratio of carbohydrate/protein/cellulose was observed to be 50:45:5, and the corresponding methane yield was 411mL/g-VS added . Methane kinetic studies suggested that the modified Gompertz model fitted better with those substrates of carbohydrate- than protein-predominated. Parameter results indicated that the maximum methane yield and production rate were enhanced firstly and then reduced with the decreasing carbohydrate and increasing protein percentages; the lag phase time however increased continuously. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Hydrogen exchange kinetics changes upon formation of the soybean trypsin inhibitor: trypsin complex

    International Nuclear Information System (INIS)

    Woodward, C.K.; Ellis, L.M.

    1975-01-01

    The hydrogen exchange kinetics of the complex of trypsin--soybean trypsin inhibitor (Kunitz) have been compared to the calculated sum of the exchange kinetics for the inhibitor and trypsin measured separately. The exchange rates observed for the complex are substantially less than the sum of the exchange rates in the two individual proteins. These results cannot be accounted for by changes in intermolecular or intramolecular hydrogen bonding. The decrease in exchange rates in the complex are ascribed to changes in solvent accessibility in the component proteins. (U.S.)

  15. Interplay of bistable kinetics of gene expression during cellular growth

    International Nuclear Information System (INIS)

    Zhdanov, Vladimir P

    2009-01-01

    In cells, the bistable kinetics of gene expression can be observed on the level of (i) one gene with positive feedback between protein and mRNA production, (ii) two genes with negative mutual feedback between protein and mRNA production, or (iii) in more complex cases. We analyse the interplay of two genes of type (ii) governed by a gene of type (i) during cellular growth. In particular, using kinetic Monte Carlo simulations, we show that in the case where gene 1, operating in the bistable regime, regulates mutually inhibiting genes 2 and 3, also operating in the bistable regime, the latter genes may eventually be trapped either to the state with high transcriptional activity of gene 2 and low activity of gene 3 or to the state with high transcriptional activity of gene 3 and low activity of gene 2. The probability to get to one of these states depends on the values of the model parameters. If genes 2 and 3 are kinetically equivalent, the probability is equal to 0.5. Thus, our model illustrates how different intracellular states can be chosen at random with predetermined probabilities. This type of kinetics of gene expression may be behind complex processes occurring in cells, e.g., behind the choice of the fate by stem cells

  16. Controlling chitosan-based encapsulation for protein and vaccine delivery

    Science.gov (United States)

    Koppolu, Bhanu prasanth; Smith, Sean G.; Ravindranathan, Sruthi; Jayanthi, Srinivas; Kumar, Thallapuranam K.S.; Zaharoff, David A.

    2014-01-01

    Chitosan-based nano/microencapsulation is under increasing investigation for the delivery of drugs, biologics and vaccines. Despite widespread interest, the literature lacks a defined methodology to control chitosan particle size and drug/protein release kinetics. In this study, the effects of precipitation-coacervation formulation parameters on chitosan particle size, protein encapsulation efficiency and protein release were investigated. Chitosan particle sizes, which ranged from 300 nm to 3 μm, were influenced by chitosan concentration, chitosan molecular weight and addition rate of precipitant salt. The composition of precipitant salt played a significant role in particle formation with upper Hofmeister series salts containing strongly hydrated anions yielding particles with a low polydispersity index (PDI) while weaker anions resulted in aggregated particles with high PDIs. Sonication power had minimal effect on mean particle size, however, it significantly reduced polydispersity. Protein loading efficiencies in chitosan nano/microparticles, which ranged from 14.3% to 99.2%, was inversely related to the hydration strength of precipitant salts, protein molecular weight and directly related to the concentration and molecular weight of chitosan. Protein release rates increased with particle size and were generally inversely related to protein molecular weight. This study demonstrates that chitosan nano/microparticles with high protein loading efficiencies can be engineered with well-defined sizes and controllable release kinetics through manipulation of specific formulation parameters. PMID:24560459

  17. Glycerol acetals, kinetic study of the reaction between glycerol and formaldehyde

    International Nuclear Information System (INIS)

    Agirre, I.; Garcia, I.; Requies, J.; Barrio, V.L.; Gueemez, M.B.; Cambra, J.F.; Arias, P.L.

    2011-01-01

    The acetalization reaction between glycerol and formaldehyde using Amberlyst 47 acidic ion exchange resin was studied. These acetals can be obtained from renewable sources (bioalcohols and bioalcohol derived aldehydes) and seem to be good candidates for different applications such as oxygenated diesel additives. A preliminary kinetic study was performed in a batch stirred tank reactor studying the influence of different process parameters like temperature, feed composition and the stirring speed. A pseudo homogenous kinetic model able to explain the reaction mechanism was adjusted. Thus, the corresponding order of reaction was determined. Amberlyst 47 acidic ion exchange resin showed a fairly good behavior allowing 100% of selectivity towards acetals formation. However, the studied acetalization reaction showed high thermodynamic limitations achieving glycerol conversions around 50% using a stoichiometric feed ratio at 353 K. The product is a mixture of two isomers (1,3-Dioxan-5-ol and 1,3-dioxolane-4-methanol) and the conversion of 1,3-dioxolane-4-methanol into 1,3-Dioxan-5-ol was also observed. -- Highlights: → The reaction between glycerol and acetaldehyde shows thermodynamic limitations. → Amberlyst 47 ion exchange resins show 100% of selectivity. → A pseudo-homogeneous kinetic model is able to predict the reaction progress. → Isomerization reactions were observed from dioxalanes to dioxanes.

  18. Cellular recovery kinetic studies relevant to combined-modality research and therapy

    International Nuclear Information System (INIS)

    Dethlefsen, L.A.

    1979-01-01

    The relevance of cellular recovery kinetics to combined-modality therapy is evaluated within the framework of an idealized experimental flow chart and published adriamycin data. Within this context, limitations for both experimental design and data interpretations are discussed. The effects of adriamycin have been documented extensively at the molecular and cellular level and its interactions with x-irradiation have been studied, both in vitro and in vivo. The limited in vivo results suggest that the end results of a given protocol correlate with cellular recovery kinetics; however, definitive experiments simply have not been done. For example, no one has used single-dose drug and irradiation data to predict the outcome and then confirm or refute the prediction even in a relatively simple 2-dose drug + 2-dose drug + 2-dose x-ray protocol. Thus, at this time, the extent of the correlations between cellular recovery kinetics and clinical response for either normal or malignant tissues is not known and the possible relevance of such studies cannot be discounted

  19. Kinetics of Single-Enzyme Reactions on Vesicles: Role of Substrate Aggregation

    Science.gov (United States)

    Zhdanov, Vladimir P.

    2015-03-01

    Enzymatic reactions occurring in vivo on lipid membranes can be influenced by various factors including macromolecular crowding in general and substrate aggregation in particular. In academic studies, the role of these factors can experimentally be clarified by tracking single-enzyme kinetics occurring on individual lipid vesicles. To extend the conceptual basis for such experiments, we analyze herein the corresponding kinetics mathematically with emphasis on the role of substrate aggregation. In general, the aggregation may occur on different length scales. Small aggregates may e.g. contain a few proteins or peptides while large aggregates may be mesoscopic as in the case of lipid domains which can be formed in the membranes composed of different lipids. We present a kinetic model describing comprehensively the effect of aggregation of the former type on the dependence of the reaction rate on substrate membrane concentration. The results obtained with physically reasonable parameters indicate that the aggregation-related deviations from the conventional Michaelis-Menten kinetics may be appreciable. Special Issue Comments: This theoretical article is focused on single-enzyme reactions occurring in parallel with substrate aggregation on individual vesicles. This subject is related to a few Special Issue articles concerning enzyme dynamics6,7 and function8 and mathematical aspects of stochastic kinetics.9

  20. Kinetic, spectroscopic and chemical modification study of iron release from transferrin; iron(III) complexation to adenosine triphosphate

    International Nuclear Information System (INIS)

    Thompson, C.P.

    1985-01-01

    Amino acids other than those that serve as ligands have been found to influence the chemical properties of transferrin iron. The catalytic ability of pyrophosphate to mediate transferrin iron release to a terminal acceptor is largely quenched by modification non-liganded histine groups on the protein. The first order rate constants of iron release for several partially histidine modified protein samples were measured. A statistical method was employed to establish that one non-liganded histidine per metal binding domain was responsible for the reduction in rate constant. These results imply that the iron mediated chelator, pyrophosphate, binds directly to a histidine residue on the protein during the iron release process. EPR spectroscopic results are consistent with this interpretation. Kinetic and amino acid sequence studies of ovotransferrin and lactoferrin, in addition to human serum transferrin, have allowed the tentative assignment of His-207 in the N-terminal domain and His-535 in the C-terminal domain as the groups responsible for the reduction in rate of iron release. The above concepts have been extended to lysine modified transferrin. Complexation of iron(II) to adenosine triphosphate (ATP) was also studied to gain insight into the nature of iron-ATP species present at physiological pH. 31 P NMR spectra are observed when ATP is presented in large excess

  1. Kinetic study of lithium-cadmium ternary amalgam decomposition

    International Nuclear Information System (INIS)

    Cordova, M.H.; Andrade, C.E.

    1992-01-01

    The effect of metals, which form stable lithium phase in binary alloys, on the formation of intermetallic species in ternary amalgams and their effect on thermal decomposition in contact with water is analyzed. Cd is selected as ternary metal, based on general experimental selection criteria. Cd (Hg) binary amalgams are prepared by direct contact Cd-Hg, whereas Li is formed by electrolysis of Li OH aq using a liquid Cd (Hg) cathodic well. The decomposition kinetic of Li C(Hg) in contact with 0.6 M Li OH is studied in function of ageing and temperature, and these results are compared with the binary amalgam Li (Hg) decomposition. The decomposition rate is constant during one hour for binary and ternary systems. Ageing does not affect the binary systems but increases the decomposition activation energy of ternary systems. A reaction mechanism that considers an intermetallic specie participating in the activated complex is proposed and a kinetic law is suggested. (author)

  2. A study of redox kinetic in silicate melt

    International Nuclear Information System (INIS)

    Magnien, V.

    2005-12-01

    The aim of this thesis is to understand better iron redox reactions and mechanisms in silicate glasses and melts. Particular interest has been paid to the influence of temperature and chemical composition. For this purpose, the influence of alkali element content, iron content and network formers on the kinetics of redox reactions has been determined through XANES and Raman spectroscopy experiments performed either near the glass transition or above the liquidus temperature. As a complement, electrical conductivity and RBS spectroscopy experiments have been made to characterize the diffusivity of the species that transport electrical charges and the reaction morphology, respectively. Temperature and composition variations can induce changes in the dominating redox mechanism. At a given temperature, the parameters that exert the strongest influence on redox mechanisms are the presence or lack of divalent cations and the existing decoupling between the mobility of network former and modifier elements. Near Tg, the diffusion of divalent cations, when present in the melt, controls the kinetics of iron redox reactions along with a flux of electron holes. Composition, through the degree of polymerization and the silicate network structure, influences the kinetics and the nature of the involved cations, but not the mechanisms of the reaction. Without alkaline earth elements, the kinetics of redox reactions are controlled by the diffusion of oxygen species. With increasing temperatures, the diffusivities of all ionic species tend to become similar. The decoupling between ionic fluxes then is reduced so that several mechanisms become kinetically equivalent and can thus coexist. (author)

  3. A study of sodium oxide crystallization mechanisms and kinetics in cold traps

    International Nuclear Information System (INIS)

    Latge, C.

    1984-04-01

    After showing up the present lack of data on crystallization mechanisms and kinetics, a number of tests were conducted on a sodium test loop equipped with two experimental cold traps. The effects of several geometric and thermohydraulic parameters on purification efficiency were also studied. The test results were used to develop a simulation model. An optimization code based on the model can be used to determine the nucleation and growth kinetics

  4. Receptor activation and 2 distinct COOH-terminal motifs control G-CSF receptor distribution and internalization kinetics

    NARCIS (Netherlands)

    L.H.J. Aarts (Bart); O. Roovers (Onno); A.C. Ward (Alister); I.P. Touw (Ivo)

    2004-01-01

    textabstractWe have studied the intracellular distribution and internalization kinetics of the granulocyte colony-stimulating factor receptor (G-CSF-R) in living cells using fusion constructs of wild-type or mutant G-CSF-R and enhanced green fluorescent protein (EGFP). Under

  5. Synthesis, structural investigation and kinetic studies of uranyl(VI) unsymmetrical Schiff base complexes

    Czech Academy of Sciences Publication Activity Database

    Asadi, Z.; Asadi, M.; Zeinali, A.; Ranjkeshshorkaei, M.; Fejfarová, Karla; Eigner, Václav; Dušek, Michal; Dehnokhalaji, A.

    2014-01-01

    Roč. 126, č. 6 (2014), s. 1673-1683 ISSN 0974-3626 R&D Projects: GA ČR(CZ) GAP204/11/0809 Institutional support: RVO:68378271 Keywords : uranyl schiff base complexes * kinetic study * kinetics of thermal decomposition * X-ray crystallography * cyclic voltammetry Subject RIV: CA - Inorganic Chemistry Impact factor: 1.191, year: 2014

  6. Chemical modification of protein A chromatography ligands with polyethylene glycol. I: Effects on IgG adsorption equilibrium, kinetics, and transport.

    Science.gov (United States)

    Weinberg, Justin; Zhang, Shaojie; Crews, Gillian; Carta, Giorgio; Przybycien, Todd

    2018-04-20

    Chemical modification of Protein A (ProA) chromatography ligands with polyethylene glycol (PEGylation) has been proposed as a strategy to increase the process selectivity and resin robustness by providing the ligand with a steric repulsion barrier against non-specific binding. This article comprises a comprehensive study of IgG adsorption and transport in Repligen CaptivA PriMAB resin with PEGylated ProA ligands that are modified using 5.2 and 21.5 kDa PEG chains. We studied the impact of the molecular weight of the PEG as well as the extent of PEGylation for the 5.2 kDa PEG modification. In all cases, PEGylation of ProA ligands decreases the resin average pore size, particle porosity, and static binding capacity for IgG proportional to the volume of conjugated PEG in the resin. Resin batch uptake experiments conducted in bulk via a stirred-tank system and with individual resin particles under confocal laser scanning microscopy suggests that PEGylation introduces heterogeneity into IgG binding kinetics: a fraction of the IgG binding sites are transformed from typical fast association kinetic behavior to slow kinetic behavior. pH gradient elution experiments of an IgG molecule on the modified resins show an increase in IgG elution pH for all modified resins, implying a decrease in IgG-ProA binding affinity on modification. Despite losses in static binding capacity for all resins with PEGylated ligands, the loss of dynamic binding capacity at 10% breakthrough (DBC 10% ) ranged more broadly from almost 0-47% depending on the PEG molecular weight and the extent of PEGylation. Minimal losses in DBC 10% were observed with a low extent of PEGylation with a smaller molecular weight PEG, while higher losses were observed at higher extents of PEGylation and with higher molecular weight PEG due to decreased static binding capacity and increased mass transfer resistance. This work provides insight into the practical implications for resin performance if PEGylation is

  7. DEFLUORIDATION OF DRINKING WATER BY ELECTROCOAGULATION/ELECTROFLOTATION - KINETIC STUDY

    Directory of Open Access Journals (Sweden)

    Bennajah Mounir

    2010-06-01

    Full Text Available A variable order kinetic (VOK model derived from the langmuir-freundlish equation was applied to determine the kinetics of fluoride removal reaction by electrocoagulation (EC. Synthetic solutions were employed to elucidate the effects of the initial fluoride concentration, the applied current and the initial acidity on the simulation results of the model. The proposed model successfully describes the fluoride removal in Airlift reactor in comparison with the experimental results. In this study two EC cells with the same capacity (V = 20 L were used to carry out fluoride removal with aluminum electrodes, the first is a stirred tank reactor (STR the second is an airlift reactor (ALR. The comparison of energy consumption demonstrates that the (ALR is advantageous for carrying out the defluoridation removal process.

  8. Kinetic model building using advanced nuclear medicine techniques: the kinetics of chromium(III) in the human body

    International Nuclear Information System (INIS)

    Lim, T.H.

    1978-06-01

    The purpose of this study is to investigate whether a valid index of chromium (III) nutritional status can be determined with satisfaction through in vivo kinetic analysis. Three normal subjects and three patients suffering from hemochromatosis were periodically scanned with the Donner Laboratory computerized whole body scanners, starting seconds after radiochromium(III) was administered intravenously, up to a period of 84 days. The activity in the liver, adipose and muscle tissues, spleen and bone was quantitated and corrected, by subtraction of the blood circulation activity in that organ; the major concentration was found in the liver and spleen. From the series of scan images, a kinetic model for the radiochromium(III) metabolic pathway was constructed. Computer analysis showed a significant difference between the two classes of subjects in organs as well as whole body radiochromium(III) transfer. Interpretation of these results showed that in patients with excessive iron stores, a smaller amount of chromium bound to plasma protein was found and a corresponding decrease in transfer of chromium into stores in the liver and other tissues was also found

  9. Glutamic Acid Signal Synchronizes Protein Synthesis Kinetics in Hepatocytes from Old Rats for the Following Several Days. Cell Metabolism Memory.

    Science.gov (United States)

    Brodsky, V Y; Malchenko, L A; Lazarev, D S; Butorina, N N; Dubovaya, T K; Zvezdina, N D

    2018-03-01

    The kinetics of protein synthesis was investigated in primary cultures of hepatocytes from old rats in serum-free medium. The rats were fed mixed fodder supplemented with glutamic acid and then transferred to a regular mixed fodder. The amplitude of protein synthesis rhythm in hepatocytes isolated from these rats increased on average 2-fold in comparison with the rats not receiving glutamic acid supplement. Based on this indicator reflecting the degree of cell-cell interactions, the cells from old rats were not different from those of young rats. The effect was preserved for 3-4 days. These results are discussed in connection with our previous data on preservation of the effect of single administration of gangliosides, noradrenaline, serotonin, and other synchronizers on various cell populations. In contrast to the other investigated factors, glutamic acid is capable of penetrating the blood-brain barrier, which makes its effect possible not only in the case of hepatocytes and other non-brain cells, but also in neurons.

  10. Experimental study and kinetic modeling of the hydro-fluorination of uranium dioxide

    International Nuclear Information System (INIS)

    Pages, Simon

    2014-01-01

    A kinetic study of hydro-fluorination of uranium dioxide was performed between 375 and 475 C under partial pressures of HF between 42 and 720 mbar. The reaction was followed by thermogravimetry in isothermal and isobaric conditions. The kinetic data obtained coupled with a characterization of the powder before, during and after reaction by SEM, EDS, BET and XRD showed that the powder grains of UO 2 are transformed according a model of instantaneous germination, anisotropic growth and internal development. The rate limiting step of the growth process is the diffusion of HF in the UF 4 layer. A mechanism of growth of the UF 4 layer has been proposed. In the temperature and pressure range studied, the reaction is of first order with respect to HF and follows an Arrhenius law. A rate equation was determined and used to perform kinetic simulations which have shown a very good correlation with experience. Coupling of this rate equation with heat and mass transport phenomena allowed to perform simulations at the scale of a powder's agglomerate. They have shown that some structures of agglomerates influence the rate of diffusion of the gases in the porous medium and thereby influence the reaction rate. Finally kinetic simulations on powder's beds and pellets were carried out and compared with experimental rates. The experimental and simulated kinetic curves have the same paces, but improvements in the simulations are needed to accurately predict rates: the coupling between the three scales (grain, agglomerate, oven) would be a good example. (author) [fr

  11. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  12. [18F]-2-FDG as a tool for studying hexokinase kinetics

    International Nuclear Information System (INIS)

    Mertens, J.; Gysemans, M.

    1990-01-01

    In the basic research related to the development of radiolabelled glucose analogues or to sugar metabolism, the measurement of hexokinase kinetics is very important. The article of S. J. Gatley et al about the quality control of [ 18 F]-2-FDG preparations using the hexokinase reaction in vitro was the basic idea of the method proposed in this paper dealing with the direct measurement of hexokinase kinetics by the measurement of the activity related to [ 18 F]-2-FDG-6-phosphate. Experimental results indicate that the method is appropriate for hexokinase studies

  13. Contribution to the study of the kinetics of maraging steel aging

    International Nuclear Information System (INIS)

    Santos Victor, O.B. dos.

    1990-01-01

    Maraging steels are materials with very low contents of C and with Ni, Co, Mo and T1 additions, that can reach very high mechanical strength values by combinations of heat treatment operations. Three 18% Ni Maraging steels have had some aspects of their aging kinetics investigated by experimental procedures using electrical resistivity, internal friction and hardness measurement techniques, in samples aged from 30 seconds to several hours. Finally, it was verified that the techniques employed were very adequate to the purposes of the present kinetics studies. (author)

  14. Kinetics of Iodine 131 labelled fibrinogen in cancerous patients. Pharmacological study

    International Nuclear Information System (INIS)

    Boneu-Valmalette, Andree; Bugat, Roland; David, J.-F.; Combes, P.-F.

    1977-01-01

    The results obtained in a previous study using 131 I fibrinogen in cancerous patients suggested a local intravascular clotting process. In order to elucidate the mechanism of fibrinogen kinetic abnormalities different drugs including heparin, prednisone, ticlopidin, aspirin and indomethacin were administred in 68 patients and their effects evaluated by change in the 131 I fibrinogen disappearance rate. The results suggest that these drugs may counteract with the early stages of coagulation (kinin-forming system, factor XII) and that abnormal 131 I fibrinogen kinetic in cancer would be a non specific phenomenon [fr

  15. Electrostatic influence of local cysteine environments on disulfide exchange kinetics.

    Science.gov (United States)

    Snyder, G H; Cennerazzo, M J; Karalis, A J; Field, D

    1981-11-10

    The ionic strength dependence of the bimolecular rate constant for reaction of the negative disulfide 5,5'-dithiobis (2-nitrobenzoic acid) with cysteines in fragments of naturally occurring proteins was determined by stopped-flow spectroscopy. The Debye-Hückel relationship was applied to determine the effective charge at the cysteine and thereby determine the extent to which nearby neighbors in the primary sequence influence the kinetics. Corrections for the secondary salt effect on cysteine pKs were determined by direct spectrometric pH titration of sulfhydryl groups or by observation of the ionic strength dependence of kinetics of cysteine reaction with the neutral disulfide 2,2'-dithiodipyridine. Quantitative expressions was verified by model studies with N-acetyl-cystein. At ionic strengths equal to or greater than 20 mM, the net charge at the polypeptide cysteine site is the sum of the single negative charge of the thiolate anion and the charges of the amino acids immediately preceding and following the cysteine in the primary sequence. At lower ionic strengths, more distant residues influence kinetics. At pH 7.0, 23 degree C, and an ionic strength of 20 mM, rate constants for reaction of the negative disulfide with a cysteine having two positive neighbors, one positive and one neutral neighbor, or two neutral neighbors are 132000, 3350, and 367 s-1 M-1, respectively. This corresponds to a contribution to the activation energy of 0.65- 1.1 kcal/mol per ion pair involved in collision between the cysteine and disulfide regions. The results permit the estimation that cysteine local environments may provide a means of achieving a 10(6)-fold range in rate constants in disulfide exchange reactions in random-coil proteins. This range may prove useful in developing strategies for directing disulfide pairing in synthetic proteins.

  16. A kinetic study of pyrolysis in pitch impregnated electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Kocaefe, D.; Charette, A.; Ferland, J.; Couderc, P.; Saint-Romain, J.L. (Universite du Quebec a Chicoutini, Chicoutini, PQ (Canada))

    1990-12-01

    A study was conducted on carbon electrodes which were impregnated with three different pitches. The focus of the study was to investigate the pyrolysis of pitch impregnated electrodes. For the purposes of the research an experimental technique and calculation procedure were developed. A kinetic model was used to interpret the data, comparison of model predictions and experimental data showed good agreement. 17 refs., 10 figs., 2 tabs.

  17. Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

    Science.gov (United States)

    Lee, Jay Min

    1990-08-01

    The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the

  18. Copper adsorption on magnetite-loaded chitosan microspheres: A kinetic and equilibrium study

    Energy Technology Data Exchange (ETDEWEB)

    Podzus, P.E., E-mail: ppodzus@gmail.com [Grupo de Aplicaciones de Materiales Biocompatibles, Departamento de Quimica, Facultad de Ingenieria, Universidad de Buenos Aires, Paseo Colon 850, C1063ACV Buenos Aires (Argentina); Debandi, M.V. [Grupo de Aplicaciones de Materiales Biocompatibles, Departamento de Quimica, Facultad de Ingenieria, Universidad de Buenos Aires, Paseo Colon 850, C1063ACV Buenos Aires (Argentina); Daraio, M.E., E-mail: medit@fi.uba.ar [Grupo de Aplicaciones de Materiales Biocompatibles, Departamento de Quimica, Facultad de Ingenieria, Universidad de Buenos Aires, Paseo Colon 850, C1063ACV Buenos Aires (Argentina)

    2012-08-15

    A composite of Fe{sub 3}O{sub 4} nanoparticles and the biopolymer chitosan, chemically crosslinked, was prepared as microspheres and used to adsorb copper ions, which were chosen as a model of contaminant metal in water. The adsorption of copper on the magnetic microspheres was studied in a batch process, with different aqueous solutions of Cu (II) at concentrations ranging from 40 to 1100 ppm. Kinetic and equilibrium aspects of the adsorption process were studied. The time-dependent Cu (II) adsorption data were well described by a pseudo-second-order kinetic model. It was found that the equilibrium data follow the Langmuir isotherm, with a maximum adsorption capacity of around 500 mg Cu/g chitosan. The used microspheres were removed and after desorption the material was able to be reused as an adsorbent. The prepared microspheres proved efficient in the removal of copper ions through an adsorption process whose kinetic and equilibrium characteristics were analyzed.

  19. Copper adsorption on magnetite-loaded chitosan microspheres: A kinetic and equilibrium study

    International Nuclear Information System (INIS)

    Podzus, P.E.; Debandi, M.V.; Daraio, M.E.

    2012-01-01

    A composite of Fe 3 O 4 nanoparticles and the biopolymer chitosan, chemically crosslinked, was prepared as microspheres and used to adsorb copper ions, which were chosen as a model of contaminant metal in water. The adsorption of copper on the magnetic microspheres was studied in a batch process, with different aqueous solutions of Cu (II) at concentrations ranging from 40 to 1100 ppm. Kinetic and equilibrium aspects of the adsorption process were studied. The time-dependent Cu (II) adsorption data were well described by a pseudo-second-order kinetic model. It was found that the equilibrium data follow the Langmuir isotherm, with a maximum adsorption capacity of around 500 mg Cu/g chitosan. The used microspheres were removed and after desorption the material was able to be reused as an adsorbent. The prepared microspheres proved efficient in the removal of copper ions through an adsorption process whose kinetic and equilibrium characteristics were analyzed.

  20. The study on highly expressed proteins as a function of an elevated ultraviolet radiation in the copepod, Tigriopus japonicus

    Science.gov (United States)

    Zubrzycki, Igor Z.; Lee, Seunghan; Lee, Kanghyun; Wiacek, Magdalena; Lee, Wonchoel

    2012-06-01

    The objective of the study was to analyze constantlyhighly expressed proteins as a function of elevated midultraviolet (UVB, 280-315 nm) radiation in Tigriopus japonicus sensu lato ( T. japonicus s.l). We also analyzed associations between kinetics of radiation avoidance, measured as a covered distance per time unit, and highly expressed proteins. The obtained results indicate an increase in T. japonicus s.l. mobility between the control (no radiation) and mild UV radiation levels (15 kJ·m-2). Two-dimensional gel electrophoresis combined with MALDI-MS-MS resulted in 2D protein map comprising of 686 protein spots, of which 19 were identified as highly expressed proteins across all experimental conditions. Obtained results indicate that calpain, vitellogenin, and collagenase are housekeeping protein that are expressed at a constant level independently of environmental changes and that adoption of a locomotive system for the avoidance of a UV source may be, at least partially, supported by hepatopancreas-driven metabolism.

  1. On the molecular basis of D-bifunctional protein deficiency type III.

    Directory of Open Access Journals (Sweden)

    Maija L Mehtälä

    Full Text Available Molecular basis of D-bifunctional protein (D-BP deficiency was studied with wild type and five disease-causing variants of 3R-hydroxyacyl-CoA dehydrogenase fragment of the human MFE-2 (multifunctional enzyme type 2 protein. Complementation analysis in vivo in yeast and in vitro enzyme kinetic and stability determinants as well as in silico stability and structural fluctuation calculations were correlated with clinical data of known patients. Despite variations not affecting the catalytic residues, enzyme kinetic performance (K(m, V(max and k(cat of the recombinant protein variants were compromised to a varying extent and this can be judged as the direct molecular cause for D-BP deficiency. Protein stability plays an additional role in producing non-functionality of MFE-2 in case structural variations affect cofactor or substrate binding sites. Structure-function considerations of the variant proteins matched well with the available data of the patients.

  2. Kinetics and hybrid kinetic-fluid models for nonequilibrium gas and plasmas

    International Nuclear Information System (INIS)

    Crouseilles, N.

    2004-12-01

    For a few decades, the application of the physics of plasmas has appeared in different fields like laser-matter interaction, astrophysics or thermonuclear fusion. In this thesis, we are interested in the modeling and the numerical study of nonequilibrium gas and plasmas. To describe such systems, two ways are usually used: the fluid description and the kinetic description. When we study a nonequilibrium system, fluid models are not sufficient and a kinetic description have to be used. However, solving a kinetic model requires the discretization of a large number of variables, which is quite expensive from a numerical point of view. The aim of this work is to propose a hybrid kinetic-fluid model thanks to a domain decomposition method in the velocity space. The derivation of the hybrid model is done in two different contexts: the rarefied gas context and the more complicated plasmas context. The derivation partly relies on Levermore's entropy minimization approach. The so-obtained model is then discretized and validated on various numerical test cases. In a second stage, a numerical study of a fully kinetic model is presented. A collisional plasma constituted of electrons and ions is considered through the Vlasov-Poisson-Fokker-Planck-Landau equation. Then, a numerical scheme which preserves total mass and total energy is presented. This discretization permits in particular a numerical study of the Landau damping. (author)

  3. Theoretical study of thin metallic deposit layers: from electronic structure to kinetics

    International Nuclear Information System (INIS)

    Senhaji, Abdelali

    1993-01-01

    We have studied the relation between the equilibrium surface segregation in an alloy A c B 1-c and the kinetics of dissolution of a few metallic layers of A (or B) deposited on a B (or A) substrate. We used an energetic model derived from the electronic structure (T.B.I.M.) allowing us to study the surface segregation both in disordered and in ordered alloys. Moreover we have developed a kinetic model (K.T.B.I.M.) consistent with the TBIM energetic model to study the kinetics both of segregation and dissolution. This process has been applied to the Cu-Pt system for which Auger, LEED and photoemission experiments are in progress at L.U.R.E. Concerning the equilibrium surface segregation in the ordered state we have studied all the possible terminations for the (111) and (100) faces in the various ordered structures occurring on the F.C.C. lattice (L1 0 , L1 1 - L1 2 and L'). In particular we have determined the domain of (meta)stability of each termination, which is very useful to understand the competition between single and double steps in ordered alloys. Studying the kinetics of dissolution of a few layers of Cu (or Pt) deposited on the (111) or (100) face of a Pt (or Cu) substrate, we have shown the formation of surface compounds with a great variety of behaviours depending on the face or on the temperature. All these behaviours can be rationalized with the local equilibrium concept, which we have defined accurately within our model and which allows to connect the dissolution mode with the equilibrium segregation. (author) [fr

  4. Physics of protein folding

    Science.gov (United States)

    Finkelstein, A. V.; Galzitskaya, O. V.

    2004-04-01

    Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.

  5. Experimental kinetic study and modeling of calcium oxide carbonation

    International Nuclear Information System (INIS)

    Rouchon, L.

    2012-01-01

    Anthropogenic carbon dioxide (CO 2 ) emissions, major contributors to the greenhouse effect, are considered as the main cause of global warming. So, decrease of CO 2 emitted by large industrial combustion sources or power plants, is an important scientific goal. One of the approaches is based on CO 2 separation and capture from flue gas, followed by sequestration in a wide range of geological formations. In this aim, CO 2 is captured by sorbents like calcium oxide (CaO) in multi-cycle process of carbonation/de-carbonation. However, it was shown that the most important limitations of such process are related to the reversibility of reaction. CaO rapidly loses activity towards CO 2 , so the maximum extent of carbonation decreases as long as the number of cycles increases. In order to well understand the processes and parameters influencing the capture capacity of CaO-based sorbents, it appears important to get details on the kinetic law governing the reaction, which have not been really studied up to now. To investigate this reaction, CaO carbonation kinetics was followed by means of thermogravimetric analysis (TGA) on divided materials. Special care was given to the validation of the usual kinetic assumptions such as steady state and rate-determining step assumptions. The aim was to obtain a model describing the reaction in order to explain the influence of intensive variables such as carbonation temperature and CO 2 partial pressure. TGA curves obtained under isothermal and isobaric conditions showed an induction period linked to the nucleation process and a strong slowing down of the reaction rate once a given fractional conversion was reached. Both phenomena were observed to depend on carbonation temperature and CO 2 partial pressure. To explain these results, the evolution of texture and microstructure of the solid during the reaction was regarded as essential. Reaction at the grain scale induces a volume increase from CaO to CaCO 3 which causes a change in the

  6. kinetic studies of colour and phenol removal from wastewater using

    African Journals Online (AJOL)

    user

    Kinetic studies by batch technique were carried out using activated carbon prepared from mango seed ... and the rate controlling steps of sorption which ... as follows (Lagergren, 1898): … ... plot of t /qt against t of Equation (6) should give a.

  7. Reverse spin-crossover and high-pressure kinetics of the heme iron center relevant for the operation of heme proteins under deep-sea conditions.

    Science.gov (United States)

    Troeppner, Oliver; Lippert, Rainer; Shubina, Tatyana E; Zahl, Achim; Jux, Norbert; Ivanović-Burmazović, Ivana

    2014-10-20

    By design of a heme model complex with a binding pocket of appropriate size and flexibility, and by elucidating its kinetics and thermodynamics under elevated pressures, some of the pressure effects are demonstrated relevant for operation of heme-proteins under deep-sea conditions. Opposite from classical paradigms of the spin-crossover and reaction kinetics, a pressure increase can cause deceleration of the small-molecule binding to the vacant coordination site of the heme-center in a confined space and stabilize a high-spin state of its Fe center. This reverse high-pressure behavior can be achieved only if the volume changes related to the conformational transformation of the cavity can offset the volume changes caused by the substrate binding. It is speculated that based on these criteria nature could make a selection of structures of heme pockets that assist in reducing metabolic activity and enzymatic side reactions under extreme pressure conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Combination of UV-vis spectroscopy and chemometrics to understand protein-nanomaterial conjugate: a case study on human serum albumin and gold nanoparticles.

    Science.gov (United States)

    Wang, Yong; Ni, Yongnian

    2014-02-01

    Study of the interactions between proteins and nanomaterials is of great importance for understanding of protein nanoconjugate. In this work, we choose human serum albumin (HSA) and citrate-capped gold nanoparticles (AuNPs) as a model of protein and nanomaterial, and combine UV-vis spectroscopy with multivariate curve resolution by an alternating least squares (MCR-ALS) algorithm to present a new and efficient method for comparatively comprehensive study of evolution of protein nanoconjugate. UV-vis spectroscopy coupled with MCR-ALS allows qualitative and quantitative extraction of the distribution diagrams, spectra and kinetic profiles of absorbing pure species (AuNPs and AuNPs-HSA conjugate are herein identified) and undetectable species (HSA) from spectral data. The response profiles recovered are converted into the desired thermodynamic, kinetic and structural parameters describing the protein nanoconjugate evolution. Analysis of these parameters for the system gives evidence that HSA molecules are very likely to be attached to AuNPs surface predominantly as a flat monolayer to form a stable AuNPs-HSA conjugate with a core-shell structure, and the binding process takes place mainly through electrostatic and hydrogen-bond interactions between the positively amino acid residues of HSA and the negatively carboxyl group of citrate on AuNPs surface. The results obtained are verified by transmission electron microscopy, zeta potential, circular dichroism spectroscopy and Fourier transform infrared spectroscopy, showing the potential of UV-vis spectroscopy for study of evolution of protein nanoconjugate. In parallel, concentration evolutions of pure species resolved by MCR-ALS are used to construct a sensitive spectroscopic biosensor for HSA with a linear range from 1.8 nM to 28.1 nM and a detection limit of 0.8 nM. © 2013 Published by Elsevier B.V.

  9. Thermogravimetric analysis and kinetic study of formation of lithium titanate by solid state route

    International Nuclear Information System (INIS)

    Sonak, Sagar; Jain, Uttam; Sahu, Ashok Kumar; Kumar, Sanjay; Krishnamurthy, Nagaiyar

    2015-01-01

    The kinetics of formation of lithium titanate from the solid state reaction of lithium carbonate and titanium oxide was studied using non-isothermal thermogravimetric technique. Thermogravimetric data for the reaction of lithium carbonate and titanium oxide was obtained at various heating rates. The methods such as Flynn–Wall–Ozawa and Kissinger–Akahira–Sunose were used to estimate the kinetic parameters from the obtained thermogravimetric data. The average activation energy for the formation of lithium titanate by solid state route was found to be 243 kJ/mol K. The reaction mechanism was determined by the method given by Malek. It was found that the three dimensional diffusion model best describes the reaction kinetics. A kinetic equation describing the reaction is proposed and reaction mechanism is discussed

  10. Strong impact of ionic strength on the kinetics of fibrilar aggregation of bovine beta-lactoglobulin

    NARCIS (Netherlands)

    Arnaudov, L.N.; Vries, de R.J.

    2006-01-01

    We investigate the effect of ionic strength on the kinetics of heat-induced fibrilar aggregation of bovine -lactoglobulin at pH 2.0. Using in situ light scattering we find an apparent critical protein concentration below which there is no significant fibril formation for all ionic strengths studied.

  11. Automated Determination of Oxygen-Dependent Enzyme Kinetics in a Tube-in-Tube Flow Reactor

    DEFF Research Database (Denmark)

    Ringborg, Rolf Hoffmeyer; Pedersen, Asbjørn Toftgaard; Woodley, John

    2017-01-01

    revealed not only the high degree of accuracy of the kinetic data obtained, but also the necessity of making measurements in this way to enable the accurate evaluation of high KMO enzyme systems. For the first time, this paves the way to integrate kinetic data into the protein engineering cycle....

  12. Studies on the kinetics and intraparticle diffusivities of BOD, colour ...

    African Journals Online (AJOL)

    Therefore, this study reveals that boiler fly ash can effectively be used as an adsorbent for POME treatment and also established the kinetic and mechanisms of the sorption process. Also, the results of this study could serve as effective design parameters for a treatment plant to further reduce BOD, colour and TSS from ...

  13. Kinetic Study on Ultrasound Assisted Biodiesel Production from Waste Cooking Oil

    Directory of Open Access Journals (Sweden)

    Widayat

    2015-09-01

    Full Text Available The objective of this research was to study a kinetic model of biodiesel production from waste cooking oil assisted by ultrasound power. The model considered the biodiesel production process as a 2nd order reversible reaction, while its kinetic parameters were estimated using MATLAB, based on data extracted from Hingu, et al. [1]. The data represented experiments under low-frequency ultrasonic wave (20 kHz and variations of temperature, power, catalyst concentration, and alcohol-oil molar ratio. Statistical analysis showed that the proposed model fits well to the experimental data with a determination coefficient (R2 higher than 0.9.

  14. Transiently disordered tails accelerate folding of globular proteins.

    Science.gov (United States)

    Mallik, Saurav; Ray, Tanaya; Kundu, Sudip

    2017-07-01

    Numerous biological proteins exhibit intrinsic disorder at their termini, which are associated with multifarious functional roles. Here, we show the surprising result that an increased percentage of terminal short transiently disordered regions with enhanced flexibility (TstDREF) is associated with accelerated folding rates of globular proteins. Evolutionary conservation of predicted disorder at TstDREFs and drastic alteration of folding rates upon point-mutations suggest critical regulatory role(s) of TstDREFs in shaping the folding kinetics. TstDREFs are associated with long-range intramolecular interactions and the percentage of native secondary structural elements physically contacted by TstDREFs exhibit another surprising positive correlation with folding kinetics. These results allow us to infer probable molecular mechanisms behind the TstDREF-mediated regulation of folding kinetics that challenge protein biochemists to assess by direct experimental testing. © 2017 Federation of European Biochemical Societies.

  15. Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations

    Energy Technology Data Exchange (ETDEWEB)

    Washington, K.E.

    1986-05-01

    The objective of this research is to develop a model that offers an alternative to the point kinetics (PK) modelling approach in the analysis of space reactor kinetics and control studies. Modelling effort will focus on the explicit treatment of control drums as reactivity input devices so that the transition to automatic control can be smoothly done. The proposed model is developed for the specific integration of automatic control and the solution of the servo mechanism problem. The integration of the kinetics model with an automatic controller will provide a useful tool for performing space reactor scoping studies for different designs and configurations. Such a tool should prove to be invaluable in the design phase of a space nuclear system from the point of view of kinetics and control limitations.

  16. Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations

    International Nuclear Information System (INIS)

    Washington, K.E.

    1986-05-01

    The objective of this research is to develop a model that offers an alternative to the point kinetics (PK) modelling approach in the analysis of space reactor kinetics and control studies. Modelling effort will focus on the explicit treatment of control drums as reactivity input devices so that the transition to automatic control can be smoothly done. The proposed model is developed for the specific integration of automatic control and the solution of the servo mechanism problem. The integration of the kinetics model with an automatic controller will provide a useful tool for performing space reactor scoping studies for different designs and configurations. Such a tool should prove to be invaluable in the design phase of a space nuclear system from the point of view of kinetics and control limitations

  17. Stochastic calculus of protein filament formation under spatial confinement

    Science.gov (United States)

    Michaels, Thomas C. T.; Dear, Alexander J.; Knowles, Tuomas P. J.

    2018-05-01

    The growth of filamentous aggregates from precursor proteins is a process of central importance to both normal and aberrant biology, for instance as the driver of devastating human disorders such as Alzheimer's and Parkinson's diseases. The conventional theoretical framework for describing this class of phenomena in bulk is based upon the mean-field limit of the law of mass action, which implicitly assumes deterministic dynamics. However, protein filament formation processes under spatial confinement, such as in microdroplets or in the cellular environment, show intrinsic variability due to the molecular noise associated with small-volume effects. To account for this effect, in this paper we introduce a stochastic differential equation approach for investigating protein filament formation processes under spatial confinement. Using this framework, we study the statistical properties of stochastic aggregation curves, as well as the distribution of reaction lag-times. Moreover, we establish the gradual breakdown of the correlation between lag-time and normalized growth rate under spatial confinement. Our results establish the key role of spatial confinement in determining the onset of stochasticity in protein filament formation and offer a formalism for studying protein aggregation kinetics in small volumes in terms of the kinetic parameters describing the aggregation dynamics in bulk.

  18. Fouling Kinetics and Associated Dynamics of Structural Modifications

    DEFF Research Database (Denmark)

    Jacob, Jerome; Prádanos, Pedro; Calvo, J. I.

    1998-01-01

    It is shown that the fouling behaviour of microfiltration membranes does not agree within all the time ranges of any of the commonly used membrane blocking models (i.e. complete, standard, intermediate or cake blocking). The resulting experimental kinetics of flux decline do not fit to only one...... of these models, but according to a successive or simultaneous coexistence of two or more of them. This is studied by analysing the structural modifications associated with the fouling kinetics. To achieve this goal, here we analyse the dynamical changes on the structure of four microporous membranes made...... by Sartorius (ST02 and ST045, neutral) and Spectrum (SP02 and SP045, positively charged) when fouled by permeating a protein aqueous solution (bovine serum albumin (BSA) at 1 g l(-1)) under 10 kPa in a dead-end device. The structure after different fouling times is obtained by using an extended bubble point...

  19. Kinetic and Thermodynamic Studies on Adsorption of Sulphate from ...

    African Journals Online (AJOL)

    DELL USER

    22, No. 1, 2017. 39. Kinetic and Thermodynamic Studies on Adsorption of Sulphate from Aqueous Solution by. Magnetite ... poison catalysts, and affect the .... C for 1 h in a stainless steel reactor placed in a furnace ... N2 gas for 30 min. 50 ml of ...... adsorption for designing and evaluating the ... is the equilibrium liquid-phase.

  20. Kinetic study of formation of sodalite from a kaolin waste of Jari river - PA, Brazil

    International Nuclear Information System (INIS)

    Silva, L.N. da; Paz, S.P.A. da; Angelica, R.S.; Neves, R.F.

    2011-01-01

    Zeolites are materials with a wide industrial application, which has motivated the development of a large number of scientific papers on this topic. This work presents a kinetic study of the formation process of sodalite produced from the reaction of the kaolin waste in the presence of sodium hydroxide solution (5M) performed at temperatures of 80, 100, 120 and 150 ° C. The process was conducted in batch, static, and autoclaves lined with Teflon, and monitoring the kinetics was performed by ex situ XRD analysis of the materials obtained in the time interval from 2 to 24 hours. The kinetic model that best describes this transformation is zero-order homogeneous reaction. Finally, we conclude that the technique of X-ray diffraction is a powerful tool to study the kinetics of phase transformation ex situ. (author)

  1. Interaction of Protease-Activated Receptor 2 with G Proteins and Beta-Arrestin 1 Studied by Bioluminescence Resonance Energy Transfer

    Directory of Open Access Journals (Sweden)

    Mohammed Akli eAyoub

    2013-12-01

    Full Text Available G protein-coupled receptors (GPCRs are well recognized as being able to activate several signaling pathways through the activation of different G proteins as well as other signaling proteins such as beta-arrestins. Therefore, understanding how such multiple GPCR-mediated signaling can be integrated constitute an important aspect. Here, we applied bioluminescence resonance energy transfer (BRET to shed more light on the G protein coupling profile of trypsin receptor, or protease-activated receptor 2 (PAR2, and its interaction with beta-arrestin1. Using YFP and Rluc fusion constructs expressed in COS-7 cells, BRET data revealed a pre-assembly of PAR2 with both Galphai1 and Galphao and a rapid and transient activation of these G proteins upon receptor activation. In contrast, no preassembly of PAR2 with Galpha12 could be detected and their physical association can be measured with a very slow and sustained kinetics similar to that of beta-arrestin1 recruitment. These data demonstrate the coupling of PAR2 with Galphai1, Galphao and Galpha12 in COS-7 cells with differences in the kinetics of GPCR-G protein coupling, a parameter that very likely influences the cellular response. Moreover, this further illustrates that preassembly or agonist-induced G protein interaction depends on receptor-G protein pairs indicating another level of complexity and regulation of the signaling of GPCR-G protein complexes and its multiplicity.

  2. Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jordan N.; Tyrrell, Kimberly J.; Hansen, Joshua R.; Thomas, Dennis G.; Murphree, Taylor A.; Shukla, Anil K.; Luders, Teresa; Madden, James M.; Li, Yunying; Wright, Aaron T.; Piehowski, Paul D.

    2017-12-06

    Protein turnover is important for general health on cellular and organism scales providing a strategy to replace old, damaged, or dysfunctional proteins. Protein turnover also informs of biomarker kinetics, as a better understanding of synthesis and degradation of proteins increases the clinical utility of biomarkers. Here, turnover rates of plasma proteins in rats were measured in vivo using a pulse-chase stable isotope labeling experiment. During the pulse, rats (n=5) were fed 13C6-labeled lysine (“heavy”) feed for 23 days to label proteins. During the chase, feed was changed to an unlabeled equivalent feed (“light”), and blood was repeatedly sampled from rats over 10 time points for 28 days. Plasma samples were digested with trypsin, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant was used to identify peptides and proteins, and quantify heavy:light lysine ratios. A system of ordinary differential equations was used to calculate protein turnover rates. Using this approach, 273 proteins were identified, and turnover rates were quantified for 157 plasma proteins with half-lives ranging 0.3-103 days. For the ~70 most abundant proteins, variability in turnover rates among rats was low (median coefficient of variation: 0.09). Activity-based protein profiling was applied to pooled plasma samples to enrich serine hydrolases using a fluorophosphonate (FP2) activity-based probe. This enrichment resulted in turnover rates for an additional 17 proteins. This study is the first to measure global plasma protein turnover rates in rats in vivo, measure variability of protein turnover rates in any animal model, and utilize activity-based protein profiling for enhancing measurements of targeted, low-abundant proteins, such as those commonly used as biomarkers. Measured protein turnover rates will be important for understanding of the role of protein turnover in cellular and organism health as well as increasing the utility of protein

  3. Equilibrium Kinetics Studies and Crystallization Aboard the International Space Station (ISS) Using the Protein Crystallization Apparatus for Microgravity (PCAM)

    Science.gov (United States)

    Achari, Aniruddha; Roeber, Dana F.; Barnes, Cindy L.; Kundrot, Craig E.; Stinson, Thomas N. (Technical Monitor)

    2002-01-01

    Protein Crystallization Apparatus in Microgravity (PCAM) trays have been used in Shuttle missions to crystallize proteins in a microgravity environment. The crystallization experiments are 'sitting drops' similar to that in Cryschem trays, but the reservoir solution is soaked in a wick. From early 2001, crystallization experiments are conducted on the International Space Station using mission durations of months rather than two weeks on previous shuttle missions. Experiments were set up in April 2001 on Flight 6A to characterize the time crystallization experiments will take to reach equilibrium in a microgravity environment using salts, polyethylene glycols and an organic solvent as precipitants. The experiments were set up to gather data for a series of days of activation with different droplet volumes and precipitants. The experimental set up on ISS and results of this study will be presented. These results will help future users of PCAM to choose precipitants to optimize crystallization conditions for their target macromolecules for a particular mission with known mission duration. Changes in crystal morphology and size between the ground and space grown crystals of a protein and a protein -DNA complex flown on the same mission will also be presented.

  4. Direct interaction between two viral proteins, the nonstructural protein 2C and the capsid protein VP3, is required for enterovirus morphogenesis.

    Directory of Open Access Journals (Sweden)

    Ying Liu

    2010-08-01

    Full Text Available In spite of decades-long studies, the mechanism of morphogenesis of plus-stranded RNA viruses belonging to the genus Enterovirus of Picornaviridae, including poliovirus (PV, is not understood. Numerous attempts to identify an RNA encapsidation signal have failed. Genetic studies, however, have implicated a role of the non-structural protein 2C(ATPase in the formation of poliovirus particles. Here we report a novel mechanism in which protein-protein interaction is sufficient to explain the specificity in PV encapsidation. Making use of a novel "reporter virus", we show that a quasi-infectious chimera consisting of the capsid precursor of C-cluster coxsackie virus 20 (C-CAV20 and the nonstructural proteins of the closely related PV translated and replicated its genome with wild type kinetics, whereas encapsidation was blocked. On blind passages, encapsidation of the chimera was rescued by a single mutation either in capsid protein VP3 of CAV20 or in 2C(ATPase of PV. Whereas each of the single-mutation variants expressed severe proliferation phenotypes, engineering both mutations into the chimera yielded a virus encapsidating with wild type kinetics. Biochemical analyses provided strong evidence for a direct interaction between 2C(ATPase and VP3 of PV and CAV20. Chimeras of other C-CAVs (CAV20/CAV21 or CAV18/CAV20 were blocked in encapsidation (no virus after blind passages but could be rescued if the capsid and 2C(ATPase coding regions originated from the same virus. Our novel mechanism explains the specificity of encapsidation without apparent involvement of an RNA signal by considering that (i genome replication is known to be stringently linked to translation, (ii morphogenesis is known to be stringently linked to genome replication, (iii newly synthesized 2C(ATPase is an essential component of the replication complex, and (iv 2C(ATPase has specific affinity to capsid protein(s. These conditions lead to morphogenesis at the site where newly

  5. Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers.

    Science.gov (United States)

    Zhang, Yongli

    2017-07-01

    Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion. A long-standing hypothesis suggests that SNAREs act like a zipper to draw the two membranes into proximity and thereby force them to fuse. However, a quantitative test of this SNARE zippering hypothesis was hindered by difficulties to determine the energetics and kinetics of SNARE assembly and to identify the relevant folding intermediates. Here, we first review different approaches that have been applied to study SNARE assembly and then focus on high-resolution optical tweezers. We summarize the folding energies, kinetics, and pathways of both wild-type and mutant SNARE complexes derived from this new approach. These results show that synaptic SNAREs assemble in four distinct stages with different functions: slow N-terminal domain association initiates SNARE assembly; a middle domain suspends and controls SNARE assembly; and rapid sequential zippering of the C-terminal domain and the linker domain directly drive membrane fusion. In addition, the kinetics and pathway of the stagewise assembly are shared by other SNARE complexes. These measurements prove the SNARE zippering hypothesis and suggest new mechanisms for SNARE assembly regulated by other proteins. © 2017 The Protein Society.

  6. Scleroglucan-borax hydrogel: a flexible tool for redox protein immobilization.

    Science.gov (United States)

    Frasconi, Marco; Rea, Sara; Matricardi, Pietro; Favero, Gabriele; Mazzei, Franco

    2009-09-15

    A highly stable biological film was prepared by casting an aqueous dispersion of protein and composite hydrogel obtained from the polysaccharide Scleroglucan (Sclg) and borax as a cross-linking agent. Heme proteins, such as hemoglobin (Hb), myoglobin (Mb), and horseradish peroxidase (HRP), were chosen as model proteins to investigate the immobilized system. A pair of well-defined quasi-reversible redox peaks, characteristics of the protein heme FeII/FeIII redox couples, were obtained at the Sclg-borax/proteins films on pyrolytic graphite (PG) electrodes, as a consequence of the direct electron transfer between the protein and the PG electrode. A full characterization of the electron transfer kinetic was performed by opportunely modeling data obtained from cyclic voltammetry and square wave voltammetry experiments. The efficiency of our cross-linking approach was investigated by studying the influence of different borax groups percentage in the Sclg matrix, revealing the versatility of this hydrogel in the immobilization of redox proteins. The native conformation of the three heme proteins entrapped in the hydrogel films were proved to be unchanged, reflected by the unaltered Soret adsorption band and by the catalytic activity toward hydrogen peroxide (H2O2). The main kinetic parameters, such as the apparent Michaelis-Menten constant, for the electrocatalytic reaction were also evaluated. The peculiar characteristics of Sclg-borax matrix make it possible to find wide opportunities as proteins immobilizing agent for studies of direct electrochemistry and biosensors development.

  7. Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

    International Nuclear Information System (INIS)

    Markin, Craig J.; Spyracopoulos, Leo

    2012-01-01

    NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

  8. Effect of protein provision via milk replacer or solid feed on protein metabolism in veal calves

    NARCIS (Netherlands)

    Berends, H.; Borne, van den J.J.G.C.; Røjen, B.A.; Hendriks, W.H.; Gerrits, W.J.J.

    2015-01-01

    The current study evaluated the effects of protein provision to calves fed a combination of solid feed (SF) and milk replacer (MR) at equal total N intake on urea recycling and N retention. Nitrogen balance traits and [15N2]urea kinetics were measured in 30 calves (23 wk of age, 180 ± 3.7 kg of body

  9. Non-kinetic capabilities: complementing the kinetic prevalence to targeting

    OpenAIRE

    Ducheine, P.

    2014-01-01

    Targeting is used in military doctrine to describe a military operational way, using (military) means to influence a target (or addressee) in order to achieve designated political and/or military goals. The four factors italicized are used to analyse non-kinetic targeting, complementing our knowledge and understanding of the kinetic prevalence. Paradoxically, non-kinetic targeting is not recognized as a separate concept: kinetic and non-kinetic are intertwined facets of targeting. Kinetic tar...

  10. Effect of protein provision via milk replacer or solid feed on protein metabolism in veal calves

    DEFF Research Database (Denmark)

    Berends, H.; van den Borne, J. J G C; Røjen, B. A.

    2015-01-01

    recycling but urea reused for anabolism remained unaffected. Total-tract neutral detergent fiber digestibility decreased (-9%) with increasing low-N SF intake, indicating reduced rumen fermentation. Increasing the N content of SF at equal total N intake resulted in decreased urea production, excretion......The current study evaluated the effects of protein provision to calves fed a combination of solid feed (SF) and milk replacer (MR) at equal total N intake on urea recycling and N retention. Nitrogen balance traits and [15N2]urea kinetics were measured in 30 calves (23 wk of age, 180±3.7kg of body...... of calves for 5 d, and for the assessment of urea recycling from [15N2]urea kinetics. Increasing low-N SF intake at equal total N intake resulted in a shift from urinary to fecal N excretion but did not affect protein retention (0.71g of N·kg of BW-0.75·d-1). Increasing low-N SF intake increased urea...

  11. Kinetic modeling studies of SOA formation from α-pinene ozonolysis

    Science.gov (United States)

    Gatzsche, Kathrin; Iinuma, Yoshiteru; Tilgner, Andreas; Mutzel, Anke; Berndt, Torsten; Wolke, Ralf

    2017-11-01

    This paper describes the implementation of a kinetic gas-particle partitioning approach used for the simulation of secondary organic aerosol (SOA) formation within the SPectral Aerosol Cloud Chemistry Interaction Model (SPACCIM). The kinetic partitioning considers the diffusion of organic compounds into aerosol particles and the subsequent chemical reactions in the particle phase. The basic kinetic partitioning approach is modified by the implementation of chemical backward reaction of the solute within the particle phase as well as a composition-dependent particle-phase bulk diffusion coefficient. The adapted gas-phase chemistry mechanism for α-pinene oxidation has been updated due to the recent findings related to the formation of highly oxidized multifunctional organic compounds (HOMs). Experimental results from a LEAK (Leipziger Aerosolkammer) chamber study for α-pinene ozonolysis were compared with the model results describing this reaction system.The performed model studies reveal that the particle-phase bulk diffusion coefficient and the particle-phase reactivity are key parameters for SOA formation. Using the same particle-phase reactivity for both cases, we find that liquid particles with higher particle-phase bulk diffusion coefficients have 310 times more organic material formed in the particle phase compared to higher viscous semi-solid particles with lower particle-phase bulk diffusion coefficients. The model results demonstrate that, even with a moderate particle-phase reactivity, about 61 % of the modeled organic mass consists of reaction products that are formed in the liquid particles. This finding emphasizes the potential role of SOA processing. Moreover, the initial organic aerosol mass concentration and the particle radius are of minor importance for the process of SOA formation in liquid particles. A sensitivity study shows that a 22-fold increase in particle size merely leads to a SOA increase of less than 10 %.Due to two additional

  12. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  13. Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy

    Science.gov (United States)

    Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

    2018-02-01

    Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (P < 0.01) rumen degradable DM (RDDM) and starch (RDSt), but decreased (P < 0.01) rumen degradable protein (RDP). (3) Molecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (P < 0.01), but protein amides associated molecular spectral intensities were lower (P < 0.01) in SFC. (4). The molecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (P < 0.10) associated with RDDM and RDSt and protein amide spectral intensities were positively (P < 0.10) associated with RDP. This results indicated that the steam flaking induced molecular structure changes had an interactive relationship with rumen degradation kinetics.

  14. Errors in Computing the Normalized Protein Catabolic Rate due to Use of Single-pool Urea Kinetic Modeling or to Omission of the Residual Kidney Urea Clearance.

    Science.gov (United States)

    Daugirdas, John T

    2017-07-01

    The protein catabolic rate normalized to body size (PCRn) often is computed in dialysis units to obtain information about protein ingestion. However, errors can manifest when inappropriate modeling methods are used. We used a variable volume 2-pool urea kinetic model to examine the percent errors in PCRn due to use of a 1-pool urea kinetic model or after omission of residual urea clearance (Kru). When a single-pool model was used, 2 sources of errors were identified. The first, dependent on the ratio of dialyzer urea clearance to urea distribution volume (K/V), resulted in a 7% inflation of the PCRn when K/V was in the range of 6 mL/min per L. A second, larger error appeared when Kt/V values were below 1.0 and was related to underestimation of urea distribution volume (due to overestimation of effective clearance) by the single-pool model. A previously reported prediction equation for PCRn was valid, but data suggest that it should be modified using 2-pool eKt/V and V coefficients instead of single-pool values. A third source of error, this one unrelated to use of a single-pool model, namely omission of Kru, was shown to result in an underestimation of PCRn, such that each ml/minute Kru per 35 L of V caused a 5.6% underestimate in PCRn. Marked overestimation of PCRn can result due to inappropriate use of a single-pool urea kinetic model, particularly when Kt/V <1.0 (as in short daily dialysis), or after omission of residual native kidney clearance. Copyright © 2017 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  15. Bridging scales through multiscale modeling: A case study on Protein Kinase A

    Directory of Open Access Journals (Sweden)

    Sophia P Hirakis

    2015-09-01

    Full Text Available The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been overlooked. However, in many cases, it remains unclear how best to synthesize information obtained from various scales and analysis approaches, such as atomistic molecular models, Markov state models (MSM, subcellular network models, and whole cell models. In this paper, we use protein kinase A (PKA activation as a case study to explore how computational methods that model different physical scales can complement each other and integrate into an improved multiscale representation of the biological mechanisms. Using measured crystal structures, we show how molecular dynamics (MD simulations coupled with atomic-scale MSMs can provide conformations for Brownian dynamics (BD simulations to feed transitional states and kinetic parameters into protein-scale MSMs. We discuss how milestoning can give reaction probabilities and forward-rate constants of cAMP association events by seamlessly integrating MD and BD simulation scales. These rate constants coupled with MSMs provide a robust representation of the free energy landscape, enabling access to kinetic and thermodynamic parameters unavailable from current experimental data. These approaches have helped to illuminate the cooperative nature of PKA activation in response to distinct cAMP binding events. Collectively, this approach exemplifies a general strategy for multiscale model development that is applicable to a wide range of biological problems.

  16. Study of strength kinetics of sand concrete system of accelerated hardening

    Science.gov (United States)

    Sharanova, A. V.; Lenkova, D. A.; Panfilova, A. D.

    2018-04-01

    Methods of calorimetric analysis are used to study the dynamics of the hydration processes of concretes with different accelerator contents. The efficiency of the isothermal calorimetry method is shown for study of strength kinetics of concrete mixtures of accelerated hardening, promising for additive technologies in civil engineering.

  17. Graphene oxide as a protein matrix: influence on protein biophysical properties.

    Science.gov (United States)

    Hernández-Cancel, Griselle; Suazo-Dávila, Dámaris; Ojeda-Cruzado, Axel J; García-Torres, Desiree; Cabrera, Carlos R; Griebenow, Kai

    2015-10-19

    This study provides fundamental information on the influence of graphene oxide (GO) nanosheets and glycans on protein catalytic activity, dynamics, and thermal stability. We provide evidence of protein stabilization by glycans and how this strategy could be implemented when GO nanosheets is used as protein immobilization matrix. A series of bioconjugates was constructed using two different strategies: adsorbing or covalently attaching native and glycosylated bilirubin oxidase (BOD) to GO. Bioconjugate formation was followed by FT-IR, zeta-potential, and X-ray photoelectron spectroscopy measurements. Enzyme kinetic parameters (k(m) and k(cat)) revealed that the substrate binding affinity was not affected by glycosylation and immobilization on GO, but the rate of enzyme catalysis was reduced. Structural analysis by circular dichroism showed that glycosylation did not affect the tertiary or the secondary structure of BOD. However, GO produced slight changes in the secondary structure. To shed light into the biophysical consequence of protein glycosylation and protein immobilization on GO nanosheets, we studied structural protein dynamical changes by FT-IR H/D exchange and thermal inactivation. It was found that glycosylation caused a reduction in structural dynamics that resulted in an increase in thermostability and a decrease in the catalytic activity for both, glycoconjugate and immobilized enzyme. These results establish the usefulness of chemical glycosylation to modulate protein structural dynamics and stability to develop a more stable GO-protein matrix.

  18. Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

    Science.gov (United States)

    Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

    2011-05-20

    Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

  19. Kinetic study of the annealing reactions in Cu-Ni-Fe alloys

    International Nuclear Information System (INIS)

    Donoso, E.

    2014-01-01

    The thermal aging of a Cu-45Ni-4Fe, Cu-34Ni-11Fe and Cu-33Ni-22Fe alloys tempered from 1173 K have been studied from Differential Scanning Calorimetry (DSC) and microhardness measurements. The analysis of DSC curves, from room temperature to 950 K, shows the presence of one exothermic reaction associated to the formation of FeNi 3 phase nucleating from a modulate structure, and one endothermic peak attributed to dissolution of this phase. Kinetic parameters were obtained using the usual Avrami-Erofeev equation, modified Kissinger method and integrated kinetic functions. Microhardness measurements confirmed the formation and dissolution of the FeNi 3 phase. (Author)

  20. Accurate label-free reaction kinetics determination using initial rate heat measurements

    Science.gov (United States)

    Ebrahimi, Kourosh Honarmand; Hagedoorn, Peter-Leon; Jacobs, Denise; Hagen, Wilfred R.

    2015-01-01

    Accurate label-free methods or assays to obtain the initial reaction rates have significant importance in fundamental studies of enzymes and in application-oriented high throughput screening of enzyme activity. Here we introduce a label-free approach for obtaining initial rates of enzyme activity from heat measurements, which we name initial rate calorimetry (IrCal). This approach is based on our new finding that the data recorded by isothermal titration calorimetry for the early stages of a reaction, which have been widely ignored, are correlated to the initial rates. Application of the IrCal approach to various enzymes led to accurate enzyme kinetics parameters as compared to spectroscopic methods and enabled enzyme kinetic studies with natural substrate, e.g. proteases with protein substrates. Because heat is a label-free property of almost all reactions, the IrCal approach holds promise in fundamental studies of various enzymes and in use of calorimetry for high throughput screening of enzyme activity. PMID:26574737

  1. Inhibition of protein tyrosine phosphatase 1B (PTP1B) and α-glucosidase by xanthones from Cratoxylum cochinchinense, and their kinetic characterization.

    Science.gov (United States)

    Li, Zuo Peng; Song, Yeong Hun; Uddin, Zia; Wang, Yan; Park, Ki Hun

    2018-02-01

    Cratoxylum cochinchinense displayed significant inhibition against protein tyrosine phosphatase 1B (PTP1B) and α-glucosidase, both of which are key target enzymes to attenuate diabetes and obesity. The compounds responsible for both enzymes inhibition were identified as twelve xanthones (1-12) among which compounds 1 and 2 were found to be new ones. All of them simultaneously inhibited PTP1B with IC 50 s of (2.4-52.5 µM), and α-glucosidase with IC 50 values of (1.7-72.7 µM), respectively. Cratoxanthone A (3) and γ-mangostin (7) were estimated to be most active inhibitors against both PTP1B (IC 50  = 2.4 µM for 3, 2.8 µM for 7) and α-glucosidase (IC 50  = 4.8 µM for 3, 1.7 µM for 7). In kinetic studies, all isolated xanthones emerged to be mixed inhibitors of α-glucosidase, whereas they behaved as competitive inhibitors of PTP1B. In time dependent experiments, compound 3 showed isomerization inhibitory behavior with following kinetic parameters: K i app  = 2.4 µM; k 5  = 0.05001 µM -1  S -1 and k 6  = 0.02076 µM -1  S -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.

    Science.gov (United States)

    Fang, Baishan; Niu, Jin; Ren, Hong; Guo, Yingxia; Wang, Shizhen

    2014-01-01

    Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.

  3. Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.

    Directory of Open Access Journals (Sweden)

    Baishan Fang

    Full Text Available Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.

  4. Kinetic study on ferulic acid production from banana stem waste via mechanical extraction

    Science.gov (United States)

    Zainol, Norazwina; Masngut, Nasratun; Khairi Jusup, Muhamad

    2018-04-01

    Banana is the tropical plants associated with lots of medicinal properties. It has been reported to be a potential source of phenolic compounds such as ferulic acid (FA). FA has excellent antioxidant properties higher than vitamin C and E. FA also have a wide range of biological activities, such as antioxidant activities and anti-microbial activities. This paper presents an experimental and kinetic study on ferulic acid (FA) production from banana stem waste (BSW) via mechanical extraction. The objective of this research is to determine the kinetic parameters in the ferulic acid production. The banana stem waste was randomly collected from the local banana plantation in Felda Lepar Hilir, Pahang. The banana stem juice was mechanically extracted by using sugarcane press machine (KR3176) and further analyzed in high performance liquid chromatography. The differential and integral method was applied to determine the kinetic parameter of the extraction process and the data obtained were fitted into the 0th, 1st and 2nd order of extraction process. Based on the results, the kinetic parameter and R2 value from were 0.05 and 0.93, respectively. It was determined that the 0th kinetic order fitted the reaction processes to best represent the mechanical extraction.

  5. A global resource allocation strategy governs growth transition kinetics of Escherichia coli.

    Science.gov (United States)

    Erickson, David W; Schink, Severin J; Patsalo, Vadim; Williamson, James R; Gerland, Ulrich; Hwa, Terence

    2017-11-02

    A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms and they remain a topic of active investigation. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions.

  6. Protein destruction by a helium atmospheric pressure glow discharge: Capability and mechanisms

    International Nuclear Information System (INIS)

    Deng, X. T.; Shi, J. J.; Kong, M. G.

    2007-01-01

    Biological sterilization represents one of the most exciting applications of atmospheric pressure glow discharges (APGD). Despite the fact that surgical instruments are contaminated by both microorganisms and proteinaceous matters, sterilization effects of APGD have so far been studied almost exclusively for microbial inactivation. This work presents the results of a detailed investigation of the capability of a helium-oxygen APGD to inactivate proteins deposited on stainless-steel surfaces. Using a laser-induced fluorescence technique for surface protein measurement, a maximum protein reduction of 4.5 logs is achieved by varying the amount of the oxygen admixture into the background helium gas. This corresponds to a minimum surface protein of 0.36 femtomole/mm 2 . It is found that plasma reduction of surface-borne protein is through protein destruction and degradation, and that its typically biphasic reduction kinetics is influenced largely by the thickness profile of the surface protein. Also presented is a complementary study of possible APGD protein inactivation mechanisms. By interplaying the protein inactivation kinetics with optical emission spectroscopy, it is shown that the main protein-destructing agents are excited atomic oxygen (via the 777 and 844 nm emission channels) and excited nitride oxide (via the 226, 236, and 246 nm emission channels). It is also demonstrated that the most effective protein reduction is achieved possibly through a synergistic effect between atomic oxygen and nitride oxide. This study is a useful step toward a full confirmation of the efficacy of APGD as a sterilization technology for surgical instruments contaminated by prion proteins

  7. Study and discretization of kinetic models and fluid models at low Mach number

    International Nuclear Information System (INIS)

    Dellacherie, Stephane

    2011-01-01

    This thesis summarizes our work between 1995 and 2010. It concerns the analysis and the discretization of Fokker-Planck or semi-classical Boltzmann kinetic models and of Euler or Navier-Stokes fluid models at low Mach number. The studied Fokker-Planck equation models the collisions between ions and electrons in a hot plasma, and is here applied to the inertial confinement fusion. The studied semi-classical Boltzmann equations are of two types. The first one models the thermonuclear reaction between a deuterium ion and a tritium ion producing an α particle and a neutron particle, and is also in our case used to describe inertial confinement fusion. The second one (known as the Wang-Chang and Uhlenbeck equations) models the transitions between electronic quantified energy levels of uranium and iron atoms in the AVLIS isotopic separation process. The basic properties of these two Boltzmann equations are studied, and, for the Wang-Chang and Uhlenbeck equations, a kinetic-fluid coupling algorithm is proposed. This kinetic-fluid coupling algorithm incited us to study the relaxation concept for gas and immiscible fluids mixtures, and to underline connections with classical kinetic theory. Then, a diphasic low Mach number model without acoustic waves is proposed to model the deformation of the interface between two immiscible fluids induced by high heat transfers at low Mach number. In order to increase the accuracy of the results without increasing computational cost, an AMR algorithm is studied on a simplified interface deformation model. These low Mach number studies also incited us to analyse on cartesian meshes the inaccuracy at low Mach number of Godunov schemes. Finally, the LBM algorithm applied to the heat equation is justified

  8. Systematic Protein-Protein Docking and Molecular Dynamics Studies of HIV-1 gp120 and CD4: Insights for New Drug Development

    Directory of Open Access Journals (Sweden)

    M. Rizman-Idid

    2011-12-01

    Full Text Available Background and the purpose of the study: The interactions between HIV-1 gp120 and mutated CD4 proteins were investigated in order to identify a lead structure for therapy based on competitive blocking of the HIV binding receptor for human T-cells. Crystal structures of HIV gp120-CD4 complexes reveal a close interaction of the virus receptor with CD4 Phe43, which is embedded in a pocket of the virus protein.Methods: This study applies computer simulations to determine the best binding of amino acid 43 CD4 mutants to HIV gp120. Besides natural CD4, three mutants carrying alternate aromatic residues His, Trp and Tyr at position 43 were investigated. Several docking programs were applied on isolated proteins based on selected crystal structures of gp120-CD4 complexes, as well as a 5 ns molecular dynamics study on the protein complexes. The initial structures were minimized in Gromacs to avoid crystal packing effects, and then subjected to docking experiments using AutoDock4, FireDock, ClusPro and ZDock. In molecular dynamics, the Gibbs free binding energy was calculated for the gp120-CD4 complexes. The docking outputs were analyzed on energy within the respective docking software.Results and conclusion: Visualization and hydrogen bonding analysis were performed using the Swiss-PdbViewer. Strong binding to HIV gp120 can be achieved with an extended aromatic group (Trp. However, the sterical demand of the interaction affects the binding kinetics. In conclusion, a ligand for an efficient blocking of HIV gp120 should involve an extended but conformational flexible aromatic group, i.e. a biphenyl. A docking study on biphenylalanine-43 confirms this expectation

  9. An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior.

    Science.gov (United States)

    Makabe, Koki; Nakamura, Takashi; Dhar, Debanjan; Ikura, Teikichi; Koide, Shohei; Kuwajima, Kunihiro

    2018-04-27

    Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions. Copyright © 2018. Published by Elsevier Ltd.

  10. Experimental and Chemical Kinetic Modeling Study of Dimethylcyclohexane Oxidation and Pyrolysis

    KAUST Repository

    Eldeeb, Mazen A.; Jouzdani, Shirin; Wang, Zhandong; Sarathy, Mani; Akih-Kumgeh, Benjamin

    2016-01-01

    A combined experimental and chemical kinetic modeling study of the high-temperature ignition and pyrolysis of 1,3-dimethylcyclohexane (13DMCH) is presented. Ignition delay times are measured behind reflected shock waves over a temperature range

  11. Evaluation of dilatometric techniques for studies of sintering kinetics

    International Nuclear Information System (INIS)

    El-Sayed Ali, M.; Toft Soerensen, O.

    1985-04-01

    The kinetics of the initial sintering stage of CeO 2 is evaluated by three different techniques: constant heating rate dilatometry, constant shrinkage rate dilatometry and a new technique recently introduced by the authors called Stepwise Isothermal Dilatometry (SID). Comparative measurements with these techniques showed that too high activation energies were obtained with the two first techniques, both of which can be termed as nonisothermal, whereas activation energies comparable to those reported for cation diffusion in other fluorite oxides were obtained with the latter technique. Of the three techniques SID is thus considered to be the most accurate for studies of the sintering kinetics. In contrast to the two nonisothermal techniques SID has the further advantage that both the controlling mechanism and its activation energy can be determined in a single experiment. From the SID-measurement it was concluded that the initial sintering stage of CeO 2 is controlled by grain-boundary diffusion. (author)

  12. Study the oxidation kinetics of uranium using XRD and Rietveld method

    Science.gov (United States)

    Zhang, Yanzhi; Guan, Weijun; Wang, Qinguo; Wang, Xiaolin; Lai, Xinchun; Shuai, Maobing

    2010-03-01

    The surface oxidation of uranium metal has been studied by X-ray diffraction (XRD) and Rietveld method in the range of 50~300°C in air. The oxidation processes are analyzed by XRD to determine the extent of surface oxidation and the oxide structure. The dynamics expression for the formation of UO2 was derived. At the beginning, the dynamic expression was nonlinear, but switched to linear subsequently for uranium in air and humid oxygen. That is, the growth kinetics of UO2 can be divided into two stages: nonlinear portion and linear portion. Using the kinetic data of linear portion, the activation energy of reaction between uranium and air was calculated about 46.0 kJ/mol. However the content of oxide as a function of time was linear in humid helium ambience. Contrast the dynamics results, it prove that the absence of oxygen would accelerate the corrosion rate of uranium in the humid gas. We can find that the XRD and Rietveld method are a useful convenient method to estimate the kinetics and thermodynamics of solid-gas reaction.

  13. Gravimetric and conductometric studies of the sedimentation kinetics in aqueous dispersions of kaoline

    International Nuclear Information System (INIS)

    Bulavyin, L.A.; Khrapatij, S.V.; Koval'chuk, V.Yi.; Klepko, V.V.; Lebovka, M.Yi.

    2006-01-01

    Using gravimetric and conductometric methods, the sedimentation kinetics in aqueous suspensions of Alekseev kaoline has been studied for pH value range from 4 to 10. It has been found that pH increasing leads to the decreasing of mean radii of flocks linearly. We found that sedimentation kinetics for intermediate pH values can be described by scaling equations that crossover time defined transition from a gravitational mechanism of deposition to the diffusion one

  14. Study of kinetics, equilibrium and isotope exchange in ion exchange systems Pt. 6

    International Nuclear Information System (INIS)

    Plicka, J.; Stamberg, K.; Cabicar, J.; Gosman, A.

    1986-01-01

    The description of kinetics of ion exchange in ternary system was based upon three Nernst-Planck equations, each of them describing the particle diffusion flux of a given counterion as an independent process. For experimental verification, the strongly acidic cation exchanger OSTION KS 08 the shallow-bed technique, and 0.2 mol x dm -3 aqueous nitrate solutions were chosen. The kinetics of ion exchange in the system of cations Na + - Mg 2+ - UO 2 2+ was studied. The values of diffusion coefficients obtained by evaluating of kinetics of isotope exchange and binary ion exchange were used for calculation. The comparison of calculated exchange rate curves with the experimental ones was made. It was found that the exchanging counterions were affected by each other. (author)

  15. Whey Protein Supplementation Enhances Whole Body Protein Metabolism and Performance Recovery after Resistance Exercise: A Double-Blind Crossover Study

    Directory of Open Access Journals (Sweden)

    Daniel W. D. West

    2017-07-01

    Full Text Available No study has concurrently measured changes in free-living whole body protein metabolism and exercise performance during recovery from an acute bout of resistance exercise. We aimed to determine if whey protein ingestion enhances whole body net protein balance and recovery of exercise performance during overnight (10 h and 24 h recovery after whole body resistance exercise in trained men. In a double-blind crossover design, 12 trained men (76 ± 8 kg, 24 ± 4 years old, 14% ± 5% body fat; means ± standard deviation (SD performed resistance exercise in the evening prior to consuming either 25 g of whey protein (PRO; MuscleTech 100% Whey or an energy-matched placebo (CHO immediately post-exercise (0 h, and again the following morning (~10 h of recovery. A third randomized trial, completed by the same participants, involving no exercise and no supplement served as a rested control trial (Rest. Participants ingested [15N]glycine to determine whole body protein kinetics and net protein balance over 10 and 24 h of recovery. Performance was assessed pre-exercise and at 0, 10, and 24 h of recovery using a battery of tests. Net protein balance tended to improve in PRO (P = 0.064; effect size (ES = 0.61, PRO vs. CHO during overnight recovery. Over 24 h, net balance was enhanced in PRO (P = 0.036 but not in CHO (P = 0.84; ES = 0.69, PRO vs. CHO, which was mediated primarily by a reduction in protein breakdown (PRO < CHO; P < 0.01. Exercise decreased repetitions to failure (REP, maximal strength (MVC, peak and mean power, and countermovement jump performance (CMJ at 0 h (all P < 0.05 vs. Pre. At 10 h, there were small-to-moderate effects for enhanced recovery of the MVC (ES = 0.56, mean power (ES = 0.49, and CMJ variables (ES: 0.27–0.49 in PRO. At 24 h, protein supplementation improved MVC (ES = 0.76, REP (ES = 0.44, and peak power (ES = 0.55. In conclusion, whey protein supplementation enhances whole body anabolism, and may improve acute recovery of

  16. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  17. Removal of mercury(II) from aqueous media using eucalyptus bark: Kinetic and equilibrium studies

    International Nuclear Information System (INIS)

    Ghodbane, Ilhem; Hamdaoui, Oualid

    2008-01-01

    In this study, eucalyptus camaldulensis bark, a forest solid waste, is proposed as a novel material for the removal of mercury(II) from aqueous phase. The operating variables studied were sorbent dosage, ionic strength, stirring speed, temperature, solution pH, contact time, and initial metal concentration. Sorption experiments indicated that the sorption capacity was dependent on operating variables and the process was strongly pH-dependent. Kinetic measurements showed that the process was uniform and rapid. In order to investigate the mechanism of sorption, kinetic data were modeled using the pseudo-first-order and pseudo-second-order kinetic equations, and intraparticle diffusion model. Among the kinetic models studied, the pseudo-second-order equation was the best applicable model to describe the sorption process. Equilibrium isotherm data were analyzed using the Langmuir and the Freundlich isotherms. The Langmuir model yields a much better fit than the Freundlich model. Isotherms have also been used to obtain the thermodynamic parameters such as free energy, enthalpy, and entropy of sorption. The maximum sorption capacity was 33.11 mg g -1 at 20 deg. C and the negative value of free energy change indicated the spontaneous nature of sorption. These results demonstrate that eucalyptus bark is very effective in the removal of Hg(II) from aqueous solutions

  18. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

    Science.gov (United States)

    Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

    2014-03-06

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu - and Arg + are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

  19. Kinetic study of the dehydration reaction of lithium sulfate monohydrate crystals using microscopy and modeling

    Energy Technology Data Exchange (ETDEWEB)

    Lan, Shuiquan [Department of Mechanical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven (Netherlands); Zondag, Herbert [Department of Mechanical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven (Netherlands); Energy research Center of the Netherlands – ECN, P.O. Box 1, 1755ZG Petten (Netherlands); Steenhoven, Anton van [Department of Mechanical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven (Netherlands); Rindt, Camilo, E-mail: c.c.m.rindt@tue.nl [Department of Mechanical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven (Netherlands)

    2015-12-10

    Highlights: • Kinetics of Li{sub 2}SO{sub 4}·H{sub 2}O single crystals were modeled based on elementary processes. • Kinetics of nucleation and nuclei growth were studied by using optical microscopy. • A novel experiment was designed to visualize the reaction front into crystal bulk. • Fractional conversion was calculated and compared with TGA-experiments. - Abstract: Simulation of gas–solid reactions occurring in industrial processes requires a robust kinetic model to be applicable in a wide range of complicated reaction conditions. However, in literature it is often seen that even the same reaction under specific controlled conditions is interpreted with different kinetic models. In the present work, a phenomenological model based on nucleation and nuclei growth processes is presented to study the kinetics of the dehydration reaction of lithium sulfate monohydrate single crystals. The two elementary processes of the reaction, nucleation and nuclei growth, are characterized and quantified as a function of temperature by using optical microscopy experiments. The in-situ measured characteristics of the dehydration reaction provided confirmatory evidence that the rate of nucleation obeys an exponential law and the rate of nuclei growth is approximately constant. With knowledge acquired from the optical observations as inputs of the kinetic model, the fractional conversion of the dehydration reaction was calculated and compared with experimental results from thermogravimetric analysis (TGA). A satisfactory comparison was found both in isothermal and non-isothermal conditions. It is demonstrated that this knowledge-based model has a great potential to represent the gas–solid reaction kinetics in a wide range of process conditions regarding temperature, pressure and particle geometry.

  20. Viral kinetics of Enterovirus 71 in human abdomyosarcoma cells

    Science.gov (United States)

    Lu, Jing; He, Ya-Qing; Yi, Li-Na; Zan, Hong; Kung, Hsiang-Fu; He, Ming-Liang

    2011-01-01

    AIM: To characterise the viral kinetics of enterovirus 71 (EV71). METHODS: In this study, human rhabdomyosarcoma (RD) cells were infected with EV71 at different multiplicity of infection (MOI). After infection, the cytopathic effect (CPE) was monitored and recorded using a phase contrast microscope associated with a CCD camera at different time points post viral infection (0, 6, 12, 24 h post infection). Cell growth and viability were measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in both EV71 infected and mock infected cells at each time point. EV71 replication kinetics in RD cells was determined by measuring the total intracellular viral RNA with real-time reverse-transcription polymerase chain reaction (qRT-PCR). Also, the intracellular and extracellular virion RNA was isolated and quantified at different time points to analyze the viral package and secretion. The expression of viral protein was determined by analyze the levels of viral structure protein VP1 with Western blotting. RESULTS: EV71 infection induced a significant CPE as early as 6 h post infection (p.i.) in both RD cells infected with high ratio of virus (MOI 10) and low ratio of virus (MOI 1). In EV71 infected cells, the cell growth was inhibited and the number of viable cells was rapidly decreased in the later phase of infection. EV71 virions were uncoated immediately after entry. The intracellular viral RNA began to increase at as early as 3 h p.i. and the exponential increase was found between 3 h to 6 h p.i. in both infected groups. For viral structure protein synthesis, results from western-blot showed that intracellular viral protein VP1 could not be detected until 6 h p.i. in the cells infected at either MOI 1 or MOI 10; and reached the peak at 9 h p.i. in the cells infected with EV71 at both MOI 1 and MOI 10. Simultaneously, the viral package and secretion were also actively processed as the virus underwent rapid replication. The viral package kinetics

  1. Mathematical Modeling of Protein Misfolding Mechanisms in Neurological Diseases: A Historical Overview.

    Science.gov (United States)

    Carbonell, Felix; Iturria-Medina, Yasser; Evans, Alan C

    2018-01-01

    Protein misfolding refers to a process where proteins become structurally abnormal and lose their specific 3-dimensional spatial configuration. The histopathological presence of misfolded protein (MP) aggregates has been associated as the primary evidence of multiple neurological diseases, including Prion diseases, Alzheimer's disease, Parkinson's disease, and Creutzfeldt-Jacob disease. However, the exact mechanisms of MP aggregation and propagation, as well as their impact in the long-term patient's clinical condition are still not well understood. With this aim, a variety of mathematical models has been proposed for a better insight into the kinetic rate laws that govern the microscopic processes of protein aggregation. Complementary, another class of large-scale models rely on modern molecular imaging techniques for describing the phenomenological effects of MP propagation over the whole brain. Unfortunately, those neuroimaging-based studies do not take full advantage of the tremendous capabilities offered by the chemical kinetics modeling approach. Actually, it has been barely acknowledged that the vast majority of large-scale models have foundations on previous mathematical approaches that describe the chemical kinetics of protein replication and propagation. The purpose of the current manuscript is to present a historical review about the development of mathematical models for describing both microscopic processes that occur during the MP aggregation and large-scale events that characterize the progression of neurodegenerative MP-mediated diseases.

  2. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

    Science.gov (United States)

    Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

    2016-08-11

    Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

  3. An experimental and kinetic modeling study of premixed nitroethane flames at low pressure

    DEFF Research Database (Denmark)

    Zhang, Kuiwen; Zhang, Lidong; Xie, Mingfeng

    2013-01-01

    An experimental and kinetic modeling study is reported on three premixed nitroethane/oxygen/argon flames at low pressure (4.655kPa) with the equivalence ratios (Φ) of 1.0, 1.5 and 2.0. Over 30 flame species were identified with tunable synchrotron vacuum ultraviolet photoionization mass spectrome......An experimental and kinetic modeling study is reported on three premixed nitroethane/oxygen/argon flames at low pressure (4.655kPa) with the equivalence ratios (Φ) of 1.0, 1.5 and 2.0. Over 30 flame species were identified with tunable synchrotron vacuum ultraviolet photoionization mass...

  4. Pyrolysis behaviors and kinetic studies on Eucalyptus residues using thermogravimetric analysis

    International Nuclear Information System (INIS)

    Chen, Zhihua; Zhu, Quanjie; Wang, Xun; Xiao, Bo; Liu, Shiming

    2015-01-01

    Highlights: • The first study on pyrolysis characteristics and kinetic of Eucalyptus residues. • Pyrolysis process can be divided into three stages using differential DTG method. • A new modified discrete DAEM showed better than Gaussian DAEM for kinetic studies. • Variations of activation energy reveal the mechanism change during pyrolysis process. - Abstract: The pyrolysis behaviors and kinetics of Eucalyptus leaves (EL), Eucalyptus bark (EB) and Eucalyptus sawdust (ESD) were investigated by using thermogravimetric analysis (TGA) technique. Three stages for EL, EB and ESD pyrolysis have been divided using differential derivative thermogravimetric (DDTG) method and the second stage is the main pyrolysis process with approximately 86.93% (EL), 88.96% (EB) and 97.84% (ESD) weight loss percentages. Kinetic parameters of Gaussian distributed activation energy model (DAEM) for EL, EB and ESD pyrolysis are: distributed centers (E_0) of 141.15 kJ/mol (EL), 149.21 kJ/mol (EB), 175.79 kJ/mol (ESD), standard deviations (σ) of 18.35 kJ/mol (EL), 18.37 kJ/mol (EB), 14.41 kJ/mol (ESD) and pre-exponential factors (A) of 1.15E+10 s"−"1 (EL), 4.34E+10 s"−"1 (EB), 7.44E+12 s"−"1 (ESD). A new modified discrete DAEM was performed and showed excellent fits to experimental data than Gaussian DAEM. According to the modified discrete DAEM, the activation energies are in ranges of 122.67–308.64 kJ/mol, 118.72–410.80 kJ/mol and 108.39–192.93 kJ/mol for EL, EB and ESD pyrolysis, respectively. The pre-exponential factors of discrete DAEM have wide ranges of 4.84E+13–6.12E+22 s"−"1 (EL), 1.91E+12–4.51E+25 s"−"1 (EB) and 63.43–4.36E+11 s"−"1 (ESD). The variation of activation energy versus conversion reveals the mechanism change during pyrolysis process. The kinetic data would be of immense benefit to model, design and develop suitable thermo-chemical systems for the application of Eucalyptus residues.

  5. ELECTRODEPOSITION OF COPPER IONS ON FIXED BED ELECTRODES: KINETIC AND HYDRODYNAMIC STUDY

    Directory of Open Access Journals (Sweden)

    L.A.M. Ruotolo

    2002-03-01

    Full Text Available The kinetic and hydrodynamic behaviour of a fixed-bed electrochemical reactor was studied in terms of current efficiency (CE and energy efficiency (EE. In the kinetic experiments the effects of fixed bed thickness (L, current density (i and initial concentration of copper (C0 were studied. In the hydrodynamic experiments the permeability (k of the electrode and the coefficient for inertial forces (c were also studied as functions of the applied current density. At low current densities and bed thicknesses greater than 1.0 cm, negative CE and EE were observed as a consequence of the dissolution of the porous matrix. At high current densities low CE and EE were observed and a powdery deposit was formed on the surface of the particles. From the results of the kinetic study bed thickness and the range of current densities employed in the hydrodynamic experiments were chosen. In these experiments the electrodeposition process continued until the whole electrode had been clogged and no more electrolyte could pass through it. The relationship between pressure drop and flow rate was well described by the Forchheimer equation. It was observed that the reduction in porosity due to copper electrodeposition causes the flow rate to decrease because of the decrease in electrode permeability, but it had no influence on current efficiency.

  6. Kinetic Study on the Esterification of Palm Fatty Acid Distillate (PFAD) Using Heterogeneous Catalyst

    Science.gov (United States)

    Rofiqah, U.; Djalal, R. A.; Sutrisno, B.; Hidayat, A.

    2018-05-01

    Esterification with heterogeneous catalysts is believed to have advantages compared to homogeneous catalysts. Palm Fatty Acid Distillate (PFAD) was esterified by ZrO2 -SO4 2-/natural zeolite at temperature variation of 55°C, 60°C, and 65°C to produce biodiesel. Determination of reaction kinetics was done by experiment and modeling. Kinetic study was approached using pseudo-homogeneous model of first order. For experiment, reaction kinetics were 0.0031 s-1, 0.0054 s-1, and 0.00937 s-1 for a temperature of 55 °C, 60 °C and 65 °C, respectively. For modelling, reaction kinetics were 0.0030 s-1, 0.0055 s-1, and 0.0090 s-1 for a temperature of 55°C, 60°C and 65°C, respectively. Rate and conversion of reaction are getting increased by increasing temperature.

  7. Slow VO2 off-kinetics in skeletal muscle is associated with fast PCr off-kinetics--and inversely.

    Science.gov (United States)

    Korzeniewski, Bernard; Zoladz, Jerzy A

    2013-09-01

    The computer model of the bioenergetic system in skeletal muscle, developed previously, was used to study the effect of the characteristic decay time of the parallel activation of oxidative phosphorylation [τ(OFF)] during muscle recovery on the muscle oxygen consumption rate (Vo2) and phosphocreatine (PCr) work-to-rest transition (off)-kinetics and on the relationship between the Vo2 and PCr rest-to-work transition (on)- and off-kinetics in moderate and heavy exercise. An increase in τ(OFF) slows down the initial phase of the muscle Vo2 off-kinetics and accelerates the PCr off-kinetics. As a result, the relationship between the initial phase of the Vo2 off-kinetics (lasting approximately 3-60 s in computer simulations) and the PCr off-kinetics is inverse: the slower the former, the faster the latter. A faster initial phase of the Vo2 off-kinetics is associated with a slower late phase of the Vo2 off-kinetics, and as a result, the integral of Vo2 above baseline during recovery, representing the oxygen debt, is identical in all cases [values of τ(OFF)] for a given PCr decrease. Depending on τ(OFF), the muscle Vo2 on-kinetics was either equally fast or slower than the Vo2 off-kinetics in moderate exercise and always slower in heavy exercise. PCr on-kinetics was always faster than PCr off-kinetics. This study clearly demonstrates that τ(OFF) has a pronounced impact on the mutual relations between the muscle Vo2 and PCr on- and off-kinetics.

  8. Comparison of Oxidation Kinetics of Nitrite-Oxidizing Bacteria: Nitrite Availability as a Key Factor in Niche Differentiation

    Science.gov (United States)

    Nowka, Boris; Daims, Holger

    2014-01-01

    Nitrification has an immense impact on nitrogen cycling in natural ecosystems and in wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially of nitrite-oxidizing bacteria (NOB) are lacking because of a limited number of pure cultures until recently. In this study, we compared the nitrite oxidation kinetics of six pure cultures and one enrichment culture representing three genera of NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 and 27 μM nitrite, Nitrospira bacteria are adapted to live under significant substrate limitation. Nitrobacter showed a wide range of lower substrate affinities, with Km values between 49 and 544 μM nitrite. However, the advantage of Nitrobacter emerged under excess nitrite supply, sustaining high maximum specific activities (Vmax) of 64 to 164 μmol nitrite/mg protein/h, contrary to the lower activities of Nitrospira of 18 to 48 μmol nitrite/mg protein/h. The Vmax (26 μmol nitrite/mg protein/h) and Km (58 μM nitrite) of “Candidatus Nitrotoga arctica” measured at a low temperature of 17°C suggest that Nitrotoga can advantageously compete with other NOB, especially in cold habitats. The kinetic parameters determined represent improved basis values for nitrifying models and will support predictions of community structure and nitrification rates in natural and engineered ecosystems. PMID:25398863

  9. Kinetic study of Chromium VI adsorption onto palm kernel shell activated carbon

    Science.gov (United States)

    Mohammad, Masita; Sadeghi Louyeh, Shiva; Yaakob, Zahira

    2018-04-01

    Heavy metal contamination of industrial effluent is one of the significant environmental problems due to their toxicity and its accumulation throughout the food chain. Adsorption is one of the promising methods for removal of heavy metals from aqua solution because of its simple technique, efficient, reliable and low-cost due to the utilization of residue from the agricultural industry. In this study, activated carbon from palm kernel shells has been produced through chemical activation process using zinc chloride as an activating agent and carbonized at 800 °C. Palm kernel shell activated carbon, PAC was assessed for its efficiency to remove Chromium (VI) ions from aqueous solutions through a batch adsorption process. The kinetic mechanisms have been analysed using Lagergren first-order kinetics model, second-order kinetics model and intra-particle diffusion model. The characterizations such as BET surface area, surface morphology, SEM-EDX have been done. The result shows that the activation process by ZnCl2 was successfully improved the porosity and modified the functional group of palm kernel shell. The result shows that the maximum adsorption capacity of Cr is 11.40mg/g at 30ppm initial metal ion concentration and 0.1g/50mL of adsorbent concentration. The adsorption process followed the pseudo second orders kinetic model.

  10. In-situ study of hydriding kinetics in Pd-based thin film systems

    Energy Technology Data Exchange (ETDEWEB)

    Delmelle, Renaud; Proost, Joris [Univ. Catholique de Louvain, Louvain-la-Neuve (Belgium). Div. of Materials and Process Engineering

    2010-07-01

    The hydriding kinetics of Pd thin films has been investigated in detail. The key experimental technique used in this work consists of a high resolution curvature measurement setup, which continuously monitors the reflections of multiple laser beams coming off a cantilevered sample. After mounting the sample inside a vacuum chamber, a H-containing gas mixture is introduced to instantaneously generate a given hydrogen partial pressure (p{sub H2}) inside the chamber. The resulting interaction of H with the Pd layer then leads to a volume expansion of the thin film system. This induces in turn changes in the sample curvature as a result of internal stresses developing in the Pd film during a hydriding cycle. Based on such curvature date obtained in-situ at different p{sub H2}, a two-step model for the kinetics of Pd-hydride formation has been proposed and expressions for the hydrogen adsorption and absorption velocities have been derived. The rate-limiting steps have been identified by studying the p{sub H2}-dependence of these velocities. Furthermore, from our in-situ experimental data, relevant kinetic parameters have been calculated. The effect of dry air exposure of the Pd films on the hydriding kinetics has been considered as well. (orig.)

  11. The shock tube as wave reactor for kinetic studies and material systems

    Energy Technology Data Exchange (ETDEWEB)

    Bhaskaran, K.A. [Indian Institute of Technology, Chennai (India). Department of Mechanical Engineering; Roth, P. [Gerhard Mercator Universitat, Duisberg (Germany). Institut fur Verbrennung und Gasdynamik

    2002-07-01

    Several important reviews of shock tube kinetics have appeared earlier, prominent among them being 'Shock Tube Technique in Chemical Kinetics' by Belford and Strehlow (Ann Rev Phys Chem 20 (1969) 247), 'Chemical Reaction of Shock Waves' by Wagner (Proceedings of the Eighth International Shock Tube Symposium (1971) 4/1), 'Shock Tube and Shock Wave Research' by Bauer and Lewis (Proceedings of the 11th International Symposium on Shock Tubes and Waves (1977) 269), 'Shock Waves in Chemistry' edited by Assa Lifshitz (Shock Waves in Chemistry, 1981) and 'Shock Tube Techniques in Chemical Kinetics' by Wing Tsang and Assa Lifshitz (Annu Rev Phys Chem 41 (1990) 559). A critical analysis of the different shock tube techniques, their limitations and suggestions to improve the accuracy of the data produced are contained in these reviews. The purpose of this article is to present the current status of kinetic research with emphasis on the diagnostic techniques. Selected studies on homogeneous and dispersed systems are presented to bring out the versatility of the shock tube technique. The use of the shock tube as high temperature wave reactor for gas phase material synthesis is also highlighted. (author)

  12. Metabolic intervention in surgical patients. An assessment of the effect of somatostatin, ranitidine, naloxone, diclophenac, dipyridamole, or salbutamol infusion on energy and protein kinetics in surgical patients using stable and radioisotopes

    International Nuclear Information System (INIS)

    Shaw, J.H.; Wolfe, R.R.

    1988-01-01

    We have assessed the effect of a variety of forms of metabolic intervention on both energy and protein metabolism in 44 severely ill surgical patients. The patients were studied either in the basal state or while receiving total parenteral nutrition (TPN), and the metabolic effects were assessed using the primed-constant infusion of a combination of stable isotopes and radioisotopes. Somatostatin infusion, either in the basal state or in the TPN, did not change glucose kinetics, but there was a significant decrease in the rate of net protein catabolism (NPC). In the basal studies the rate of NPC decreased from 3.4 +/- 0.7 g/kg/d to 2.9 +/- 0.7 g/kg/d (p less than 0.002), while in the TPN patients the corresponding values were 1.48 +/- 0.61 g/kg/d and 1.10 +/- 0.50 g/kg/d, respectively (p less than 0.005). Histamine type 2 blockade with ranitidine did not significantly alter glucose kinetics, but in both the TPN patients and in the basal state ranitidine was associated with a significant decrease in the rate of NPC. In the basal state rate of NPC was 2.44 +/- 0.53 g/kg/d and during ranitidine infusion the value was 2.08 +/- 0.42 g/kg/d (p less than 0.04). Naloxone infusion did not alter glucose kinetics, but there was a significant decrease in the rate of NPC from a basal value of 2.6 +/- 0.6 g/kg/d to 2.3 +/- 0.5 g/kg/d (p less than 0.04). The infusion of the prostaglandin antagonists diclofenac or dipyridamole resulted in increases in the plasma insulin level, and as a result glucose turnover decreased in both groups. In the diclofenac group the rate of glucose turnover decreased from 14.4 +/- 1.7 mumol/kg/min to 12.6 +/- 1.3 mumol/kg/min (p less than 0.02). Neither prostaglandin antagonist resulted in any significant change in the rate of NPC

  13. Autoradiographic and cytochemical studies on the intracellular transport of secreted proteins in the lacrimal ducts (glandula extraorbitalis) of the rat

    International Nuclear Information System (INIS)

    Vogel, H.

    1982-01-01

    Azini was isolated from the glandula lacrimalis of the rat. Its vitality was proven by oxygen use measurements. In autoradiographic studies isolated Azini was marked with L-(4,5- 3 H)-leucine and fixed at various times thereafter. The light microscopic autoradiography showed a time dependent distribution of the silver grains whose association with membrane-enclosed compartments made the electron microscopic autoradiography possible. This distribution allows an analysis of the kinetics of the intracellular transport of secreted proteins. Because of its limited spatial resolution the autoradiographic research methods were combined with the cytochemical presentation of the peroxidase, a secreted protein, of the lacrimal duct. (orig./MG) [de

  14. Impact of contamination with long-lived radionuclides on PET kinetics modelling in multitracer studies

    DEFF Research Database (Denmark)

    Jødal, Lars; Hansen, Søren Baarsgaard; Jensen, Svend B

    2016-01-01

    Introduction: An important issue in multitracer studies is the separation of signals from the different radiotracers. This is especially the case when an early tracer has a long physical half-life and kinetic modelling has to be performed, because the early tracer can confer a long-lived contamin......Introduction: An important issue in multitracer studies is the separation of signals from the different radiotracers. This is especially the case when an early tracer has a long physical half-life and kinetic modelling has to be performed, because the early tracer can confer a long...... of subsequent PET tracers. Blood sample counts were corrected by recounting the samples a few days later. A more optimal choice of energy window was also explored. The effect of correction versus noncorrection was investigated using a two-tissue kinetic model with irreversible uptake (K1, k2, k3). Results: K1...... counting of blood samples can lead to a contaminating background not observed in PET imaging and this background can affect kinetic modelling. If the contaminating tracer has a much longer half-life than the foreground tracer, then the problem can be solved by late recounting of the samples....

  15. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions

    International Nuclear Information System (INIS)

    Salmon, L.; Licinio, A.; Jensen, M.R.; Blackledge, M.; Ortega Roldan, J.L.; Van Nuland, N.; Lescop, E.

    2011-01-01

    We have recently presented a titration approach for the determination of residual dipolar couplings (RDCs) from experimentally inaccessible complexes. Here, we extend this approach to the measurement of 15 N spin relaxation rates and demonstrate that this can provide long-range structural, dynamic, and kinetic information about these elusive systems. (authors)

  16. Removal Rate of Organic Matter Using Natural Cellulose via Adsorption Isotherm and Kinetic Studies.

    Science.gov (United States)

    Din, Mohd Fadhil Md; Ponraj, Mohanadoss; Low, Wen-Pei; Fulazzaky, Mohamad Ali; Iwao, Kenzo; Songip, Ahmad Rahman; Chelliapan, Shreeshivadasan; Ismail, Zulhilmi; Jamal, Mohamad Hidayat

    2016-02-01

    In this study, the removal of natural organic matter (NOM) using coconut fiber (CF) and palm oil fiber (POF) was investigated. Preliminary analysis was performed using a jar test for the selection of optimal medium before the fabricated column model experiment. The equilibrium studies on isotherms and kinetic models for NOM adsorption were analyzed using linearized correlation coefficient. Results showed that the equilibrium data were fitted to Langmuir isotherm model for both CF and POF. The most suitable adsorption model was the pseudo-first-order kinetic model for POF and pseudo-second-order kinetic model for CF. The adsorption capacities achieved by the CF and POF were 15.67 and 30.8 mg/g respectively. Based on this investigation, it can be concluded that the POF is the most suitable material for the removal of NOM in semi polluted river water.

  17. Kinetic analysis of a monoclonal therapeutic antibody and its single-chain homolog by surface plasmon resonance.

    Science.gov (United States)

    Patel, Rekha; Andrien, Bruce A

    2010-01-01

    Monoclonal antibodies (mAbs) and antibody fragments have become an emerging class of therapeutics since 1986. Their versatility enables them to be engineered for optimal efficiency and decreased immunogenicity, and the path to market has been set by recent regulatory approvals. One of the initial criteria for success of any protein or antibody therapeutic is to understand its binding characteristics to the target antigen. Surface plasmon resonance (SPR) has been widely used and is an important tool for ligand-antigen binding characterization. In this work, the binding kinetics of a recombinant mAb and its single-chain antibody homolog, single-chain variable fragment (scFv), was analyzed by SPR. These two proteins target the same antigen. The binding kinetics of the mAb (bivalent antibody) and scFv (monovalent scFv) for this antigen was analyzed along with an assessment of the thermodynamics of the binding interactions. Alternative binding configurations were investigated to evaluate potential experimental bias because theoretically experimental binding configuration should have no impact on binding kinetics. Self-association binding kinetics in the proteins' respective formulation solutions and antigen epitope mapping were also evaluated. Functional characterization of monoclonal and single-chain antibodies has become just as important as structural characterization in the biotechnology field.

  18. Kinetic Modeling of the Release of Ethylene Oxide from Sterilized Plastic Containers and its Interaction with Monoclonal Antibodies.

    Science.gov (United States)

    Yu, Bryan Lei; Han, Jun; Hammond, Matthew; Wang, Xuemei; Zhang, Qingchun; Clausen, Andrew; Forster, Ronald; Eu, Mingda

    Ethylene oxide (ETO) is commonly used to sterilize plastic containers, but the effects of residual amounts left after sterilization on protein therapeutics are still not well understood. Here we focus primarily on the factors that influence concentrations of ETO migrating from ETO-treated plastic containers into aqueous solution. A study was designed to investigate the kinetics of this process at various temperatures, and the kinetic data could be fit with a model based on a combination of Fickean diffusion and first-order chemical reaction (to account for observed hydrolysis of ETO). The diffusion and reaction rate constants thus obtained obey Arrhenius-like temperature dependence. These results indicate that for analytical methods involving extraction into water, measurements of residual ETO in a container must account for the effects of ETO hydrolysis. Further, the effects of salt concentration and pH of the fluid in the container on accumulated ETO levels were explored. Finally, interactions of ETO with anti-streptavidin (AntiSA) Immunoglobulin G1 (IgG1) and IgG2 antibodies were studied, with ETO adducts found on all methionine residues when incubated in solutions spiked with ETO at concentrations that could be reached (based on the kinetic studies) in ETO-treated plastic vials. Overall, the likelihood of observable ETO-protein modifications upon storage in ETO-sterilized containers will depend on a complex interplay of protein properties, formulation details, storage conditions, and amount of residual ETO initially in the container. Ethylene oxide (ETO) is commonly used to sterilize plastic containers, but the effects of residual amounts left after sterilization on protein therapeutics are still not well understood. Here we describe experiments exploring the factors that influence concentrations of ETO migrating from ETO-treated plastic containers into aqueous solution over time. Additionally, interactions of ETO with model antibodies were studied, with ETO

  19. PROTEIN FRACTIONS AND IN VITRO FERMENTATION OF PROTEIN FEEDS FOR RUMINANTS

    Directory of Open Access Journals (Sweden)

    Angel L. Guevara-Mesa

    2011-05-01

    Full Text Available The objective of this study was to evaluate 20 protein feeds grouped in forages, vegetal by- products and animal by-products used for ruminant diets. Protein fractions (PF: A, non-protein nitrogen (NPN; B1, buffer-soluble protein; B2, buffer-insoluble, NDF-soluble protein; B3, NDF-insoluble, ADF-soluble protein; and C, ADF-insoluble protein, were determined for each ingredient.  Protein composition was correlated with total gas production in vitro (GP, gas production rate (S, lag time (L, DM disappearance (DMDIV and residual protein (RPIV. The completely randomised designed was analysed using mixed proc. and Tukey contrasts. Forages contained 18.29, 7.86, 66.00, 2.96, 4.89% of fractions A, B1, B2, B3 and C, respectively. Vegetable by-products contained 22.55, 4.55, 59.51, 8.84, 4.55% of each fraction, in the same order. Animal by-products contained 19.13, 4.52, 70.24, 3.74, 2.37% of each fraction, in the same order. Vetch, wheat bran and poultry litter had the greatest Vmax in each group. Vmax was correlated (P≤0.01 with total protein (r = -0.45, ADF (r = 0.27 and DMDIV (r = 0.61. In conclusion, there were differences in protein composition and kinetics of in vitro gas production among ingredients.

  20. Effects of Toasting Time on Digestive Hydrolysis of Soluble and Insoluble 00-Rapeseed Meal Proteins

    NARCIS (Netherlands)

    Salazar-Villanea, Sergio; Bruininx, Erik M.A.M.; Gruppen, Harry; Carré, Patrick; Quinsac, Alain; Poel, van der Thomas

    2017-01-01

    Thermal damage to proteins can reduce their nutritional value. The effects of toasting time on the kinetics of hydrolysis, the resulting molecular weight distribution of 00-rapeseed meal (RSM) and the soluble and insoluble protein fractions separated from the RSM were studied. Hydrolysis was

  1. A kinetic study of 1,3-dipolar cycloadditions in micellar media

    NARCIS (Netherlands)

    Rispens, T; Engberts, JBFN

    2003-01-01

    The kinetics of the 1,3-dipolar cycloadditions (DC) of benzonitrile oxide with a series of N-substituted maleimides in micellar media have been investigated. Surfactants studied include anionic sodium dodecyl sulfate, cationic cetyltrimethylammonium bromide, and a series of nonionic alkyl

  2. The anabolic response to a meal containing different amounts of protein is not limited by the maximal stimulation of protein synthesis in healthy young adults.

    Science.gov (United States)

    Kim, Il-Young; Schutzler, Scott; Schrader, Amy; Spencer, Horace J; Azhar, Gohar; Ferrando, Arny A; Wolfe, Robert R

    2016-01-01

    We have determined whole body protein kinetics, i.e., protein synthesis (PS), breakdown (PB), and net balance (NB) in human subjects in the fasted state and following ingestion of ~40 g [moderate protein (MP)], which has been reported to maximize the protein synthetic response or ~70 g [higher protein (HP)] protein, more representative of the amount of protein in the dinner of an average American diet. Twenty-three healthy young adults who had performed prior resistance exercise (X-MP or X-HP) or time-matched resting (R-MP or R-HP) were studied during a primed continuous infusion of l-[(2)H5]phenylalanine and l-[(2)H2]tyrosine. Subjects were randomly assigned into an exercise (X, n = 12) or resting (R, n = 11) group, and each group was studied at the two levels of dietary protein intake in random order. PS, PB, and NB were expressed as increases above the basal, fasting values (mg·kg lean body mass(-1)·min(-1)). Exercise did not significantly affect protein kinetics and blood chemistry. Feeding resulted in positive NB at both levels of protein intake: NB was greater in response to the meal containing HP vs. MP (P < 0.00001). The greater NB with HP was achieved primarily through a greater reduction in PB and to a lesser extent stimulation of protein synthesis (for all, P < 0.0001). HP resulted in greater plasma essential amino acid responses (P < 0.01) vs. MP, with no differences in insulin and glucose responses. In conclusion, whole body net protein balance improves with greater protein intake above that previously suggested to maximally stimulating muscle protein synthesis because of a simultaneous reduction in protein breakdown. Copyright © 2016 the American Physiological Society.

  3. Supercritical kinetic analysis in simplified system of fuel debris using integral kinetic model

    International Nuclear Information System (INIS)

    Tuya, Delgersaikhan; Obara, Toru

    2016-01-01

    Highlights: • Kinetic analysis in simplified weakly coupled fuel debris system was performed. • The integral kinetic model was used to simulate criticality accidents. • The fission power and released energy during simulated accident were obtained. • Coupling between debris regions and its effect on the fission power was obtained. - Abstract: Preliminary prompt supercritical kinetic analyses in a simplified coupled system of fuel debris designed to roughly resemble a melted core of a nuclear reactor were performed using an integral kinetic model. The integral kinetic model, which can describe region- and time-dependent fission rate in a coupled system of arbitrary geometry, was used because the fuel debris system is weakly coupled in terms of neutronics. The results revealed some important characteristics of coupled systems, such as the coupling between debris regions and the effect of the coupling on the fission rate and released energy in each debris region during the simulated criticality accident. In brief, this study showed that the integral kinetic model can be applied to supercritical kinetic analysis in fuel debris systems and also that it can be a useful tool for investigating the effect of the coupling on consequences of a supercritical accident.

  4. Effects of preservation conditions of canine feces on in vitro gas production kinetics and fermentation end-products

    NARCIS (Netherlands)

    Bosch, G.; Wrigglesworth, D.J.; Cone, J.W.; Pellikaan, W.F.; Hendriks, W.H.

    2013-01-01

    This study investigated the effect of chilling and freezing (for 24 h) canine feces on in vitro gas production kinetics and fermentation end-product profiles from carbohydrate-rich (in vitro run 1) and protein-rich substrates (in vitro run 2). Feces were collected from 3 adult Retriever-type dogs

  5. Understanding ensemble protein folding at atomic detail

    International Nuclear Information System (INIS)

    Wallin, Stefan; Shakhnovich, Eugene I

    2008-01-01

    Although far from routine, simulating the folding of specific short protein chains on the computer, at a detailed atomic level, is starting to become a reality. This remarkable progress, which has been made over the last decade or so, allows a fundamental aspect of the protein folding process to be addressed, namely its statistical nature. In order to make quantitative comparisons with experimental kinetic data a complete ensemble view of folding must be achieved, with key observables averaged over the large number of microscopically different folding trajectories available to a protein chain. Here we review recent advances in atomic-level protein folding simulations and the new insight provided by them into the protein folding process. An important element in understanding ensemble folding kinetics are methods for analyzing many separate folding trajectories, and we discuss techniques developed to condense the large amount of information contained in an ensemble of trajectories into a manageable picture of the folding process. (topical review)

  6. Thermogravimetric Analysis and Kinetic Study on Pyrolysis of Veteri-narian Solid Waste

    Directory of Open Access Journals (Sweden)

    Andrés Felipe Rojas González

    2016-10-01

    Full Text Available Context: Institutional waste from clinical centers can be classified as those coming from health institutions dedicated to human attention and those coming from centers for animal veterinary care. The latter are mainly hazardous wastes, hence their disposal requires incineration. Most of such waste is organic, and it is possible, therefore, to take advantage of their energetic power in combustion or pyrolysis processes. This work is motivated because no literature was found on the pyrolysis kinetics veterinary waste, as this kind of studies are mainly focused on hospital waste of human health care. Method: The kinetics of pyrolysis is characterized and studied by means of thermogravimetric analysis of 6 major veterinary waste (gauze, cotton swabs, cotton, nails, hair, plastic syringes. The characterization is performed by proximate and elemental analysis, and thermogravimetric analysis. Reactivity characteristics and pyrolytic capability of wastes are established. The kinetics study on pyrolysis was carried out by determining the kinetic triplet by isoconversional Starink method. Results: It was established that the pyrolysis index increases with the heating rate and that the thermal degradation depends on the material type of the waste. Similarly, it was found that the temperature (ΔT = Tf - Ti for the thermal decomposition of veterinary waste is: ΔTnails> ΔThair > ΔTcotton swabs > ΔTgauze > ΔTcotton > ΔTplastic syringes; the activation energy is Enails> E hair > Eplastic syringes > Ecotton swabs > E gauze > Ecotton, and the reaction order is: n hair > nnails > ncotton swabs > ncotton > n gauze > n plastic syringes. Conclusions: These results suggest the possibility of using veterinary wastes for power generation, providing an alternative for sustainable energy development to cities in continuous growth, from both, energetic and environmental points of view.

  7. Study of kinetics and mechanism of diazo compound reactions using nuclear chemical polarization

    International Nuclear Information System (INIS)

    Gragerov, I.P.; Levit, A.F.; Kiprianova, L.A.; Buchachenko, A.L.; Sterleva, T.G.

    1975-01-01

    It has been established that at the rate-determining steps of the radical reactions in which aniline interacts with isoamyl nitrite and substituted diazo salts interact with sodium methylate, tertiary fatty amines, or phosphinic acid, no transfer of a single electron occurs. The processes of single electron transfer do not seem to play a decisive role in the kinetics of most transformations of diazo compounds. Chemical nuclear polarization is shown to be suitable for kinetic studies of fast radical processes

  8. Using a split luciferase assay (SLA) to measure the kinetics of cell-cell fusion mediated by herpes simplex virus glycoproteins.

    Science.gov (United States)

    Saw, Wan Ting; Matsuda, Zene; Eisenberg, Roselyn J; Cohen, Gary H; Atanasiu, Doina

    2015-11-15

    Herpes simplex virus (HSV) entry and cell-cell fusion require the envelope proteins gD, gH/gL and gB. We propose that receptor-activated conformational changes to gD activate gH/gL, which then triggers gB (the fusogen) into an active form. To study this dynamic process, we have adapted a dual split protein assay originally developed to study the kinetics of human immunodeficiency virus (HIV) mediated fusion. This assay uses a chimera of split forms of renilla luciferase (RL) and green fluorescent protein (GFP). Effector cells are co-transfected with the glycoproteins and one of the split reporters. Receptor-bearing target cells are transfected with the second reporter. Co-culture results in fusion and restoration of RL, which can convert a membrane permeable substrate into a luminescent product, thereby enabling one to monitor initiation and extent of fusion in live cells in real time. Restoration of GFP can also be studied by fluorescence microscopy. Two sets of split reporters have been developed: the original one allows one to measure fusion kinetics over hours whereas the more recent version was designed to enhance the sensitivity of RL activity allowing one to monitor both initiation and rates of fusion in minutes. Here, we provide a detailed, step-by-step protocol for the optimization of the assay (which we call the SLA for split luciferase assay) using the HSV system. We also show several examples of the power of this assay to examine both the initiation and kinetics of cell-cell fusion by wild type forms of gD, gB, gH/gL of both serotypes of HSV as well as the effect of mutations and antibodies that alter the kinetics of fusion. The SLA can be applied to other viral systems that carry out membrane fusion. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Numerical Simulations of Kinetic Alfvén Waves to Study Spectral ...

    Indian Academy of Sciences (India)

    Numerical Simulations of Kinetic Alfvén Waves to Study Spectral. Index in Solar Wind Turbulence and Particle Heating. R. P. Sharma. ∗. & H. D. Singh. Center for Energy Studies, Indian Institute of Technology, Delhi 110 016, India. ∗ e-mail: rpsharma@ces.iitd.ernet.in. Abstract. We present numerical simulations of the ...

  10. Kinetics and

    Directory of Open Access Journals (Sweden)

    Mojtaba Ahmadi

    2016-11-01

    Full Text Available The aqueous degradation of Reactive Yellow 84 (RY84 by potassium peroxydisulfate (K2S2O8 has been studied in laboratory scale experiments. The effect of the initial concentrations of potassium peroxydisulfate and RY84, pH and temperature on RY84 degradation were also examined. Experimental data were analyzed using first and second-order kinetics. The degradation kinetics of RY84 of the potassium peroxydisulfate process followed the second-order reaction kinetics. These rate constants have an extreme values similar to of 9.493 mM−1min−1 at a peroxydisulfate dose of 4 mmol/L. Thermodynamic parameters such as activation (Ea and Gibbs free energy (ΔG° were also evaluated. The negative value of ΔGo and Ea shows the spontaneous reaction natural conditions and exothermic nature.

  11. Physicochemical analysis and nonisothermal kinetic study of sertraline–lactose binary mixtures

    Directory of Open Access Journals (Sweden)

    Faranak Ghaderi

    2017-07-01

    Full Text Available In the present study the physicochemical stability of sertraline with lactose was evaluated in drug-excipient binary mixtures. Different physicochemical methods such as differential scanning calorimetry (DSC, Fourier-transform infrared spectroscopy, and mass spectrometry were applied to confirm the incompatibility. The final aim of this study was to evaluate the kinetic parameters using a fast and sensitive DSC method. Solid-state kinetic parameters were derived from nonisothermally stressed physical mixtures using different thermal models such as Friedman, Flynn–Wall–Ozawa, and Kissinger–Akahira–Sunose. Overall, the instability of sertraline with lactose was successfully evaluated. Further confirmation was made by tracking the Maillard reaction product of sertraline and lactose by mass spectrometry. DSC scans provided important information about the stability of sertraline in solid-state condition and also revealed the related thermokinetic parameters in order to understand the nature of the chemical instability.

  12. Physicochemical analysis and nonisothermal kinetic study of sertraline-lactose binary mixtures.

    Science.gov (United States)

    Ghaderi, Faranak; Nemati, Mahboob; Siahi-Shadbad, Mohammad Reza; Valizadeh, Hadi; Monajjemzadeh, Farnaz

    2017-07-01

    In the present study the physicochemical stability of sertraline with lactose was evaluated in drug-excipient binary mixtures. Different physicochemical methods such as differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy, and mass spectrometry were applied to confirm the incompatibility. The final aim of this study was to evaluate the kinetic parameters using a fast and sensitive DSC method. Solid-state kinetic parameters were derived from nonisothermally stressed physical mixtures using different thermal models such as Friedman, Flynn-Wall-Ozawa, and Kissinger-Akahira-Sunose. Overall, the instability of sertraline with lactose was successfully evaluated. Further confirmation was made by tracking the Maillard reaction product of sertraline and lactose by mass spectrometry. DSC scans provided important information about the stability of sertraline in solid-state condition and also revealed the related thermokinetic parameters in order to understand the nature of the chemical instability. Copyright © 2016. Published by Elsevier B.V.

  13. Lipase-catalyzed synthesis of palmitanilide: Kinetic model and antimicrobial activity study.

    Science.gov (United States)

    Liu, Kuan-Miao; Liu, Kuan-Ju

    2016-01-01

    Enzymatic syntheses of fatty acid anilides are important owing to their wide range of industrial applications in detergents, shampoo, cosmetics, and surfactant formulations. The amidation reaction of Mucor miehei lipase Lipozyme IM20 was investigated for direct amidation of triacylglycerol in organic solvents. The process parameters (reaction temperature, substrate molar ratio, enzyme amount) were optimized to achieve the highest yield of anilide. The maximum yield of palmitanilide (88.9%) was achieved after 24 h of reaction at 40 °C at an enzyme concentration of 1.4% (70 mg). Kinetics of lipase-catalyzed amidation of aniline with tripalmitin has been investigated. The reaction rate could be described in terms of the Michaelis-Menten equation with a Ping-Pong Bi-Bi mechanism and competitive inhibition by both the substrates. The kinetic constants were estimated by using non-linear regression method using enzyme kinetic modules. The enzyme operational stability study showed that Lipozyme IM20 retained 38.1% of the initial activity for the synthesis of palmitanilide (even after repeated use for 48 h). Palmitanilide, a fatty acid amide, exhibited potent antimicrobial activity toward Bacillus cereus. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Study the oxidation kinetics of uranium using XRD and Rietveld method

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yanzhi; Guan Weijun; Wang Qinguo; Wang Xiaolin; Lai Xinchun; Shuai Maobing, E-mail: yanzhizh@163.com [China Academy of Engineering Physics, PO Box 919-71, Mianyang, Sichuan, 621900 (China)

    2010-03-15

    The surface oxidation of uranium metal has been studied by X-ray diffraction (XRD) and Rietveld method in the range of 50{approx}300deg. C in air. The oxidation processes are analyzed by XRD to determine the extent of surface oxidation and the oxide structure. The dynamics expression for the formation of UO{sub 2} was derived. At the beginning, the dynamic expression was nonlinear, but switched to linear subsequently for uranium in air and humid oxygen. That is, the growth kinetics of UO{sub 2} can be divided into two stages: nonlinear portion and linear portion. Using the kinetic data of linear portion, the activation energy of reaction between uranium and air was calculated about 46.0 kJ/mol. However the content of oxide as a function of time was linear in humid helium ambience. Contrast the dynamics results, it prove that the absence of oxygen would accelerate the corrosion rate of uranium in the humid gas. We can find that the XRD and Rietveld method are a useful convenient method to estimate the kinetics and thermodynamics of solid-gas reaction.

  15. DSC and curing kinetics study of epoxy grouting diluted with furfural -acetone slurry

    Science.gov (United States)

    Yin, H.; Sun, D. W.; Li, B.; Liu, Y. T.; Ran, Q. P.; Liu, J. P.

    2016-07-01

    The use of furfural-acetone slurry as active diluents of Bisphenol-A epoxy resin (DGEBA) groutings has been studied by dynamic and non-isothermal DSC for the first time. Curing kinetics study was investigated by non-isothermal differential scanning calorimetries at different heating rates. Activation enery (Ea) was calculated based on Kissinger and Ozawa Methods, and the results showed that Ea increased from 58.87 to 71.13KJ/mol after the diluents were added. The furfural-acetone epoxy matrix could cure completely at the theoretical curing temperature of 365.8K and the curing time of 139mins, which were determined by the kinetic model parameters.

  16. Biophysical characterization of the complex between human papillomavirus E6 protein and synapse-associated protein 97

    DEFF Research Database (Denmark)

    Chi, Celestine Ngang; Bach, Anders; Engström, Åke

    2011-01-01

    The E6 protein of human papillomavirus exhibits complex interaction patterns with several host proteins and their roles in HPV mediated oncogenesis have proved challenging to study. Here we use several biophysical techniques to explore the binding of E6 to the three PDZ domains of the tumor......, this quaternary complex has the same apparent hydrodynamic volume as the unliganded PDZ region, suggesting that a conformational change occurs in the PDZ region upon binding, a conclusion supported by kinetic experiments. Using NMR, we discovered a new mode of interaction between E6 and PDZ: a subset of residues...

  17. Selecting for Fast Protein-Protein Association As Demonstrated on a Random TEM1 Yeast Library Binding BLIP.

    Science.gov (United States)

    Cohen-Khait, Ruth; Schreiber, Gideon

    2018-04-27

    Protein-protein interactions mediate the vast majority of cellular processes. Though protein interactions obey basic chemical principles also within the cell, the in vivo physiological environment may not allow for equilibrium to be reached. Thus, in vitro measured thermodynamic affinity may not provide a complete picture of protein interactions in the biological context. Binding kinetics composed of the association and dissociation rate constants are relevant and important in the cell. Therefore, changes in protein-protein interaction kinetics have a significant impact on the in vivo activity of the proteins. The common protocol for the selection of tighter binders from a mutant library selects for protein complexes with slower dissociation rate constants. Here we describe a method to specifically select for variants with faster association rate constants by using pre-equilibrium selection, starting from a large random library. Toward this end, we refine the selection conditions of a TEM1-β-lactamase library against its natural nanomolar affinity binder β-lactamase inhibitor protein (BLIP). The optimal selection conditions depend on the ligand concentration and on the incubation time. In addition, we show that a second sort of the library helps to separate signal from noise, resulting in a higher percent of faster binders in the selected library. Fast associating protein variants are of particular interest for drug development and other biotechnological applications.

  18. Kinetics Studies on citric acid production by gamma ray induced mutant of Aspergillus niger

    International Nuclear Information System (INIS)

    Begum, A.A.; Choudhury, N.; Islam, M.S.

    1991-01-01

    Effect of cultural pH and incubation temperature on citric acid yield and kinetic patterns of citric acid fermentation by a natural isolate of aspergillus niger as CA16 and one of its gamma ray induced mutants were studied using cane molasses as growth and fermentation substrate. Mutant strain, 277/30 gave maximum citric acid yield of 85 g/l at pH 3.5 and 28 degree centigrade in molasses medium adjusted to 16% sugar and 25% prescott salt in the medium. Parent strain, CA16 gave a maximum yield of 34 g/l at pH 4.0 and 26 degree centigrade in molasses medium adjusted to 16% sugar and 100% prescott salt in the medium. In kinetic studies, strains showed combination kinetics of citric acid fermentation where product formation is directly related to growth and cell mass and indirectly related to carbohydrate uptake

  19. Batch study, equilibrium and kinetics of adsorption of naphthalene using waste tyre rubber granules

    Directory of Open Access Journals (Sweden)

    Felix A. Aisien

    2014-04-01

    Full Text Available The potential use of waste tyre rubber granules (WTRG for the batch adsorption of naphthalene from aqueous solutions was investigated. The effect of various operational variables such as contact time, initial naphthalene concentration, adsorbent dose, size of adsorbent particles, and temperature of solution on the adsorption capacity of WTRG was evaluated. The adsorption of naphthalene by WTRG was a fast kinetic process with an equilibrium contact time of 60 min. A low temperature (5°C, small adsorbent particle size (0.212 mm and higher adsorbent dosage favored the adsorption process. Results of isotherm studies revealed that adsorption of naphthalene was best described by the Langmuir isotherm equation (R2=0.997 while the kinetics of the process was best described by the Lagergren pseudofirst order kinetic equation (R2=0.998. This study has demonstrated the suitability of WTRG for the removal of naphthalene from aqueous solution.

  20. Kinetic studies of ICF target dynamics with ePLAS

    Science.gov (United States)

    Mason, R. J.

    2016-10-01

    The ePLAS code was recently used1 to show that a modeling change from artificial to real viscosity can result in a decrease of the predicted performance of ICF targets. This code typically follows either fluid or PIC electrons with fluid ions in self-consistent E - and B - fields computed by the Implicit Moment Method2. For the present study the ions have instead been run as PIC particles undergoing Krook-like self-collisions. The ePLAS collision model continually redistributes the ion particle properties toward a local Maxwellian, while conserving the mean density, momentum and energy. Whereas the use of real viscosity captures large Knudsen Number effects as the active target dimensions shrink below the ion mean-free-path, the new kinetic modeling can manifest additional effects such as collisional shock precursors3 from the escape and streaming of the fastest particle ions. In 2D cylindrical geometry we will explore how such kinetic shock extensions might affect shell and core compression dynamics in ICF target implosions.

  1. Kinetic study of corn straw pyrolysis: comparison of two different three-pseudocomponent models.

    Science.gov (United States)

    Li, Zhengqi; Zhao, Wei; Meng, Baihong; Liu, Chunlong; Zhu, Qunyi; Zhao, Guangbo

    2008-11-01

    With heating rates of 20, 50 and 100 K min(-1), the thermal decomposition of corn straw samples (corn stalks skins, corn stalks cores, corn bracts and corn leaves) were studied using thermogravimetric analysis. The maximum pyrolysis rates increased with the heating rate increasing and the temperature at the peak pyrolysis rate also increased. Assuming the addition of three independent parallel reactions, corresponding to three pseudocomponents linked to the hemicellulose, cellulose and lignin, two different three-pseudocomponent models were used to simulate the corn straw pyrolysis. Model parameters of pyrolysis were given. It was found that the three-pseudocomponent model with n-order kinetics was more accurate than the model with first-order kinetics at most cases. It showed that the model with n-order kinetics was more accurate to describe the pyrolysis of the hemicellulose.

  2. A new study of the kinetics of curd production in the process of cheese manufacture.

    Science.gov (United States)

    Muñoz, Susana Vargas; Torres, Maykel González; Guerrero, Francisco Quintanilla; Talavera, Rogelio Rodríguez

    2017-11-01

    We studied the role played by temperature and rennet concentration in the coagulation process for cheese manufacture and the evaluation of their kinetics. We concluded that temperature is the main factor that determines the kinetics. The rennet concentration was unimportant probably due to the fast action of the enzyme chymosin. The Dynamic light scattering technique allowed measuring the aggregate's size and their formation kinetics. The volume fraction of solids was determined from viscosity measurements, showing profiles that are in agreement with the size profiles. The results indicate that the formation of the aggregates for rennet cheese is strongly dependent on temperature and rennet concentration. The results revealed that at 35·5 °C the volume fraction of solids has the maximum slope, indicating that at this temperature the curd is formed rapidly. The optimal temperature throughout the process was established. Second-order kinetics were obtained for the process. We observed a quadratic dependence between the rennet volume and the volume fraction of solids (curd), thereby indicating that the kinetics of the curd production should be of order two.

  3. A kinetic study of the mechanism of radiation induced agglomeration of ovalbumin in aqueous solution

    International Nuclear Information System (INIS)

    Tuce, Zorana; Janata, Eberhard; Radojcic, Marija; Milosavljevic, B.H.

    2001-01-01

    The effect of concentration on the protein radiolytic damage resulting in a change in molecular mass was measured in the concentration range from 0.2 to 2 mmolxdm -3 ovalbumin in phosphate buffered solutions saturated with N 2 O. The electrophoretic analysis of samples on discontinuous SDS-polyacrylamide gels in the presence or absence of 5% β-mercaptoethanol showed an expected result, i.e. that the protein scission did not take place in the absence of oxygen. Only ovalbumin agglomerates, bonded by covalent bonds other than S-S bridges, were observed. The G-value for the formation of ovalbumin agglomerates increased linearly from 1.1 to 2.4 by increasing the ovalbumin concentration from 0.2 to 2 mmolxdm -3 . The result is interpreted as to be owing to the competition between ovalbumin agglomeration and some intramolecular reactions which did not lead to the change in the molecular mass. It was also found that the G-value is independent of irradiation dose rate. The result was rationalized as a kinetic evidence that the agglomeration is not a cross-linking process, i.e. it does not occur via recombination of the protein radicals produced in the interaction of ovalbumin and · OH radical. The result suggested that the agglomeration takes place via the process of grafting, i.e. it occurs in the reaction of ovalbumin radical and an intact ovalbumin molecule. The time-resolved light scattering experiments provided an additional proof, supporting the reaction scheme of radiation-induced protein agglomeration. The biological consequences of the proposed mechanism of protein agglomeration are also discussed

  4. Binding kinetics of five drugs to beta2-adrenoceptor using peak profiling method and nonlinear chromatography.

    Science.gov (United States)

    Liang, Yuan; Wang, Jing; Fei, Fuhuan; Sun, Huanmei; Liu, Ting; Li, Qian; Zhao, Xinfeng; Zheng, Xiaohui

    2018-02-23

    Investigations of drug-protein interactions have advanced our knowledge of ways to design more rational drugs. In addition to extensive thermodynamic studies, ongoing works are needed to enhance the exploration of drug-protein binding kinetics. In this work, the beta2-adrenoceptor (β 2 -AR) was immobilized on N, N'-carbonyldiimidazole activated amino polystyrene microspheres to prepare an affinity column (4.6 mm × 5.0 cm, 8 μm). The β 2 -AR column was utilized to determine the binding kinetics of five drugs to the receptor. Introducing peak profiling method into this receptor chromatographic analysis, we determined the dissociation rate constants (k d ) of salbutamol, terbutaline, methoxyphenamine, isoprenaline hydrochloride and ephedrine hydrochloride to β 2 -AR to be 15 (±1), 22 (±1), 3.3 (±0.2), 2.3 (±0.2) and 2.1 (±0.1) s -1 , respectively. The employment of nonlinear chromatography (NLC) in this case exhibited the same rank order of k d values for the five drugs bound to β 2 -AR. We confirmed that both the peak profiling method and NLC were capable of routine measurement of receptor-drug binding kinetics. Compared with the peak profiling method, NLC was advantageous in the simultaneous assessment of the kinetic and apparent thermodynamic parameters. It will become a powerful method for high throughput drug-receptor interaction analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Kinetic Study on Channelling of Protons in Metallic Carbon Nanotubes

    International Nuclear Information System (INIS)

    Dan, Zhao; Yuan-Hong, Song; You-Nian, Wang

    2008-01-01

    Based on the kinetic model and the dielectric response theory, a theoretical model is put forward to describe the transport of protons along nanotube axes. With the introduction of electron band structure for different nanotubes like zigzag and armchair nanotubes of metallic properties, the collective excitation of electrons on the cylinders induced by the incident ions is studied, showing several distinct peaks in the curves of the energy loss function. Furthermore, the stopping power and the self-energy are calculated as functions of ion velocities, especially taking into account the influence of damping coefficients. It is conceivable from the results that, in the kinetic formulation, plasmon excitation plays a major role in the stopping. And as the damping increases, the peaks of the stopping power shift to the lower velocities, with the broadening of the plasmon resonance. (condensed matter: structure, mechanical and thermal properties)

  6. A chimeric LysK-lysostaphin fusion enzyme lysing Staphylococcus aureus cells: a study of both kinetics of inactivation and specifics of interaction with anionic polymers

    Science.gov (United States)

    A staphylolytic fusion protein (K-L) was created, harboring three unique lytic activities comprised of the LysK CHAP endopeptidase, and amidase domains, and the lysostaphin glycyl-glycine endopeptidase domain. To assess the potential of possible therapeutic applications, the kinetic behavior of K-L...

  7. Casein and soy protein meals differentially affect whole-body and splanchnic protein metabolism in healthy humans.

    Science.gov (United States)

    Luiking, Yvette C; Deutz, Nicolaas E P; Jäkel, Martin; Soeters, Peter B

    2005-05-01

    Dietary protein quality is considered to be dependent on the degree and velocity with which protein is digested, absorbed as amino acids, and retained in the gut as newly synthesized protein. Metabolic animal studies suggest that the quality of soy protein is inferior to that of casein protein, but confirmatory studies in humans are lacking. The study objective was to assess the quality of casein and soy protein by comparing their metabolic effects in healthy human subjects. Whole-body protein kinetics, splanchnic leucine extraction, and urea production rates were measured in the postabsorptive state and during 8-h enteral intakes of isonitrogenous [0.42 g protein/(kg body weight . 8 h)] protein-based test meals, which contained either casein (CAPM; n = 12) or soy protein (SOPM; n = 10) in 2 separate groups. Stable isotope techniques were used to study metabolic effects. With enteral food intake, protein metabolism changed from net protein breakdown to net protein synthesis. Net protein synthesis was greater in the CAPM group than in the SOPM group [52 +/- 14 and 17 +/- 14 nmol/(kg fat-free mass (FFM) . min), respectively; P CAPM (P = 0.07). Absolute splanchnic extraction of leucine was higher in the subjects that consumed CAPM [306 +/- 31 nmol/(kg FFM . min)] vs. those that consumed SOPM [235 +/- 29 nmol/(kg FFM . min); P < 0.01]. In conclusion, a significantly larger portion of soy protein is degraded to urea, whereas casein protein likely contributes to splanchnic utilization (probably protein synthesis) to a greater extent. The biological value of soy protein must be considered inferior to that of casein protein in humans.

  8. Granulocyte kinetics

    International Nuclear Information System (INIS)

    Peters, A.M.; Lavender, J.P.; Saverymuttu, S.H.

    1985-01-01

    By using density gradient materials enriched with autologous plasma, the authors have been able to isolate granulocutes from other cellular elements and label them with In-111 without separation from a plasma environment. The kinetic behavior of these cells suggests that phenomena attributed to granulocyte activation are greatly reduced by this labeling. Here, they review their study of granulocyte kinetics in health and disease in hope of quantifying sites of margination and identifying principal sites of destruction. The three principle headings of the paper are distribution, life-span, and destruction

  9. Combustion Kinetic Studies of Gasolines and Surrogates

    KAUST Repository

    Javed, Tamour

    2016-01-01

    . These measurements were performed in shock tubes and rapid compression machines over a wide range of experimental conditions (650 – 1250 K, 10 – 40 bar) relevant to internal combustion engines. Using the measured the data and chemical kinetic analyses, the surrogate

  10. Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway.

    Science.gov (United States)

    Dana, Saswati; Nakakuki, Takashi; Hatakeyama, Mariko; Kimura, Shuhei; Raha, Soumyendu

    2011-01-01

    Mutation and/or dysfunction of signaling proteins in the mitogen activated protein kinase (MAPK) signal transduction pathway are frequently observed in various kinds of human cancer. Consistent with this fact, in the present study, we experimentally observe that the epidermal growth factor (EGF) induced activation profile of MAP kinase signaling is not straightforward dose-dependent in the PC3 prostate cancer cells. To find out what parameters and reactions in the pathway are involved in this departure from the normal dose-dependency, a model-based pathway analysis is performed. The pathway is mathematically modeled with 28 rate equations yielding those many ordinary differential equations (ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations (RDE) system in which the parameters are random variables. We show that our RDE model captures the uncertainty in the kinetic rate constants as seen in the behavior of the experimental data and more importantly, upon simulation, exhibits the abnormal EGF dose-dependency of the activation profile of MAP kinase signaling in PC3 prostate cancer cells. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. The last computation identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behavior in the PC3 prostate cancer cells. The reactions in which these most sensitive parameters participate emerge as candidate drug targets on the signaling pathway. 2011 Elsevier Ireland Ltd. All rights reserved.

  11. Protein Colloidal Aggregation Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  12. Alpha Shapes and Proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Sterner, Henrik; Sterner, Peter

    2009-01-01

    We provide a unified description of (weighted) alpha shapes, beta shapes and the corresponding simplicialcomplexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha shapes and touch upon related persistence issues.We claim that the full...... potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementation....

  13. Anticariogenic and Hemolytic Activity of Selected Seed Protein Extracts In vitro conditions.

    Directory of Open Access Journals (Sweden)

    Kalpesh B Ishnava

    2014-10-01

    Full Text Available This study aimed to assess the anticariogenic and hemolytic activity of crude plant seed protein extracts against tooth decaying bacteria.The proteins from seeds of 12 different plants were extracted and used for antimicrobial assay against six different organisms. The extraction was carried out in 10mM of sodium phosphate buffer (pH 7.0. Protein concentrations were determined as described by Bradford method. Anticariogenic activity was studied by agar well diffusion method and Minimum Inhibitory Concentration (MIC was evaluated by the two-fold serial broth dilution method. Hemolytic activity, treatment of proteinase K and Kinetic study in Mimusops elengi crude seed protein extract.The anticariogenic assay demonstrated the activity of Mimusops elengi against Staphylococcus aureus and Streptococcus pyogenes. A minor activity of Glycine wightii against Streptococcus mutans was also found. The protein content of Mimusops elengi seed protein extract was 5.84mg/ml. The MIC values for Staphylococcus aureus and Streptococcus pyogenes against Mimusops elengi seed protein extract were 364.36μg/ml and 182.19μg/ml, respectively. Kinetic study further elucidated the mode of inhibition in the presence of the Mimusops elengi plant seed protein with respect to time. The concentration of crude extract which gave 50% hemolysis compared to Triton X-100 treatment (HC50 value was 1.58 mg/ml; which is more than five times larger than that of the MIC. Treatment with proteinase K of the Mimusops elengi seed protein resulted in absence of the inhibition zone; which clearly indicates that the activity was only due to protein.Our results showed the prominence of Mimusops elengi plant seed protein extract as an effective herbal medication against tooth decaying bacteria.

  14. Automated Determination of Oxygen-Dependent Enzyme Kinetics in a Tube-in-Tube Flow Reactor.

    Science.gov (United States)

    Ringborg, Rolf H; Toftgaard Pedersen, Asbjørn; Woodley, John M

    2017-09-08

    Enzyme-mediated oxidation is of particular interest to synthetic organic chemists. However, the implementation of such systems demands knowledge of enzyme kinetics. Conventionally collecting kinetic data for biocatalytic oxidations is fraught with difficulties such as low oxygen solubility in water and limited oxygen supply. Here, we present a novel method for the collection of such kinetic data using a pressurized tube-in-tube reactor, operated in the low-dispersed flow regime to generate time-series data, with minimal material consumption. Experimental development and validation of the instrument revealed not only the high degree of accuracy of the kinetic data obtained, but also the necessity of making measurements in this way to enable the accurate evaluation of high K MO enzyme systems. For the first time, this paves the way to integrate kinetic data into the protein engineering cycle.

  15. A study of kinetic friction: The Timoshenko oscillator

    Science.gov (United States)

    Henaff, Robin; Le Doudic, Gabriel; Pilette, Bertrand; Even, Catherine; Fischbach, Jean-Marie; Bouquet, Frédéric; Bobroff, Julien; Monteverde, Miguel; Marrache-Kikuchi, Claire A.

    2018-03-01

    Friction is a complex phenomenon that is of paramount importance in everyday life. We present an easy-to-build and inexpensive experiment illustrating Coulomb's law of kinetic friction. The so-called friction, or Timoshenko, oscillator consists of a plate set into periodic motion through the competition between gravity and friction on its rotating supports. The period of such an oscillator gives a measurement of the coefficient of kinetic friction μk between the plate and the supports. Our prototype is mainly composed of a motor, LEGO blocks, and a low-cost microcontroller, but despite its simplicity, the results obtained are in good agreement with values of μk found in the literature (enhanced online).

  16. Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.

    Science.gov (United States)

    Michaels, Thomas C T; Šarić, Anđela; Habchi, Johnny; Chia, Sean; Meisl, Georg; Vendruscolo, Michele; Dobson, Christopher M; Knowles, Tuomas P J

    2018-04-20

    Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.

  17. Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation

    Science.gov (United States)

    Michaels, Thomas C. T.; Šarić, Anđela; Habchi, Johnny; Chia, Sean; Meisl, Georg; Vendruscolo, Michele; Dobson, Christopher M.; Knowles, Tuomas P. J.

    2018-04-01

    Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.

  18. Kinetic Study of Denatonium Sorption to Smectite Clay Minerals.

    Science.gov (United States)

    Crosson, Garry S; Sandmann, Emily

    2013-06-01

    The denatonium cation, as a benzoate salt, is the most bitter cation known to modern society and is frequently added to consumer products to reduce accidental and intentional consumption by humans and animals. Denatonium can enter the environment by accidental discharges, potentially rendering water supplies undrinkable. Interactions of denatonium with soil components ( i.e. , smectite minerals) ultimately control the environmental fate of denatonium, but the current literature is devoid of studies that evaluate denatonium sorption to smectite minerals. This study investigated the mechanism and kinetics of denatonium sorption to smectite clay minerals as a function of smectite type, temperature, pH and ionic strength. Uptake by synthetic mica montmorillonite (Syn-1), Wyoming montmorillonite (SWy-2), and Texas montmorillonite (STx-1b) at 305K was rapid, with equilibrium being reached within 2 min for all clays. Complete removal of denatonium was observed for STx-1b at pH 6.9, while partial removal was observed for Syn-1 and SWy-2. Kinetic behavior of SWy-2 and Syn-1 is consistent with a pseudo-second-order model at 305K. An activation energy of +25.9 kJ/mol was obtained for sorption to Syn-1 and was independent of temperature between 286K and 338K. Activation-free energy (Δ G *), activation enthalpy (Δ H *), and activation entropy (Δ S *) for Syn-1 were found to be +62.91 kJ/mol, +23.36 kJ/mol, and -0.130 kJ/(K·mol), respectively. Sorption capacities at pH 3.6, 6.9, and 8.2 were constant at 1.3×10 -2 g denatonium/g clay; however, the kinetic rate constant increased by 56%, going from acidic to basic solution conditions. Distribution coefficients were negatively correlated with ionic strength, suggesting cation exchange. Collectively, results suggested that smectite minerals can serve as efficient sinks for denatonium cations. This is much-needed information for agencies developing regulations regarding denatonium usage and for water treatment professionals

  19. Facilitated diffusion in a crowded environment: from kinetics to stochastics

    International Nuclear Information System (INIS)

    Meroz, Yasmine; Klafter, Joseph; Eliazar, Iddo

    2009-01-01

    Facilitated diffusion is a fundamental search process used to describe the problem of a searcher protein finding a specific target site over a very large DNA strand. In recent years macromolecular crowding has been recognized to affect this search process. In this paper, we bridge between two different modelling methodologies of facilitated diffusion: the physics-oriented kinetic approach, which yields the reaction rate of the search process, and the probability-oriented stochastic approach, which yields the probability distribution of the search duration. We translate the former approach to the latter, ascertaining that the two approaches yield coinciding results, both with and without macromolecular crowding. We further show that the stochastic approach markedly generalizes the kinetic approach by accommodating a vast array of search mechanisms, including mechanisms having no reaction rates, and thus being beyond the realm of the kinetic approach.

  20. Characterization of ligand binding to melanocortin 4 receptors using fluorescent peptides with improved kinetic properties.

    Science.gov (United States)

    Link, Reet; Veiksina, Santa; Rinken, Ago; Kopanchuk, Sergei

    2017-03-15

    Melanocortin 4 (MC 4 ) receptors are important drug targets as they regulate energy homeostasis, eating behaviour and sexual functions. The ligand binding process to these G protein-coupled receptors is subject to considerable complexity. Different steps in the complex dynamic regulation can be characterized by ligand binding kinetics. Optimization of these kinetic parameters in terms of on-rate and residence time can increase the rapid onset of drug action and reduce off-target effects. Fluorescence anisotropy (FA) is one of the homogeneous fluorescence-based assays that enable continuous online monitoring of ligand binding kinetics. FA has been implemented for the kinetic study of melanocortin MC 4 receptors expressed on budded baculoviruses. However, the slow dissociation of the fluorescently labelled peptide NDP-α-MSH does not enable reaching equilibrium nor enable more in-depth study of the binding mechanisms. To overcome this problem, two novel red-shifted fluorescent ligands were designed. These cyclized heptapeptide derivatives (UTBC101 and UTBC102) exhibited nanomolar affinity toward melanocortin MC 4 receptors but had relatively different kinetic properties. The dissociation half-lives of UTBC101 (τ 1/2 =160min) and UTBC102 (τ 1/2 =7min) were shorter compared to that what was previously reported for Cy3B-NDP-α-MSH (τ 1/2 =224min). The significantly shorter dissociation half-life of UTBC102 enables equilibrium in screening assays, whereas the higher affinity of UTBC101 helps to resolve a wider range of competitor potencies. These two ligands are suitable for further kinetic screening of novel melanocortin MC 4 receptor specific ligands and could complement each other in these studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Kinetic studies on the degradation of crystal violet by the Fenton oxidation process.

    Science.gov (United States)

    Wu, H; Fan, M M; Li, C F; Peng, M; Sheng, L J; Pan, Q; Song, G W

    2010-01-01

    The degradation of dye crystal violet (CV) by Fenton oxidation process was investigated. The UV-Vis spectrogram has shown that CV can be degraded effectively by Fenton oxidation process. Different system variables namely initial H(2)O(2) concentration, initial Fe(2 + ) concentration and reaction temperature, which have effect on the degradation of CV by Fenton oxidation process, have been studied systematically. The degradation kinetics of CV was also elucidated based on the experimental data. The degradation of CV obeys the first-order reaction kinetics. The kinetic model can be described as k=1.5 exp(-(7.5)/(RT))[H(2)O(2)](0)(0.8718)[Fe(2+)](0)(0.5062). According to the IR spectrogram, it is concluded that the benzene ring of crystal violet has been destroyed by Fenton oxidation. The result will be useful in treating dyeing wastewater containing CV by Fenton oxidation process.

  2. Rapid kinetics of iron responsive element (IRE) RNA/iron regulatory protein 1 and IRE-RNA/eIF4F complexes respond differently to metal ions.

    Science.gov (United States)

    Khan, Mateen A; Ma, Jia; Walden, William E; Merrick, William C; Theil, Elizabeth C; Goss, Dixie J

    2014-06-01

    Metal ion binding was previously shown to destabilize IRE-RNA/IRP1 equilibria and enhanced IRE-RNA/eIF4F equilibria. In order to understand the relative importance of kinetics and stability, we now report rapid rates of protein/RNA complex assembly and dissociation for two IRE-RNAs with IRP1, and quantitatively different metal ion response kinetics that coincide with the different iron responses in vivo. kon, for FRT IRE-RNA binding to IRP1 was eight times faster than ACO2 IRE-RNA. Mn(2+) decreased kon and increased koff for IRP1 binding to both FRT and ACO2 IRE-RNA, with a larger effect for FRT IRE-RNA. In order to further understand IRE-mRNA regulation in terms of kinetics and stability, eIF4F kinetics with FRT IRE-RNA were determined. kon for eIF4F binding to FRT IRE-RNA in the absence of metal ions was 5-times slower than the IRP1 binding to FRT IRE-RNA. Mn(2+) increased the association rate for eIF4F binding to FRT IRE-RNA, so that at 50 µM Mn(2+) eIF4F bound more than 3-times faster than IRP1. IRP1/IRE-RNA complex has a much shorter life-time than the eIF4F/IRE-RNA complex, which suggests that both rate of assembly and stability of the complexes are important, and that allows this regulatory system to respond rapidly to change in cellular iron. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Kinetic Typography

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Djonov, Emilia

    2014-01-01

    After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images.......After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....

  4. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

    Science.gov (United States)

    Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

    2014-12-23

    To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

  5. A kinetic study on the conversion of glucose to levulinic acid

    NARCIS (Netherlands)

    Girisuta, B; Janssen, LPBM; Heeres, HJ

    Levulinic acid has been identified as a promising green. biomass derived platform chemical. A kinetic study oil one of the key steps in the conversion of biomass to levulinic acid, i.e., the acid catalysed decomposition of glucose to levulinic acid has been performed. The experiments were Performed

  6. Gyrocenter-gauge kinetic theory

    International Nuclear Information System (INIS)

    Qin, H.; Tang, W.M.; Lee, W.W.

    2000-01-01

    Gyrocenter-gauge kinetic theory is developed as an extension of the existing gyrokinetic theories. In essence, the formalism introduced here is a kinetic description of magnetized plasmas in the gyrocenter coordinates which is fully equivalent to the Vlasov-Maxwell system in the particle coordinates. In particular, provided the gyroradius is smaller than the scale-length of the magnetic field, it can treat high frequency range as well as the usual low frequency range normally associated with gyrokinetic approaches. A significant advantage of this formalism is that it enables the direct particle-in-cell simulations of compressional Alfven waves for MHD applications and of RF waves relevant to plasma heating in space and laboratory plasmas. The gyrocenter-gauge kinetic susceptibility for arbitrary wavelength and arbitrary frequency electromagnetic perturbations in a homogeneous magnetized plasma is shown to recover exactly the classical result obtained by integrating the Vlasov-Maxwell system in the particle coordinates. This demonstrates that all the waves supported by the Vlasov-Maxwell system can be studied using the gyrocenter-gauge kinetic model in the gyrocenter coordinates. This theoretical approach is so named to distinguish it from the existing gyrokinetic theory, which has been successfully developed and applied to many important low-frequency and long parallel wavelength problems, where the conventional meaning of gyrokinetic has been standardized. Besides the usual gyrokinetic distribution function, the gyrocenter-gauge kinetic theory emphasizes as well the gyrocenter-gauge distribution function, which sometimes contains all the physics of the problems being studied, and whose importance has not been realized previously. The gyrocenter-gauge distribution function enters Maxwell's equations through the pull-back transformation of the gyrocenter transformation, which depends on the perturbed fields. The efficacy of the gyrocenter-gauge kinetic approach is

  7. PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics.

    Science.gov (United States)

    Jemimah, Sherlyn; Yugandhar, K; Michael Gromiha, M

    2017-09-01

    We have developed PROXiMATE, a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and functional information, experimental conditions and literature information. Additional features include complex structure visualization, search and display options, download options and a provision for users to upload their data. The database is freely available at http://www.iitm.ac.in/bioinfo/PROXiMATE/ . The website is implemented in Python, and supports recent versions of major browsers such as IE10, Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  8. Study on the Hydrolysis Kinetics of Xylan on Different Acid Catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Na, Byeong-Il; Lee, Jae-Won [Chonnam National University, Gwangju (Korea, Republic of)

    2014-04-15

    In this study, we investigated kinetic model for the acid-catalyzed xylan hydrolysis at temperature 120-150 .deg. C. Also, we analyzed the kinetic parameters for xylose production and furfural decomposition. The hydrolysis of xylan and the degradation of xylose were promoted by high reaction temperature and acid concentration. The optimal hydrolysis condition for the highest reaction rate constants (k{sub 1}) was different depending on the acid catalysts. Among sulfuric, oxalic and maleic acid, the xylan reaction rate constants (k{sub 1}) to xylose had the highest value of 0.0241 min{sup -1} when 100 mM sulfuric acid was used at 120 .deg. C. However, sulfuric acid induced more xylose degradation compared to oxalic and maleic acid hydrolysis. The activation energy for xylan degradation was the highest when sulfuric acid was used.

  9. Isotherm, kinetic, and thermodynamic study of ciprofloxacin sorption on sediments.

    Science.gov (United States)

    Mutavdžić Pavlović, Dragana; Ćurković, Lidija; Grčić, Ivana; Šimić, Iva; Župan, Josip

    2017-04-01

    In this study, equilibrium isotherms, kinetics and thermodynamics of ciprofloxacin on seven sediments in a batch sorption process were examined. The effects of contact time, initial ciprofloxacin concentration, temperature and ionic strength on the sorption process were studied. The K d parameter from linear sorption model was determined by linear regression analysis, while the Freundlich and Dubinin-Radushkevich (D-R) sorption models were applied to describe the equilibrium isotherms by linear and nonlinear methods. The estimated K d values varied from 171 to 37,347 mL/g. The obtained values of E (free energy estimated from D-R isotherm model) were between 3.51 and 8.64 kJ/mol, which indicated a physical nature of ciprofloxacin sorption on studied sediments. According to obtained n values as measure of intensity of sorption estimate from Freundlich isotherm model (from 0.69 to 1.442), ciprofloxacin sorption on sediments can be categorized from poor to moderately difficult sorption characteristics. Kinetics data were best fitted by the pseudo-second-order model (R 2  > 0.999). Thermodynamic parameters including the Gibbs free energy (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) were calculated to estimate the nature of ciprofloxacin sorption. Results suggested that sorption on sediments was a spontaneous exothermic process.

  10. Kinetics of Anti-Phlebotomus perniciosus Saliva Antibodies in Experimentally Bitten Mice and Rabbits.

    Directory of Open Access Journals (Sweden)

    Inés Martín-Martín

    Full Text Available Sand flies are hematophagous arthropods that act as vectors of Leishmania parasites. When hosts are bitten they develop cellular and humoral responses against sand fly saliva. A positive correlation has been observed between the number of bites and antibody levels indicating that anti-saliva antibody response can be used as marker of exposure to sand flies. Little is known about kinetics of antibodies against Phlebotomus perniciosus salivary gland homogenate (SGH or recombinant salivary proteins (rSP. This work focused on the study of anti-P. perniciosus saliva antibodies in sera of mice and rabbits that were experimentally exposed to the bites of uninfected sand flies.Anti-saliva antibodies were evaluated by ELISA and Western blot. In addition, antibody levels against two P. perniciosus rSP, apyrase rSP01B and D7 related protein rSP04 were determined in mice sera. Anti-saliva antibody levels increased along the immunizations and correlated with the number of sand fly bites. Anti-SGH antibody levels were detected in sera of mice five weeks after exposure, and persisted for at least three months. Anti-apyrase rSP01B antibodies followed similar kinetic responses than anti-SGH antibodies while rSP04 showed a delayed response and exhibited a greater variability among sera of immunized mice. In rabbits, anti-saliva antibodies appeared after the second week of exposure and IgG antibodies persisted at high levels, even 7 months post-exposure.Our results contributed to increase the knowledge on the type of immune response P. perniciosus saliva and individual proteins elicited highlighting the use of rSP01B as an epidemiological marker of exposure. Anti-saliva kinetics in sera of experimentally bitten rabbits were studied for the first time. Results with rabbit model provided useful information for a better understanding of the anti-saliva antibody levels found in wild leporids in the human leishmaniasis focus in the Madrid region, Spain.

  11. NMR Studies of Protein Hydration and Protein-Ligand Interactions

    Science.gov (United States)

    Chong, Yuan

    Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

  12. Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

    International Nuclear Information System (INIS)

    Welzel, S; Rousseau, A; Davies, P B; Roepcke, J

    2007-01-01

    Within the last decade mid infrared absorption spectroscopy between 3 and 20 μm, known as Infrared Laser Absorption Spectroscopy (IRLAS) and based on tuneable semiconductor lasers, namely lead salt diode lasers, often called tuneable diode lasers (TDL), and quantum cascade lasers (QCL) has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, organo-silicon and boron compounds has lead to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present article is threefold: (i) to review recent achievements in our understanding of molecular phenomena in plasmas (ii) to report on selected studies of the spectroscopic properties and kinetic behaviour of radicals, and (iii) to describe the current status of advanced instrumentation for TDLAS in the mid infrared

  13. Differences in postprandial protein handling after beef compared with milk ingestion during postexercise recovery: a randomized controlled trial.

    Science.gov (United States)

    Burd, Nicholas A; Gorissen, Stefan H; van Vliet, Stephan; Snijders, Tim; van Loon, Luc Jc

    2015-10-01

    Protein consumed after resistance exercise increases postexercise muscle protein synthesis rates. To date, dairy protein has been studied extensively, with little known about the capacity of other protein-dense foods to augment postexercise muscle protein synthesis rates. We aimed to compare protein digestion and absorption kinetics, postprandial amino acid availability, anabolic signaling, and the subsequent myofibrillar protein synthetic response after the ingestion of milk compared with beef during recovery from resistance-type exercise. In crossover trials, 12 healthy young men performed a single bout of resistance exercise. Immediately after cessation of exercise, participants ingested 30 g protein by consuming isonitrogenous amounts of intrinsically l-[1-(13)C]phenylalanine-labeled beef or milk. Blood and muscle biopsy samples were collected at rest and after exercise during primed continuous infusions of l-[ring-(2)H5]phenylalanine and l-[ring-3,5-(2)H2]tyrosine to assess protein digestion and absorption kinetics, plasma amino acid availability, anabolic signaling, and subsequent myofibrillar protein synthesis rates in vivo in young men. Beef protein-derived phenylalanine appeared more rapidly in circulation compared with milk ingestion (P Nutrition.

  14. Equilibrium, kinetic and thermodynamic studies of adsorption of Th(IV) from aqueous solution onto kaolin

    International Nuclear Information System (INIS)

    Hongxia Zhang; Zhiwei Niu; Zhi Liu; Zhaodong Wen; Weiping Li; Xiaoyun Wang; Wangsuo Wu

    2015-01-01

    The kinetics and thermodynamics of the adsorption of Th(IV) on the kaolin were studied by using batch method. In addition, the experimental data were studied by dynamic and thermodynamic models. The results showed that the adsorption capacity of the adsorbent increased with increasing temperature and solid liquid ratio, but decreased with increasing initial Th(IV) ion concentration, and the best fit was obtained for the pseudo-second-order kinetics model. The calculated activation energy for adsorption was about 45 kJ/mol, which indicated the adsorption process to be chemisorption. The adsorption isotherm data could be well described by the Langmuir as well as Dubinin-Radushkevich model. The mean free energy (E) of adsorption was calculated to be about 15 kJ/mol. The thermodynamic data calculated showed that the adsorption was spontaneous and enhanced at higher temperature. Considering kinetics and equilibrium studies, the adsorption on the sites was the rate-limiting step and that adsorption was mainly a chemisorption process through cation exchange. (author)

  15. Powder X-ray diffraction studies of structural and kinetic aspects of polymorphism

    International Nuclear Information System (INIS)

    Chan, F.C.

    1999-01-01

    Polymorphism is a poorly understood phenomenon that is of considerable technological interest to the pharmaceutical industry. The polymorph selected can influence the bioavailability, processing and stability of the pharmaceutical dosage form. In this study structural, kinetic and thermodynamics aspects of polymorphism and polymorphic phase transformations have been examined using powder X-ray diffraction (PXRD). The compound sulphathiazole is a well-studied model in the investigation of polymorphism and crystal growth. There are five known polymorphic forms and the structure of form V was unknown until this study. The difficulty has been that it has not been possibly to prepare crystals of appropriate size and quality for single crystal diffraction. Furthermore, structure solution from powder data for organic molecules is almost impossible. Despite the challenge the structure of sulphathiazole form V have been solved ab initio from powder data using direct methods. With 16 non-hydrogen atoms in the molecule and two molecules in the asymmetric unit, this structure represents a significant advance in terms of the complexity of an organic structure solved from PXRD data. The structural data should be invaluable for rationalizing experimental observations and the development of theoretical ideas regarding polymorphism and crystal growth. The second part of the study, has examined kinetics of polymorphic phase transformations as a function of pressure combined with temperature using real-time synchrotron PXRD. The significance of pressure arises from the fact that phase transitions can be induced in pharmaceuticals during tabletting. The phase transformation behaviour of rubidium iodide (chosen as a simple test model) has been investigated as a function of isobaric pressure at ambient and elevated temperatures. The kinetics have been characterized by using the Johnson-Melil-Avrami equation. The effect of successive cycling across the transition pressure was also

  16. Fouling kinetics in microfiltration of protein solutions using different membrane configurations

    DEFF Research Database (Denmark)

    Jakobsen, Sune; Jonsson, Gunnar Eigil

    1997-01-01

    Protein fouling in microfiltration has a large impact on the permeate flux and observed retention of the proteins despite the fact that the protein molecule is several times smaller than the average pore size in microfiltration membranes. This is due to adsorption and deposition of protein...... molecules and aggregates. The effect of membrane configuration upon protein fouling was investigated in crossflow filtration with asymmetric membranes either in a normal mode or in a reverse mode. It was observed by Jonsson et al. [1] that beer filtration in a reverse mode results in a smaller decrease...... in the flux compared to beer filtration in a normal mode. Similar results for protein filtration were observed by Bowen et al. [2]. One possible way to avoid fouling is the novel backshock technique (see Jonsson et al. [1]). The effect of backshock on protein filtration was investigated using a hollow fiber...

  17. Pleural liquid and kinetic friction coefficient of mesothelium after mechanical ventilation.

    Science.gov (United States)

    Bodega, Francesca; Sironi, Chiara; Porta, Cristina; Zocchi, Luciano; Agostoni, Emilio

    2015-01-15

    Volume and protein concentration of pleural liquid in anesthetized rabbits after 1 or 3h of mechanical ventilation, with alveolar pressure equal to atmospheric at end expiration, were compared to those occurring after spontaneous breathing. Moreover, coefficient of kinetic friction between samples of visceral and parietal pleura, obtained after spontaneous or mechanical ventilation, sliding in vitro at physiological velocity under physiological load, was determined. Volume of pleural liquid after mechanical ventilation was similar to that previously found during spontaneous ventilation. This finding is contrary to expectation of Moriondo et al. (2005), based on measurement of lymphatic and interstitial pressure. Protein concentration of pleural liquid after mechanical ventilation was also similar to that occurring after spontaneous ventilation. Coefficient of kinetic friction after mechanical ventilation was 0.023±0.001, similar to that obtained after spontaneous breathing. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Study of the dissolution velocity of dispersed solid particles. Development of a calculation method for analyzing the kinetic curves. Extension to the study of composed kinetics

    International Nuclear Information System (INIS)

    Jorda, Michel.

    1976-01-01

    The dissolution of a solid in an aqueous phase is studied, the solid consisting of dispersed particles. A continuous colorimetric analysis method is developed to study the dissolution process and a two-parameter optimization method is established to investigate the kinetic curves obtained. This method is based on the differential equation dx/dt=K(1-x)sup(n). (n being the decrease in the dissolution velocity when the dissolved part increases and K a velocity parameter). The dissolution of SO 4 Cu and MnO 4 K in water and UO 3 in SO 4 H 2 is discussed. It is shown that the dissolution velocity of UO 3 is proportional to the concentration of the H + ions in the solution as far as this one is not higher than 0.25N. The study of the temperature dependence of the UO 3 dissolution reaction shows that a transition phase takes place from 25 to 65 0 C between a phase in which the dissolution is controlled by the diffusion of the H + ions and the chemical reaction at the interface and a phase in which the kinetics is only controlled by the diffusion [fr

  19. A Study of the Optimal Model of the Flotation Kinetics of Copper Slag from Copper Mine BOR

    Science.gov (United States)

    Stanojlović, Rodoljub D.; Sokolović, Jovica M.

    2014-10-01

    In this study the effect of mixtures of copper slag and flotation tailings from copper mine Bor, Serbia on the flotation results of copper recovery and flotation kinetics parameters in a batch flotation cell has been investigated. By simultaneous adding old flotation tailings in the ball mill at the rate of 9%, it is possible to increase copper recovery for about 20%. These results are compared with obtained copper recovery of pure copper slag. The results of batch flotation test were fitted by MatLab software for modeling the first-order flotation kinetics in order to determine kinetics parameters and define an optimal model of the flotation kinetics. Six kinetic models are tested on the batch flotation copper recovery against flotation time. All models showed good correlation, however the modified Kelsall model provided the best fit.

  20. Electrochemistry of metalloproteins: protein film electrochemistry for the study of E. coli [NiFe]-hydrogenase-1.

    Science.gov (United States)

    Evans, Rhiannon M; Armstrong, Fraser A

    2014-01-01

    Protein film electrochemistry is a technique which allows the direct control of redox-active enzymes, providing particularly detailed information on their catalytic properties. The enzyme is deposited onto a working electrode tip, and through control of the applied potential the enzyme activity is monitored as electrical current, allowing for direct study of inherent activity as electrons are transferred to and from the enzyme redox center(s). No mediators are used. Because the only enzyme present in the experiment is bound at the electrode surface, gaseous and liquid phase inhibitors can be introduced and removed whilst the enzyme remains in situ. Potential control means that kinetics and thermodynamics are explored simultaneously; the kinetics of a reaction can be studied as a function of potential. Steady-state catalytic rates are observed directly as current (for a given potential) and non-steady-state rates (such as interconversions between different forms of the enzyme) are observed from the change in current with time. The more active the enzyme, the higher the current and the better the signal-to-noise. In this chapter we outline the practical aspects of PFE for studying electroactive enzymes, using the Escherichia coli [NiFe]-hydrogenase 1 (Hyd-1) as an example.

  1. Modularity in protein structures: study on all-alpha proteins.

    Science.gov (United States)

    Khan, Taushif; Ghosh, Indira

    2015-01-01

    Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

  2. Kinetic parameters from thermogravimetric analysis

    Science.gov (United States)

    Kiefer, Richard L.

    1993-01-01

    High performance polymeric materials are finding increased use in aerospace applications. Proposed high speed aircraft will require materials to withstand high temperatures in an oxidative atmosphere for long periods of time. It is essential that accurate estimates be made of the performance of these materials at the given conditions of temperature and time. Temperatures of 350 F (177 C) and times of 60,000 to 100,000 hours are anticipated. In order to survey a large number of high performance polymeric materials on a reasonable time scale, some form of accelerated testing must be performed. A knowledge of the rate of a process can be used to predict the lifetime of that process. Thermogravimetric analysis (TGA) has frequently been used to determine kinetic information for degradation reactions in polymeric materials. Flynn and Wall studied a number of methods for using TGA experiments to determine kinetic information in polymer reactions. Kinetic parameters, such as the apparent activation energy and the frequency factor, can be determined in such experiments. Recently, researchers at the McDonnell Douglas Research Laboratory suggested that a graph of the logarithm of the frequency factor against the apparent activation energy can be used to predict long-term thermo-oxidative stability for polymeric materials. Such a graph has been called a kinetic map. In this study, thermogravimetric analyses were performed in air to study the thermo-oxidative degradation of several high performance polymers and to plot their kinetic parameters on a kinetic map.

  3. Effects of multi-frequency power ultrasound on the enzymolysis of corn gluten meal: Kinetics and thermodynamics study.

    Science.gov (United States)

    Jin, Jian; Ma, Haile; Qu, Wenjuan; Wang, Kai; Zhou, Cunshan; He, Ronghai; Luo, Lin; Owusu, John

    2015-11-01

    The effects of multi-frequency power ultrasound (MPU) pretreatment on the kinetics and thermodynamics of corn gluten meal (CGM) were investigated in this research. The apparent constant (KM), apparent break-down rate constant (kA), reaction rate constants (k), energy of activation (Ea), enthalpy of activation (ΔH), entropy of activation (ΔS) and Gibbs free energy of activation (ΔG) were determined by means of the Michaelis-Menten equation, first-order kinetics model, Arrhenius equation and transition state theory, respectively. The results showed that MPU pretreatment can accelerate the enzymolysis of CGM under different enzymolysis conditions, viz. substrate concentration, enzyme concentration, pH, and temperature. Kinetics analysis revealed that MPU pretreatment decreased the KM value by 26.1% and increased the kA value by 7.3%, indicating ultrasound pretreatment increased the affinity between enzyme and substrate. In addition, the values of k for ultrasound pretreatment were increased by 84.8%, 41.9%, 28.9%, and 18.8% at the temperature of 293, 303, 313 and 323 K, respectively. For the thermodynamic parameters, ultrasound decreased Ea, ΔH and ΔS by 23.0%, 24.3% and 25.3%, respectively, but ultrasound had little change in ΔG value in the temperature range of 293-323 K. In conclusion, MPU pretreatment could remarkably enhance the enzymolysis of CGM, and this method can be applied to protein proteolysis industry to produce peptides. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. A note on the use of ellipsometry for studying the kinetics of ...

    Indian Academy of Sciences (India)

    Unknown

    encountered in organic monolayer films, as would occur for example in ... dology advanced is applied to the kinetics of formation of a self-assembled monolayer of a well-studied ... Colvin et al 1992), this aspect of research assumes greater.

  5. Stopped-flow kinetic studies of poly(amidoamine) dendrimer-calf thymus DNA to form dendriplexes.

    Science.gov (United States)

    Dey, Debabrata; Kumar, Santosh; Maiti, Souvik; Dhara, Dibakar

    2013-11-07

    Poly(amidoamine) (PAMAM) dendrimers are known to be highly efficient nonviral carriers in gene delivery. Dendrimer-mediated transfection is known to be a function of the dendrimer to DNA charge ratio as well as the size of the dendrimer. In the present study, the binding kinetics of four PAMAM dendrimers (G1, G2, G3, and G4) with calf thymus DNA (CT-DNA) has been studied using stopped-flow fluorescence spectroscopy. The effect of dendrimer-to-DNA charge ratio and dendrimer generation on the binding kinetics was investigated. In most cases, the results of dendrimer-CT-DNA binding can be explained by a two-step reaction mechanism: a rapid electrostatic binding between the dendrimer and DNA, followed by a conformational change of the dendrimer-DNA complex that ultimately leads to DNA condensation. It was observed that the charge ratio on the dendrimer and the DNA phosphate groups, as well as the dendrimer generation (size), has a marked effect on the kinetics of binding between the DNA and the dendrimers. The rate constant (k'1) of the first step was much higher compared to that of the second step (k'2), and both were found to increase with an increase in dendrimer concentration. Among the four generations of dendrimers, G4 exhibited significantly faster binding kinetics compared to the three smaller generation dendrimers.

  6. In vitro characterization of luseogliflozin, a potent and competitive sodium glucose co-transporter 2 inhibitor: Inhibition kinetics and binding studies

    Directory of Open Access Journals (Sweden)

    Saeko Uchida

    2015-05-01

    Full Text Available In this study, we evaluated an inhibition model of luseogliflozin on sodium glucose co-transporter 2 (SGLT2. We also analyzed the binding kinetics of the drug to SGLT2 protein using [3H]-luseogliflozin. Luseogliflozin competitively inhibited human SGLT2 (hSGLT2-mediated glucose uptake with a Ki value of 1.10 nM. In the absence of glucose, [3H]-luseogliflozin exhibited a high affinity for hSGLT2 with a Kd value of 1.3 nM. The dissociation half-time was 7 h, suggesting that luseogliflozin dissociates rather slowly from hSGLT2. These profiles of luseogliflozin might contribute to the long duration of action of this drug.

  7. A study of the static to kinetic friction transition of polymers

    OpenAIRE

    Lee, Edward Chungjen

    1995-01-01

    This study investigates the transition from static to kinetic friction for structural polymers and continues previous research conducted by Dr. N. S. Eiss, B. McCann, and R. Molique. A new test apparatus which simultaneously measures friction, normal load, and relative velocity was developed to study this transition. The polymers used in this study were nylon, ABS, polycarbonate, and fiberglass filled and unfilled polypropylene. Creep effects of polymers on the static coefficie...

  8. Kinetics of concentration decay of specific organic matter in UASB reactors operating with and without return of aerobic sludge.

    Science.gov (United States)

    Pontes, P P; Chernicharo, C A L; Von Sperling, M

    2014-08-01

    This study aimed at assessing the influence of the return of excess aerobic sludge from a trickling filter (TF) upon the anaerobic digestion process in an upflow anaerobic sludge blanket (UASB) reactor, by evaluating its effect on the kinetics of the decay of specific organic matter (carbohydrates, proteins and lipids), as well as on the concentrations of volatile fatty acids in the UASB reactor. A pilot-scale UASB/TF system was used to perform the experiments, operating with (phase 2) and without (phase 1) excess sludge return from the TF to the UASB reactor. Sampling was carried out at different heights of the UASB reactor (0, 25, 125 and 225-cm height), and profile concentrations were determined for the following parameters: carbohydrates, proteins, lipids and volatile fatty acids. First-order kinetics showed the best fit to the decay of concentrations of carbohydrates, proteins, lipids and chemical oxygen demand (COD) in the UASB reactor. The parameters showing the best fit to the first-order kinetics were proteins and COD, during the sludge return phase. The occurrence of higher apparent reaction constants was further observed during the sludge return phase. For an influent COD concentration of 600 mg L-1 and hydraulic retention times of 2.1, 2.6 and 3.0 h in phase 1, the effluent COD concentrations were 125.3, 88.4 and 62.4 mg L-1, respectively, whereas in phase 2, the effluent COD concentrations were 75.5, 47.6 and 30.1 mg L-1, respectively.

  9. Kinetic study of nucleation and crystal growth during oxalic precipitation in the nuclear industry

    International Nuclear Information System (INIS)

    Andrieu, Murielle

    1999-01-01

    In spite of an extensive use in chemical industry, most of precipitation processes are based on global and empirical knowledge. However, in the recent years, fundamental and phenomenological theories have been developed and they can be used to better understand the mechanisms of precipitation of plutonium IV oxalate, which is a significant stage of the irradiated fuel reprocessing. For this reason, appropriate methods were developed to study nucleation and crystal growth kinetics in a nuclear environment under a wide range of operating conditions. Each phenomena was studied individually in order to reduce the free parameters of the System. This study bears on the oxalates of plutonium and elements which simulate plutonium behaviour during the precipitation, neodymium III and uranium IV. A compact apparatus of a specific construction was used for nucleation measurements in accordance with the Nielsen's method. The state of the mixing was characterised at the reactor scale (macro-mixing) and at molecular scale (micro-mixing). The experimental results for the studied oxalates are in good agreement with the Volmer and Weber's theory. We propose primary nucleation kinetic laws over a wide range of operating conditions (temperature, non-stoichiometric conditions, acidity...). An original method, using a high seed charge, was developed for the determination of crystal growth kinetics, in a batch crystallizer. The crystal growth rate is first order with respect to the supersaturation and the kinetic constant follows an Arrhenius type relation with activation energies of 14, 29 and 36 kJ.mol -1 for respectively neodymium III, uranium IV and plutonium IV oxalates. The overall growth process is surface integration controlled, with a screw dislocation mechanism. [fr

  10. Exploring the interaction of silver nanoparticles with pepsin and its adsorption isotherms and kinetics.

    Science.gov (United States)

    Li, Xiangrong; Wang, Kaiwei; Peng, Yanru

    2018-04-25

    The interaction of nanoparticles (NPs) with proteins is a topic of high relevance for the medical application of nanomaterials. In the study, a comprehensive investigation was performed for the binding properties of silver nanoparticles (AgNPs) to pepsin. The results indicate that the binding of AgNPs to pepsin may be a static quenching mechanism. Thermodynamic analysis reveals that AgNPs binds to pepsin is synergistically driven by enthalpy and entropy, and the major driving forces are hydrophobic and electrostatic interactions. Synchronous fluorescence spectroscopy shows that AgNPs may induce microenvironmental changes of pepsin. The hydrophobicity of Trp is increased while the hydrophility of Tyr is increased. The adsorption of pepsin on AgNPs was analyzed by Langmuir and Freundlich models, suggesting that the equilibrium adsorption data fit well with Freundlich model. The equilibrium adsorption data were modeled using the pseudo-first-order and pseudo-second-order kinetic equations. The results indicate that pseudo-second-order kinetic equation better describes the adsorption kinetics. The study provides an accurate and full basic data for clarifying the binding mechanism, adsorption isotherms and kinetic behaviors of AgNPs with pepsin. These fundamental works will provide some new insights into the safe and effective application of AgNPs in biological and medical areas. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Revisiting the description of Protein-Protein interfaces. Part II: Experimental study

    OpenAIRE

    Cazals , Frédéric; Proust , Flavien

    2006-01-01

    This paper provides a detailed experimental study of an interface model developed in the companion article F. Cazals and F. Proust, Revisiting the description of Protein-Protein interfaces. Part I: algorithms. Our experimental study is concerned with the usual database of protein-protein complexes, split into five families (Proteases, Immune system, Enzyme Complexes, Signal transduction, Misc.) Our findings, which bear some contradictions with usual statements are the following: (i)Connectivi...

  12. High-temperature dehydration of talc: a kinetics study using in situ X-ray powder diffraction

    Science.gov (United States)

    Wang, Duojun; Yi, Li; Huang, Bojin; Liu, Chuanjiang

    2015-06-01

    High-temperature in situ X-ray powder diffraction patterns were used to study the dehydration kinetics of natural talc with a size of 10-15 µm. The talc was annealed from 1073 to 1223 K, and the variations in the characteristic peaks corresponding to talc with the time were recorded to determine the reaction progress. The decomposition of talc occurred, and peaks corresponding to talc and peaks corresponding to enstatite and quartz were observed. The enstatite and talc exhibited a topotactic relationship. The dehydration kinetics of talc was studied as a function of temperature between 1073 and 1223 K. The kinetics data could be modeled using an Avrami equation that considers nucleation and growth processes ? where n varies from 0.4 to 0.8. The rate constant (k) equation for the natural talc is ? The reaction mechanism for the dehydration of talc is a heterogeneous nucleation and growth mechanism.

  13. Novel synthetic approach to the prion protein: Kinetic study optimization of a native chemical ligation

    Czech Academy of Sciences Publication Activity Database

    Zawada, Zbigniew; Šebestík, Jaroslav; Bouř, Petr; Hlaváček, Jan; Stibor, Ivan

    2008-01-01

    Roč. 14, č. 8 (2008), s. 76-77 ISSN 1075-2617. [European Peptide Symposium /30./. 31.08.2008-05.09.2008, Helsinki] R&D Projects: GA ČR GA203/07/1517 Institutional research plan: CEZ:AV0Z40550506 Keywords : prion protein * neurodegenerative diseases * chemical synthesis * ligation conditions Subject RIV: CC - Organic Chemistry

  14. Tunneling Kinetics and Nonadiabatic Proton-Coupled Electron Transfer in Proteins: The Effect of Electric Fields and Anharmonic Donor-Acceptor Interactions.

    Science.gov (United States)

    Salna, Bridget; Benabbas, Abdelkrim; Russo, Douglas; Champion, Paul M

    2017-07-20

    A proper description of proton donor-acceptor (D-A) distance fluctuations is crucial for understanding tunneling in proton-coupled electron transport (PCET). The typical harmonic approximation for the D-A potential results in a Gaussian probability distribution, which does not appropriately reflect the electronic repulsion forces that increase the energetic cost of sampling shorter D-A distances. Because these shorter distances are the primary channel for thermally activated tunneling, the analysis of tunneling kinetics depends sensitively on the inherently anharmonic nature of the D-A interaction. Thus, we have used quantum chemical calculations to account for the D-A interaction and developed an improved model for the analysis of experimental tunneling kinetics. Strong internal electric fields are also considered and found to contribute significantly to the compressive forces when the D-A distance distribution is positioned below the van der Waals contact distance. This model is applied to recent experiments on the wild type (WT) and a double mutant (DM) of soybean lipoxygenase-1 (SLO). The compressive force necessary to prepare the tunneling-active distribution in WT SLO is found to fall in the ∼ nN range, which greatly exceeds the measured values of molecular motor and protein unfolding forces. This indicates that ∼60-100 MV/cm electric fields, aligned along the D-A bond axis, must be generated by an enzyme conformational interconversion that facilitates the PCET tunneling reaction. Based on the absolute value of the measured tunneling rate, and using previously calculated values of the electronic matrix element, the population of this tunneling-active conformation is found to lie in the range 10 -5 -10 -7 , indicating this is a rare structural fluctuation that falls well below the detection threshold of recent ENDOR experiments. Additional analysis of the DM tunneling kinetics leads to a proposal that a disordered (high entropy) conformation could be

  15. Kinetic study of carbon dioxide absorption into glycine promoted diethanolamine (DEA)

    Science.gov (United States)

    Pudjiastuti, Lily; Susianto, Altway, Ali; IC, Maria Hestia; Arsi, Kartika

    2015-12-01

    In industry, especially petrochemical, oil and natural gas industry, required separation process of CO2 gas which is a corrosive gas (acid gas). This characteristic can damage the plant utility and piping systems as well as reducing the caloric value of natural gas. Corrosive characteristic of CO2 will appear in areas where there is a decrease in temperature and pressure, such as at the elbow pipe, tubing, cooler and injector turbine. From disadvantages as described above, then it is important to do separation process in the CO2 gas stream, one of the method for remove CO2 from the gas stream is reactive absorption using alkanolamine based solution with promotor. Therefore, this study is done to determine the kinetics constant of CO2 absorption in diethanolamine (DEA) solution using a glycine promoter. Glycine is chosen as a promoter because glycine is a primary amine compound which is reactive, moreover, glycine has resistance to high temperatures so it will not easy to degradable and suitable for application in industry. The method used in this study is absorption using laboratory scale wetted wall column equipment at atmospheric of pressure. This study will to provide the reaction kinetics data information in order to optimize the separation process of CO2 in the industrialized world. The experimental results show that rising temperatures from 303,15 - 328,15 K and the increase of concentration of glycine from 1% - 3% weight will increase the absorption rate of carbon dioxide in DEA promoted with glycine by 24,2% and 59,764% respectively, also the reaction kinetic constant is 1.419 × 1012 exp (-3634/T) (m3/kmol.s). This result show that the addition of glycine as a promoter can increase absorption rate of carbon dioxide in diethanolamine solution and cover the weaknesses of diethanolamine solution.

  16. Towards accurate free energy calculations in ligand protein-binding studies.

    Science.gov (United States)

    Steinbrecher, Thomas; Labahn, Andreas

    2010-01-01

    Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties of biomolecule binding, would be invaluable in the study of biological systems. In addition, as the mode of action of many pharmaceuticals is based upon their inhibition or activation of biomolecule targets, predictive models of small molecule receptor binding are very helpful tools in rational drug design. Since the goal here is normally to design a new compound with a high inhibition strength, one of the most important thermodynamic properties is the binding free energy DeltaG(0). The prediction of binding constants has always been one of the major goals in the field of computational chemistry, because the ability to reliably assess a hypothetical compound's binding properties without having to synthesize it first would save a tremendous amount of work. The different approaches to this question range from fast and simple empirical descriptor methods to elaborate simulation protocols aimed at putting the computation of free energies onto a solid foundation of statistical thermodynamics. While the later methods are still not suited for the screenings of thousands of compounds that are routinely performed in computational drug design studies, they are increasingly put to use for the detailed study of protein ligand interactions. This review will focus on molecular mechanics force field based free energy calculations and their application to the study of protein ligand interactions. After a brief overview of other popular methods for the calculation of free energies, we will describe recent advances in methodology and a variety of exemplary studies of molecular dynamics

  17. Ultrasound Pretreatment as an Useful Tool to Enhance Egg White Protein Hydrolysis: Kinetics, Reaction Model, and Thermodinamics.

    Science.gov (United States)

    Jovanović, Jelena R; Stefanović, Andrea B; Šekuljica, Nataša Ž; Tanasković, Sonja M Jakovetić; Dojčinović, Marina B; Bugarski, Branko M; Knežević-Jugović, Zorica D

    2016-09-28

    The impact of ultrasound waves generated by probe-type sonicator and ultrasound cleaning bath on egg white protein susceptibility to hydrolysis by alcalase compared to both thermal pretreatment and conventional enzymatic hydrolysis was quantitatively investigated. A series of hydrolytic reactions was carried out in a stirred tank reactor at different substrate concentrations, enzyme concentrations, and temperatures using untreated, and pretreated egg white proteins (EWPs). The kinetic model based on substrate inhibition and second-order enzyme deactivation successfully predicts the experimental behavior providing an effective tool for comparison and optimization. The ultrasound pretreatments appear to greatly improve the enzymatic hydrolysis of EWPs under different conditions when compare to other methods. The apparent reaction rate constants for proteolysis (k 2 ) are 0.009, 0.011, 0.053, and 0.045 min -1 for untreated EWPs, and those pretreated with heat, probe-type sonicator, and ultrasound cleaning bath technologies, respectively. The ultrasound pretreatment also decreases hydrolysis activation (E a ) and enzyme deactivation (E d ) energy, enthalpy (ΔH), and entropy (ΔS) of activation and for the probe-type sonication this decrease is 61.7%, 61.6%, 63.6%, and 32.2%, respectively, but ultrasound has little change in Gibbs free energy value in the temperature range of 318 to 338 K. The content of sulfhydryl groups and ζ potential show a significant increase (P < 0.05) for both applied ultrasound pretreatments and the reduction of particle size distribution are achieved, providing some evidence that the ultrasound causes EWP structural changes affecting the proteolysis rate. © 2016 Institute of Food Technologists®

  18. Domain-growth kinetics and aspects of pinning: A Monte Carlo simulation study

    DEFF Research Database (Denmark)

    Castán, T.; Lindgård, Per-Anker

    1991-01-01

    By means of Monte Carlo computer simulations we study the domain-growth kinetics after a quench across a first-order line to very low and moderate temperatures in a multidegenerate system with nonconserved order parameter. The model is a continuous spin model relevant for martensitic transformati......By means of Monte Carlo computer simulations we study the domain-growth kinetics after a quench across a first-order line to very low and moderate temperatures in a multidegenerate system with nonconserved order parameter. The model is a continuous spin model relevant for martensitic...... to cross over from n = 1/4 at T approximately 0 to n = 1/2 with temperature for models with pinnings of types (a) and (b). For topological pinnings at T approximately 0, n is consistent with n = 1/8, a value conceivable for several levels of hierarchically interrelated domain-wall movement. When...

  19. Fundamentals of Protein NMR Spectroscopy

    CERN Document Server

    Rule, Gordon S

    2006-01-01

    NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data pr...

  20. Sampling the equilibrium kinetic network of Trp-cage in explicit solvent

    NARCIS (Netherlands)

    Du, W.; Bolhuis, P.G.

    2014-01-01

    We employed the single replica multiple state transition interface sampling (MSTIS) approach to sample the kinetic (un) folding network of Trp-cage mini-protein in explicit water. Cluster analysis yielded 14 important metastable states in the network. The MSTIS simulation thus resulted in a full 14

  1. STUDY ON THE KINETICS OF POLYMERIZATION OF MMA BY COPPER(Ⅱ) CHELATING RESINS

    Institute of Scientific and Technical Information of China (English)

    WangHongzuo; JiangYuanzhang; 等

    1993-01-01

    The polymerization of MMA initiated by copper(Ⅱ) chelating resins/CCl4 system was studied.From the kinetic data,the kinetic equation of polymerization can be expressed as Rp=Ke-56400/RT[MMA]1.57[CCl4]m[RESIN-Cu]0.18 where m:3-4.5,when[CCl4] 0.1-6.93M.The free radical polymerization mechanism is proposed.The primary radicals are formed by the process of complexation-chlorine transformation among the copper(Ⅱ) chelating resin,CCl4 and methacrylate.

  2. ELECTROCHEMICAL STUDIES OF URANIUM METAL CORROSION MECHANISM AND KINETICS IN WATER

    International Nuclear Information System (INIS)

    Boudanova, Natalya; Maslennikov, Alexander; Peretroukhine, Vladimir F.; Delegard, Calvin H.

    2006-01-01

    During long-term underwater storage of low burn-up uranium metal fuel, a corrosion product sludge forms containing uranium metal grains, uranium dioxide, uranates and, in some cases, uranium peroxide. Literature data on the corrosion of non-irradiated uranium metal and its alloys do not allow unequivocal prediction of the paragenesis of irradiated uranium in water. The goal of the present work conducted under the program 'CORROSION OF IRRADIATED URANIUM ALLOYS FUEL IN WATER' is to study the corrosion of uranium and uranium alloys and the paragenesis of the corrosion products during long-term underwater storage of uranium alloy fuel irradiated at the Hanford Site. The elucidation of the physico-chemical nature of the corrosion of irradiated uranium alloys in comparison with non-irradiated uranium metal and its alloys is one of the most important aspects of this work. Electrochemical methods are being used to study uranium metal corrosion mechanism and kinetics. The present part of work aims to examine and revise, where appropriate, the understanding of uranium metal corrosion mechanism and kinetics in water

  3. Identification of a key structural element for protein folding within beta-hairpin turns.

    Science.gov (United States)

    Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

    2003-05-09

    Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

  4. Study of water vapour adsorption kinetics on aluminium oxide materials

    Science.gov (United States)

    Livanova, Alesya; Meshcheryakov, Evgeniy; Reshetnikov, Sergey; Kurzina, Irina

    2017-11-01

    Adsorbents on the basis of active aluminum oxide are still of demand on the adsorbent-driers market. Despite comprehensive research of alumina adsorbents, and currently is an urgent task to improve their various characteristics, and especially the task of increasing the sorption capacity. In the present work kinetics of the processes of water vapours' adsorption at room temperature on the surface of desiccant samples has been studied. It was obtained on the basis of bayerite and pseudoboehmite experimentally. The samples of pseudoboehmite modified with sodium and potassium ions were taken as study objects. The influence of an adsorbent's grain size on the kinetics of water vapours' adsorption was studied. The 0.125-0.25 mm and 0.5-1.0 mm fractions of this sample were used. It has been revealed that the saturation water vapor fine powder (0.125-0.25 mm) is almost twofold faster in comparison with the sample of fraction 0.5-1.0 mm due to the decrease in diffusion resistance in the pores of the samples when moving from the sample of larger fraction to the fine-dispersed sample. It has been established that the adsorption capacity of the pseudoboehmite samples, modified by alkaline ions, is higher by ˜40 %, than for the original samples on the basis of bayerite and pseudoboehmite.

  5. A computational study on kinetics, mechanism and thermochemistry ...

    Indian Academy of Sciences (India)

    level procedure employing the optimization at .... for a better understanding of mechanistic pathways, kinetics and thermochemistry we must rely on quantum chemical methods. The aim of this paper is to have .... The search was made along.

  6. Influence of lysozyme on the precipitation of calcium carbonate: a kinetic and morphologic study

    Science.gov (United States)

    Jimenez-Lopez, Concepcion; Rodriguez-Navarro, Alejandro; Dominguez-Vera, Jose M.; Garcia-Ruiz, Juan M.

    2003-05-01

    Several mechanisms have been proposed to explain the interactions between proteins and mineral surfaces, among them a combination of electrostatic, stereochemical interactions and molecular recognition between the protein and the crystal surface. To identify the mechanisms of interaction in the lysozyme-calcium carbonate model system, the effect of this protein on the precipitation kinetics and morphology of calcite crystals was examined. The solution chemistry and morphology of the solid were monitored over time in a set of time-series free-drift experiments in which CaCO 3 was precipitated from solution in a closed system at 25°C and 1 atm total pressure, in the presence and absence of lysozyme. The precipitation of calcite was preceded by the precipitation of a metastable phase that later dissolved and gave rise to calcite as the sole phase. With increasing lysozyme concentration, the nucleation of both the metastable phase and calcite occurred at lower Ω calcite, indicating that lysozyme favored the nucleation of both phases. Calcite growth rate was not affected by the presence of lysozyme, at least at protein concentrations ranging from 0 mg/mL to 10 mg/mL. Lysozyme modified the habit of calcite crystals. The degree of habit modification changed with protein concentration. At lower concentrations of lysozyme, the typical rhombohedral habit of calcite crystals was modified by the expression of {110} faces, which resulted from the preferential adsorption of protein on these faces. With increasing lysozyme concentration, the growth of {110}, {100}, and finally {001} faces was sequentially inhibited. This adsorption sequence may be explained by an electrostatic interaction between lysozyme and calcite, in which the inhibition of the growth of {110}, {100}, and {001} faces could be explained by a combined effect of the density of carbonate groups in the calcite face and the specific orientation (perpendicular) of these carbonate groups with respect to the calcite

  7. Cesium removal and kinetics equilibrium: Precipitation kinetics

    International Nuclear Information System (INIS)

    Barnes, M.J.

    1999-01-01

    This task consisted of both non-radioactive and radioactive (tracer) tests examining the influence of potentially significant variables on cesium tetraphenylborate precipitation kinetics. The work investigated the time required to reach cesium decontamination and the conditions that affect the cesium precipitation kinetics

  8. Differential metabolic effects of casein and soy protein meals on skeletal muscle in healthy volunteers.

    Science.gov (United States)

    Luiking, Yvette C; Engelen, Mariëlle P K J; Soeters, Peter B; Boirie, Yves; Deutz, Nicolaas E P

    2011-02-01

    Dietary protein intake is known to affect whole body and interorgan protein turnover. We examined if moderate-nitrogen and carbohydrate casein and soy meals have a different effect on skeletal muscle protein and amino acid kinetics in healthy young subjects. Muscle protein and amino acid kinetics were measured in the postabsorptive state and during 4-h enteral intake of isonitrogenous [0.21 g protein/(kg body weight. 4 h)] protein-based test meals, which contained either casein (CAPM; n = 12) or soy protein (SOPM; n = 10) in 2 separate groups. Stable isotope and muscle biopsy techniques were used to study metabolic effects. The net uptake of glutamate, serine, histidine, and lysine across the leg was larger during CAPM than during SOPM intake. Muscle concentrations of glutamate, serine, histidine, glutamine, isoleucine and BCAA changed differently after CAPM and SOPM (P CAPM and SOPM, but differences in their (net) breakdown rates were not significant. Muscle protein synthesis was not different between CAPM and SOPM. Moderate-nitrogen casein and soy protein meals differently alter leg amino acid uptake without a significant difference in influencing acute muscle protein metabolism. Copyright © 2010 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  9. A kinetic study on the decomposition of 5-hydroxymethylfurfural into levulinic acid

    NARCIS (Netherlands)

    Girisuta, B.; Janssen, L. P. B. M.; Heeres, H. J.

    2006-01-01

    Levulinic acid (LA), accessible by the acid catalyzed degradation of biomass, is potentially a very versatile green intermediate chemical for the synthesis of various (bulk) chemicals for applications like fuel additives, polymers, and resin precursors. We report here a kinetic study on one of the

  10. Kinetic study on the acid-catalyzed hydrolysis of cellulose to levulinic acid

    NARCIS (Netherlands)

    Girisuta, B.; Janssen, L. P. B. M.; Heeres, H. J.

    2007-01-01

    A variety of interesting bulk chemicals is accessible by the acid-catalyzed hydrolysis of cellulose. An interesting example is levulinic acid, a versatile precursor for fuel additives, polymers, and resins. A detailed kinetic study on the acid-catalyzed hydrolysis of cellulose to levulinic acid is

  11. Radioimmunoassay of protein hormones

    International Nuclear Information System (INIS)

    Talas, M.; Fingerova, H.

    1976-01-01

    A survey is presented of the history of RIA methods for FSH, LH, HCG, HPL and prolactin determinations with special regard to the double antibody method in a kinetic system. Problems are shown in 125 I-labelling protein hormones in preparing own antisera. (L.O.)

  12. Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

    Science.gov (United States)

    Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

    2015-12-01

    Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models

  13. Effects of replacing soybean meal with canola meal differing in rumen-undegradable protein content on ruminal fermentation and gas production kinetics using 2 in vitro systems.

    Science.gov (United States)

    Paula, E M; Monteiro, H F; Silva, L G; Benedeti, P D B; Daniel, J L P; Shenkoru, T; Broderick, G A; Faciola, A P

    2017-07-01

    Previous research indicated that there were significant differences in rumen-undegradable protein (RUP) among canola meals (CM), which could influence the nutritional value of CM. The objectives of this study were to (1) evaluate the effects of feeding CM with different RUP contents on ruminal fermentation, nutrient digestion, and microbial growth using a dual-flow continuous culture system (experiment 1) and (2) evaluate ruminal gas production kinetics, in vitro organic matter (OM) digestibility, and methane (CH 4 ) production of soybean meal (SBM) and CM with low or high RUP in the diet or as a sole ingredient using a gas production system (experiments 2 and 3). In experiment 1, diets were randomly assigned to 6 fermentors in a replicated 3 × 3 Latin square. The only ingredient that differed among diets was the protein supplement. The treatments were (1) solvent-extracted SBM, (2) low-RUP solvent-extracted CM (38% RUP as a percentage of crude protein), and (3) high-RUP solvent-extracted CM (50% RUP). Diets were prepared as 3 concentrate mixtures that were combined with 25% orchardgrass hay and 15% wheat straw (dry matter basis). Experiments 2 and 3 had the same design with 24 bottles incubated 3 times for 48 h each. During the 48-h incubation, the cumulative pressure was recorded to determine gas production kinetics, in vitro OM digestibility, and CH 4 production. In experiment 1, N flow (g/d), efficiency of N use, efficiency of bacterial N synthesis, total volatile fatty acids (mM), and molar proportion of acetate, propionate, and isobutyrate were not affected by treatments. There were tendencies for a decrease in ruminal NH 3 -N and an increase in molar proportion of butyrate for the SBM diet compared with both CM diets. The molar proportion of valerate was greater in both CM diets, whereas the molar proportion of isovalerate and total branched-chain volatile fatty acids was lower for the CM diets compared with the SBM diet. In experiments 2 and 3, the SBM

  14. Training-induced acceleration of oxygen uptake kinetics in skeletal muscle: the underlying mechanisms.

    Science.gov (United States)

    Zoladz, J A; Korzeniewski, B; Grassi, B

    2006-11-01

    It is well known that the oxygen uptake kinetics during rest-to-work transition (V(O2) on-kinetics) in trained subjects is significantly faster than in untrained individuals. It was recently postulated that the main system variable that determines the transition time (t(1/2)) of the V(O2) on-kinetics in skeletal muscle, at a given moderate ATP usage/work intensity, and under the assumption that creatine kinase reaction works near thermodynamic equilibrium, is the absolute (in mM) decrease in [PCr] during rest-to-work transition. Therefore we postulate that the training-induced acceleration of the V(O2) on-kinetics is a marker of an improvement of absolute metabolic stability in skeletal muscles. The most frequently postulated factor responsible for enhancement of muscle metabolic stability is the training-induced increase in mitochondrial proteins. However, the mechanism proposed by Gollnick and Saltin (1982) can improve absolute metabolic stability only if training leads to a decrease in resting [ADP(free)]. This effect is not observed in many examples of training causing an acceleration of the V(O2) on-kinetics, especially in early stages of training. Additionally, this mechanism cannot account for the significant training-induced increase in the relative (expressed in % or as multiples of the resting values) metabolic stability at low work intensities, condition in which oxidative phosphorylation is not saturated with [ADP(free)]. Finally, it was reported that in the early stage of training, acceleration in the V(O2) on-kinetics and enhancement of muscle metabolic stability may precede adaptive responses in mitochondrial enzymes activities or mitochondria content. We postulate that the training-induced acceleration in the V(O2) on-kinetics and the improvement of the metabolite stability during moderate intensity exercise in the early stage of training is mostly caused by an intensification of the "parallel activation" of ATP consumption and ATP supply pathways

  15. Kinetic Study of the Catalytic Pyrolysis of Oil-Containing Waste

    Directory of Open Access Journals (Sweden)

    Kirill Chalov

    2016-10-01

    Full Text Available Basing on the experimental data the optimal parameters of the pyrolysis of heavy and residual hydrocarbons of oil were defined as follows: temperature of 500 °С; catalyst  of CoCl2 with the catalyst loading 5% (wt. of the substrate weight. Under the optimal conditions the kinetic investigation of the pyrolysis process was carried out using the thermogravimetric method. According to the investigation, it was found that the activation energy of the catalytic pyrolysis of oil-containing waste decreased by 20-30 kJ/mol in comparison to non-catalytic process. Copyright © 2016 BCREC GROUP. All rights reserved Received: 13th July 2015; Revised: 25th March 2016; Accepted: 1st April 2016 How to Cite: Chalov, K., Lugovoy, Y., Kosivtsov, Y., Sulman, M., Sulman, E., Matveeva, V., Stepacheva, A. (2016. Kinetic Study of the Catalytic Pyrolysis of Oil-Containing Waste. Bulletin of Chemical Reaction Engineering & Catalysis, 11 (3: 330-338 (doi:10.9767/bcrec.11.3.572.330-338 Permalink/DOI: http://doi.org/10.9767/bcrec.11.3.572.330-338

  16. Kinetic study on anaerobic oxidation of methane coupled to denitrification.

    Science.gov (United States)

    Yu, Hou; Kashima, Hiroyuki; Regan, John M; Hussain, Abid; Elbeshbishy, Elsayed; Lee, Hyung-Sool

    2017-09-01

    Monod kinetic parameters provide information required for kinetic analysis of anaerobic oxidation of methane coupled to denitrification (AOM-D). This information is critical for engineering AOM-D processes in wastewater treatment facilities. We first experimentally determined Monod kinetic parameters for an AOM-D enriched culture and obtained the following values: maximum specific growth rate (μ max ) 0.121/d, maximum substrate-utilization rate (q max ) 28.8mmol CH 4 /g cells-d, half maximum-rate substrate concentration (K s ) 83μΜ CH 4 , growth yield (Y) 4.76gcells/mol CH 4 , decay coefficient (b) 0.031/d, and threshold substrate concentration (S min ) 28.8μM CH 4 . Clone library analysis of 16S rRNA and mcrA gene fragments suggested that AOM-D reactions might have occurred via the syntrophic interaction between denitrifying bacteria (e.g., Ignavibacterium, Acidovorax, and Pseudomonas spp.) and hydrogenotrophic methanogens (Methanobacterium spp.), supporting reverse methanogenesis-dependent AOM-D in our culture. High μ max and q max , and low K s for the AOM-D enrichment imply that AOM-D could play a significant role in mitigating atmospheric methane efflux. In addition, these high kinetic features suggest that engineered AOM-D systems may provide a sustainable alternative to nitrogen removal in wastewater treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Thermodynamics and kinetics of graphene chemistry: a graphene hydrogenation prototype study.

    Science.gov (United States)

    Pham, Buu Q; Gordon, Mark S

    2016-12-07

    The thermodynamic and kinetic controls of graphene chemistry are studied computationally using a graphene hydrogenation reaction and polyaromatic hydrocarbons to represent the graphene surface. Hydrogen atoms are concertedly chemisorped onto the surface of graphene models of different shapes (i.e., all-zigzag, all-armchair, zigzag-armchair mixed edges) and sizes (i.e., from 16-42 carbon atoms). The second-order Z-averaged perturbation theory (ZAPT2) method combined with Pople double and triple zeta basis sets are used for all calculations. It is found that both the net enthalpy change and the barrier height of graphene hydrogenation at graphene edges are lower than at their interior surfaces. While the thermodynamic product distribution is mainly determined by the remaining π-islands of functionalized graphenes (Phys. Chem. Chem. Phys., 2013, 15, 3725-3735), the kinetics of the reaction is primarily correlated with the localization of the electrostatic potential of the graphene surface.

  18. Synchrotron Study on Crystallization Kinetics of Milk Fat under Shear Flow

    International Nuclear Information System (INIS)

    Mazzanti, G.; Marangoni, A.; Idziak, S.

    2009-01-01

    A detailed synchrotron X-ray diffraction study on the kinetics of crystallization of anhydrous milk fat (AMF) and milk fat triacylglycerols (MFT) was done in a Couette cell at 17 C, 17.5 C and 20 C under shear rates between 0 and 2880 s-1. We observed shear-induced acceleration of the transition from phase ? to ?? and the presence of crystalline orientation, but no effect of shear on the onset time of phase ? was observed. A two stage regime was observed for the growth of phase ??. The first stage follows a series-parallel system of differential equations describing the conversion between liquid and crystalline phases. The second stage follows a diffusion-controlled regime. These mechanisms are consistent with the crystalline orientation, the growth of the crystalline domains and the observed displacement of the diffraction peak positions. The absence of the polar lipids explains the faster kinetics of MFT.

  19. Present status on numerical algorithms and benchmark tests for point kinetics and quasi-static approximate kinetics

    International Nuclear Information System (INIS)

    Ise, Takeharu

    1976-12-01

    Review studies have been made on algorithms of numerical analysis and benchmark tests on point kinetics and quasistatic approximate kinetics computer codes to perform efficiently benchmark tests on space-dependent neutron kinetics codes. Point kinetics methods have now been improved since they can be directly applied to the factorization procedures. Methods based on Pade rational function give numerically stable solutions and methods on matrix-splitting are interested in the fact that they are applicable to the direct integration methods. An improved quasistatic (IQ) approximation is the best and the most practical method; it is numerically shown that the IQ method has a high stability and precision and the computation time which is about one tenth of that of the direct method. IQ method is applicable to thermal reactors as well as fast reactors and especially fitted for fast reactors to which many time steps are necessary. Two-dimensional diffusion kinetics codes are most practicable though there exist also three-dimensional diffusion kinetics code as well as two-dimensional transport kinetics code. On developing a space-dependent kinetics code, in any case, it is desirable to improve the method so as to have a high computing speed for solving static diffusion and transport equations. (auth.)

  20. Study of the effect of anions and mixed solvents on the kinetics of reduction of Eu(III)

    International Nuclear Information System (INIS)

    Chandrasekaran, V.R.; Sundaram, A.K.

    1983-01-01

    The kinetics of reduction of Eu(III) to Eu(II) in aqueous solutions of perchlorate, chloride, sulphate, acetate and lactate anions and water-methanol and water-acetone mixtures containing potassium chloride as the inert electrolyte is reported and the effect of anions and solvent on the kinetics is studied. (author)

  1. Differential equation methods for simulation of GFP kinetics in non-steady state experiments.

    Science.gov (United States)

    Phair, Robert D

    2018-03-15

    Genetically encoded fluorescent proteins, combined with fluorescence microscopy, are widely used in cell biology to collect kinetic data on intracellular trafficking. Methods for extraction of quantitative information from these data are based on the mathematics of diffusion and tracer kinetics. Current methods, although useful and powerful, depend on the assumption that the cellular system being studied is in a steady state, that is, the assumption that all the molecular concentrations and fluxes are constant for the duration of the experiment. Here, we derive new tracer kinetic analytical methods for non-steady state biological systems by constructing mechanistic nonlinear differential equation models of the underlying cell biological processes and linking them to a separate set of differential equations governing the kinetics of the fluorescent tracer. Linking the two sets of equations is based on a new application of the fundamental tracer principle of indistinguishability and, unlike current methods, supports correct dependence of tracer kinetics on cellular dynamics. This approach thus provides a general mathematical framework for applications of GFP fluorescence microscopy (including photobleaching [FRAP, FLIP] and photoactivation to frequently encountered experimental protocols involving physiological or pharmacological perturbations (e.g., growth factors, neurotransmitters, acute knockouts, inhibitors, hormones, cytokines, and metabolites) that initiate mechanistically informative intracellular transients. When a new steady state is achieved, these methods automatically reduce to classical steady state tracer kinetic analysis. © 2018 Phair. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  2. Kinetic study and growth behavior of template-based electrodeposited platinum nanotubes controlled by overpotential

    Energy Technology Data Exchange (ETDEWEB)

    Yousefi, E. [Department of Materials Science and Engineering, Sharif University of Technology, Azadi Ave., P.O.Box 11155-9466, Tehran (Iran, Islamic Republic of); Dolati, A., E-mail: dolati@sharif.edu [Department of Materials Science and Engineering, Sharif University of Technology, Azadi Ave., P.O.Box 11155-9466, Tehran (Iran, Islamic Republic of); Imanieh, I. [Department of Materials Science and Engineering, Sharif University of Technology, Azadi Ave., P.O.Box 11155-9466, Tehran (Iran, Islamic Republic of); Yashiro, H.; Kure-Chu, S.-Z. [Department of Chemistry and Bioengineering, Faculty of Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 (Japan)

    2017-02-01

    Platinum nanotubes (PtNTs) are fabricated by potentiostatic electrodeposition at various overpotentials (−200 up to −400 mV versus SCE) in polycarbonate templates (PCTs) with pore diameter of 200 nm in a solution containing 5 mM H{sub 2}PtCl{sub 6} and 0.1 M H{sub 2}SO{sub 4}. The synthesized PtNTs are characterized by field emission scanning electron microscopy (FE-SEM), and transmission electron microscopy (TEM). The electrochemical growth mechanism within nanoscopic pores and the relationship between morphological variations and kinetic parameters are investigated for the first time. It is shown that more porous structure of nanotubes forms at high overpotentials possibly due to preferably nucleation. The kinetics of electrodeposition process is studied by electrochemical techniques such as voltammetry and chronoamperometry. The linear diffusion coefficient at the early stage of the deposition and the radial diffusion coefficients at steady state regime are calculated as D = 8.39 × 10{sup −5} and 2.33–13.26 × 10{sup −8} cm{sup 2}/s, respectively. The synthesized PtNT electrode is tested as electrocatalyst for hydrogen peroxide oxidation in phosphate buffer solution (PBS) and shows a sensitivity as high as 2.89 mA per 1 μM that is an indication to its enlarged electrochemical surface area. - Highlights: • PtNT is electrodeposited in a 3-aminopropyltrimethoxysilane-modified PCT. • The electrochemical growth mechanism within nanoscopic pores is discussed. • The kinetics of PtNT electrodeposition is studied based on models for UME arrays. • Relationship between morphological variations vs. kinetic parameters is studied.

  3. Prediction of the optimal set of contacts to fold the smallest knotted protein

    International Nuclear Information System (INIS)

    Dabrowski-Tumanski, P; Jarmolinska, A I; Sulkowska, J I

    2015-01-01

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map. (paper)

  4. Prediction of the optimal set of contacts to fold the smallest knotted protein

    Science.gov (United States)

    Dabrowski-Tumanski, P.; Jarmolinska, A. I.; Sulkowska, J. I.

    2015-09-01

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

  5. Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease.

    Science.gov (United States)

    Gable, Jonathan E; Lee, Gregory M; Acker, Timothy M; Hulce, Kaitlin R; Gonzalez, Eric R; Schweigler, Patrick; Melkko, Samu; Farady, Christopher J; Craik, Charles S

    2016-04-19

    Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Fourier transform infrared microspectroscopic analysis of the effects of cereal type and variety within a type of grain on structural makeup in relation to rumen degradation kinetics.

    Science.gov (United States)

    Walker, Amanda M; Yu, Peiqiang; Christensen, Colleen R; Christensen, David A; McKinnon, John J

    2009-08-12

    The objectives of this study were to use Fourier transform infrared microspectroscopy (FTIRM) to determine structural makeup (features) of cereal grain endosperm tissue and to reveal and identify differences in protein and carbohydrate structural makeup between different cereal types (corn vs barley) and between different varieties within a grain (barley CDC Bold, CDC Dolly, Harrington, and Valier). Another objective was to investigate how these structural features relate to rumen degradation kinetics. The items assessed included (1) structural differences in protein amide I to nonstructural carbohydrate (NSC, starch) intensity and ratio within cellular dimensions; (2) molecular structural differences in the secondary structure profile of protein, alpha-helix, beta-sheet, and their ratio; (3) structural differences in NSC to amide I ratio profile. From the results, it was observed that (1) comparison between grain types [corn (cv. Pioneer 39P78) vs barley (cv. Harrington)] showed significant differences in structural makeup in terms of NSC, amide I to NSC ratio, and rumen degradation kinetics (degradation ratio, effective degradability of dry matter, protein and NSC) (P makeup in terms of amide I, NSC, amide I to NSC ratio, alpha-helix and beta-sheet protein structures, and rumen degradation kinetics (effective degradability of dry matter, protein, and NSC) (P makeup differences between cereal types and between different varieties within a type of grain could be revealed. These structural makeup differences were related to the rate and extent of rumen degradation.

  7. Dsc cure kinetics of an unsaturated polyester resin using empirical kinetic model

    International Nuclear Information System (INIS)

    Abdullah, I.

    2015-01-01

    In this paper, the kinetics of curing of unsaturated polyester resin initiated with benzoyl peroxide was studied. In case of unsaturated polyester (UP) resin, isothermal test alone could not predict correctly the curing time of UP resin. Therefore, isothermal kinetic analysis through isoconventional adjustment was used to correctly predict the curing time and temperature of UP resin. Isothermal kinetic analysis through isoconversional adjustment indicated that 97% of UP resin cures in 33 min at 120 degree C. Curing of UP resin through microwaves was also studied and found that 67% of UP resin cures in 1 min at 120 degree C. The crosslinking reaction of UP resin is so fast at 120 degree C that it becomes impossible to predict correctly the curing time of UP resin using isothermal test and the burial of C=C bonds in microgels makes it impossible to be fully cured by microwaves at 120 degree C. The rheological behaviour of unsaturated polyester resin was also studied to observe the change in viscosity with respect to time and temperature. (author)

  8. Effects of knot type in the folding of topologically complex lattice proteins

    Science.gov (United States)

    Soler, Miguel A.; Nunes, Ana; Faísca, Patrícia F. N.

    2014-07-01

    The folding properties of a protein whose native structure contains a 52 knot are investigated by means of extensive Monte Carlo simulations of a simple lattice model and compared with those of a 31 knot. A 52 knot embedded in the native structure enhances the kinetic stability of the carrier lattice protein in a way that is clearly more pronounced than in the case of the 31 knot. However, this happens at the expense of a severe loss in folding efficiency, an observation that is consistent with the relative abundance of 31 and 52 knots in the Protein Data Bank. The folding mechanism of the 52 knot shares with that of the 31 knot the occurrence of a threading movement of the chain terminus that lays closer to the knotted core. However, co-concomitant knotting and folding in the 52 knot occurs with negligible probability, in sharp contrast to what is observed for the 31 knot. The study of several single point mutations highlights the importance in the folding of knotted proteins of the so-called structural mutations (i.e., energetic perturbations of native interactions between residues that are critical for knotting but not for folding). On the other hand, the present study predicts that mutations that perturb the folding transition state may significantly enhance the kinetic stability of knotted proteins provided they involve residues located within the knotted core.

  9. Kinetics study of levulinic acid production from corncobs by tin tetrachloride as catalyst.

    Science.gov (United States)

    Qing, Qing; Guo, Qi; Wang, Pengbo; Qian, Hongjia; Gao, Xiaohang; Zhang, Yue

    2018-07-01

    Levulinic acid (LA) is an ideal platform chemical that can be produced through acid-catalyzed dehydration and hydrolysis of hexose sugars obtained from lignocellulosic materials. In this study, SnCl 4 was identified as an efficient catalyst for LA production and the reaction kinetics was investigated in a single water phase under different reaction conditions. The Box-Behnken design response surface methodology (RSM) was applied to determine the optimized reaction conditions and three individual variables including reaction temperature, duration, and catalyst concentration were evaluated. An appealing LA yield of 76.0% was achieved at 193 °C and 17 min with 82 mM SnCl 4 catalyst. A kinetics model was developed to predict the yields of glucose, HMF, and LA, which are tally with the experimental results. The analysis of the related kinetic parameters and the results of the RSM experiment helped to provide insights into the interplay between various reaction steps with SnCl 4 as catalysts. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Muscular Oxygen Uptake Kinetics in Aged Adults.

    Science.gov (United States)

    Koschate, J; Drescher, U; Baum, K; Eichberg, S; Schiffer, T; Latsch, J; Brixius, K; Hoffmann, U

    2016-06-01

    Pulmonary oxygen uptake (V˙O2) kinetics and heart rate kinetics are influenced by age and fitness. Muscular V˙O2 kinetics can be estimated from heart rate and pulmonary V˙O2. In this study the applicability of a test using pseudo-random binary sequences in combination with a model to estimate muscular V˙O2 kinetics was tested. Muscular V˙O2 kinetics were expected to be faster than pulmonary V˙O2 kinetics, slowed in aged subjects and correlated with maximum V˙O2 and heart rate kinetics. 27 elderly subjects (73±3 years; 81.1±8.2 kg; 175±4.7 cm) participated. Cardiorespiratory kinetics were assessed using the maximum of cross-correlation functions, higher maxima implying faster kinetics. Muscular V˙O2 kinetics were faster than pulmonary V˙O2 kinetics (0.31±0.1 vs. 0.29±0.1 s; p=0.004). Heart rate kinetics were not correlated with muscular or pulmonary V˙O2 kinetics or maximum V˙O2. Muscular V˙O2 kinetics correlated with maximum V˙O2 (r=0.35; p=0.033). This suggests, that muscular V˙O2 kinetics are faster than estimates from pulmonary V˙O2 and related to maximum V˙O2 in aged subjects. In the future this experimental approach may help to characterize alterations in muscular V˙O2 under various conditions independent of motivation and maximal effort. © Georg Thieme Verlag KG Stuttgart · New York.

  11. Predicting Protein-Protein Interactions Using BiGGER: Case Studies

    Directory of Open Access Journals (Sweden)

    Rui M. Almeida

    2016-08-01

    Full Text Available The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A in which no specific contact data is available; (Case Study B when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling on one of the partners is available; and (Case Study C when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.

  12. The porcine acute phase response to infection with Actinobacillus pleuropneumoniae. Haptoglobin, C-reactive protein, major acute phase protein and serum amyloid a protein are sensitive indicators of infection

    DEFF Research Database (Denmark)

    Heegaard, Peter M. H.; Klausen, Joan; Nielsen, J.P.

    1998-01-01

    response peaking at around 2 days after infection. Haptoglobin, C-reactive protein (CRP), and major acute phase protein (MAP) responded with large increases in serum levels, preceding the development of specific antibodies by 4-5 days. Serum amyloid A protein (SAA) was also strongly induced. The increase......, kinetics of induction and normalization were different between these proteins. It is concluded that experimental Ap-infection by the aerosol route induces a typical acute phase reaction in the pig, and that pig Hp, CRP, MAP, and SAA are major acute phase reactants. These findings indicate the possibility...

  13. Biomarkers kinetics in the assessment of ventilator-associated pneumonia response to antibiotics - results from the BioVAP study

    NARCIS (Netherlands)

    Póvoa, Pedro; Martin-Loeches, Ignacio; Ramirez, Paula; Bos, Lieuwe D.; Esperatti, Mariano; Silvestre, Joana; Gili, Gisela; Goma, Gemma; Berlanga, Eugenio; Espasa, Mateu; Gonçalves, Elsa; Torres, Antoni; Artigas, Antonio

    2017-01-01

    Purpose: Our aim was to evaluate the role of biomarker kinetics in the assessment of ventilator-associated pneumonia (VAP) response to antibiotics. Materials and methods: We performed a prospective, multicenter, observational study to evaluate in 37 microbiologically documented VAP, the kinetics of

  14. Structural, kinetic, and docking studies of artificial imine reductases based on biotin-streptavidin technology: an induced lock-and-key hypothesis.

    Science.gov (United States)

    Robles, Victor Muñoz; Dürrenberger, Marc; Heinisch, Tillmann; Lledós, Agustí; Schirmer, Tilman; Ward, Thomas R; Maréchal, Jean-Didier

    2014-11-05

    An artificial imine reductase results upon incorporation of a biotinylated Cp*Ir moiety (Cp* = C5Me5(-)) within homotetrameric streptavidin (Sav) (referred to as Cp*Ir(Biot-p-L)Cl] ⊂ Sav). Mutation of S112 reveals a marked effect of the Ir/streptavidin ratio on both the saturation kinetics as well as the enantioselectivity for the production of salsolidine. For [Cp*Ir(Biot-p-L)Cl] ⊂ S112A Sav, both the reaction rate and the selectivity (up to 96% ee (R)-salsolidine, kcat 14-4 min(-1) vs [Ir], KM 65-370 mM) decrease upon fully saturating all biotin binding sites (the ee varying between 96% ee and 45% ee R). In contrast, for [Cp*Ir(Biot-p-L)Cl] ⊂ S112K Sav, both the rate and the selectivity remain nearly constant upon varying the Ir/streptavidin ratio [up to 78% ee (S)-salsolidine, kcat 2.6 min(-1), KM 95 mM]. X-ray analysis complemented with docking studies highlight a marked preference of the S112A and S112K Sav mutants for the SIr and RIr enantiomeric forms of the cofactor, respectively. Combining both docking and saturation kinetic studies led to the formulation of an enantioselection mechanism relying on an "induced lock-and-key" hypothesis: the host protein dictates the configuration of the biotinylated Ir-cofactor which, in turn, by and large determines the enantioselectivity of the imine reductase.

  15. One step sintering of homogenized bauxite raw material and kinetic study

    Science.gov (United States)

    Gao, Chang-he; Jiang, Peng; Li, Yong; Sun, Jia-lin; Zhang, Jun-jie; Yang, Huan-ying

    2016-10-01

    A one-step sintering process of bauxite raw material from direct mining was completed, and the kinetics of this process was analyzed thoroughly. The results show that the sintering kinetics of bauxite raw material exhibits the liquid-phase sintering behavior. A small portion of impurities existed in the raw material act as a liquid phase. After X-ray diffraction analyses, scanning electron microscopy observations, and kinetics calculations, sintering temperature and heating duration were determined as the two major factors contributing to the sintering process and densification of bauxite ore. An elevated heating temperature and longer duration favor the densification process. The major obstacle for the densification of bauxite material is attributed to the formation of the enclosed blowhole during liquid-phase sintering.

  16. Impact of hydrodynamic interactions on protein folding rates depends on temperature

    Science.gov (United States)

    Zegarra, Fabio C.; Homouz, Dirar; Eliaz, Yossi; Gasic, Andrei G.; Cheung, Margaret S.

    2018-03-01

    We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α /β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β -barrel α -spectrin Src-homology 3 domain (SH3) protein. When comparing the protein folding kinetics simulated with Brownian dynamics in the presence of HI to that in the absence of HI, we find that the effect of HI on protein folding appears to have a "crossover" behavior about the folding temperature. This means that at a temperature greater than the folding temperature, the enhanced friction from the hydrodynamic solvents between the beads in an unfolded configuration results in lowered folding rate; conversely, at a temperature lower than the folding temperature, HI accelerates folding by the backflow of solvent toward the folded configuration of a protein. Additionally, the extent of acceleration depends on the topology of a protein: for a protein like CI2, where its folding nucleus is rather diffuse in a transition state, HI channels the formation of contacts by favoring a major folding pathway in a complex free energy landscape, thus accelerating folding. For a protein like SH3, where its folding nucleus is already specific and less diffuse, HI matters less at a temperature lower than the folding temperature. Our findings provide further theoretical insight to protein folding kinetic experiments and simulations.

  17. Kinetic study on the effect of temperature on biogas production using a lab scale batch reactor.

    Science.gov (United States)

    Deepanraj, B; Sivasubramanian, V; Jayaraj, S

    2015-11-01

    In the present study, biogas production from food waste through anaerobic digestion was carried out in a 2l laboratory-scale batch reactor operating at different temperatures with a hydraulic retention time of 30 days. The reactors were operated with a solid concentration of 7.5% of total solids and pH 7. The food wastes used in this experiment were subjected to characterization studies before and after digestion. Modified Gompertz model and Logistic model were used for kinetic study of biogas production. The kinetic parameters, biogas yield potential of the substrate (B), the maximum biogas production rate (Rb) and the duration of lag phase (λ), coefficient of determination (R(2)) and root mean square error (RMSE) were estimated in each case. The effect of temperature on biogas production was evaluated experimentally and compared with the results of kinetic study. The results demonstrated that the reactor with operating temperature of 50°C achieved maximum cumulative biogas production of 7556ml with better biodegradation efficiency. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Size dependence of adsorption kinetics of nano-MgO: a theoretical and experimental study

    International Nuclear Information System (INIS)

    Wang, Shuting; Wen, Yanzhen; Cui, Zixiang; Xue, Yongqiang

    2016-01-01

    Nanoparticles present tremendous differences in adsorption kinetics compared with corresponding bulk particles which have great influences on the applications of nanoparticles. A size-dependent adsorption kinetic theory was proposed, the relations between adsorption kinetic parameters, respectively, and particle size of nano-adsorbent were derived theoretically, and the influence mechanism of particle size on the adsorption kinetic parameters was discussed. In experiment, nanoscale magnesium oxide (nano-MgO) with different diameters between 11.5 and 41.4 nm with narrow size distribution and low agglomeration were prepared, and the kinetic parameters of adsorption of benzene on nano-MgO in aqueous solution were obtained. Then the influence regularities of the particle size on the adsorption kinetic parameters were obtained. The experimental results are consistent with the nano-adsorption kinetic theory. With particle size decreasing, the adsorption rate constant increases; the adsorption activation energy and the adsorption pre-exponential factor decrease. Furthermore, the logarithm of adsorption rate constant, the adsorption activation energy, and the logarithm of adsorption pre-exponential factor are linearly related to the reciprocal of particle diameter, respectively. The mechanism of particle size influence on the kinetic parameters is that the activation energy is influenced by the molar surface enthalpy of nano-adsorbent, the pre-exponential factor by the molar surface entropy, and the rate constant by both the molar surface enthalpy and the molar surface entropy

  19. Electrochemical oxidation of COD from real textile wastewaters: Kinetic study and energy consumption.

    Science.gov (United States)

    Zou, Jiaxiu; Peng, Xiaolan; Li, Miao; Xiong, Ying; Wang, Bing; Dong, Faqin; Wang, Bin

    2017-03-01

    In the present study, the electrochemical oxidation of real wastewaters discharged by textile industry was carried out using a boron-doped diamond (BDD) anode. The effect of operational variables, such as applied current density (20-100 mA·cm -2 ), NaCl concentration added to the real wastewaters (0-3 g·L -1 ), and pH value (2.0-10.0), on the kinetics of COD oxidation and on the energy consumption was carefully investigated. The obtained experimental results could be well matched with a proposed kinetic model, in which the indirect oxidation mediated by electrogenerated strong oxidants would be described through a pseudo-first-order kinetic constant k. Values of k exhibited a linear increase with increasing applied current density and decreasing pH value, and an exponential increase with NaCl concentration. Furthermore, high oxidation kinetics resulted in low specific energy consumption, but this conclusion was not suitable to the results obtained under different applied current density. Under the optimum operational conditions, it only took 3 h to complete remove the COD in the real textile wastewaters and the specific energy consumption could be as low as 11.12 kWh·kg -1  COD. The obtained results, low energy consumption and short electrolysis time, allowed to conclude that the electrochemical oxidation based on BDD anodes would have practical industrial application for the treatment of real textile wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Differences in kinetic variables between injured and noninjured novice runners : A prospective cohort study

    NARCIS (Netherlands)

    Bredeweg, Steef W.; Kluitenberg, Bas; Bessem, Bram; Buist, Ida

    Objectives: This prospective study examined differences in kinetic variables between injured and noninjured novice female and male runners and their potential contribution to RRIs. Design: A prospective cohort study. Methods: At baseline vertical ground reaction forces were assessed with an

  1. Study of extraction kinetics of lanthanides(III) and actinides(III) nitrates by the molecule N, N'-dimethyl-N, N'-dibutyl, tetradecylmalonamide

    International Nuclear Information System (INIS)

    Daldon, M.

    1999-01-01

    The kinetics of extraction of lanthanides (III) and actinides (III) nitrates by the molecule N, N'-dimethyl - N, N'-dibutyl tetra-decyl malonamide has been investigated. This study was realised with a new constant interfacial-area-stirred cell. During the qualification step of the device it appears that the reduction of the device can lead to hydrolytic perturbations. The main conclusions are: - after the determination of conditions which provide kinetics regime (diffusion of species neglectable), partial orders of the kinetics law have been obtained and lead to the establishment of the law J = k [Nd 3+ ] [NO 3 - ] 3 [diamide] 1 , - interfacial tension measurements and kinetics study in presence of surface-active compounds proved that the chemical limiting reaction for Nd(III) is interfacial, - the results allow to propose an adsorption-desorption reaction mechanism, - a comprehensive study of the extraction kinetics of the lanthanides(III) series and also Am(III) and Cm(III) nitrates has been realised. The lighter lanthanides (La, Ce and Pr) exhibit higher kinetics rate of extraction than the others, which differs from the tendency observed with distribution coefficients which exhibit tetrad effect. The kinetics rate of extraction of Am(III) and Cm(III) is closed to the value of Eu(III). (author)

  2. Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

    Directory of Open Access Journals (Sweden)

    Miguel Fribourg

    2017-02-01

    Full Text Available Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic processes from the overall (macroscopic response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE. SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology

  3. Kinetic study of the alkaline metals oxidation by dry oxygen

    International Nuclear Information System (INIS)

    Touzain, Ph.

    1967-06-01

    The oxidation of lithium, sodium, potassium, rubidium, cesium and sodium-potassium alloys by dry oxygen is studied at several temperatures and in the oxygen pressure range 40 to 400 mmHg. One distinguishes three different oxidation behaviours (inflammation, ignition and slow combustion) whose zones are precised in function of the temperature. The slow oxidation kinetic laws, the composition of oxides and the motive of oxides colorations are determined. At least, the experimental data are construed theoretically. (author) [fr

  4. Study of the kinetics parameters for subcritical media driven by source

    International Nuclear Information System (INIS)

    Lee, S.M.; Maiorino, J.R.

    2009-01-01

    This paper presents a theoretical study of reactor kinetics focusing on the methodology of calculation and the experimental measurements of the so-called kinetic parameters. A comparison between the methodology based on the Dulla's formalism and the classical method is made. The objective is to exhibit the dependence of the parameters on sub criticality level and perturbation. Two different slab type systems were considered: thermal one and fast one, both with homogeneous media. One group diffusion model was used for the fast reactor, and for the thermal system, two group diffusion model, considering, in both case only one precursor's family. For reason of simplicity, several additional assumptions were made for calculation of two group method: no up-scattering, fission reaction occurring only in thermal group, etc. The solutions for subcritical systems were obtained using the expansion method, and for critical systems, the methods presented in classical textbooks of reactor physics were applied. The numerical results presented their dependence on sub criticality level and perturbation. (author)

  5. NMRKIN: Simulating line shapes from two-dimensional spectra of proteins upon ligand binding

    International Nuclear Information System (INIS)

    Guenther, Ulrich L.; Schaffhausen, Brian

    2002-01-01

    The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Guenther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT)

  6. Effects of different per translational kinetics on the dynamics of a core circadian clock model.

    Science.gov (United States)

    Nieto, Paula S; Revelli, Jorge A; Garbarino-Pico, Eduardo; Condat, Carlos A; Guido, Mario E; Tamarit, Francisco A

    2015-01-01

    Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

  7. Kinetic Modelling and Experimental Study of Small Esters: Methyl Acetate and Ethyl Acetate

    KAUST Repository

    Ahmed, Ahfaz; Mehl, Marco; Lokachari, Nitin; Nilsson, Elna J.K.; Konnov, Alexander A.; Wagnon, Scott W.; Pitz, William J.; Curran, Henry J.; Roberts, William L.; Sarathy, Mani

    2017-01-01

    A detailed chemical kinetic mechanism comprising methyl acetate and ethyl acetate has been developed based on the previous work by Westbrook et al. [1]. The newly developed kinetic mechanism has been updated with new reaction rates from recent theoretical studies. To validate this model, shock tube experiments measuring ignition delay time have been conducted at 15 & 30 bar and equivalence ratio 0.5, 1.0 and 2.0. Another set of experiments measuring laminar burning velocity was also performed on a heat flux burner at atmospheric pressure over wide range of equivalence ratios [~0.7-1.4]. The new mechanism shows significant improvement in prediction of experimental data over earlier model across the range of experiments.

  8. Kinetic Modelling and Experimental Study of Small Esters: Methyl Acetate and Ethyl Acetate

    KAUST Repository

    Ahmed, Ahfaz

    2017-12-14

    A detailed chemical kinetic mechanism comprising methyl acetate and ethyl acetate has been developed based on the previous work by Westbrook et al. [1]. The newly developed kinetic mechanism has been updated with new reaction rates from recent theoretical studies. To validate this model, shock tube experiments measuring ignition delay time have been conducted at 15 & 30 bar and equivalence ratio 0.5, 1.0 and 2.0. Another set of experiments measuring laminar burning velocity was also performed on a heat flux burner at atmospheric pressure over wide range of equivalence ratios [~0.7-1.4]. The new mechanism shows significant improvement in prediction of experimental data over earlier model across the range of experiments.

  9. A Kinetic Study of the Diels-Alder Reaction. An Experiment Illustrating Simple Second-Order Reaction Kinetics.

    Science.gov (United States)

    Silvestri, Michael G.; Dills, Charles E.

    1989-01-01

    Describes an organic chemistry experiment for teaching the basic concepts of chemical kinetics. Provides background information about first- and second-order reactions, experimental procedures of the Diels-Alder reaction between cyclopentadiene and dimethyl fumarate, and the experimental results. (YP)

  10. Kinetic study of sphingomyelin hydrolysis for ceramide production

    DEFF Research Database (Denmark)

    Zhang, Long; Hellgren, Lars; Xu, Xuebing

    2008-01-01

    in cosmetic and pharmaceutical industries such as in hair and skin care products. The enzymatic hydrolysis of sphingomyelin has been proved to be a feasible method to produce ceramide. The kinetic performance of sphingomyelin hydrolysis in the optimal two-phase (water:organic solvent) reaction system...

  11. Study of kinetics of 2,3-diphosphoglycerate degradation by 31P-NMR technique in depleted human erythrocytes

    International Nuclear Information System (INIS)

    Ataullakhanov, F.I.; Vitvitskii, V.M.; Dubinskaya, E.I.; Dubinskii, V.Z.

    1986-01-01

    The kinetics of 2,3-diphosphoglycerate degradation in depleted human erythrocytes was studied by the high-resolution 31 P-NMR technique. A plateau was found on the kinetic curve in the first 1.5-2 h after the beginning of depletion. The mechanisms that may be responsible for the existence of such a plateau are discussed

  12. Kinetic theory of nonideal gases and nonideal plasmas

    CERN Document Server

    Klimontovich, Yu L

    2013-01-01

    Kinetic Theory of Nonideal Gases and Nonideal Plasmas presents the fundamental aspects of the kinetic theory of gases and plasmas. The book consists of three parts, which attempts to present some of the ideas, methods and applications in the study of the kinetic processes in nonideal gases and plasmas. The first part focuses on the classical kinetic theory of nonideal gases. The second part discusses the classical kinetic theory of fully ionized plasmas. The last part is devoted to the quantum kinetic theory of nonideal gases and plasmas. A concluding chapter is included, which presents a shor

  13. The Feasibility of Bulk Crystallization as an Industrial Purification and Production Technique for Proteins

    Science.gov (United States)

    Judge, Russell A.; Forsythe, Elizabeth L.; Johns, Michael R.; Pusey, Marc L.; White, Edward T.

    1998-01-01

    Bulk crystallization in stirred vessels is used industrially for the recovery and purification of many inorganic and organic materials. Although much has been written on the crystallization of proteins for X-ray diffraction analysis, very little has been reported on the application of bulk crystallization in stirred vessels. In this study, a 1-liter, seeded, stirred, batch crystallizer was used with ovalbumin as a model protein to test the feasibility of this crystallization method as a recovery and purification process for proteins. Results were obtained for ovalbumin solubility, nucleation thresholds, crystal breakage and crystal growth kinetics in bulk solution under a range of operating conditions of pH and ammonium sulphate concentration (Judge et al., 1996). Experiments were also performed to determine the degree of purification that can be achieved by the crystallization of ovalbumin from a mixture of proteins. The effect of the presence of these proteins upon the ovalbumin crystal growth kinetics was also investigated (Judge et al., 1995). All of these aspects are essential for the design of bulk crystallization processes which have not previously been reported for proteins. Results from a second study that investigated the effect of structurally different proteins on the solubility, crystal growth rates and crystal purity of chicken egg white lysozyme are also presented (Judge et al., 1997). In this case face growth rates were measured using lysozyme purified by liquid chromatography and the effect of the addition of specific protein impurities were observed on the (110) and (101) crystal faces. In these two studies the results are presented to show the feasibility and purifying ability of crystallization as a production process for proteins.

  14. Photo-assisted Fenton type processes for the degradation of phenol: A kinetic study

    International Nuclear Information System (INIS)

    Kusic, Hrvoje; Koprivanac, Natalija; Bozic, Ana Loncaric; Selanec, Iva

    2006-01-01

    In this study the application of advanced oxidation processes (AOPs), dark Fenton and photo-assisted Fenton type processes; Fe 2+ /H 2 O 2 , Fe 3+ /H 2 O 2 , Fe 0 /H 2 O 2 , UV/Fe 2+ /H 2 O 2 , UV/Fe 3+ /H 2 O 2 and UV/Fe 0 /H 2 O 2 , for degradation of phenol as a model organic pollutant in the wastewater was investigated. A detail kinetic modeling which describes the degradation of phenol was performed. Mathematical models which predict phenol decomposition and formation of primary oxidation by-products: catechol, hydroquinone and benzoquinone, by applied processes were developed. The study also consist the modeling of mineralization kinetic of the phenol solution by applied AOPs. This part, besides well known reactions of Fenton and photo-Fenton chemistry, involves additional reactions which describe removal of iron from catalytic cycle through formation of ferric complexes and its regeneration induced by UV radiation. Phenol decomposition kinetic was monitored by HPLC analysis and total organic carbon content measurements (TOC). Complete phenol removal was obtained by all applied processes. Residual TOC by applied Fenton type processes ranged between 60.2 and 44.7%, while the efficiency of those processes was significantly enhanced in the presence of UV light, where residual TOC ranged between 15.2 and 2.4%

  15. High-Throughput Study of Diffusion and Phase Transformation Kinetics of Magnesium-Based Systems for Automotive Cast Magnesium Alloys

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Alan A [The Ohio State Univ., Columbus, OH (United States); Zhao, Ji-Cheng [The Ohio State Univ., Columbus, OH (United States); Riggi, Adrienne [National Energy Technology Lab. (NETL), Morgantown, WV (United States); Joost, William [US Dept. of Energy, Washington, DC (United States)

    2017-10-02

    The objective of the proposed study is to establish a scientific foundation on kinetic modeling of diffusion, phase precipitation, and casting/solidification, in order to accelerate the design and optimization of cast magnesium (Mg) alloys for weight reduction of U.S. automotive fleet. The team has performed the following tasks: 1) study diffusion kinetics of various Mg-containing binary systems using high-throughput diffusion multiples to establish reliable diffusivity and mobility databases for the Mg-aluminum (Al)-zinc (Zn)-tin (Sn)-calcium (Ca)-strontium (Sr)-manganese (Mn) systems; 2) study the precipitation kinetics (nucleation, growth and coarsening) using both innovative dual-anneal diffusion multiples and cast model alloys to provide large amounts of kinetic data (including interfacial energy) and microstructure atlases to enable implementation of the Kampmann-Wagner numerical model to simulate phase transformation kinetics of non-spherical/non-cuboidal precipitates in Mg alloys; 3) implement a micromodel to take into account back diffusion in the solid phase in order to predict microstructure and microsegregation in multicomponent Mg alloys during dendritic solidification especially under high pressure die-casting (HPDC) conditions; and, 4) widely disseminate the data, knowledge and information using the Materials Genome Initiative infrastructure (http://www.mgidata.org) as well as publications and digital data sharing to enable researchers to identify new pathways/routes to better cast Mg alloys.

  16. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY

    International Nuclear Information System (INIS)

    Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley, D; Schuler, B; Bakajin, O

    2006-01-01

    The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein secondary structure formation with Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy. The mixers are designed to rapidly initiate protein folding reaction through the dilution of denaturant. The devices are fabricated out of fused silica, so that they are transparent in the UV. We present characterization of mixing in the fabricated devices, as well as the initial SRCD data on proteins inside the mixers

  17. A comparative study of ethylene growth response kinetics in eudicots and monocots reveals a role for gibberellin in growth inhibition and recovery.

    Science.gov (United States)

    Kim, Joonyup; Wilson, Rebecca L; Case, J Brett; Binder, Brad M

    2012-11-01

    Time-lapse imaging of dark-grown Arabidopsis (Arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. This study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. Although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. In contrast, with continued application of ethylene, white millet (Panicum miliaceum) seedlings had a rapid and transient growth inhibition response, rice (Oryza sativa 'Nipponbare') seedlings had a slow onset of growth stimulation, and barley (Hordeum vulgare) had a transient growth inhibition response followed, after a delay, by a prolonged inhibition response. Growth stimulation in rice correlated with a decrease in the levels of rice ETHYLENE INSENSTIVE3-LIKE2 (OsEIL2) and an increase in rice F-BOX DOMAIN AND LRR CONTAINING PROTEIN7 transcripts. The gibberellin (GA) biosynthesis inhibitor paclobutrazol caused millet seedlings to have a prolonged growth inhibition response when ethylene was applied. A transient ethylene growth inhibition response has previously been reported for Arabidopsis ethylene insensitive3-1 (ein3-1) eil1-1 double mutants. Paclobutrazol caused these mutants to have a prolonged response to ethylene, whereas constitutive GA signaling in this background eliminated ethylene responses. Sensitivity to paclobutrazol inversely correlated with the levels of EIN3 in Arabidopsis. Wild-type Arabidopsis seedlings treated with paclobutrazol and mutants deficient in GA levels or signaling had a delayed growth recovery after ethylene removal. It is interesting to note that ethylene caused alterations in gene expression that are predicted to increase GA levels in the ein3-1 eil1-1 seedlings. These results indicate that ethylene affects GA levels leading to modulation of ethylene growth inhibition kinetics.

  18. Binding of Cimetidine to Balb/C Mouse Liver Catalase; Kinetics and Conformational Studies.

    Science.gov (United States)

    Jahangirvand, Mahboubeh; Minai-Tehrani, Dariush; Yazdi, Fatemeh; Minai-Tehrani, Arash; Razmi, Nematollah

    2016-01-01

    Catalase is responsible for converting hydrogen peroxide (H2O2) into water and oxygen in cells. This enzyme has high affinity for hydrogen peroxide and can protect the cells from oxidative stress damage. Catalase is a tetramer protein and each monomer contains a heme group. Cimetidine is a histamine H2 receptor blocker which inhibits acid release from stomach and is used for gasterointestinal diseases. In this research, effect of cimetidine on the activity of liver catalase was studied and the kinetic parameters of this enzyme and its conformational changes were investigated. Cell free extract of mouse liver was used for the catalase assay. The activity of the catalase was detected in the absence and presence of cimetidine by monitoring hydrogen peroxide reduction absorbance at 240 nm. The purified enzyme was used for conformational studies by Fluorescence spectrophotometry. The data showed that cimetidine could inhibit the enzyme in a non-competitive manner. Ki and IC50 values of the drug were determined to be about 0.75 and 0.85 uM, respectively. The Arrhenius plot showed that activation energy was 6.68 and 4.77 kJ/mol in the presence and absence of the drug, respectively. Fluorescence spectrophotometry revealed that the binding of cimetidine to the purified enzyme induced hyperchromicity and red shift which determined the conformational change on the enzyme. Cimetidine could non-competitively inhibit the liver catalase with high affinity. Binding of cimetidine to the enzyme induced conformational alteration in the enzyme.

  19. Kinetics of immobilisation and release of tryptophan, riboflavin and peptides from whey protein microbeads.

    Science.gov (United States)

    O'Neill, Graham J; Egan, Thelma; Jacquier, Jean Christophe; O'Sullivan, Michael; Dolores O'Riordan, E

    2015-08-01

    This study investigated the kinetics of immobilisation and release of riboflavin, amino acids and peptides from whey microbeads. Blank whey microbeads were placed in solutions of the compounds. As the volume of microbeads added to the solution was increased, the uptake of the compounds increased, to a maximum of 95% for the pentapeptide and 56%, 57% and 45% for the dipeptide, riboflavin and tryptophan respectively, however, the rate of uptake remained constant. The rate of uptake increased with increasing molecule hydrophobicity. The opposite was observed in the release studies, the more hydrophobic compounds had lower release rate constants (kr). When whey microbeads are used as sorbents, they show excellent potential to immobilise small hydrophobic molecules and minimise subsequent diffusion, even in high moisture environments. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. A kinetic study of mercury(II transport through a membrane assisted by new transport reagent

    Directory of Open Access Journals (Sweden)

    Görgülü Ahmet

    2011-07-01

    Full Text Available Abstract Background A new organodithiophosphorus derivative, namely O-(1,3-Bispiperidino-2-propyl-4-methoxy phenyldithiophosphonate, was synthesized and then the kinetic behavior of the transport process as a function of concentration, temperature, stirring rate and solvents was investigated. Results The compound 1 was characterized by elemental analysis, IR, 1H and 31P NMR spectroscopies. The transport of mercury(II ion by a zwitterionic dithiophosphonate 1 in the liquid membrane was studied and the kinetic behavior of the transport process as a function of concentration, temperature, stirring rate and solvents was investigated. The compound 1 is expected to serve as a model liquid membrane transport with mercury(II ions. Conclusion A kinetic study of mercury(II transport through a membrane assisted by O-(1,3-Bispiperidino-2-propyl-4-methoxy phenyldithiophosphonate was performed. It can be concluded that the compound 1 can be provided a general and straightforward route to remove toxic metals ions such as mercury(II ion from water or other solution.