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Sample records for binding constant studies

  1. Binding constants of phenylalanine for the four mononucleotides

    Science.gov (United States)

    Khaled, M. A.; Mullins, D. W., Jr.; Lacey, J. C., Jr.

    1984-01-01

    Earlier work has shown that several properties of amino acids correlate directly with properties of their anticodonic nucleotides. Furthermore, in precipitation studies with thermal proteinoids and homopolyribonucleotides, an anticodonic preference was displayed between Lys-rich, Pro-rich and Gly-rich thermal proteinoids and their anticodonic polyribonucleotides. However, Phe-rich thermal proteinoid displayed a preference for its codonic nucleotide, poly U. This inconsistency seemed to be explained by a folding in of the hydrophobic residues of Phe causing the proteinoid to appear more hydrophilic. The present work used nuclear magnetic resonance techniques to resolve a limited question: to which of the four nucleotides does Phe bind most strongly? The results show quite clearly that Phe binds most strongly to its anticodonic nucleotide, AMP.

  2. Prediction and dissection of widely-varying association rate constants of actin-binding proteins.

    Directory of Open Access Journals (Sweden)

    Xiaodong Pang

    Full Text Available Actin is an abundant protein that constitutes a main component of the eukaryotic cytoskeleton. Its polymerization and depolymerization are regulated by a variety of actin-binding proteins. Their functions range from nucleation of actin polymerization to sequestering G-actin in 1∶1 complexes. The kinetics of forming these complexes, with rate constants varying at least three orders of magnitude, is critical to the distinct regulatory functions. Previously we have developed a transient-complex theory for computing protein association mechanisms and association rate constants. The transient complex refers to an intermediate in which the two associating proteins have near-native separation and relative orientation but have yet to form short-range specific interactions of the native complex. The association rate constant is predicted as k(a = k(a0 e(-ΔG(el*/k(BT, where k(a0 is the basal rate constant for reaching the transient complex by free diffusion, and the Boltzmann factor captures the bias of long-range electrostatic interactions. Here we applied the transient-complex theory to study the association kinetics of seven actin-binding proteins with G-actin. These proteins exhibit three classes of association mechanisms, due to their different molecular shapes and flexibility. The 1000-fold k(a variations among them can mostly be attributed to disparate electrostatic contributions. The basal rate constants also showed variations, resulting from the different shapes and sizes of the interfaces formed by the seven actin-binding proteins with G-actin. This study demonstrates the various ways that actin-binding proteins use physical properties to tune their association mechanisms and rate constants to suit distinct regulatory functions.

  3. New Quasar Studies Keep Fundamental Physical Constant Constant

    Science.gov (United States)

    2004-03-01

    Very Large Telescope sets stringent limit on possible variation of the fine-structure constant over cosmological time Summary Detecting or constraining the possible time variations of fundamental physical constants is an important step toward a complete understanding of basic physics and hence the world in which we live. A step in which astrophysics proves most useful. Previous astronomical measurements of the fine structure constant - the dimensionless number that determines the strength of interactions between charged particles and electromagnetic fields - suggested that this particular constant is increasing very slightly with time. If confirmed, this would have very profound implications for our understanding of fundamental physics. New studies, conducted using the UVES spectrograph on Kueyen, one of the 8.2-m telescopes of ESO's Very Large Telescope array at Paranal (Chile), secured new data with unprecedented quality. These data, combined with a very careful analysis, have provided the strongest astronomical constraints to date on the possible variation of the fine structure constant. They show that, contrary to previous claims, no evidence exist for assuming a time variation of this fundamental constant. PR Photo 07/04: Relative Changes with Redshift of the Fine Structure Constant (VLT/UVES) A fine constant To explain the Universe and to represent it mathematically, scientists rely on so-called fundamental constants or fixed numbers. The fundamental laws of physics, as we presently understand them, depend on about 25 such constants. Well-known examples are the gravitational constant, which defines the strength of the force acting between two bodies, such as the Earth and the Moon, and the speed of light. One of these constants is the so-called "fine structure constant", alpha = 1/137.03599958, a combination of electrical charge of the electron, the Planck constant and the speed of light. The fine structure constant describes how electromagnetic forces hold

  4. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay

    OpenAIRE

    Win, Maung Nyan; Klein, Joshua S.; Smolke, Christina D.

    2006-01-01

    RNA aptamers that bind the opium alkaloid codeine were generated using an iterative in vitro selection process. The binding properties of these aptamers, including equilibrium and kinetic rate constants, were determined through a rapid, high-throughput approach using surface plasmon resonance (SPR) analysis to measure real-time binding. The approach involves direct coupling of the target small molecule onto a sensor chip without utilization of a carrier protein. Two highest binding aptamer se...

  5. Palmitate and stearate binding to human serum albumin. Determination of relative binding constants

    DEFF Research Database (Denmark)

    Vorum, H; Fisker, K; Honoré, B

    1997-01-01

    Multiple binding equilibria of two apparently insoluble ligands, palmitate and stearate, to defatted human serum albumin were studied in a 66 mM sodium phosphate buffer (pH 7.4) at 37 degrees C, by determination of dialytic exchange rates of ligands among identical equilibrium solutions. The expe...

  6. The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

    Science.gov (United States)

    Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

    2013-11-01

    We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens.

  7. A 1H NMR titration study on the binding constants for D- and L-tryptophan inclusion complexes with 6-O-α-D-glucosyl-β-cyclodextrin. Formation of 1:1 and 2:1 (host:guest) complexes

    Science.gov (United States)

    Akita, Tomoki; Matsui, Yoshihisa; Yamamoto, Tatsuyuki

    2014-02-01

    A 1H NMR titration study revealed that 6-O-α-D-glucosyl-β-cyclodextrin (G1-β-CD) forms 1:1 and 2:1 (host:guest) inclusion complexes with D- and L-tryptophan in alkaline D2O solutions (pD 11.0). The binding constants (K1's) for the 1:1 complexes of D-isomer at 298 K (59 mol-1 dm3) were virtually equal to that of L-isomer (54 mol-1 dm3). On the other hand, the K2 values for 2:1 complexes of D-isomer (42 mol-1 dm3) were larger than that of L-counterpart (12 mol-1 dm3). These facts suggest that the first CD molecule includes the indole ring moiety of tryptophan, followed by inclusion with the second CD molecule in the vicinity of chiral center, α-carbon of the guest, to result in the difference in K2's for two enantiomers. Two-dimensional NMR measurement (Rotating-frame nuclear Overhauser Effect SpectroscopY, ROESY) supported this interpretation.

  8. Calculation of binding constants and concentration of binding sites in a reaction of a ligand with a heterogeneous system of binding sites

    International Nuclear Information System (INIS)

    A method is presented for the calculation of association constants and the concentration of binding sites in a reaction of a ligand with a heterogeneous system of binding sites. The Scatchard plot for such a system is curvelinear and the method employs previously established relationships between the parameters of the limiting slopes to such a curve and the above mentioned association constants and concentrations of binding sites. The special case of a system with two different and non-interacting groups of binding sites was solved. The expressions thus obtained were used to characterize the reaction of a polypeptide neurotoxin with its specific binding sites in a membranal preparation from insect central nervous system. Moreover it is evident from these expressions that the widely accepted method to analyze such system, by an intuitive generalization of the method applicable to homogeneous systems, is erroneous and should be avoided. (author)

  9. CONSTANTS FOR MERCURY BINDING BY DISSOLVED ORGANIC MATTER ISOLATES FROM THE FLORIDA EVERGLADES. (R827653)

    Science.gov (United States)

    Dissolved organic matter (DOM) has been implicated as an important complexing agent for Hg that can affect its mobility and bioavailability in aquatic ecosystems. However, binding constants for natural Hg-DOM complexes are not well known. We employed a competitive ligand appro...

  10. Thermodynamics of Calcium binding to the Calmodulin N-terminal domain to evaluate site-specific affinity constants and cooperativity.

    Science.gov (United States)

    Beccia, Maria Rosa; Sauge-Merle, Sandrine; Lemaire, David; Brémond, Nicolas; Pardoux, Romain; Blangy, Stéphanie; Guilbaud, Philippe; Berthomieu, Catherine

    2015-07-01

    Calmodulin (CaM) is an essential Ca(II)-dependent regulator of cell physiology. To understand its interaction with Ca(II) at a molecular level, it is essential to examine Ca(II) binding at each site of the protein, even if it is challenging to estimate the site-specific binding properties of the interdependent CaM-binding sites. In this study, we evaluated the site-specific Ca(II)-binding affinity of sites I and II of the N-terminal domain by combining site-directed mutagenesis and spectrofluorimetry. The mutations had very low impact on the protein structure and stability. We used these binding constants to evaluate the inter-site cooperativity energy and compared it with its lower limit value usually reported in the literature. We found that site I affinity for Ca(II) was 1.5 times that of site II and that cooperativity induced an approximately tenfold higher affinity for the second Ca(II)-binding event, as compared to the first one. We further showed that insertion of a tryptophan at position 7 of site II binding loop significantly increased site II affinity for Ca(II) and the intra-domain cooperativity. ΔH and ΔS parameters were studied by isothermal titration calorimetry for Ca(II) binding to site I, site II and to the entire N-terminal domain. They showed that calcium binding is mainly entropy driven for the first and second binding events. These findings provide molecular information on the structure-affinity relationship of the individual sites of the CaM N-terminal domain and new perspectives for the optimization of metal ion binding by mutating the EF-hand loops sequences.

  11. Application of quantitative structure-activity relationship to the determination of binding constant based on fluorescence quenching

    Energy Technology Data Exchange (ETDEWEB)

    Wen Yingying [Department of Applied Chemistry, Yantai University, Yantai 264005 (China); Liu Huitao, E-mail: liuht-ytu@163.co [Department of Applied Chemistry, Yantai University, Yantai 264005 (China); Luan Feng; Gao Yuan [Department of Applied Chemistry, Yantai University, Yantai 264005 (China)

    2011-01-15

    Quantitative structure-activity relationship (QSAR) model was used to predict and explain binding constant (log K) determined by fluorescence quenching. This method allowed us to predict binding constants of a variety of compounds with human serum albumin (HSA) based on their structures alone. Stepwise multiple linear regression (MLR) and nonlinear radial basis function neural network (RBFNN) were performed to build the models. The statistical parameters provided by the MLR model (R{sup 2}=0.8521, RMS=0.2678) indicated satisfactory stability and predictive ability while the RBFNN predictive ability is somewhat superior (R{sup 2}=0.9245, RMS=0.1736). The proposed models were used to predict the binding constants of two bioactive components in traditional Chinese medicines (isoimperatorin and chrysophanol) whose experimental results were obtained in our laboratory and the predicted results were in good agreement with the experimental results. This QSAR approach can contribute to a better understanding of structural factors of the compounds responsible for drug-protein interactions, and can be useful in predicting the binding constants of other compounds. - Research Highlights: QSAR models for binding constants of some compounds to HSA were developed. The models provide a simple and straightforward way to predict binding constant. QSAR can give some insight into structural features related to binding behavior.

  12. Kinetic mechanism of phenylalanine hydroxylase: intrinsic binding and rate constants from single-turnover experiments.

    Science.gov (United States)

    Roberts, Kenneth M; Pavon, Jorge Alex; Fitzpatrick, Paul F

    2013-02-12

    Phenylalanine hydroxylase (PheH) catalyzes the key step in the catabolism of dietary phenylalanine, its hydroxylation to tyrosine using tetrahydrobiopterin (BH(4)) and O(2). A complete kinetic mechanism for PheH was determined by global analysis of single-turnover data in the reaction of PheHΔ117, a truncated form of the enzyme lacking the N-terminal regulatory domain. Formation of the productive PheHΔ117-BH(4)-phenylalanine complex begins with the rapid binding of BH(4) (K(d) = 65 μM). Subsequent addition of phenylalanine to the binary complex to form the productive ternary complex (K(d) = 130 μM) is approximately 10-fold slower. Both substrates can also bind to the free enzyme to form inhibitory binary complexes. O(2) rapidly binds to the productive ternary complex; this is followed by formation of an unidentified intermediate, which can be detected as a decrease in absorbance at 340 nm, with a rate constant of 140 s(-1). Formation of the 4a-hydroxypterin and Fe(IV)O intermediates is 10-fold slower and is followed by the rapid hydroxylation of the amino acid. Product release is the rate-determining step and largely determines k(cat). Similar reactions using 6-methyltetrahydropterin indicate a preference for the physiological pterin during hydroxylation.

  13. Cyclodextrins in pharmaceutical formulations II: solubilization, binding constant, and complexation efficiency.

    Science.gov (United States)

    Jambhekar, Sunil S; Breen, Philip

    2016-02-01

    Cyclodextrins are cyclic oligosaccharides that have been recognized as pharmaceutical adjuvants for the past 20 years. The molecular structure of these glucose derivatives, which approximates a truncated cone, bucket, or torus, generates a hydrophilic exterior surface and a nonpolar interior cavity. Cyclodextrins can interact with appropriately sized drug molecules to yield an inclusion complex. These noncovalent inclusion complexes offer a variety of advantages over noncomplexed forms of a drug. Cyclodextrins are carbohydrates that are primarily used to enhance the aqueous solubility, physical chemical stability, and bioavailability of drugs. Their other applications include preventing drug-drug interactions, converting liquid drugs into microcrystalline powders, minimizing gastrointestinal and ocular irritation, and reducing or eliminating unpleasant taste and smell. Here, we focus on the solubilization of drugs by complexation, and discuss the determination and significance of binding constants for cyclodextrin complexes, and the determination of complexation efficiency and factors that influence it. We also make some general observations on cyclodextrin complexation and the use of cyclodextrins in solid, as well as parenteral, dosage forms. PMID:26687191

  14. Structural studies of sugar binding proteins

    OpenAIRE

    Sooriyaarachchi, Sanjeewani

    2010-01-01

    Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose bindin...

  15. Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity.

    Directory of Open Access Journals (Sweden)

    Marcela Torres

    Full Text Available Mouse-human chimeric antibodies composed of murine variable (V and human (C chains are useful therapeutic reagents. Consequently, we investigated whether heterologous C-regions from mice and humans affected specificity and affinity, and determined the contribution of C(H glycosylation to antigen binding. The interaction of a 12-mer peptide mimetic with monoclonal antibody (mAb 18B7 to Cryptococcus neoformans glucuronoxylomannan, and its chimeric (ch and deglycosylated forms were studied by surface plasmon resonance. The equilibrium and rate association constants for the chAb were higher than for mAb 18B7. V region affinity was not affected by C(H region glycosylation whereas heterologous C region of the same isotype altered the Ab binding affinity and the specificity for self-antigens. Structural models displayed local differences that implied changes on the connectivity of residues. These findings suggest that V region conformational changes can be dictated by the C(H domains through an allosteric effect involving networks of highly connected amino acids.

  16. Competitive counterion complexation allows the true host : guest binding constants from a single titration by ionic receptors.

    Science.gov (United States)

    Pessêgo, Márcia; Basílio, Nuno; Muñiz, M Carmen; García-Río, Luis

    2016-07-01

    Counterion competitive complexation is a background process currently ignored by using ionic hosts. Consequently, guest binding constants are strongly affected by the design of the titration experiments in such a way that the results are dependent on the guest concentration and on the presence of added salts, usually buffers. In the present manuscript we show that these experimental difficulties can be overcome by just considering the counterion competitive complexation. Moreover a single titration allows us to obtain not only the true binding constants but also the stoichiometry of the complex showing the formation of 1 : 1 : 1 (host : guest : counterion) complexes. The detection of high stoichiometry complexes is not restricted to a single titration experiment but also to a displacement assay where both competitive and competitive-cooperative complexation models are taken into consideration. PMID:27278457

  17. In vitro DNA binding studies of Aspartame, an artificial sweetener.

    Science.gov (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Kheirdoosh, Fahimeh

    2013-03-01

    A number of small molecules bind directly and selectively to DNA, by inhibiting replication, transcription or topoisomerase activity. In this work the interaction of native calf thymus DNA (CT-DNA) with Aspartame (APM), an artificial sweeteners was studied at physiological pH. DNA binding study of APM is useful to understand APM-DNA interaction mechanism and to provide guidance for the application and design of new and safer artificial sweeteners. The interaction was investigated using spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD). Hypochromism and red shift are shown in UV absorption band of APM. A strong fluorescence quenching reaction of DNA to APM was observed and the binding constants (Kf) of DNA with APM and corresponding number of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be +181kJmol(-1) and +681Jmol(-1)K(-1) according to Van't Hoff equation, which indicated that reaction is predominantly entropically driven. Moreover, spectrofluorometric competition experiment and circular dichroism (CD) results are indicative of non-intercalative DNA binding nature of APM. We suggest that APM interacts with calf thymus DNA via groove binding mode with an intrinsic binding constant of 5×10(+4)M(-1).

  18. Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

    International Nuclear Information System (INIS)

    Highlights: • Energetics of the interaction of proflavine with DNA has been studied. • The binding reaction was favored by both negative enthalpy and positive entropy. • Enthalpy–entropy compensation phenomenon was observed. • Non-polyelectrolytic forces played a dominant role in the binding process. • Proflavine enhanced the thermal stability of DNA remarkably. - Abstract: The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 105 · M−1 at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation

  19. Study on cipher propertys of constant weight codes

    Institute of Scientific and Technical Information of China (English)

    Lin Bogang

    2006-01-01

    Constant weight code is an important error-correcting control code in communications. Basic structure of constant weight codes for some arriving at Johnson bound, A(n, 2u, w), is presented. Some correlative propertys of the codes, the solution of arriving at Johnson bound, and the results on the couple constant code and some constant weight codes are discussed. The conclusion is verified through four examples.

  20. Computational study on Kerr constants of neutral and ionized gases

    Science.gov (United States)

    Sato, M.; Kumada, A.; Hidaka, K.

    2015-08-01

    In order to quantitatively examine the measurement capability of Poisson's field using electro-optic Kerr-effect (EOKE), Kerr constants of neutral molecules and ions are examined by means of first principle calculations. We have systematically computed Kerr constants of neutral molecules and ions of several molecular symmetry groups, with consistent theory level and basis sets. Computed Kerr constants of neutral molecules (N2, CO2, SF6, and CF3I) ranging across two orders of magnitudes are within 50% error of the experimental values, which are comparable to the scattering between experimental values itself. The results show that SF6 has smaller Kerr constant due to its high molecular symmetry compared to those of N2 and CO2. In contrast, CF3I has large Kerr constant due to its permanent dipole. Computed Kerr constants for anions are larger by two orders of magnitude than those of neutral molecules, probably due to the shielding effect. For cations, the opposite holds true; however, due to anisotropic polarizability, computed Kerr constants for some cations are comparable to neutral molecules, while others show smaller values. The ratio of Kerr constants of ions to those of neutral molecules are at most 102; EOKE is valid for measuring electric field in weakly ionized gas whose ionization degree is smaller than 10-3.

  1. Fluorescence Studied of Dissociation Constant of Cyclodextrin With Phenol Derivatives

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ α-and β-cyclodextrins consisting of six and seven glucose residues respectively, have lipophilic cavities with different inner diameters. They form host-guest inclusion complexes with hydrophobic organic and organometallic guest molecules in aqueous solution. These host-guest complexes have proved to be excellent model systems for studying the nature of noncovalent bonding forces in aqueous media. They have provided valuable insights into the hydrophobic effect and London dispersion forces and are good model for understanding the specificity of enzyme substrate interactions [1] Evidence for the formation of inclusion complexes have been provided from calovimetric titration [2] NMR[33], circular dichroism[4], U V[1] and fluorescence spectra[5] and conductometric method[6] etc. H ere we report a new fluorimetric method for a study on the reaction of the host-guest inclusion complexes of cyclodextrin with phenols. Dissociation constants (Kd) of the inclusion complexes of some phenols with α-β-cyclodextrin are estimated based on the variation of the fluorescent intensity and modified Harad' equations.

  2. Fluorescence Studied of Dissociation Constant of Cyclodextrin With Phenol Derivatives

    Institute of Scientific and Technical Information of China (English)

    ZHANG; YouMing

    2001-01-01

    α-and β-cyclodextrins consisting of six and seven glucose residues respectively, have lipophilic cavities with different inner diameters. They form host-guest inclusion complexes with hydrophobic organic and organometallic guest molecules in aqueous solution. These host-guest complexes have proved to be excellent model systems for studying the nature of noncovalent bonding forces in aqueous media. They have provided valuable insights into the hydrophobic effect and London dispersion forces and are good model for understanding the specificity of enzyme substrate interactions [1] Evidence for the formation of inclusion complexes have been provided from calovimetric titration [2] NMR[33], circular dichroism[4], U V[1] and fluorescence spectra[5] and conductometric method[6] etc. H ere we report a new fluorimetric method for a study on the reaction of the host-guest inclusion complexes of cyclodextrin with phenols. Dissociation constants (Kd) of the inclusion complexes of some phenols with α-β-cyclodextrin are estimated based on the variation of the fluorescent intensity and modified Harad' equations.……

  3. Flexible Acyclic Polyol-Chloride Anion Complexes and Their Characterization by Photoelectron Spectroscopy and Variable Temperature Binding Constant Determinations.

    Science.gov (United States)

    Shokri, Alireza; Wang, Xue-Bin; Wang, Yanping; O'Doherty, George A; Kass, Steven R

    2016-03-17

    Flexible acyclic alcohols with one to five hydroxyl groups were bound to a chloride anion and these complexes were interrogated by negative ion photoelectron spectroscopy and companion density functional theory computations. The resulting vertical detachment energies are reproduced on average to 0.10 eV by M06-2X/aug-cc-pVTZ predictions and range from 4.45-5.96 eV. These values are 0.84-2.35 eV larger than the adiabatic detachment energy of Cl(-) as a result of the larger hydrogen bond networks in the bigger polyols. Adiabatic detachment energies of the alcohol-Cl(-) clusters are more difficult to determine both experimentally and computationally. This is due to the large geometry changes that occur upon photodetachment and the large bond dissociation energy of H-Cl which enables the resulting chlorine atom to abstract a hydrogen from any of the methylene (CH2) or methine (CH) positions. Both ionic and nonionic hydrogen bonds (i.e., OH···Cl(-) and OH···OH···Cl(-)) form in the larger polyols complexes and are found to be energetically comparable. Subtle structural differences, consequently can lead to the formation of different types of hydrogen bonds, and maximizing the ionic ones is not always preferred. Solution equilibrium binding constants between the alcohols and tetrabutylammonium chloride (TBACl) in acetonitrile at -24.2, +22.0, and +53.6 °C were also determined. The free energies of association are nearly identical for all of the substrates (i.e., ΔG° = -2.8 ± 0.7 kcal mol(-1)). Compensating enthalpy and entropy values reveal, contrary to expectation and the intrinsic gas-phase preferences, that the bigger systems with more hydroxyl groups are entropically favored and enthalpically disfavored relative to the smaller species. This suggests that more solvent molecules are released upon binding TBACl to alcohols with more hydroxyl groups and is consistent with the measured negative heat capacities. These quantities increase with molecular

  4. Flexible Acyclic Polyol-Chloride Anion Complexes and Their Characterization by Photoelectron Spectroscopy and Variable Temperature Binding Constant Determinations

    Energy Technology Data Exchange (ETDEWEB)

    Shokri, Alireza; Wang, Xue B.; Wang, Yangping; O' Doherty, George A.; Kass, Steven R.

    2016-03-17

    Flexible acyclic alcohols with 1–5 hydroxyl groups were bound to chloride anion and these complexes were interrogated by negative ion photoelectron spectroscopy and companion density functional theory computations. The resulting vertical detachment energies are reproduced on average to 0.10 eV by M06-2X/aug-cc-pVTZ predictions and range from 4.45 – 5.96 eV. These values are 0.84 – 2.35 eV larger than the adiabatic detachment energy of Cl– as a result of the larger hydrogen bond networks in the bigger polyols. Adiabatic detachment energies of the alcohol–Cl– clusters are more difficult to determine both experimentally and computationally. This is due to the large geometry changes that occur upon photodetachment and the large bond dissociation energy of H–Cl which enables the resulting chlorine atom to abstract a hydrogen from any of the methylene (CH2) or methine (CH) positions. Both ionic and non-ionic hydrogen bonds (i.e., OH•••Cl– and OH•••OH•••Cl–) form in the larger polyols complexes, and are found to be energetically comparable. Subtle structural differences, consequently can lead to the formation of different types of hydrogen bonds and maximizing the ionic ones is not always preferred. Solution equilibrium binding constants between the alcohols and tetrrabuylammonium chloride (TBACl) in acetonitrile at -24.2, 22.0, and 53.6 °C were also determined. The free energies of association are nearly identical for all of the substrates (i.e., ΔG° = -2.8 ± 0.7 kcal mol–1). Compensating enthalpy and entropy values reveal, contrary to expectation and the intrinsic gas-phase preferences, that the bigger systems with more hydroxyl groups are entropically favored and enthalpically disfavored relative to the smaller species. This suggests that more solvent molecules are released upon binding TBACl to alcohols with more hydroxyl groups and is consistent with the measured negative heat capacities. These quantities increase with

  5. Estimation of the pH-independent binding constants of alanylphenylalanine and leucylphenylalanine stereoisomers with beta-cyclodextrin in the presence of urea.

    Science.gov (United States)

    Li, J; Waldron, K C

    1999-01-01

    The separation of stereoisomers, particularly enantiomers, is important when their physiological activity differs. We have resolved the four stereoisomers each of alanylphenylalanine (Ala-Phe) and of leucylphenylalanine (Leu-Phe) by capillary electrophoresis using beta-cyclodextrin as a buffer additive and urea to enhance its solubility. A study of the influence of pH and beta-cyclodextrin concentration on the separations showed that weak inclusion complexes were formed between the dipeptides and chiral selector. It was found that pH could alter the migration order of enantiomers L-Ala-L-Phe and D-Ala-D-Phe, as well as L-Leu-L-Phe and D-Leu-D-Phe; however, there was no change in order for the other pairs of optical isomers. Electrophoretic mobility data were used to estimate the acid dissociation constants of the dipeptide isomers at pH < 7 with no chiral selector present. By varying the concentration of beta-cyclodextrin, the chiral selector, the binding constants of Ala-Phe and Leu-Phe optical isomers in their fully protonated and zwitterionic forms were estimated. For the four Ala-Phe stereoisomers, K = 42-66 M(-1) and 4-41 M(-1) for the cationic and zwitterionic forms, respectively. For the four Leu-Phe stereoisomers, K = 43-94 M(-1) and 1-28 M(-1) for the cationic and zwitterionic forms, respectively.

  6. Binding equilibrium study between Mn( Ⅱ ) and HSA or BSA

    Institute of Scientific and Technical Information of China (English)

    LIANG, Hong; TU, Chu-Qiao; ZHANG, Hong-Zhi; SHEN, Xing-Can; ZHOU, Yong-Qia; SHEN, Pan-Wen

    2000-01-01

    The binding of Mn( Ⅱ ) to human serum allbumin (HSA) or bovine serum albumin (BSA) has been studied by equilibrium dialysis at physiological pH (7.43). The Scatchard analysis indicates that there are 1.8 and 1.9 strong binding sites of Mn( Ⅱ ) in HSA and BSA, respectively. The successive stobility constants which are reported for the first time are obtained by non-linear least-squares methods fitting Bjerrum formula.For both Mn( Ⅱ )-HSA and Mn( Ⅱ )-BSA systems, the order of magnitude of K1 was found to be 104. The analyses of Hill plots and free energy coupling show that the positive cooperative effect was found in both Mn( Ⅱ )-HSA and Mn(Ⅱ)-BSA systems. The results of Mn ( Ⅱ ) competing with Cu ( Ⅱ )、Zn( Ⅱ )、Cd( Ⅱ ) or Ca( Ⅱ ) to bind to HSA or BSA further support the conjecture that there are two strong binding sites of Mn( Ⅱ ) in both HSA and BSA. One is most probably located at the tripeptide segment of N-terminal sequence of HSA and BSA molecules involving four groups composed of nitrogen atoms, and the fifth coordination atom is the carboxyl oxygen of Asp1. The coordinated atoms of the other are most probably almost all oxygen atoms.

  7. [Spectroscopic studies on the binding of phenazopyridine hydrochloride and bovine serum albumin].

    Science.gov (United States)

    Zhou, Hong; Chen, Chang-Yun; Xie, An-Jian

    2007-09-01

    The binding of phenazopyridine hydrochloride and bovine serum albumin under physiological conditions was studied by spectroscopic method. The quenching mechanism of the fluorescence of bovine serum albumin by phenazopyridine hydrochloride was studied with fluorescence and absorption spectroscopy. The binding constant Kb and the number of binding sites n were determined at different temperatures according to Scatchard equation, and the main binding force was discussed by thermodynamic equations. The effect of the drug on bovine serum albumin conformation was also studied by using synchronous fluorescence spectroscopy. The quenching mechanism of phenazopyridine hydrochloride to bovine serum albumin is static quenching and non-radiation energy transfer. The binding constants Kb at 15, 25 and 37 degrees C are 2.47 x 10(7), 9.15 x 10(6) and 4.36 x 10(6) mol(-1) with one binding site, respectively. The thermodynamic parameters of the reaction are DeltaH = -71.2 kJ x mol(-1), and DeltaS = 124.8 J x mol(-1) x K(-1). Binding phenazopyridine hydrochloride to bovine serum albumin is a spontaneous inter-molecular interaction in which entropy increases and Gibbs free energy decreases. The binding distance r between phenazopyridine hydrochloride and bovine serum albumin is 1.61 nm according to Forster theory of non-radiation energy transfer. The binding force is electrostatic interaction. Phenazopyridine hydrochloride can be deposited and transported by serum protein in vivo. Phenazopyridine hydrochloride does affect the serum protein conformation. PMID:18051539

  8. Binding of amifostine to human serum albumin: a biophysical study.

    Science.gov (United States)

    Sun, Yifu; Wu, Han; Zhao, Guoqing; Shi, Ying

    2015-02-01

    The aim of this present work is to investigate the interaction between amifostine and human serum albumin (HSA) in simulated physiological conditions by spectroscopic methods to reveal potential toxic effects of the drug. The results reflected that amifostine caused fluorescence quenching of HSA through a static quenching process, which was further confirmed by the electrochemical experiments. The binding constants at 290, 297 and 304 K were obtained as 2.53 × 10(5) /M, 8.13 × 10(4) /M and 3.59 × 10(4) /M, respectively. There may be one binding site of amifostine on HSA. The thermodynamic parameters indicated that the interaction between amifostine and HSA was driven mainly by hydrogen bonding and electrostatic forces. Synchronous fluorescence spectra, circular dichroism and Fourier transform infrared spectroscopy results showed amifostine binding slightly changed the conformation of HSA with secondary structural content changes. Förster resonance energy transfer study revealed high possibility of energy transfer with amifostine-Trp-214 distance of 3.48 nm. The results of the present study may provide valuable information for studying the distribution, toxicological and pharmacological mechanisms of amifostine in vivo. PMID:24962599

  9. Study on the proteins-luminol binding by use of luminol as a fluorescence probe

    Science.gov (United States)

    He, Xili; Song, Zhenghua

    2013-10-01

    In this paper, a new mathematical equation of lg(F0 - F)/F = 1/nlg[P] + 1/nlgKa, which was used to obtain interaction parameters (the binding constant Ka and the number of binding sites n) between the protein and the small molecule ligand by using the ligand as a fluorescence (FL) probe, was constructed for the first time. The interaction parameters between myoglobin, catalase, lysozyme, bovine serum albumin (BSA) and luminol were obtained by this equation with luminol used as a FL probe, showing that the binding constants Ka were 8.78 × 105, 4.47 × 105, 4.21 × 104 and 3.95 × 104 respectively, and the number of binding sites n approximately equaled to 1.0 for myoglobin, catalase, and 2.0 for lysozyme, BSA. The interactions of ferritin, ovalbumin, aldolase, chymotrypsinogen and ribonuclease with luminol were also studied by this method. The binding constants Ka were at 104-105 level, and the number of binding sites n mostly approximately equaled to 2.0. The binding ability of luminol to the studied proteins followed the pattern: myoglobin > aldolase > ferritin > ovalbumin > catalase > ribonuclease > lysozyme > BSA > chymotrypsinoge.

  10. Binding constants of inclusion complexes of nitroimidazoles with {beta}-cyclodextrins in the absence and presence of PVP

    Energy Technology Data Exchange (ETDEWEB)

    Chadha, Renu [University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014 (India)]. E-mail: renukchadha2004@yahoo.co.in; Jain, D.V.S. [Depatment of Chemistry, Panjab University, Chandigarh 160014 (India); Aggarwal, Amit [University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014 (India); Singh, Surjit [GND University, Amritsar, Panjab (India); Thakur, Deepika [University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014 (India)

    2007-07-01

    Thermodynamics of complexation of 5-nitroimidazoles with {beta}-cyclodextrin and its methylated and hydroxypropyl derivatives in water and in 0.25% polyvinylpyrrolidone are determined by solution calorimetry. A 1:1 stoichiometry was established. The equilibrium constant (K) for all the nitroimidazoles fall in the range 1000-1900 M{sup -1} suitable for use of cyclodextrins as drug carriers. The complexation ability is significantly enhanced by methylation of the {beta}-cyclodextrin. The stability constant increased in the order metronidazole < ornidazole < tinidazole < secnidazole. The presence of polyvinylpyrrolidone enhances the stability constants.

  11. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism

    Science.gov (United States)

    Zeng, Hua-jin; Yang, Ran; You, Jing; Qu, Ling-bo; Sun, Yan-jun

    2016-01-01

    The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly through electrostatic and hydrophobic interactions with one binding site. Synchronous fluorescence, three-dimensional fluorescence, and molecular docking results revealed that liquiritigenin bound directly to the enzyme cavity site and this binding influenced the microenvironment of the hyaluronidase activity site, resulting in reduced hyaluronidase activity. The present study provides useful information for clinical applications of liquiritigenin as a hyaluronidase inhibitor. PMID:27313960

  12. BDflex: A method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations

    Science.gov (United States)

    Greives, Nicholas; Zhou, Huan-Xiang

    2012-10-01

    A method developed by Northrup et al. [J. Chem. Phys. 80, 1517 (1984)], 10.1063/1.446900 for calculating protein-ligand binding rate constants (ka) from Brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long BD simulations necessary for ka calculation. Here, we propose a new method called BDflex for ka calculation that circumvents this problem. The basic idea is to separate the whole space into an outer region and an inner region, and formulate ka as the product of kE and bar η _d, which are obtained by separately solving exterior and interior problems. kE is the diffusion-controlled rate constant for the ligand in the outer region to reach the dividing surface between the outer and inner regions; in this exterior problem conformational fluctuations can be neglected. bar η _d is the probability that the ligand, starting from the dividing surface, will react at the binding site rather than escape to infinity. The crucial step in reducing the determination of bar η _d to a problem confined to the inner region is a radiation boundary condition imposed on the dividing surface; the reactivity on this boundary is proportional to kE. By confining the ligand to the inner region and imposing the radiation boundary condition, we avoid multiple-crossing of the dividing surface before reaction at the binding site and hence dramatically cut down the total simulation time, making the treatment of conformational fluctuations affordable. BDflex is expected to have wide applications in problems where conformational fluctuations of the molecules are crucial for productive ligand binding, such as in cases where transient widening of a bottleneck allows the ligand to access the binding pocket, or the binding site is properly formed only after ligand entrance induces the closure of a lid.

  13. Fluorescence spectroscopic studies on binding of a flavonoid antioxidant quercetin to serum albumins

    Indian Academy of Sciences (India)

    Beena Mishra; Atanu Barik; K Indira Priyadarsini; Hari Mohan

    2005-11-01

    Binding of quercetin to human serum albumin (HSA) was studied and the binding constant measured by following the red-shifted absorption spectrum of quercetin in the presence of HSA and the quenching of the intrinsic protein fluorescence in the presence of different concentrations of quercetin. Fluorescence lifetime measurements of HSA showed decrease in the average lifetimes indicating binding at a location, near the tryptophan moiety, and the possibility of fluorescence energy transfer between excited tryptophan and quercetin. Critical transfer distance () was determined, from which the mean distance between tryptophan-214 in HSA and quercetin was calculated. The above studies were also carried out with bovine serum albumin (BSA).

  14. Dimer self-association via hydrogen bonding: Measurement and comparison of binding constants with 2-amidopyrimidine derivatives

    Science.gov (United States)

    Bednar, Victor; Elliott, K. Wade; Byrd, Emily; Woodford, Jeffrey N.

    2012-09-01

    A method based on 1H NMR was used to measure the self-assembly equilibrium constants for three acylated derivatives of 2-aminopyrimidine: 2-acetamidopyrimidine (1), 2-isopropylamidopyrimidine (2), and 2-neopentylamidopyrimidine (3). The synthesis of the latter two compounds is described. The self-association constant decreases from 1 to 2 to 3, which is attributed to the syn/anti conformational preference of the amide bond. For 1, complexation with chloroform must be included in order to explain the observed chemical shift values. Complementary density functional theory calculations (MP2/cc-pVTZ//B3LYP-D/cc-pVDZ) suggest a direct relationship between conformational preference of the amide bond and the self-assembly constant.

  15. Using Electrophoretic Mobility Shift Assays to Measure Equilibrium Dissociation Constants: GAL4-p53 Binding DNA as a Model System

    Science.gov (United States)

    Heffler, Michael A.; Walters, Ryan D.; Kugel, Jennifer F.

    2012-01-01

    An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (K[subscript D]) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel;…

  16. Dielectric constant of the polarizable dipolar hard sphere fluid studied by Monte Carlo simulation and theories

    OpenAIRE

    M. Valiskó; D. Boda

    2005-01-01

    A systematic Monte Carlo (MC) simulation and perturbation theoretical (PT) study is reported for the dielectric constant of the polarizable dipolar hard sphere (PDHS) fluid. We take the polarizability of the molecules into account in two different ways. In a continuum approach we place the permanent dipole of the molecule into a sphere of dielectric constant ε∞ in the spirit of Onsager. The high frequency dielectric constant ε∞ is calculated from the Clausius-Mosotti relation, while the diele...

  17. A model of mitochondrial creatine kinase binding to membranes: adsorption constants, essential amino acids and the effect of ionic strength

    DEFF Research Database (Denmark)

    Fedosov, Sergey; Belousova, Lubov; Plesner, Igor

    1993-01-01

    of mitCK adsorption capacity by another method at pH 7.4, when the enzyme is almost protonated, gave View the MathML source. The effect of ionic strength on mitCK adsorption may be described in terms of Debye-Hückel's theory for activity coefficients assuming the charges of the interacting species......The quantitative aspects of mitochondrial creatinekinase (mitCK) binding to mitochondrial membranes were investigated. A simple adsorption and binding model was used for data fitting, taking into account the influence of protein concentration, pH, ionic strength and substrate concentration...... on the enzyme adsorption. An analysis of our own data as well as of the data from the literature is consistent with the adsorption site of the octameric mitCK being composed of 4 amino acid residues with pK = 8.8 in the free enzyme. The pK value changes to 9.8 upon binding of the protein to the membrane. Lysine...

  18. Study of cylindrically symmetric solutions in metric f(R) gravity with constant R

    CERN Document Server

    Rincon-Ramirez, Monica Tatiana

    2013-01-01

    Solutions for cylindrically symmetric spacetimes in f(R) gravity are studied. As a first approach, R=constant is assumed. A solution was found such that it is equivalent to a result given by Azadi et al. for R=0 and a metric was found for R=constant different from zero. Comparison with the case of general relativity with cosmological constant is made and the metric constants are given in terms of \\Lambda. Overlap with arXiv:0810.4673 [gr-qc] by A. Azadi, D. Momeni and M. Nouri-Zonoz

  19. HypCal, a general-purpose computer program for the determination of standard reaction enthalpy and binding constant values by means of calorimetry.

    Science.gov (United States)

    Arena, Giuseppe; Gans, Peter; Sgarlata, Carmelo

    2016-09-01

    The program HypCal has been developed to provide a means for the simultaneous determination, from data obtained by isothermal titration calorimetry, of both standard enthalpy of reaction and binding constant values. The chemical system is defined in terms of species of given stoichiometry rather than in terms of binding models (e.g., independent or cooperative). The program does not impose any limits on the complexity of the chemical systems that can be treated, including competing ligand systems. Many titration curves may be treated simultaneously. HypCal can also be used as a simulation program when designing experiments. The use of the program is illustrated with data obtained with nicotinic acid (niacin, pyridine-3 carboxylic acid). Preliminary experiments were used to establish the rather different titration conditions for the two sets of titration curves that are needed to determine the parameters for protonation of the carboxylate and amine groups.

  20. The complexity of condensed tannin binding to bovine serum albumin--An isothermal titration calorimetry study.

    Science.gov (United States)

    Kilmister, Rachel L; Faulkner, Peta; Downey, Mark O; Darby, Samuel J; Falconer, Robert J

    2016-01-01

    Isothermal titration calorimetry was applied to study the binding of purified proanthocyanidin oligomers to bovine serum albumin (BSA). The molecular weight of the proanthocyanidin oligomer had a major impact on its binding to BSA. The calculated change in enthalpy (ΔH) and association constant (Ka) became greater as the oligomer size increased then plateaued at the heptameric oligomer. These results support a model for precipitation of proteins by proanthocyanidin where increased oligomer size enhanced the opportunity for cross linkages between proteins ultimately forming sediment-able complexes. The authors suggest tannin binding to proteins is opportunistic and involves multiple sites, each with a different Ka and ΔH of binding. The ΔH of binding comprises both an endothermic hydrophobic interaction and exothermic hydrogen bond component. This suggests the calculated entropy value (ΔS) for tannin-protein interactions is subject to a systematic error and should be interpreted with caution.

  1. Study on the bindings of dichlorprop and diquat dibromide herbicides to human serum albumin by spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Tunç, Sibel, E-mail: stunc@akdeniz.edu.tr; Duman, Osman, E-mail: osmanduman@akdeniz.edu.tr; Soylu, İnanç; Kancı Bozoğlan, Bahar

    2014-05-01

    Highlights: • The affinity of DCP to HSA is higher than DQ. • DCP and DQ have quenched the fluorescence emission spectrum of HSA by static quenching mechanism. • Electrostatic interactions are very important in HSA-DCP and HSA-DQ complexes. • Binding constants, numbers of binding sites and thermodynamic parameters have been calculated. • The binding of DQ changes the conformation of protein, on the contrary to DCP. - Abstract: The interactions of dichlorprop (DCP) and diquat dibromide (DQ) herbicides with human serum albumin (HSA) protein were studied by UV absorption, fluorescence, synchronous fluorescence and circular dichroism (CD) spectroscopy. Both DCP and DQ quenched the fluorescence emission spectrum of HSA through the static quenching mechanism. The Stern–Volmer quenching constant, binding constant, the number of binding sites and thermodynamic parameters were determined at 288 K, 298 K, 310 K and 318 K. In HSA-DCP and HSA-DQ systems, an increase in temperature led to a decrease in the Stern–Volmer quenching constant and binding constant. One binding site was obtained for DCP and DQ on HSA. It was found that DCP can bind to HSA with higher affinity than DQ. Negative ΔH and positive ΔS values were obtained for the binding processes between protein and herbicide molecules. This result displayed that electrostatic interactions play a major role in the formation of HSA-DCP and HSA-DQ complexes. The binding processes were exothermic reactions and spontaneous. In addition, synchronous fluorescence and CD spectra of HSA revealed that the binding of DCP to HSA did not cause a significant conformational change in protein, but the interaction of DQ with HSA led to an alteration in the protein structure.

  2. Receptor binding studies of the living heart

    International Nuclear Information System (INIS)

    Receptors form a class of intrinsic membrane proteins (or glycoproteins) defined by the high affinity and specificity with which they bind ligands. Many receptors are associated directly or indirectly with membrane ion channels that open or close after a conformational change of the receptor induced by the binding of the neurotransmitter. Changes in number and/or affinity of cardiac neurotransmitter receptors have been associated with myocardial ischemia and infarction, congestive heart failure, and cardiomyopathy as well as diabetes or thyroid-induced heart muscle disease. These alterations of cardiac receptors have been demonstrated in vitro on membrane homogenates from samples collected mainly during surgery or postmortem. The disadvantage of these in vitro binding techniques is that receptors lose their natural environment and their relationships with the other components of the tissue

  3. Study on Optical Constants and Refractive Index Dispersion of Neutral red Doped Polymer Film

    Directory of Open Access Journals (Sweden)

    Hussain A. Badran

    2012-01-01

    Full Text Available Problem statement: The some optical constants polymer thin film with red dye 3-amino-7-dimethylamino-2-methyl phenazine (NR as the guest material and Polyvinylpyrrolidone (PVP as the host material were prepared by adulteration and spin-coating methods. Approach: The values of some important parameters (refractive index n, extinction coefficient K and dielectric constant ε∞ of polymer thin film are determined from these spectra. Results: It has been found that the dispersion data obey the single oscillator relation of the Wemple-DiDomenico model, from which the dispersion parameters and high-frequency dielectric constant were determined. The estimation of the E0, Ed and ε∞ are 1.27, 3.175 and 3.5 eV respectively. Conclusion: The single oscillator model was used to calculate their optical constants from the transmittance and reflectance spectra. The dispersion of the refractive index in film follow the single electronic oscillator mode relation. The UV-Visible spectroscopic studies showed that, the NR film have high refractive index and high dielectric constant. The variation of the dielectric constant with the wavelength indicates that some interactions between photon and electrons in the films are produced in this wavelength range. These interactions are observed on the shapes of the real and imaginary parts of the dielectric constant and they cause the formation of peaks in the dielectric spectra which depends on the material type.

  4. Microdialysis-liquid chromatographic study on competitive binding of drugs to protein

    Institute of Scientific and Technical Information of China (English)

    汪海林; 邹汉法; 张玉奎

    1997-01-01

    A new method to determine the interaction between drug and protein has been developed by utilizing the technique of microdialysis sampling with the ketoprofen and the human serum albumin (HSA) as the model of drug and protein.Two kinds of binding sites of HSA to ketoprofen have been observed.The binding constants and number of binding sites obtained by the Scatchard equation are 0.799,3.18×106 mol-1 L and 2.15,2.01×105 mol-1 L,respectively The displacement binding of drugs to HSA has also been studied.The strong displacement of competitive binding of ibuprofen with ketoprofen to HSA was observed,which means that the primary binding site of HSA to ketoprofen and that to ibuprofen are the same.However,only a weaker displacement of warfarin for the association of ketoprofen with HSA was observed,which may suggest that the primary binding site of HSA to ketoprofen is different from that to warfarin.Such a displacement effect for competitive binding of drugs to HSA was explained by the displacement model i

  5. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism

    OpenAIRE

    Hua-jin Zeng; Ran Yang; Jing You; Ling-bo Qu; Yan-jun Sun

    2016-01-01

    The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly thro...

  6. Study of caffeine binding to human serum albumin using optical spectroscopic methods

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The binding of caffeine to human serum albumin (HSA) under physiological conditions has been stud-ied by the methods of fluorescence,UV-vis absorbance and circular dichroism (CD) spectroscopy. The mechanism of quenching of HSA fluorescence by caffeine was shown to involve a dynamic quenching procedure. The number of binding sites n and apparent binding constant Kb were measured by the fluorescence quenching method and the thermodynamic parameters △H,△G,△S were calculated. The results indicate that the binding is mainly enthalpy-driven,with van der Waals interactions and hydrogen bonding playing major roles in the reaction. The distance r between donor (HSA) and acceptor (caffeine) was obtained according to the Frster theory of non-radiative energy transfer. Synchronous fluorescence,CD and three-dimensional fluorescence spectroscopy showed that the microenvironment and conformation of HSA were altered during the reaction.

  7. Study of Stability Constants of Fe (Iii And Mn (Ii with Chloramphenicol by Paper Electrophoretic Technique

    Directory of Open Access Journals (Sweden)

    Arvind Singh

    2014-12-01

    Full Text Available Stabilty constant of binary complexes of Fe(III and Mn(II with medicinally important ligand chloramphenicol antibiotics in solution were determined by paper electrophoretic technique. Stability constant of the complexes were determined at 25°C temperature and 0.1M (HClO4 ionic strength. Our study is based upon the migration of a spot of metal ions on a paper strip at different pH against mobility gives information about the binary complexes and permits to calculate their stability constant. The stability constant data revealed that chloramphenicol may be used as chelating agent in chelation for medical treatment of metal overload or poisoning.

  8. Novel chiral N4S2- and N6S3-donor macrocyclic ligands: synthesis, protonation constants, metal-ion binding and asymmetric catalysis in the Henry reaction.

    Science.gov (United States)

    Gao, Jian; Martell, A E

    2003-08-01

    New hydrophobic chiral macrocyclic ligands L1-L3 with chiral diamino and thiophene moieties have been synthesized by the Schiff base condensation approach. Protonation constants of L1 and L2 were determined by potentiometry titration. Metal-ion binding experiments exhibited that L1 and L3 are pronounced in selective recognition, Ag+, Cu2+ and Ca2+ ions among the surveyed metal ions (Cu2+, Co2+, Ni2+, Zn2+, Cd2+, Pb2+, Ag+, Li+, Na+, K+, and Ca2+). L1 was found to spectroscopically detect the presence of Cu2+ and Ca2+ to function as a multiple readout sensor. The detection limit for Ca2+ ions was found to be 9.8 x 10(-5) M in CH2Cl2-MeOH solution. The trimeric chiral ligand L3 has been shown to be an efficient auxiliary in a Zn(II)-mediated enantioselective Henry reaction. PMID:12948208

  9. Dielectric constant of the polarizable dipolar hard sphere fluid studied by Monte Carlo simulation and theories

    Directory of Open Access Journals (Sweden)

    M.Valiskó

    2005-01-01

    Full Text Available A systematic Monte Carlo (MC simulation and perturbation theoretical (PT study is reported for the dielectric constant of the polarizable dipolar hard sphere (PDHS fluid. We take the polarizability of the molecules into account in two different ways. In a continuum approach we place the permanent dipole of the molecule into a sphere of dielectric constant ε∞ in the spirit of Onsager. The high frequency dielectric constant ε∞ is calculated from the Clausius-Mosotti relation, while the dielectric constant of the polarizable fluid is obtained from the Kirkwood-Fröhlich equation. In the molecular approach, the polarizability is built into the model on the molecular level, which makes the interactions non-pairwise additive. Here we use Wertheim's renormalized PT method to calculate the induced dipole moment, while the dielectric constant is calculated from our recently introduced formula. We also apply a series expansion for the dielectric constant both in the continuum and the molecular approach. These series expansions ensure a better agreement with simulation results. The agreement between our MC data and the PT results in the molecular approach is excellent for low to moderate dipole moments and polarizabilities. At stronger dipolar interactions ergodicity problems and anizotropic behaviour appear where simulation results become uncertain and the theoretical approach becomes invalid.

  10. AFM studies of nonspecific binding of enzyme on DNA

    Institute of Scientific and Technical Information of China (English)

    张益; 谢恒月; 等

    1996-01-01

    Atomic force microscope(AFM) is used to study restriction endonuclease digestion of plasmid DNA,pWRr plasmid DNA is digested by Hind Ⅲ,and the specific and the nonspecific binding of the restriction endonuclease are imaged,and the biological function of the enzyme binding to nonspecific sites is discussed.In addition,it is found that nonspecific binding of Hind ǚ could not induce the DNA characteristic bending angle.

  11. An Empirical Rate Constant Based Model to Study Capacity Fading in Lithium Ion Batteries

    Directory of Open Access Journals (Sweden)

    Srivatsan Ramesh

    2015-01-01

    Full Text Available A one-dimensional model based on solvent diffusion and kinetics to study the formation of the SEI (solid electrolyte interphase layer and its impact on the capacity of a lithium ion battery is developed. The model uses the earlier work on silicon oxidation but studies the kinetic limitations of the SEI growth process. The rate constant of the SEI formation reaction at the anode is seen to play a major role in film formation. The kinetics of the reactions for capacity fading for various battery systems are studied and the rate constants are evaluated. The model is used to fit the capacity fade in different battery systems.

  12. Study of MMLV RT- Binding with DNA using Surface Plasmon Resonance Biosensor

    Institute of Scientific and Technical Information of China (English)

    Lei WU; Ming-Hui HUANG; Jian-Long ZHAO; Meng-Su YANG

    2005-01-01

    Surface plasmon resonance biosensor technique was used to study the binding of Moloney murine leukemia virus reverse transcriptase without RNase H domain (MMLV RT-) with DNA in the absence and in the presence of inhibitors. Different DNA substrates, including single-stranded DNA (ssDNA),DNA template-primer (T-P) duplex and gapped DNA, were immobilized on the biosensor chip surface using streptavidin-biotin, and MMLV RT--DNA binding kinetics were analyzed by different models. MMLV RT-could bind with ssDNA and the binding was involved in conformation change. MMLV RT- binding DNA T-P duplex and gapped DNA could be analyzed using the simple 1:1 Langmuir model. The lack of RNase H domain reduced the affinity between MMLV RT- and T-P duplex. The effects of RT inhibitors, including efavirenz, nevirapine and quercetin, on the interaction between MMLV RT- and gapped DNA were analyzed according to recovered kinetics parameters. Efavirenz slightly interfered with the binding between RT and DNA and the affinity constant in the presence of the inhibitor (KA=1.21× 106 M-1) was lower than in the absence of the inhibitor (KA=4.61× 106 M-1). Nevirapine induced relatively tight binding between RT and DNA and the affinity constant in the presence of the inhibsitor (KA=l.47×107 M-1) was approximately three folds higher than without nevirapine, mainly due to rapid association and slow dissociation. Quercetin, a flavonoid originating from plant which has previously shown strong inhibition of the activity of RT, was found to have minimal effect on the RT-DNA binding.

  13. Direct zonal liquid chromatographic method for the kinetic study of actinomycin-DNA binding.

    Science.gov (United States)

    Vidal-Madjar, Claire; Florentina, Cañada-Cañada; Gherghi, Ioanna; Jaulmes, Alain; Pantazaki, Anastasia; Taverna, Myriam

    2004-07-01

    The binding of an anticancer drug (actinomycin D or ACTD) to double-stranded DNA (dsDNA) was studied by means of high-performance liquid chromatography (HPLC). ACTD is an antitumor antibiotic containing one chromophore group and two pentapeptidic lactone cycles that binds dsDNA. Incubations of ACTD with DNA were performed at physiological pH. The complexed and free ligand concentrations of the mixture were quantified at 440 nm from their separation on a size-exclusion chromatographic (SEC) column using the same buffer for the elution and the sample incubation. The DNA and the ACTD-DNA complexes were eluted at the column exclusion volume while the ligand was retained on the support. An apparent binding curve was obtained by plotting the amount emerging at the exclusion column volume against that eluted at free ACTD retention volume. A dissociating effect was evidenced and the binding parameters were significantly different from those obtained at equilibrium by visible absorbance titration. The equilibrium binding parameters determined by absorption spectroscopy were used as starting data in the numerical simulations of the chromatographic process. The results showed a strong dependency of the apparent binding parameters on the reaction kinetics. Finally the comparison of the apparent binding curve obtained from the HPLC experiments and from the numerical simulations permitted an evaluation of the dissociation rate constant (kd = 0.004 s(-1)). PMID:15296384

  14. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

    Directory of Open Access Journals (Sweden)

    Ankur Bikash Pradhan

    Full Text Available Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride with single and double stranded form of polyriboadenylic acid (hereafter poly-A using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A with high affinity while it does not interact at all with the double stranded (ds form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

  15. Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: a basis set and correlation study.

    Science.gov (United States)

    Kjaer, Hanna; Nielsen, Monia R; Pagola, Gabriel I; Ferraro, Marta B; Lazzeretti, Paolo; Sauer, Stephan P A

    2012-09-01

    In this article, we present the so far most extended investigation of the calculation of the coupling constant polarizability of a molecule. The components of the coupling constant polarizability are derivatives of the nuclear magnetic resonance (NMR) indirect nuclear spin-spin coupling constant with respect to an external electric field and play an important role for both chiral discrimination and solvation effects on NMR coupling constants. In this study, we illustrate the effects of one-electron basis sets and electron correlation both at the level of density functional theory as well as second-order polarization propagator approximation for the small molecule hydrogen peroxide, which allowed us to perform calculations with the largest available basis sets optimized for the calculation of NMR coupling constants. We find a systematic but rather slow convergence with the one-electron basis set and that augmentation functions are required. We observe also large and nonsystematic correlation effects with significant differences between the density functional and wave function theory methods. PMID:22618604

  16. Influence of turbulence on power quality. Comparative study between constant and variable wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Longatt, Francisco M. [Universidad Nacional Experimental Politecnica de la Fuerza Armada Nacional (UNEFA), Aragua (Venezuela). Grupo de Investigaciones Avanzadas en Energia

    2008-07-01

    Turbulence is clearly a complex process, and one which cannot be represented simply in terms of deterministic equations. The main objective of this paper is a comparative study of impact on dynamic behavior on constant and variable speed wind turbines considering several turbulence sceneries. We consider integration on a test system of squirrel cage induction generator for constant speed wind turbine, and doubly fed induction generator for variable speed wind turbine. Several simulations with different intensity of turbulences were developed, and conclusions are presented. Good dynamic behavior is evident on doubly fed induction generator, with controls. (orig.)

  17. Study of coupled-cluster correlations on electromagnetic transitions and hyperfine structure constants of W VI

    CERN Document Server

    Bhowmik, Anal; Roy, Sourav; Majumder, Sonjoy

    2016-01-01

    This work presents precise calculations of important electromagnetic transition amplitudes along with detail of their many-body correlations using relativistic coupled cluster method. Studies of hyperfine interaction constants, useful for plasma diagnostic, with this correlation exhaustive many-body approach are another important area of this work. The calculated oscillator strengths of allowed transitions, amplitudes of forbidden transitions and lifetimes are compared with the other theoretical results wherever available and they show a good agreement. Hyperfine constants of ?different isotopes of W VI, presented in this paper will be helpful to get accurate picture of abundances of this element in different astronomical bodies.

  18. Studies on dissociation energies of diatomic molecules using vibrational spectroscopic constants

    Institute of Scientific and Technical Information of China (English)

    HOU; Shilin(侯世林); SUN; Weiguo(孙卫国)

    2003-01-01

    New analytical expression and numerical approach are suggested to calculate dissociation energies De of diatomic molecular states using an extreme value method (EVM). Studies on some electronic states of OH, BH, N2, Br2, ClF and CO molecules show that the accuracy of the EVM dissociation energies depends on the number of correct vibrational constants used in the calculations. The convergence qualities of De are suggested to be an alternative physical criterion to measure the qualities of the various sets of vibrational constants from different literature for the same diatomic state.

  19. Study of surface cell Madelung constant and surface free energy of nanosized crystal grain

    Institute of Scientific and Technical Information of China (English)

    Zhang Wei-Jia; Wang Tian-Min; Rong Ai-Lun; Cui Min

    2006-01-01

    Surface cell Madelung constant is firstly defined for calculating the surface free energy of nanosized crystal grains,which explains the physical performance of small crystals and may be greatly beneficial to the analysis of surface states and the study of the dynamics of crystal nucleation and growth.A new approximative expression of the surface energy and relevant thermodynamic data are used in this calculation.New formula and computing method for calculating the Madelung constant α of any complex crystals are proposed,and the surface free energies and surface electrostatic energies of nanosized crystal grains and the Madelung constant of some complex crystals are theoretically calculated in this paper.The surface free energy of nanosized-crystal-grain TiO2 and the surface electrostatic energy (absolute value) of nanosized-crystal-grain α-A12O3 are found to be the biggest among all the crystal grains including those of other species.

  20. Study of Surface Cell Madelung Constant and Surface Free Energy of Nanosized Crystal Grain

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jia; WANG Tian-Min; CUI Min

    2005-01-01

    Surface cell Madelung constant is firstly defined in calculating surface free energy of nanosized crystal grains, which explains the physical performance of small crystals and may be great benefit to make surface analysis and study dynamics of crystal nucleus growth. A new ap- proximative expression of surface energy and relevant thermodynamic data was used in this cal- culation. A new formula and computing method for calculating the Madelung constant α of any complex crystals is proposed, and surface free energies and surface electrostatic energies of nano- sized crystal grains as well as Madelung constant of some complex crystals are theoretically cal- culated in this paper. The surface free energy of nanosized crystal grain TiO2 and surface elec- trostatic energy(absolute value) of nanosized crystal grain α-Al2O3 are found to be the biggest among other crystal grains.

  1. A single center study of the effects of trained fathers' participation in constant breastfeeding.

    Directory of Open Access Journals (Sweden)

    Khadijeh Raeisi

    2014-09-01

    Full Text Available Constant breastfeeding that depends on the family support. Fathers' involvement is as an important factor of successful breastfeeding. The aim of this study was to evaluate the influence of fathers' participation in constant breastfeeding in Vali-E-Asr Hospital, Tehran, Iran. This interventional study was piloted on spouses of pregnant women participating in pregnancy courses. The case group consisted of fathers attending training courses of breastfeeding during pregnancy (Group A, and the control group was made up of fathers who did not take part in training courses (Group B. The courses were held three times from the 30th week of gestation to the end of pregnancy in a family health research center. Fathers attended three training sessions where they were trained by brochures. After delivery newborns were weighted and examined for jaundice (3-5 days, 30 days, three and six months after birth. According to mothers' views, spouses' participation, encouragement and support in group A, was 11 times more than group B. It means that 47 (94% of spouses in the group A participated in mothers' constant breastfeeding, but fathers' participation in group B was 60% (30 spouses. This study showed that breastfeeding was more constant in the group that fathers participated in breastfeeding training course. One of the reasons for such a significant difference was spouses' participation, encouragement and support in the trained group. This study showed that fathers' involvement in training programs may influence constancy of breastfeeding.

  2. Novel Bioluminescent Binding Assays for Ligand–Receptor Interaction Studies of the Fibroblast Growth Factor Family

    Science.gov (United States)

    Song, Ge; Shao, Xiao-Xia; Wu, Qing-Ping; Xu, Zeng-Guang; Liu, Ya-Li; Guo, Zhan-Yun

    2016-01-01

    We recently developed novel bioluminescent binding assays for several protein/peptide hormones to study their interactions with receptors using the so far brightest NanoLuc reporter. To validate the novel bioluminescent binding assay using a variety of protein/peptide hormones, in the present work we applied it to the fibroblast growth factor (FGF) family using the prototype member FGF2 as an example. A fully active recombinant FGF2 retaining a unique exposed cysteine (Cys) residue was chemically conjugated with an engineered NanoLuc carrying a unique exposed Cys residue at the C-terminus via formation of an intermolecular disulfide linkage. The NanoLuc-conjugated FGF2 (FGF2-Luc) retained high binding affinity to the overexpressed FGFR1 and the endogenous FGF receptor with the calculated dissociation constants of 161 ± 21 pM (n = 3) and 25 ± 4 pM (n = 3), respectively. In competition binding assays using FGF2-Luc as a tracer, receptor-binding potencies of wild-type or mutant FGF2s were accurately quantified. Thus, FGF2-Luc represents a novel non-radioactive tracer for the quantitative measurement of ligand–receptor interactions in the FGF family. These data suggest that the novel bioluminescent binding assay can be applied to a variety of protein/peptide hormones for ligand–receptor interaction studies. PMID:27414797

  3. Revised stability constant, spectroscopic properties and binding mode of Zn(II) to FluoZin-3, the most common zinc probe in life sciences.

    Science.gov (United States)

    Marszałek, I; Krężel, A; Goch, W; Zhukov, I; Paczkowska, I; Bal, W

    2016-08-01

    2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) is used very broadly in life sciences as intra- and extracellular Zn(II) sensor selective for Zn(II) over Co(II), Ca(II) and Mg(II) ions at their physiological concentrations. It has been used for determination of relative and absolute levels of exchangeable Zn(II) in cells and extracellular fluids. Despite its popularity, the knowledge of its acid/base and Zn(II) coordination abilities and of its spectroscopic properties remained very limited. Also the published conditional dissociation constant ((C)Kd) values at pH7.4 are slightly discrepant, (15nM or 8.9nM). In this work we determined the (C)Kd for Zn(II) complexation by FluoZin-3 at pH7.4 with nitrilotriacetic acid (NTA) as competitor using two independent methods: fluorimetry and UV-Vis spectroscopy. For the first time, we investigated FluoZin-3 alone and complexed with Zn(II) in the wide range of pH, determining the total of eight pKa values from fluorescence spectra and from various regions of UV-Vis spectra. The validated values of (C)Kd (9.1±0.4nM; -log (C)Kd=8.04) and of the absolute (pH-independent) stability constant log βZnL (8.16±0.05) were provided by fluorescence spectroscopy experiments performed at 1μM concentrations. Our experiments demonstrated that both of aminocarboxylate moieties of FluoZin-3 bind the Zn(II) ion synergistically. PMID:27216451

  4. [Electron paramagnetic resonance study of the interactions between steroid hormones and binding proteins].

    Science.gov (United States)

    Basset, M; Chambaz, E M; Defaye, G; Metz, B

    1978-01-01

    Interaction of a spin labeled corticosteroid (desoxycorticosterone nitroxyde: DOC -NO) with three purified proteins (albumin, transcortin, progesterone binding protein: PBG) was studied by electron spin resonance (ESR) spectroscopy. DOC-NO was competitive with natural corticosteroids and therefore bound at the same site to specific binding proteins. ESR spectra in the presence of each of the proteins showed an immobilized (bound) form of the spin labeled steroid and allowed the calculation of the corresponding association constant (Ka) at equilibrium. The three binding proteins could be characterized by the ESR parameters of the DOC-NO bound form. The thermodynamic parameters (deltaH, deltaS) of the steroid-protein interactions were calculated from the ESR data obtained within a wide temperature range (3--40 degrees C). The ESR spectra width (2T) was used to evaluate the polarity of the spin label environment within the steroid binding site: a hydrophobic character was observed for transcortin whereas PBG exhibited a more hydrophilic steroid binding sits. The rotational correlation time of the three protein DOC-NO complexes at equilibrium were calculated from ESR data; the results were correlated with the protein molecular size and suggested a non spherical shape for the binding macromolecule in solution. Spin labelling of biologically active steroids thus provides a novel approach for the study of the interaction of these hormones with their binding protein. Providing a suitable spin label, the ESR parameters may allow the characterization of several types of binding sites of different biological significance for the same hormone, in biological fluids as well as in target tissues. PMID:83166

  5. Binding Equilibrium Studies Between Co2+ and HAS or BSA

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ Introduction Up to now,the interactions of Cu2+,Ni2+ and Zn2+ with serum albumin have been extensively studied[1-3].However,the interaction of serum with Co2+ has rarely been studied.Our study of Co2+-HSA by means of charge transfer spectra indicated that the metal center took an octahedron configuration and the binding site was probably located at the tripeptide segment of the N-terminal of albumin[4].Sadler et al.[5]has reported that the binding site of Co2+ in HSA is located at the tripeptide segment of HSA involving the four nitrogen atoms and a carboxyl oxygen atom of Aspl.In this paper the interaction of HSA and BSA with Co2+ at physiological pH is further studied by equilibrium dialysis.The number of binding sites and the cooperation among the binding sites are reported.According to the equilibrium dialysis results and the study of competition between Co2+ and Cu2+,Ca2+ or Zn2+ to be bound to HSA or BSA,it is suggested that there are three strong binding sites in both HSA and BSA.The possible locations of the strong binding sites of Co2+ in HSA and BSA have also been determined.

  6. Binding equilibrium study of phosphotungstic acid and HSA or BSA with UV spectrum, fluorescence spectrum and equilibrium dialysis

    Institute of Scientific and Technical Information of China (English)

    黄瑾; 袁余洲; 梁宏

    2002-01-01

    The binding equilibrium between phosphotungstic acid (H7[P(W2O7)6]@XH2O;PTA) and human serum albumin (HSA) or bovine serum albumin (BSA) has been studied by UV-Vis, fluorescence spectroscopies and equilibrium dialysis. It has been observed that UV absorption enhanced and the fluorescence quenched as the PTA binding to HSA or BSA at physiological pH 7.43( ± 0.02). The Scatchard analysis indicated that there exists a strong binding site of PTA in both HSA and BSA, and the successive stability constants of these two systems are obtained by nonlinear least-squares methods fitting Bjerrum formula.

  7. Competing binding of metal ions with protein studied by microdialysis

    Institute of Scientific and Technical Information of China (English)

    郭明; 孔亮; 毛希琴; 历欣; 邹汉法

    2002-01-01

    A method has been established to study the competing binding of metal ions with protein by a combined technique of microdialysis with high performance liquid chromatography (HPLC). Ni2+, Cd2+, Zn2+, Cu2+ and human serum albumin (HSA) were chosen as model metal ions and protein. The experimental results show that Ni2+ and Cu2+ share a common primary binding site on HSA, and Zn2+ and Cd2+ share a different common primary binding site from them, but there is a common multi-metal binding site for all of those four metal ions. This method show advantages of fast sampling, easily to be operated and especially to be useful when ideal spectroscopic probes are not available for the study of interaction between protein and metal ions.

  8. Model test study of evaporation mechanism of sand under constant atmospheric condition

    OpenAIRE

    Cui, Yu Jun; DING, Wenqi; Song, Weikang

    2014-01-01

    The evaporation mechanism of Fontainebleau sand using a large-scale model chamber is studied. First, the evaporation test on a layer of water above sand surface is performed under various atmospheric conditions, validating the performance of the chamber and the calculation method of actual evaporation rate by comparing the calculated and measured cumulative evaporations. Second,the evaporation test on sand without water layer is conducted under constant atmospheric condition. Both the evoluti...

  9. Study on the Interaction of Zinc Ion Binding with Human Serum Albumin using Isothermal Titration Calorimetry

    International Nuclear Information System (INIS)

    The interaction between zinc ion and human serum albumin (HSA) was investigated by nano-Watt- scale isothermal titration calorimetry (ITC). From the analysis of the ITC data, the binding characteristics and thermodynamic properties of the system were obtained and the binding mechanism was discussed. It was found that the experimental data fit well with the Langmuir's binding theory and the system behaved as a system with two classes of binding sites (high-affinity and low-affinity binding site). The binding number of high-affinity binding site (N1) is 1.40 and the binding constant (K1) is 2.72*105 L/mol. For the low-affinity binding site, the binding number (N2) is 1.55 and the binding constant (K2) is 3.78*103 L/mol. Moreover, it was indicated by the thermodynamic analysis that the binding processes of both types of binding sites were exothermic and spontaneous. The high-affinity binding was an enthalpy-entropy synergically driven process and the electrostatic interaction was the main force, while the low-affinity binding was an enthalpy driven process and this process was mainly driven by the van der Waals forces. (author)

  10. Study of binding glycyrrhetic acid to AT1 receptor

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Fengyun; (张凤云); YUE; Baozhen; (岳保珍); HE; Shipeng; (贺师鹏)

    2003-01-01

    To analyze the binding of glycyrrhetic acid (GA) to angiotensin II type I (AT1) receptor and to explore the mechanisms underlying the binding, primary cell culture of rat vascular smooth muscle cell (VSMC), radioactive ligand-receptor binding assay, lascer confocal scanning microscope (LCSM), Northern blot, 3H-TdR incorporation DNA assay were used in this study. The results suggest that specific binding of GA to AT1 receptor (IC50 value was 35.0 μmol/L) increases intracellular [Ca2+]i of VSMC, activates transcription factor c-myc and promotes the proliferation of VSMC, therefore GA was probably an agonist of AT1 receptor, providing a new target for GA's pharmaceutical effects.

  11. Experimental study of prompt neutron decay constant α for 300# pool reactor under mixed core

    International Nuclear Information System (INIS)

    The experimental study of prompt neutron decay constant α for 300# pool reactor under mixed core was carried out through a suit of reactor power spectral density measurement system. The two channel continuous current signals of neutron in the reactor were acquired by ionization chamber DL129 which was symmetrically putted in reactor core. The power spectral density, for two channel signals, was computed using the application program of data acquirement and data process analysis. Finally, by using the non-linear least squares method, the prompt neutron decay constant α was fitted. By comparison, the experimental results well accord to the theory calculation within the error range. The deviation can meet the actual need of project. (authors)

  12. A facile method for studying interaction of rhodamine B and bovine serum albumin:Towards physical-binding mediated fluorescence labeling of proteins

    Institute of Scientific and Technical Information of China (English)

    马宇星; 钟睿博; 郭俊; 刘雨双; 袁鸣; 白志军; 刘涛涛; 赵欣敏; 张峰

    2015-01-01

    Strategies for labeling proteins with fluorophores are always important for biotechnology. Here we take a model protein (bovine serum albumin) and a typical fluorophore (rhodamine B) to demonstrate a direct labeling method just by physical adsorption. In combination with size exclusion chromatography and the Scartchard equation, we have developed a facile analysis method for calculating the binding constant and binding sites. The molecular docking method has been used to study the binding site in amino acid level.

  13. pH and ionic strength effects on the binding constant between a nitrogen-containing polycyclic aromatic compound and humic acid.

    Science.gov (United States)

    Chang, Kuei-Chen; Lee, Chon-Lin; Hsieh, Ping-Chieh; Brimblecombe, Peter; Kao, Shu-Min

    2015-09-01

    Polycyclic aromatic compounds (PACs) are widespread environmental pollutants with a high potential to act as human carcinogens and mutagens. The behavior of PACs is significantly affected by their interactions with dissolved organic matter (DOM), such as their transport, solubility, bioavailability, and bioaccumulation in the aquatic environment. Being a basic PAC, benzo(h)quinoline (BQ) is the dominant species, as the solution's pH value is higher than BQ's pK a (pK a of BQ = 4.2). In contrast, benzo(h)quinolinium (BQH(+)) is the major species, as the solution's pH value is lower than its pK a. The binding constant (K DOC), measured by fluorescence quenching, between BQ/BQH(+) and Leonardite humic acid (LHA) would decrease 70 to 95 % and 20 to 90 % when increasing the ionic strength in acidic and neutral to basic conditions, respectively. The results can be attributed to the added cation (Na(+) and Mg(2+)), which forms a bridge with LHA and enhances the intramolecular reaction among these functional groups, therefore inducing the coiling up within the LHA molecule. In addition, the decrease of the K DOC with added MgCl2/MgSO4 (75-95 %) is higher than that with added NaCl/Na2SO4 (20-75 %), indicating that the K DOC was affected by the charge density of cations. The fluorescence intensity of BQH(+) in the absence of LHA (F 0) was found to decay only in the acidic solution with Cl(-), suggesting that Cl(-) might be a heavy atom serving as a quencher in an acidic solution. PMID:25940463

  14. Alteration of methotrexate binding to human serum albumin induced by oxidative stress. Spectroscopic comparative study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Sułkowska, A.; Równicka-Zubik, J.

    2016-01-01

    Changes of oxidative modified albumin conformation by comparison of non-modified (HSA) and modified (oHSA) human serum albumin absorption spectra, Red Edge Excitation Shift (REES) effect and fluorescence synchronous spectra were investigated. Studies of absorption spectra indicated that changes in the value of absorbance associated with spectral changes in the region from 200 to 250 nm involve structural alterations related to variations in peptide backbone conformation. Analysis of the REES effect allowed for the observation of changes caused by oxidation in the region of the hydrophobic pocket containing the tryptophanyl residue. Synchronous fluorescence spectroscopy confirmed changes of the position of the tryptophanyl and tyrosil residues fluorescent band. Effect of oxidative stress on binding of methotrexate (MTX) was investigated by spectrofluorescence, UV-VIS and 1HNMR spectroscopy. MTX caused the fluorescence quenching of non-modified (HSA) and modified (oHSA) human serum albumin molecule. The values of binding constants, Hill's coefficients and a number of binding sites in the protein molecule in the high affinity binding site were calculated for the binary MTX-HSA and MTX-oHSA systems. For these systems, qualitative analysis in the low affinity binding sites was performed with the use of the 1HNMR technique.

  15. Proton and iodine-127 nuclear magnetic resonance studies on the binding of iodide by lactoperoxidase

    Energy Technology Data Exchange (ETDEWEB)

    Sakurada, J.; Takahashi, S.; Shimizu, T.; Hatano, M.; Nakamura, S.; Hosoya, T.

    1987-10-06

    Interaction of an iodide ion with lactoperoxidase was studied by the use of /sup 1/H NMR, /sup 127/I NMR, and optical difference spectrum techniques. /sup 1/H NMR spectra demonstrated that a major broad hyperfine-shifted signal at about 60 ppm, which is ascribed to the heme peripheral methyl protons, was shifted toward high field by adding KI, indicating the binding of iodide to the active site of the enzyme; the dissociation constant was estimated to be 38 mM at pH 6.1. The binding was further detected by /sup 127/I NMR, showing no competition with cyanide. Both /sup 1/H NMR and /sup 127/I NMR revealed that the binding of iodide to the enzyme is facilitated by the protonation of an ionizable group with a pK/sup a/ value of 6.0-6.8, which is presumably the distal histidyl residue. Optical difference spectra showed that the binding of an aromatic donor molecule to the enzyme is slightly but distinctly affected by adding KI. On the basis of these results, it was suggested that an iodide ion binds to lactoperoxidase outside the heme crevice but at the position close enough to interact with the distal histidyl residue which possibly mediates electron transport in the iodide oxidation reaction.

  16. A study of the formation constants of ternary and quaternary complexes of some bivalent transition metals

    Directory of Open Access Journals (Sweden)

    MADHURJYA NEOG

    2010-01-01

    Full Text Available The formation of hetero-ligand 1:1:1, M(II-Opda-Sal/Gly ternary and 1:1:1:1, M(II-Opda-Sal-Gly quaternary complexes, where M(II = Ni, Cu, Zn and Cd; Opda = o‑phenylenediamine, Sal = salicylic acid, Gly = glycine, was studied pH-metrically in aqueous medium. The formation constants for the resulting ternary and quaternary complexes were evaluated at a constant ionic strength, μ = 0.20 mol dm-3 and temperature, 30±0.1 °C. The order of the formation constants in terms of the metal ion for both type of complexes was found to be Cu(II > Ni(II > Zn(II > Cd(II. This order was explained based on the increasing number of fused rings, the coordination number of the metal ions, the Irving – William order and the stability of various species. The expected species formed in solution were pruned with the Fortran IV program SPEPLOT and the stability of the ternary and quaternary complexes is explained.

  17. Study of the behaviour of the dielectric constant in Cu, Fe: BaTiO3

    Institute of Scientific and Technical Information of China (English)

    Alioune OUEDRAOGO; Kalifa PALM; Issaka OUEDRAOGO; Guy CHANUSSOT

    2008-01-01

    In this work we study the behaviour of the dielectric constant of BaTiO3 single crystals doped with Cu and Fe for different ion percentages, particularly, the influence of these heterovalent substitutions on the ferroelectric-paraelectric phase transition whose temperature is found at Tc=120 ℃ for pure samples. The dielectric constant ε in terms of temperature shows that the Curie temperature decreases when the quantity of impurities increases and presents a broadening and flattering of the maximum of ε(T) within higher values, with the transition becoming more and more diffuse. It is interesting to have a material with very high permittivity (high-k) because of its capacity to store an important quantity of electric charges. The ε anisotropy and the Curie-Weiss law are also verified with a good ratio between the slopes ofε-1(T) from both sides of the transition, leading to a Curie constant: C= 13×104 K for BaTiO3:1.6%Fe in the polar phase. BaTiO3 is a displacive ferroelectric going through a first-order phase transition. The substitutions have an effect on the dynamics of the perovskite lattice. They induce charges transfer to Ti and a diminution of elastic forces in BaTiO3. Then we discuss the fact that the maximum of permittivity does not depend on the phase transition but on the nature of the material.

  18. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, A.

    1997-10-08

    The author`s group has previously shown that isocyanides are readily adsorbed from solutions to Au powder and bind to the Au surface in an end-on fashion through the terminal carbon. Later work demonstrated that the equilibrium constants for the reversible adsorption of electronically inequivalent isocyanides could be obtained using the Langmuir isotherm technique. This dissertation describes two projects completed which complement the initial findings of this group. Initially, several alkylisocyanides were synthesized to examine the effect of tail length on Au powder adsorption. It was observed that the length of the alkyl chain affected not only the Au surface binding affinity, but also the rate of surface saturation and saturation coverage values. Direct competition studies were also studied using a {sup 13}C-labeled isocyanide. These studies demonstrated the stabilization afforded by substrate-substrate packing forces in SAM`s formed by the longer chain isocyanides. In a second study, di and triisocyanides were synthesized to determine the effect that the length of the connecting link and the number of isocyanide groups (as points of attachment) have on Au adsorption stability. The work in this area describes the binding modes, relative binding affinities and surface coverage values for a series of flexible alkyl and xylyldiisocyanides on Au powder surfaces. This report contains only the introductory material, and general summary. Two chapters have been processed separately. 56 refs.

  19. Spectroscopic studies on Titanium ion binding to the apo lactoferrin

    International Nuclear Information System (INIS)

    Titanium is a relatively abundant element that has found growing applications in medical science and recently some of Titanium compounds are introduced as anticancer drugs. In spite of very limited data which exist on the Titanium metabolism, some proteins might be involved in the mechanism of action of Titanium up to our knowledge, there is not any report in the literature concerning binding of Titanium to apo lactoferrin. Binding of apo lactoferrin with Ti(IV)-citrate was studied by spectroflourimeterey and spectrophotometery techniques under physiological conditions. The spectroflourimeteric studies revealed a significant fluorescence quenching, that indicated binding of apo lactoferrin with Ti(IV). The same reaction was monitored through spectrophotometry technique; this represents a characteristic UV difference band at 267 nm, which is different from lac-Fe (III). Titration studies how that lactoferrin specifically binds two moles Ti(IV) as complex with citrate per mol protein. Spectroflourimeterey and spectrophotometery techniques indicated that Ti(IV) ions cause a reduction (13%-14%) in binding of Fe(III) to lactoferrin. In overall, we may come to this conclusion that this element might be involved in the iron metabolism

  20. Curcumin Binding to Beta Amyloid: A Computational Study.

    Science.gov (United States)

    Rao, Praveen P N; Mohamed, Tarek; Teckwani, Karan; Tin, Gary

    2015-10-01

    Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding  = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding  = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates.

  1. Comparative studies on insulin binding human erythrocytes by immunoradiometric techniques

    International Nuclear Information System (INIS)

    Blood cells have been widely used to evaluate the status of the insulin receptor in man. The receptors exhibited competitive inhibition curves and nonlinear Scatchard plots similar to those reported for insulin target tissues, such as the hepatocyte and the adipocytes. This study demonstrated specific insulin binding by the erythrocytes (RBCs) of infants, children and adults. The total insulin bound by the RBCs from both children and adults gave a small difference over the physiologic range of insulin concentrations. blood RBCs of infants showed greater numbers of insulin receptors per cell and significant increase in the total amount of insulin binding than that in either children (ps for of infants, children and adults were similar to each other. It is clear that, the measurement of insulin binding by RBCs may be particularly useful in the study of infants and children with disorders of carbohydrate metabolism to elucidate the role, if any, of abnormal receptor function in their conditions

  2. Basic study on relationship between estimated rate constants and noise in FDG kinetic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, Yuichi [Tokyo Medical and Dental Univ. (Japan). Inst. for Medical and Dental Engineering; Toyama, Hinako; Senda, Michio

    1996-02-01

    For accurate estimation of the rate constants in {sup 18}F-FDG dynamic study, the shape of the estimation function ({Phi}) is crucial. In this investigation, the relationship between the noise level in tissue time activity curve and the shape of the least squared estimation function which is the sum of squared error between a function of model parameters and a measured data is calculated in 3 parameter model of {sup 18}F-FDG. In the first simulation, by using actual plasma time activity curve, the true tissue curve was generated from known sets of rate constants ranging 0.05{<=}k{sub 1}{<=}0.15, 0.1{<=}k{sub 2}{<=}0.2 and 0.01{<=}k{sub 3}{<=}0.1 in 0.01 step. This procedure was repeated under various noise levels in the tissue time activity curve from 1 to 8% of the maximum value in the tissue activity. In the second simulation, plasma and tissue time activity curves from clinical {sup 18}F-FDG dynamic study were used to calculate the {Phi}. In the noise-free case, because the global minima is separated from neighboring local minimums, it was easy to find out the optimum point. However, with increasing noise level, the optimum point was buried in many neighboring local minima. Making it difficult to find out the optimum point. The optimum point was found within 20% of the convergence point by standard non-linear optimization method. The shape of {Phi} for the clinical data was similar to that with the noise level of 3 or 5% in the first simulation. Therefore direct search within the area extending 20% from the result of usual non-linear curve fitting procedure is recommended for accurate estimation of the constants. (author).

  3. Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution.

    Science.gov (United States)

    Singh, Amit K; Kumar, Ramasamy P; Pandey, Nisha; Singh, Nagendra; Sinha, Mau; Bhushan, Asha; Kaur, Punit; Sharma, Sujata; Singh, Tej P

    2010-01-01

    Isoniazid (INH) is an anti-tuberculosis prodrug that is activated by mammalian lactoperoxidase and Mycobacterium tuberculosis catalase peroxidase (MtCP). We report here binding studies, an enzyme assay involving INH, and the crystal structure of the complex of bovine lactoperoxidase (LPO) with INH to illuminate binding properties and INH activation as well as the mode of diffusion and interactions together with a detailed structural and functional comparison with MtCP. The structure determination shows that isoniazid binds to LPO at the substrate binding site on the distal heme side. The substrate binding site is connected to the protein surface through a long hydrophobic channel. The acyl hydrazide moiety of isoniazid interacts with Phe(422) O, Gln(423) O(epsilon1), and Phe(254) O. In this arrangement, pyridinyl nitrogen forms a hydrogen bond with a water molecule, W-1, which in turn forms three hydrogen bonds with Fe(3+), His(109) N(epsilon2), and Gln(105) N(epsilon2). The remaining two sides of isoniazid form hydrophobic interactions with the atoms of heme pyrrole ring A, C(beta) and C(gamma) atoms of Glu(258), and C(gamma) and C(delta) atoms of Arg(255). The binding studies indicate that INH binds to LPO with a value of 0.9 x 10(-6) m for the dissociation constant. The nitro blue tetrazolium reduction assay shows that INH is activated by the reaction of LPO-H(2)O(2) with INH. This suggests that LPO can be used for INH activation. It also indicates that the conversion of INH into isonicotinoyl radical by LPO may be the cause of INH toxicity.

  4. Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies.

    Science.gov (United States)

    Ruan, Qiaoqiao; Skinner, Joseph P; Tetin, Sergey Y

    2009-10-15

    The purpose of this article is to highlight the versatility of nonfluorescent Förster resonance energy transfer (FRET) acceptors in determination of protein equilibrium dissociation constants and kinetic rates. Using a nonfluorescent acceptor eliminates the necessity to spectrally isolate the donor fluorescence when performing binding titrations covering a broad range of reagent concentrations. Moreover, random distribution of the donor and acceptor chromophores on the surface of proteins increases the probability of FRET occurring on their interaction. Three high-affinity antibodies are presented in this study as characteristic protein systems. Monoclonal antibody (mAb) 106.3 binds brain natriuretic peptide (BNP)5-13(C10A) and full-length BNP1-32 with the dissociation constants 0.26+/-0.01 and 0.05+/-0.02 nM, respectively, which was confirmed by kinetic measurements. For anti-hCG (human chorionic gonadotropin) mAb 8F11, studied at two incorporation ratios (IRs=1.9 and 3.8) of the nonfluorescent FRET acceptor, K(D) values of 0.04+/-0.02 and 0.059(-0.004)(+0.006) nM, respectively, were obtained. Likewise, the binding of goat anti-hamster immunoglobulin G (IgG) antibody was not affected by conjugation and yielded K(D) values of 1.26+/-0.04, 1.25+/-0.05, and 1.14+/-0.04 nM at IRs of 1.7, 4.7, and 8.1, respectively. We conclude that this FRET-based method offers high sensitivity, practical simplicity, and versatility in protein binding studies. PMID:19563765

  5. PRELIMINARY STUDY OF EXTRACTABLE PROTEIN BINDING USING MALEIC ANHYDRIDE COPOLYMER

    Institute of Scientific and Technical Information of China (English)

    Thirawan Nipithakul; Ladawan Watthanachote; Nanticha Kalapat

    2012-01-01

    A preliminary study of using maleic anhydride copolymer for protein binding has been carried out.The polymeric films were prepared by compression of the purified resin and annealing the film to induce efficient back formation of the anhydride groups.The properties of the film surface were analyzed by attenuated total reflection Fourier transforms infrared spectroscopy and water contact angle measurements.The protein content was determined by Bradford assay.To obtain optimum conditions,immersion time for protein binding was examined.Results revealed that proteins can be successfully immobilized onto the film surface via covalent linkage.The efficiency of the covalent binding of the extractable protein to maleic anhydride-polyethylene film was estimated at 69.87 μtg/cm2,although the film had low anhydride content (3%) on the surface.

  6. Spectroscopic Studies on the Binding of Bacteriophage Mequindox with Bovine Serum Albumin

    Institute of Scientific and Technical Information of China (English)

    ZENG,Zhouhua; LIU,Yi; HU,Xianming; XU,Zhenqiang; ZENG,Kun

    2009-01-01

    Fluorescence spectra and UV-Vis absorption spectra have been used to study the binding of bacteriophage mequindox (MEQ) with bovine serum albumin (BSA),which performed a dynamic quenching process.The quenching constants and thermodynamic parameters at different temperatures were calculated.The binding was primarily driven by entropy,and hydrophobic forces also played a significant role.The distance between BSA and MEQ was estimated to be 4.5 nm based on the theory of F(o)rster's non-radioactive energy transfer.Furthermore,synchronous fluorescence spectra and 3-dimensional fluorescence spectra were used to figure out the configuration of BSA in the presence or absence of MEQ,which indicated that it was basically the same.

  7. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Science.gov (United States)

    Sanders, Jeffrey M; Wampole, Matthew E; Thakur, Mathew L; Wickstrom, Eric

    2013-01-01

    The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF

  8. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Sanders

    Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

  9. Binding of nucleotides to nucleoside diphosphate kinase: a calorimetric study.

    Science.gov (United States)

    Cervoni, L; Lascu, I; Xu, Y; Gonin, P; Morr, M; Merouani, M; Janin, J; Giartosio, A

    2001-04-17

    The source of affinity for substrates of human nucleoside diphosphate (NDP) kinases is particularly important in that its knowledge could be used to design more effective antiviral nucleoside drugs (e.g., AZT). We carried out a microcalorimetric study of the binding of enzymes from two organisms to various nucleotides. Isothermal titration calorimetry has been used to characterize the binding in terms of Delta G degrees, Delta H degrees and Delta S degrees. Thermodynamic parameters of the interaction of ADP with the hexameric NDP kinase from Dictyostelium discoideum and with the tetrameric enzyme from Myxococcus xanthus, at 20 degrees C, were similar and, in both cases, binding was enthalpy-driven. The interactions of ADP, 2'deoxyADP, GDP, and IDP with the eukaryotic enzyme differed in enthalpic and entropic terms, whereas the Delta G degrees values obtained were similar due to enthalpy--entropy compensation. The binding of the enzyme to nonphysiological nucleotides, such as AMP--PNP, 3'deoxyADP, and 3'-deoxy-3'-amino-ADP, appears to differ in several respects. Crystallography of the protein bound to 3'-deoxy-3'-amino-ADP showed that the drug was in a distorted position, and was unable to interact correctly with active site side chains. The interaction of pyrimidine nucleoside diphosphates with the hexameric enzyme is characterized by a lower affinity than that with purine nucleotides. Titration showed the stoichiometry of the interaction to be abnormal, with 9--12 binding sites/hexamer. The presence of supplementary binding sites might have physiological implications. PMID:11294625

  10. Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Morgunova, Ekaterina [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden); Illarionov, Boris; Saller, Sabine [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Popov, Aleksander [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX 09 (France); Sambaiah, Thota [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Bacher, Adelbert [Chemistry Department, Technical University of Munich, 85747 Garching (Germany); Cushman, Mark [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Fischer, Markus [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Ladenstein, Rudolf, E-mail: rudolf.ladenstein@ki.se [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden)

    2010-09-01

    Crystallographic studies of lumazine synthase, the penultimate enzyme of the riboflavin-biosynthetic pathway in B. anthracis, provide a structural framework for the design of antibiotic inhibitors, together with calorimetric and kinetic investigations of inhibitor binding. The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R{sub cryst} = 23.7% (R{sub free} = 28.4%) at a resolution of 3.5 Å. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.

  11. First-Principles Studies the Lattice Constants and the Electronic Structures of Diluted Magnetic Semiconductors (In,Mn)As

    Institute of Scientific and Technical Information of China (English)

    WEI Shuyi; YAN Yuli; XIA Congxin; LIU Guangsheng

    2006-01-01

    Lattice constants and electronic structures of diluted magnetic semiconductors (In,Mn)As were investigated using the first principles LMTO-ASA band calculation by assuming supercell structures. Three concentrations of the 3d impurities were studied (x=1/2, 1/4, 1/8). The effect of varying Mn concentrations on the lattice constants and the electronic structures are shown.

  12. Spectroscopy and molecular docking studies on the binding of propyl gallate to human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Guo-fei; Wang, Yu; Xi, Lei; Liu, Jin; Wang, Hao; Du, Lin-fang, E-mail: dulinfang@scu.edu.cn

    2015-03-15

    The interaction of propyl gallate (PG) with human serum albumin (HSA) was investigated by fluorescence, far-UV CD and FT-IR spectroscopic methods as well as molecular docking. Fluorescence emission spectra demonstrated that the HSA fluorescence was quenched by PG through static quenching and energy transfer with the binding constants in the order of 10{sup 5} L mol{sup −1}. The thermodynamic parameters (ΔH=−29.64 KJ mol{sup −1}, ΔS=2.7 J mol{sup −1} K{sup −1}) indicated that both hydrophobic force and hydrogen bond interactions played a leading role in the formation of PG–HSA complex. The results also showed the existence of a single binding site, which was located in subdomain IIA (site I) as revealed by molecular docking and competitive binding experiments. Molecular docking studies further showed the participation of several amino acids in PG–HSA complexation, which stabilized by H-bonding systems. The synchronous fluorescence spectra showed that the binding of drug caused the environment of tryptophan residues became more polar. FT-IR and CD spectroscopic further showed that drug complexation altered protein conformation by a major reduction of α-helix inducing a partial protein destabilization. - Highlights: • The interaction between propyl gallate and HSA has been investigated. • HSA fluorescence is quenched by propyl gallate through static quenching mechanism. • Both hydrophobic force and hydrogen bond play major role in the binding process. • Site I of the HSA is found to be the main binding site for propyl gallate. • The structure of HSA has been changed upon the interaction with propyl gallate.

  13. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B;

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

  14. Average and equilibrium structures of methyl flouride studied by electron diffraction. A joint analysis with rotational constants and cubic force constants

    Science.gov (United States)

    Egawa, Toru; Yamamoto, Satoshi; Nakata, Munetaka; Kuchitsu, Kozo

    1987-02-01

    Electron diffraction intensity of methyl fluoride was measured and analyzed jointly with the rotational constants, Ao and Bo, of the normal species. The following structure was derived: rg(CF) = 1.391(1) Å, rg(CH) = 1.108(1) Å and β z(FCH) = 108.7(2)°, where the numbers in parentheses represent estimated limits of error. The effective anharmonic constants were derived using the rotational constants and the l-type doubling constants; the cubic force constants calculated by Kondo using a 6-311G** (MP2) basis set were also incorporated in the analysis. The following equilibrium structure was derived from the rz structure and the effective anharmonic constants: re(CF) = 1.383(1) Å, re(CH) = 1.086(2) Å and β e(FCH) = 108.8(3)°.

  15. First-principles study of the elastic constants and optical properties of uranium metal

    Institute of Scientific and Technical Information of China (English)

    Chen Qiu-Yun; Tan Shi-Yong; Lai Xin-Chun; Chen Jun

    2012-01-01

    We perform first-principles calculations of the lattice constants,elastic constants,and optical properties for alphaand gamma-uranium based on the ultra-soft pseudopotential method.Lattice constants and equilibrium atomic volume are consistent pretty well with the experimental results.Some difference exists between our calculated elastic constants and the experimental data.Based on the satisfactory ground state electronic structure calculations,the optical conductivity,dielectric function,refractive index,and extinction coefficients are also obtained.These calculated optical properties are compared with our results and other published experimental data.

  16. Effect of the Experimental Design in Automatic Attention Shift Studies : A Comparison of Constant vs. Randmized Stimulus Onset Asynchrony (SOA)

    OpenAIRE

    Yuri, HASHIMOTO; Narisuke, Utsuki

    2011-01-01

    The present study compared two experimental designs used in response time (RT) studies: constant and randomized stimulus onset asynchrony (SOA). Both designs are commonly used in studies of automatic attention shifts. The results revealed that RTs at SOAs of 105 ms and 300 ms with a randomized SOA design were significantly longer than with a constant SOA design. The RT gain (i.e. RTs to uncued stimuli minus RTs to cued stimuli) measured in the constant SOA method was maximal when the SOA was ...

  17. Binding of the neuroleptic drug, gabapentin, to bovine serum albumin: Insights from experimental and computational studies

    International Nuclear Information System (INIS)

    The interaction between antiepileptic drug, gabapentin (GP), and bovin serum albumin (BSA) was studied by spectroscopic and computational methods. The native fluorescence of BSA was quenched by GP. Stern–Volmer quenching constant was calculated at different temperatures which suggested a static mechanism. The association constant (Ka) was calculated from fluorescence quenching studies, which increased with temperature rising. GP competed well with warfarine for hydrophobic subdomain IIA (Sudlow's site I) on the protein. Enthalpy and entropy changes during the interaction of GP with BSA were obtained using van't Hoff plot, which showed an entropy-driven process and involvement of hydrophobic forces (ΔH>0 and ΔS>0). Synchronous fluorescence measurements of BSA solution in the presence of GP showed a considerable blue shift when Δλ=15 nm, therefore, GP interacts with tyrosine-rich sites on BSA. Optimized docked model of BSA–GP mixture confirmed the experimental results. -- Highlights: • Interaction of gabapentin and bovine serum albumin (BSA) is investigated by spectroscopic techniques. • Gabapentin can quench the fluorescence of BSA through a static quenching procedure. • The binding of gabapentin to BSA is driven mainly by hydrophobic interactions. • Subdomain IIA (Sudlow's site I) of BSA is found to be the main binding site for gabapentin. • Molecular docking modeling confirmed the experimental results

  18. Binding of the neuroleptic drug, gabapentin, to bovine serum albumin: Insights from experimental and computational studies

    Energy Technology Data Exchange (ETDEWEB)

    Jalali, Fahimeh, E-mail: fahimehjalali@yahoo.com [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Dorraji, Parisa S. [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Mahdiuni, Hamid [Department of Biology, Razi University, 67346 Kermanshah (Iran, Islamic Republic of)

    2014-04-15

    The interaction between antiepileptic drug, gabapentin (GP), and bovin serum albumin (BSA) was studied by spectroscopic and computational methods. The native fluorescence of BSA was quenched by GP. Stern–Volmer quenching constant was calculated at different temperatures which suggested a static mechanism. The association constant (K{sub a}) was calculated from fluorescence quenching studies, which increased with temperature rising. GP competed well with warfarine for hydrophobic subdomain IIA (Sudlow's site I) on the protein. Enthalpy and entropy changes during the interaction of GP with BSA were obtained using van't Hoff plot, which showed an entropy-driven process and involvement of hydrophobic forces (ΔH>0 and ΔS>0). Synchronous fluorescence measurements of BSA solution in the presence of GP showed a considerable blue shift when Δλ=15 nm, therefore, GP interacts with tyrosine-rich sites on BSA. Optimized docked model of BSA–GP mixture confirmed the experimental results. -- Highlights: • Interaction of gabapentin and bovine serum albumin (BSA) is investigated by spectroscopic techniques. • Gabapentin can quench the fluorescence of BSA through a static quenching procedure. • The binding of gabapentin to BSA is driven mainly by hydrophobic interactions. • Subdomain IIA (Sudlow's site I) of BSA is found to be the main binding site for gabapentin. • Molecular docking modeling confirmed the experimental results.

  19. XAS and Pulsed EPR Studies of the Copper Binding Site in Riboflavin Binding Protein

    Energy Technology Data Exchange (ETDEWEB)

    Smith,S.; Bencze, K.; Wasiukanis, K.; Benore-Parsons, T.; Stemmler, T.

    2008-01-01

    Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 Angstroms, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a CuO3N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

  20. Study of Antigravity in an F(R) Model and in Brans-Dicke Theory with Cosmological Constant

    OpenAIRE

    Oikonomou, V. K.; N. Karagiannakis

    2014-01-01

    We study antigravity, that is having an effective gravitational constant with a negative sign, in scalar-tensor theories originating from $F(R)$-theory and in a Brans-Dicke model with cosmological constant. For the $F(R)$ theory case, we obtain the antigravity scalar-tensor theory in the Jordan frame by using a variant of the Lagrange multipliers method and we numerically study the time dependent effective gravitational constant. As we shall demonstrate by using a specific $F(R)$ model, altho...

  1. Binding of Cu(II) ions to peptides studied by fluorescence spectroscopy and isothermal titration calorimetry.

    Science.gov (United States)

    Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech

    2016-01-15

    Steady-state and time-resolved fluorescence quenching measurements supported by Isothermal Titration Calorimetry (ITC) were used to study the interactions of Cu(2+) with four peptides. Two of them were taken from the N-terminal part of the FBP28 protein (formin binding protein) WW domain: Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr-NH2 (D9) and its mutant Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr-NH2 (D9_M) as well as two mutated peptides from the B3 domain of the immunoglobulin binding protein G derived from Streptococcus: Asp-Val-Ala-Thr-Tyr-Thr-NH2 (J1) and Glu-Val-Ala-Thr-Tyr-Thr-NH2 (J2). The measurements were carried out at 298.15K in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution with a pH of 6. The fluorescence of all peptides was quenched by Cu(2+) ions. The stoichiometry, conditional stability constants and thermodynamic parameters for the interactions of the Cu(2+) ions with D9 and D9_M were determined from the calorimetric data. The values of the conditional stability constants were additionally determined from fluorescence quenching measurements and compared with those obtained from calorimetric studies. There was a good correlation between data obtained from the two techniques. On the other hand, the studies revealed that J1 and J2 do not exhibit an affinity towards metal ions. The obtained results prove that fluorescence quenching experiments may be successfully used in order to determine stability constants of complexes with fluorescent ligands. Finally, based on the obtained results, the coordinating properties of the peptides towards the Cu(2+) ions are discussed.

  2. Theoretical studies of binding of mannose-binding protein to monosaccharides

    Science.gov (United States)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  3. Studies of the binding mode of TXNHCH2COOH with calf thymus DNA by spectroscopic methods.

    Science.gov (United States)

    Ataci, Nese; Arsu, Nergis

    2016-12-01

    In this study, a thioxanthone derivative named 2-(9-oxo-9H-thioxanthen-2ylamino) acetic acid (TX-NHCH2COOH) was used to investigate small molecule and DNA binding interactions. Absorption and fluorescence emission spectroscopy were used and melting studies were used to explain the binding mode of TXNHCH2COOH-DNA. Intrinsic binding constant Kb TXNHCH2COOH was found 6×10(5)M(-1)from UV-Vis absorption spectroscopy. Fluorescence emmision intensity increased by adding ct-DNA to the TXNHCH2COOH and KI quenching experiments resulted with low Ksv value. Additionally, 3.7°C increase for Tm was observed. The observed quenching of EB and ct-DNA complex and increase viscosity values of ct-DNA by addition of TXNHCH2COOH was determined. All those results indicate that TXNHCH2COOH can intercalate into DNA base pairs. Fluorescence microscopy helped to display imaging of the TXNHCH2COOH-DNA solution. PMID:27367618

  4. Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: daniel.sem@cuw.edu [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

  5. Study on geometric models of non-numerically controlled machining revolving cutter with constant pitch

    Institute of Scientific and Technical Information of China (English)

    韩成顺; 尚元江; 王景贺; 唐余勇; 董申

    2004-01-01

    This paper presents a new approach of designing the revolving cutter with constant pitch, and pro-vides geometric models. The corresponding models in the non-numerically controlled manufacturing, such asdesigning the helical groove, grinding wheel, relative feeding motion, and calculating the helical angle of thecutting edge, are introduced. The examples are given to testify that the design approach is simple and readilyrealized in machining the revolving cutter with constant pitch. The effective design and manufacture method pro-vides general references for non-NC machining revolving cutter with constant pitch and reducing the equipmentsinput.

  6. Calorimetric study of binding of some disaccharides with crown ethers

    Energy Technology Data Exchange (ETDEWEB)

    Davydova, Olga I.; Lebedeva, Nataliya Sh.; Parfenyuk, Elena V

    2004-11-01

    Isothermal titration calorimetry has been applied to the determination of the thermodynamic parameters of binding of {beta}-lactose, {alpha},{alpha}-trehalose and sucrose with 15-crown-5 and 18-crown-6 in water at 298.15 K. The formation of 1:1 molecular associates has been found for the systems studied except 18-crown-6 and {beta}-lactose. The associates are preferentially or completely entropy stabilized. The most stable associate is formed between {alpha},{alpha}-trehalose and 18-crown-6. The obtained values of thermodynamic parameters of binding are discussed from the point of view of solute-solvent interactions as well as conformational and structural peculiarities of the disaccharides (DS) and crown ethers (CE)

  7. Numerical study on the cooling performance of natural draft dry cooling tower with vertical delta radiators under constant heat load

    International Nuclear Information System (INIS)

    Highlights: • A 3D numerical model for NDDCTV under constant heat load was set and validated. • The ambient temperature effect on NDDCTV under constant heat load had been studied. • A suitable crosswind profile index was ascertained by sensitivity analysis. • The crosswind effect on NDDCTV under constant heat load has studied from columns. • The crosswind effect mechanism was clarified from the air inflow deviation angle. - Abstract: From the view of cooling system, the natural draft dry cooling tower with vertical delta radiators (NDDCTV) under constant heat load can be studied by keeping constant water temperature drop Δtw. With computed entry water temperature tw1 as the sum of tower exit water temperature tw2 and the constant Δtw, a three-dimensional (3D) numerical model for NDDCTV under constant heat load was established. Through analyses about mesh-independence, sensitivity about crosswind profile index and comparison with published results, the accuracy and credibility of the established numerical model for NDDCTV were confirmed. The aerodynamic field around cooling deltas was analyzed at windless and crosswind conditions, so as to clarify the impacts of ambient air temperature and air inflow deviation angle θd on the performance of cooling columns. With constant heat load and uniform entry water temperature, the cooling performance of each sector was analyzed under crosswind impact. With increasing crosswind velocity vc, the cooling performance of NDDCTV under constant heat load deteriorates sharply at low vc, but varies slightly at high vc, which can be improved by air deflectors

  8. Fundamental Constants

    CERN Document Server

    Wilczek, Frank

    2007-01-01

    The notion of ``fundamental constant'' is heavily theory-laden. A natural, fairly precise formulation is possible in the context of the standard model (here defined to include gravity). Some fundamental constants have profound geometric meaning. The ordinary gravitational constant parameterizes the stiffness, or resistance to curvature, of space-time. The cosmological term parameterizes space-time's resistance to expansion -- which may be, and apparently is at present, a {\\it negative} resistance, i.e. a tendency toward expansion. The three gauge couplings of the strong, electromagnetic, and weak interactions parameterize resistance to curvature in internal spaces. The remaining fundamental couplings, of which there are a few dozen, supply an ungainly accommodation of inertia. The multiplicity and variety of fundamental constants are esthetic and conceptual shortcomings in our present understanding of foundational physics. I discuss some ideas for improving the situation. I then briefly discuss additional con...

  9. Varying Constants

    CERN Document Server

    Damour, Thibault Marie Alban Guillaume

    2003-01-01

    We review some string-inspired theoretical models which incorporate a correlated spacetime variation of coupling constants while remaining naturally compatible both with phenomenological constraints coming from geochemical data (Oklo; Rhenium decay) and with present equivalence principle tests. Barring unnatural fine-tunings of parameters, a variation of the fine-structure constant as large as that recently ``observed'' by Webb et al. in quasar absorption spectra appears to be incompatible with these phenomenological constraints. Independently of any model, it is emphasized that the best experimental probe of varying constants are high-precision tests of the universality of free fall, such as MICROSCOPE and STEP. Recent claims by Bekenstein that fine-structure-constant variability does not imply detectable violations of the equivalence principle are shown to be untenable.

  10. Varying Constants

    CERN Document Server

    Barrow, J D

    2005-01-01

    We review properties of theories for the variation of the gravitation and fine structure 'constants'. We highlight some general features of the cosmological models that exist in these theories with reference to recent quasar data that are consistent with time-variation in the fine structure 'constant' since a redshift of 3.5. The behaviour of a simple class of varying-alpha cosmologies is outlined in the light of all the observational constraints.

  11. Peptide Arrays for Binding Studies of E3 Ubiquitin Ligases.

    Science.gov (United States)

    Klecker, Maria; Dissmeyer, Nico

    2016-01-01

    The automated SPOT (synthetic peptide arrays on membrane support technique) synthesis technology has entrenched as a rapid and robust method to generate peptide libraries on cellulose membrane supports. The synthesis method is based on conventional Fmoc chemistry building up peptides with free N-terminal amino acids starting at their cellulose-coupled C-termini. Several hundreds of peptide sequences can be assembled with this technique on one membrane comprising a strong binding potential due to high local peptide concentrations. Peptide orientation on SPOT membranes qualifies this array type for assaying substrate specificities of N-recognins, the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Pioneer studies described binding capability of mammalian and yeast enzymes depending on a peptide's N-terminus. SPOT arrays have been successfully used to describe substrate specificity of N-recognins which are the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Here, we describe the implementation of SPOT binding assays with focus on the identification of N-recognin substrates, applicable also for plant NERD enzymes. PMID:27424747

  12. Experimental study of the complex resistivity and dielectric constant of chrome-contaminated soil

    Science.gov (United States)

    Liu, Haorui; Yang, Heli; Yi, Fengyan

    2016-08-01

    Heavy metals such as arsenic and chromium often contaminate soils near industrialized areas. Soil samples, made with different water content and chromate pollutant concentrations, are often needed to test soil quality. Because complex resistivity and complex dielectric characteristics of these samples need to be measured, the relationship between these measurement results and chromium concentration as well as water content was studied. Based on soil sample observations, the amplitude of the sample complex resistivity decreased with an increase of contamination concentration and water content. The phase of complex resistivity takes on a tendency of initially decrease, and then increase with the increasing of contamination concentration and water content. For a soil sample with the same resistivity, the higher the amplitude of complex resistivity, the lower the water content and the higher the contamination concentration. The real and imaginary parts of the complex dielectric constant increase with an increase in contamination concentration and water content. Note that resistivity and complex resistivity methods are necessary to adequately evaluate pollution at various sites.

  13. Comprehensive Study of Lanthanum Aluminate High-Dielectric-Constant Gate Oxides for Advanced CMOS Devices

    Directory of Open Access Journals (Sweden)

    Masamichi Suzuki

    2012-03-01

    Full Text Available A comprehensive study of the electrical and physical characteristics of Lanthanum Aluminate (LaAlO3 high-dielectric-constant gate oxides for advanced CMOS devices was performed. The most distinctive feature of LaAlO3 as compared with Hf-based high-k materials is the thermal stability at the interface with Si, which suppresses the formation of a low-permittivity Si oxide interfacial layer. Careful selection of the film deposition conditions has enabled successful deposition of an LaAlO3 gate dielectric film with an equivalent oxide thickness (EOT of 0.31 nm. Direct contact with Si has been revealed to cause significant tensile strain to the Si in the interface region. The high stability of the effective work function with respect to the annealing conditions has been demonstrated through comparison with Hf-based dielectrics. It has also been shown that the effective work function can be tuned over a wide range by controlling the La/(La + Al atomic ratio. In addition, gate-first n-MOSFETs with ultrathin EOT that use sulfur-implanted Schottky source/drain technology have been fabricated using a low-temperature process.

  14. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

    Science.gov (United States)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  15. Characterisation of peptide microarrays for studying antibody-antigen binding using surface plasmon resonance imagery.

    Directory of Open Access Journals (Sweden)

    Claude Nogues

    Full Text Available BACKGROUND: Non-specific binding to biosensor surfaces is a major obstacle to quantitative analysis of selective retention of analytes at immobilized target molecules. Although a range of chemical antifouling monolayers has been developed to address this problem, many macromolecular interactions still remain refractory to analysis due to the prevalent high degree of non-specific binding. We describe how we use the dynamic process of the formation of self assembling monolayers and optimise physical and chemical properties thus reducing considerably non-specific binding and allowing analysis of specific binding of analytes to immobilized target molecules. METHODOLOGY/PRINCIPAL FINDINGS: We illustrate this approach by the production of specific protein arrays for the analysis of interactions between the 65kDa isoform of human glutamate decarboxylase (GAD65 and a human monoclonal antibody. Our data illustrate that we have effectively eliminated non-specific interactions with the surface containing the immobilised GAD65 molecules. The findings have several implications. First, this approach obviates the dubious process of background subtraction and gives access to more accurate kinetic and equilibrium values that are no longer contaminated by multiphase non-specific binding. Second, an enhanced signal to noise ratio increases not only the sensitivity but also confidence in the use of SPR to generate kinetic constants that may then be inserted into van't Hoff type analyses to provide comparative DeltaG, DeltaS and DeltaH values, making this an efficient, rapid and competitive alternative to ITC measurements used in drug and macromolecular-interaction mechanistic studies. Third, the accuracy of the measurements allows the application of more intricate interaction models than simple Langmuir monophasic binding. CONCLUSIONS: The detection and measurement of antibody binding by the type 1 diabetes autoantigen GAD65 represents an example of an antibody

  16. Effects of deuterium oxide on the rate and dissociation constants for saxitoxin and tetrodotoxin action. Voltage-clamp studies on frog myelinated nerve

    International Nuclear Information System (INIS)

    The actions of tetrodotoxin (TTX) and saxitoxin (STX) in normal water and in deuterium oxide (D20) have been studied in frog myelinated nerve. Substitution of D20 for H20 in normal Ringer's solution has no effect on the potency of TTX in blocking action potentials but increases the potency of STX by approximately 50%. Under voltage clamp, the steady-state inhibition of sodium currents by 1 nM STX is doubled in D20 as a result of a halving of the rate of dissociation of STX from the sodium channel; the rate of block by STX is not measurably changed by D20. Neither steady-state inhibition nor the on- or off-rate constants of TTX are changed by D20 substitution. The isotopic effects on STX binding are observed less than 10 min after the toxin has been added to D20, thus eliminating the possibility that slow-exchange (t 1/2 greater than 10 h) hydrogen-binding sites on STX are involved. The results are consistent with a hypothesis that attributes receptor-toxin stabilization to isotopic changes of hydrogen bonding; this interpretation suggests that hydrogen bonds contribute more to the binding of STX than to that of TTX at the sodium channel

  17. Molar absorption coefficients and stability constants of metal complexes of 4-(2-pyridylazo)resorcinol (PAR): Revisiting common chelating probe for the study of metalloproteins.

    Science.gov (United States)

    Kocyła, Anna; Pomorski, Adam; Krężel, Artur

    2015-11-01

    4-(2-Pyridylazo)resorcinol (PAR) is one of the most popular chromogenic chelator used in the determination of the concentrations of various metal ions from the d, p and f blocks and their affinities for metal ion-binding biomolecules. The most important characteristics of such a sensor are the molar absorption coefficient and the metal-ligand complex dissociation constant. However, it must be remembered that these values are dependent on the specific experimental conditions (e.g. pH, solvent components, and reactant ratios). If one uses these values to process data obtained in different conditions, the final result can be under- or overestimated. We aimed to establish the spectral properties and the stability of PAR and its complexes accurately with Zn(2+), Cd(2+), Hg(2+), Co(2+), Ni(2+), Cu(2+), Mn(2+) and Pb(2+) at a multiple pH values. The obtained results account for the presence of different species of metal-PAR complexes in the physiological pH range of 5 to 8 and have been frequently neglected in previous studies. The effective molar absorption coefficient at 492 nm for the ZnHx(PAR)2 complex at pH7.4 in buffered water solution is 71,500 M(-1) cm(-1), and the dissociation constant of the complex in these conditions is 7.08×10(-13) M(2). To confirm these values and estimate the range of the dissociation constants of zinc-binding biomolecules that can be measured using PAR, we performed several titrations of zinc finger peptides and zinc chelators. Taken together, our results provide the updated parameters that are applicable to any experiment conducted using inexpensive and commercially available PAR.

  18. A study on the jet characteristic by using of Coanda effect in constant expansion rate nozzle

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sak; Lee, Dong Won; Kwon, Soon Bum [Kyungpook National Univ., Daegu (Korea, Republic of); Kim, Byung Ji [Catholic Sangji College, Andong (Korea, Republic of)

    2005-07-01

    Jets issuing from a conventional nozzle and convergent nozzles of a constant expansion rates and a certain normal using an annular slit are compared to investigate the characteristics of the 3 jets. In experiments, to compare the characteristics between jets, the nozzle exit mean velocity is fixed as 90m/s. The pressures along the jet axis and radial directions is measured by scanning valve system moving with 3-axis auto-traverse unit, and the velocity distribution can be obtained by calculation from the measured static and total pressures. To obtain the highly stable and convergency jets, a nozzle has to be designed with an annular slit connected to an conical cylinder, furthermore, the flow through a constant expansion rate nozzle using annular slit is the most probable. And the pressure drop along the nozzle for the constant expansion rate nozzle is small.

  19. Multispectroscopic DNA-binding studies of a terbium(III) complex containing 2,2'-bipyridine ligand.

    Science.gov (United States)

    Aramesh-Boroujeni, Zahra; Khorasani-Motlagh, Mozhgan; Noroozifar, Meissam

    2016-01-01

    Agarose gel electrophoresis, absorption, fluorescence, viscosity, and circular dichroism (CD) have been used in exploring the interaction of terbium(III) complex, [Tb(bpy)2Cl3(OH2)] where bipy is 2,2'-bipyridine, with Fish salmon DNA. Agarose gel electrophoresis assay, along with absorption and fluorescence studies, reveal interaction between the corresponding complex and FS-DNA. Also, the binding constants (Kb) and the Stern-Volmer quenching constants (Ksv) of Tb(III) complex with FS-DNA were determined. The calculated thermodynamic parameters suggested that the binding of mentioned complex to FS-DNA was driven mainly by hydrophobic interactions. A comparative study of this complex with respect to the effect of iodide-induced quenching, ionic strength effect, and ethidium bromide exclusion assay reflects binding of explicit to the FS-DNA primarily in a groove fashion. CD and viscosity data also support the groove binding mode. Furthermore, Tb(III) complex have been simultaneously screened for their antibacterial and antifungal activities.

  20. STUDY OF ESTROGEN BINDING SITE ON HUMAN EJACULATED SPERMATOZOA

    Institute of Scientific and Technical Information of China (English)

    CHUJin-Shong; WANGYi-Fei

    1989-01-01

    The specific estrogen binding site for 17β-estradiol has been investigated on human spermatozoa by electron microscopec autoradiography. The results show that the binding sites were distributed over the surface of human spermatozoa: acrosomal cap, equatorial

  1. Influence of humic acid on plutonium sorption to gibbsite. Determination of Pu-humic acid complexation constants and ternary sorption studies

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, Trevor; Powell, Brian A. [Clemson Univ., Anderson, SC (United States). Environmental Engineering and Earth Sciences; Zavarin, Mavrik [Lawrence Livermore National Laboratory, Livermore, CA (United States). Glenn T. Seaborg Institute

    2014-10-01

    In this work stability constants describing Pu(IV), Th(IV), and Np(V) binding to Leonardite humic acid (HA) were determined using a discrete pK{sub a} model. A hybrid ultra-filtration/equilibrium dialysis, ligand exchange technique was used to generate the partitioning data. Ethylenediaminetetraacetic acid (EDTA) was used as a reference ligand to allow the aqueous chemistry of the Pu(IV)-HA system to be examined over a range of pH values, while minimizing the possibility of precipitation of Pu(IV). The conditional stability constant for Pu(IV) complexation with HA determined as part of this work is logβ{sub 112} = 6.76 ± 0.14 based on the equation: Pu{sup 4+} + HL3 + 2H{sub 2}O <-> Pu(OH){sub 2}L3{sup +} + 3H{sup +} where HA is represented by HL3 (a binding site on the HA with a pK{sub a} value of 7). This value is three orders of magnitude higher than the Th(IV)-HA constant and between six and eight orders of magnitude higher than the Np(V)-HA complex. The magnitude of the stability constants and the general trend of increasing complexation strength with increasing pH is consistent with previous observations. The Pu(IV)-HA stability constants were used to model sorption of Pu(IV) to gibbsite in the presence of HA. Assuming only aqueous Pu-HA complexes and AlOH-Pu surface complexes, the model was unable to predict the observed data which exhibited greater sorption at pH 4 relative to pH 6; a phenomenon which does not occur in the absence of HA. Therefore, this study demonstrates that ternary Pu-HA-gibbsite complexes may form under low pH conditions and exhibit greater sorption than that observed in the absence of HA. Although the presence of HA may increase the solubility/aqueous concentrations of Pu in the absence of a solid phase, formation of ternary complexes may indeed retard the subsurface migration of Pu. The corollary to this finding is that increased mobility may occur if the ternary surface complex forms on a mobile colloid rather than part of the

  2. Binding of several anti-tumor drugs to bovine serum albumin: Fluorescence study

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun [College of Chemistry, Changchun Normal University, Changchun 130032 (China)], E-mail: sy_bi@sina.com; Sun Yantao [College of Chemistry, Jilin University, Changchun 130023 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Qiao Chunyu; Zhang Hanqi [College of Chemistry, Jilin University, Changchun 130023 (China); Liu Chunming [College of Chemistry, Changchun Normal University, Changchun 130032 (China)

    2009-05-15

    The interactions of mitomycin C (MMC), fluorouracil (FU), mercaptopurine (MP) and doxorubicin hydrochloride (DXR) with bovine serum albumin (BSA) were studied by spectroscopic method. Quenching of fluorescence of serum albumin by these drugs was found to be a static quenching process. The binding constants (K{sub A}) were 9.66x10{sup 3}, 2.08x10{sup 3}, 8.20x10{sup 2} and 7.50x10{sup 3} L mol{sup -1} for MMC-, FU-, MP- and DXR-BSA, respectively, at pH 7.4 Britton-Robinson buffer at 28 deg. C. The thermodynamic functions such as enthalpy change ({delta}H), entropy change ({delta}S) and Gibbs free-energy change ({delta}G) for the reactions were also calculated according to the thermodynamic equations. The main forces in the interactions of these drugs with BSA were evaluated. It was found that the interactions of MMC and FU with BSA were exothermic processes and those of MP and DXR with BSA were endothermic. In addition, the binding sites on BSA for the four drugs were probed by the changes of binding properties of these drugs with BSA in the presence of two important site markers such as ibuprofen and indomethacin. Based on the Foester theory of non-radiation energy transfer, the binding distances between the drugs and tryptophane were calculated and they were 3.00, 1.14, 2.85, and 2.79 nm for MMC, FU, MP and DXR, respectively.

  3. Equilibrium binding constants for Tl+ with gramicidins A, B and C in a lysophosphatidylcholine environment determined by 205Tl nuclear magnetic resonance spectroscopy.

    OpenAIRE

    Hinton, J F; Koeppe, R E; Shungu, D; Whaley, W L; Paczkowski, J A; Millett, F S

    1986-01-01

    Nuclear Magnetic Resonance (NMR) 205Tl spectroscopy has been used to monitor the binding of Tl+ to gramicidins A, B, and C packaged in aqueous dispersions of lysophosphatidylcholine. For 5 mM gramicidin dimer in the presence of 100 mM lysophosphatidylcholine, only approximately 50% or less of the gramicidin appears to be accessible to Tl+. Analysis of the 205Tl chemical shift as a function of Tl+ concentration over the 0.65-50 mM range indicates that only one Tl+ ion can be bound by gramicidi...

  4. Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors, Hanna E. [Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories (Netherlands); Koning, Peter E. de; Wouter Drijfhout, Jan [Leiden University Medical Centre, Department of Immunohematology and Blood Transfusion (Netherlands); Venezia, Brigida; Ubbink, Marcellus [Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories (Netherlands)], E-mail: m.ubbink@chem.leidenuniv.nl

    2008-07-15

    Paramagnetic relaxation enhancement provides a tool for studying the dynamics as well as the structure of macromolecular complexes. The application of side-chain coupled spin-labels is limited by the mobility of the free radical. The cyclic, rigid amino acid spin-label TOAC (2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid), which can be incorporated straightforwardly by peptide synthesis, provides an attractive alternative. In this study, TOAC was incorporated into a peptide derived from focal adhesion kinase (FAK), and the interaction of the peptide with the Src homology 3 (SH3) domain of Src kinase was studied, using paramagnetic NMR. Placing TOAC within the binding motif of the peptide has a considerable effect on the peptide-protein binding, lowering the affinity substantially. When the TOAC is positioned just outside the binding motif, the binding constant remains nearly unaffected. Although the SH3 domain binds weakly and transiently to proline-rich peptides from FAK, the interaction is not very dynamic and the relative position of the spin-label to the protein is well-defined. It is concluded that TOAC can be used to generate reliable paramagnetic NMR restraints.

  5. Multi-spectroscopic studies on the interaction of human serum albumin with astilbin: Binding characteristics and structural analysis

    International Nuclear Information System (INIS)

    Five spectroscopic techniques were used to investigate the interaction of astilbin (ASN) with human serum albumin (HSA). UV–vis absorption measurements prove that ASN–HSA complex can be formed. The analysis of fluorescence spectra reveal that in the presence of ASN, quenching mechanism of HSA is considered as static quenching. The quenching rate constant kq, KSV and the binding constant K were estimated. According to the van't Hoff equation, the thermodynamic parameters enthalpy change (ΔΗ) and entropy change (ΔS) were calculated to be −12.94 kJ mol−1 and 35.92 J mol−1 K−1, respectively. These indicate that the hydrophobic interaction is the major forces between ASN and HSA, but the hydrogen bond interaction cannot be excluded. The changes in the secondary structure of HSA which was induced by ASN were determined by circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and Raman spectroscopy. -- Graphical abstract: In this paper, the interaction of HSA with ASN was systematically studied under simulated physiological conditions by using UV–vis absorption, CD, FT-IR, fluorescence and Raman spectroscopic approaches. The quenching constant kq, KSV and the binding constant K were estimated. The changes in the secondary structure of HSA were studied by Circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and Raman spectroscopy. The UV–visible absorption spectra of HSA in the absence and presence of different concentration of ASN (1) and fluorescence spectra of HSA in the absence and the presence of ASN (2). Highlights: ► Interaction of ASN and HSA has been studied by five spectroscopic techniques. ► Hydrophobic interaction is the major forces between ASN and HSA. ► Binding of ASN induced the changes in the secondary structure of HSA

  6. Pressure dependent elastic constants of alpha and gamma cyclotrimethylene trinitramine: A quantum mechanical study

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, DeCarlos E., E-mail: decarlos.e.taylor.civ@mail.mil [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)

    2014-08-07

    The elastic constants of the α and γ polymorphs of cyclotrimethylene trinitramine (RDX) have been computed using dispersion corrected density functional theory (DFT). The DFT results validate the values obtained in several experiments using ultrasonic and impulsive stimulated thermal scattering techniques and disagree with those obtained using Brillouin scattering which, in general, exceed the other experimental and theoretical results. Compressibility diagrams at zero pressure are presented for the ab, ac, and bc crystallographic planes, and the anisotropic linear compressibility within the ac plane of α-RDX at 0 GPa, observed using ultrasonic and impulsive stimulated thermal scattering measurements, is verified using DFT. The pressure dependence of the elastic constants of α-RDX (0–4 GPa) and γ-RDX (4–8 GPa) is also presented.

  7. Comparative study of methyl-CpG-binding domain proteins

    Directory of Open Access Journals (Sweden)

    Ropers H Hilger

    2003-01-01

    Full Text Available Abstract Background Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD can bind to single methylated CpGs and most of them are involved in transcription control. So far, five vertebrate MBD proteins have been described as MBD family members: MBD1, MBD2, MBD3, MBD4 and MECP2. Results We performed database searches for new proteins containing an MBD and identified six amino acid sequences which are different from the previously described ones. Here we present a comparison of their MBD sequences, additional protein motifs and the expression of the encoding genes. A calculated unrooted dendrogram indicates the existence of at least four different groups of MBDs within these proteins. Two of these polypeptides, KIAA1461 and KIAA1887, were only present as predicted amino acid sequences based on a partial human cDNA. We investigated their expression by Northern blot analysis and found transcripts of ~8 kb and ~5 kb respectively, in all eight normal tissues studied. Conclusions Eleven polypeptides with a MBD could be identified in mouse and man. The analysis of protein domains suggests a role in transcriptional regulation for most of them. The knowledge of additional existing MBD proteins and their expression pattern is important in the context of Rett syndrome.

  8. Hemaka's constant

    CERN Document Server

    Sparavigna, Amelia Carolina

    2012-01-01

    As proposed in a previous paper, the decorations of ancient objects can provide some information on the approximate evaluations of constant {\\pi}, the ratio of circumference to diameter. Here we discuss some disks found in the tomb of Hemaka, the chancellor of a king of the First Dynasty of Egypt, about 3000 BC. The discussion is based on measurements of the dimensionless ratio of lengths.

  9. MATHEMATICAL CONSTANTS.

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, H.P.; Potter, Elinor

    1971-03-01

    This collection of mathematical data consists of two tables of decimal constants arranged according to size rather than function, a third table of integers from 1 to 1000, giving some of their properties, and a fourth table listing some infinite series arranged according to increasing size of the coefficients of the terms. The decimal values of Tables I and II are given to 20 D.

  10. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

    OpenAIRE

    Andreas Gansäuer; Meriam Seddiqzai; Tobias Dahmen; Rebecca Sure; Stefan Grimme

    2013-01-01

    The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol−1 and was therefore employed in furthe...

  11. Study on forming directivity with constant beam width in low frequency based on small sensor

    Institute of Scientific and Technical Information of China (English)

    HUI Junying; LIU Hong; YU Huabing; LIANG Guolong

    2001-01-01

    Based on a combined sensor with the size of 10 cm, a narrow beam with a constant receiving beam width of 20 degree has been formed in low frequency from several Hz to thousands of Hz by using simple adaptive algorithm. The results of theoretical simulation,laboratory experiment and lake experiment with one-dimension and two-dimension combined sensors have been given.

  12. Study on the relationship between soil moisture and its dielectric constant obtained by space-borne microwave radiometers and scatterometers

    International Nuclear Information System (INIS)

    For obtaining spatial-temporal soil moisture information in large range, a study on the relationship of soil moisture and dielectric constant obtained by space-borne microwave radiometers and scatterometers data was performed. Microwave signal is much related to dielectric constant of object observed, and soil dielectric constant is decided by soil moisture, this is the basis of using microwave remote sensing technology for soil moisture monitoring. This study focuses on the transformation of soil moisture and soil dielectric constant. The Dobson semi-empirical model was used to build a simulated database, then, the coefficients calibrated of Hallikainen formula by the least square regression method at radiometer SMOS(1.4GHz), AMSR-E(6.9GHz), and scatterometer ERS-WCS and METOP-ASCAT (both at 5.3GHz) frequency-points were performed to set up the simplified models to related the real part of the dielectric constant and the soil volumetric moisture content. The validations are performed using both simulated data of the Dobson model and in-situ observations, the results show that the simplified models have good accuracy and practicality

  13. Synthesis, Characterization, and DNA Binding Studies of Nanoplumbagin

    Directory of Open Access Journals (Sweden)

    Sheik Dawood Shahida Parveen

    2014-01-01

    Full Text Available The traditional anticancer medicine plumbagin (PLN was prepared as nanostructured material (nanoplumbagin, NPn1 from its commercial counterparts, simultaneously coencapsulating with cetyltrimethylammonium bromide or cyclodextrin as stabilizers using ultrasonication technique. Surface morphology of NPn analysed from atomic force microscopy (AFM indicates that NPn has tunable size between 75 nm and 100 nm with narrow particle size distribution. Its binding efficiency with herring sperm DNA was studied using spectral and electrochemical techniques and its efficiency was found to be more compared to the commercial microcrystalline plumbagin (PLN. DNA cleavage was also studied by gel electrophoresis. The observed results indicate that NPn1 has better solubility in aqueous medium and hence showed better bioavailability compared to its commercial counterparts.

  14. Study of Antigravity in an F(R) Model and in Brans-Dicke Theory with Cosmological Constant

    CERN Document Server

    Oikonomou, V K

    2014-01-01

    We study antigravity, that is having an effective gravitational constant with a negative sign, in scalar-tensor theories originating from $F(R)$-theory and in a Brans-Dicke model with cosmological constant. For the $F(R)$ theory case, we obtain the antigravity scalar-tensor theory in the Jordan frame by using a variant of the Lagrange multipliers method and we numerically study the time dependent effective gravitational constant. As we shall demonstrate by using a specific $F(R)$ model, although there is no antigravity in the initial model, it might occur or not in the scalar-tensor counterpart, mainly depending on the parameter that characterizes antigravity. Similar results hold true in the Brans-Dicke model.

  15. Study of Antigravity in an F(R Model and in Brans-Dicke Theory with Cosmological Constant

    Directory of Open Access Journals (Sweden)

    V. K. Oikonomou

    2014-01-01

    Full Text Available We study antigravity, that is, having an effective gravitational constant with a negative sign, in scalar-tensor theories originating from F(R theory and in a Brans-Dicke model with cosmological constant. For the F(R theory case, we obtain the antigravity scalar-tensor theory in the Jordan frame by using a variant of the Lagrange multipliers method and we numerically study the time dependent effective gravitational constant. As we will demonstrate by using a specific F(R model, although there is no antigravity in the initial model, it might occur or not in the scalar-tensor counterpart, mainly depending on the parameter that characterizes antigravity. Similar results hold true in the Brans-Dicke model.

  16. Study on improving the turbidity measurement of the absolute coagulation rate constant.

    Science.gov (United States)

    Sun, Zhiwei; Liu, Jie; Xu, Shenghua

    2006-05-23

    The existing theories dealing with the evaluation of the absolute coagulation rate constant by turbidity measurement were experimentally tested for different particle-sized (radius = a) suspensions at incident wavelengths (lambda) ranging from near-infrared to ultraviolet light. When the size parameter alpha = 2pi a/lambda > 3, the rate constant data from previous theories for fixed-sized particles show significant inconsistencies at different light wavelengths. We attribute this problem to the imperfection of these theories in describing the light scattering from doublets through their evaluation of the extinction cross section. The evaluations of the rate constants by all previous theories become untenable as the size parameter increases and therefore hampers the applicable range of the turbidity measurement. By using the T-matrix method, we present a robust solution for evaluating the extinction cross section of doublets formed in the aggregation. Our experiments show that this new approach is effective in extending the applicability range of the turbidity methodology and increasing measurement accuracy.

  17. Spectroscopic and molecular docking studies of binding interaction of gefitinib, lapatinib and sunitinib with bovine serum albumin (BSA).

    Science.gov (United States)

    Shen, Guo-Feng; Liu, Ting-Ting; Wang, Qi; Jiang, Min; Shi, Jie-Hua

    2015-12-01

    The binding interactions of three kinds of tyrosine kinase inhibitors (TKIs), such as gefitinib, lapatinib and sunitinib, with bovine serum albumin (BSA) were studied using ultraviolet spectrophotometry, fluorescence spectroscopy, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and molecular docking methods. The experimental results showed that the intrinsic fluorescence quenching of BSA induced by the three TKIs resulted from the formation of stable TKIs-BSA complexes through the binding interaction of TKIs with BSA. The stoichiometry of three stable TKIs-BSA complexes was 1:1 and the binding constants (Kb) of the three TKIs-BSA complexes were in the order of 10(4)M(-1) at 310 K, indicating that there was a strong binding interaction of the three TKIs with BSA. Based on the analysis of the signs and magnitudes of the free energy change (ΔG(0)), enthalpic change (ΔH(0)) and entropic change (ΔS(0)) in the binding process, it can be deduced that the binding process of the three TKIs with BSA was spontaneous and enthalpy-driven process, and the main interaction forces between the three TKIs and BSA were van der Waals force and hydrogen bonding interaction. Moreover, from the results of CD, FT-IR and molecular docking, it can be concluded that there was a significant difference between the three TKIs in the binding site on BSA, lapatinib was located on site II (m) of BSA while gefitinib and sunitinib were bound on site I of BSA, and there were some changes in the BSA conformation when binding three TKIs to BSA but BSA still retains its secondary structure α-helicity.

  18. How does fatty acid influence anti-thyroid drugs binding and specificity toward protein human serum albumin? A blind docking simulation study

    Indian Academy of Sciences (India)

    Bijan K Paul; Nikhil Guchhait

    2014-11-01

    This study reports an AutoDock-based blind docking simulation investigation to characterize the binding interaction of a series of anti-thyroid drugs (2-mercapto-1-methylimidazole (MMI), 2-thiouracil (TU), 6-methyl-2-thiouracil (MTU), 6--propyl-2-thiouracil (PTU) with a model plasma protein Human SerumAlbumin (HSA) in the presence and absence of fatty acid (FA). The drug-protein binding efficiency is characterized in terms of binding free energy and the association constant (Ka, which is estimated as the reciprocal of the inhibition constant, Ki) of the drugs to the transport protein. The study also unveils the substantial impact of the presence of fatty acid (FA) on the binding interaction process. It is shown that in the presence of FA the drug-protein binding efficiency is markedly enhanced (except for MTU) and the binding location is changed. Hydrogen bonding interaction appears to play a governing role in the process of FA-induced modifications of binding efficiency and location.

  19. PET physiological measurements using constant infusion

    International Nuclear Information System (INIS)

    A wide range of study designs can be used with positron emission tomography methods to provide quantitative measurements of physiological parameters. While bolus injection of tracer is the conventional approach, use of combined bolus plus constant infusion provides a number of advantages for receptor-binding tracers. Of recent interest is the use of this approach to dynamically follow the displacement of tracer during in vivo changes in neurotransmitter concentrations. This paper provides an overview of the tradeoffs in using bolus/infusion methods versus conventional bolus injection for receptor binding studies

  20. Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies.

    Science.gov (United States)

    Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G

    2016-03-28

    We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies. PMID:27036466

  1. Atomic Transition Frequencies, Isotope Shifts, and Sensitivity to Variation of the Fine Structure Constant for Studies of Quasar Absorption Spectra

    Science.gov (United States)

    Berengut, J. C.; Dzuba, V. A.; Flambaum, V. V.; King, J. A.; Kozlov, M. G.; Murphy, M. T.; Webb, J. K.

    Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, α = {e}2/hslash c , could be detected via shifts in the frequencies of atomic transitions in quasar absorption systems. Recent studies using 140 absorption systems from the Keck telescope and 153 from the Very Large Telescope, suggest that α varies spatially (61). That is, in one direction on the sky α seems to have been smaller at the time of absorption, while in the opposite direction it seems to have been larger.

  2. Coupled cluster study of spectroscopic constants of ground states of heavy rare gas dimers with spin-orbit interaction

    Science.gov (United States)

    Tu, Zhe-Yan; Wang, Wen-Liang; Li, Ren-Zhong; Xia, Cai-Juan; Li, Lian-Bi

    2016-07-01

    The CCSD(T) approach based on two-component relativistic effective core potential with spin-orbit interaction just included in coupled cluster iteration is adopted to study the spectroscopic constants of ground states of Kr2, Xe2 and Rn2 dimers. The spectroscopic constants have significant basis set dependence. Extrapolation to the complete basis set limit provides the most accurate values. The spin-orbit interaction hardly affects the spectroscopic constants of Kr2 and Xe2. However, the equilibrium bond length is shortened about 0.013 Å and the dissociation energy is augmented about 18 cm-1 by the spin-orbit interaction for Rn2 in the complete basis set limit.

  3. Hydrocephalus associated with subarachnoid hemorrhage: clinical study by computed tomography, radioisotope cisternography and constant infusion test.

    Directory of Open Access Journals (Sweden)

    Nosaka,Yoshiki

    1981-02-01

    Full Text Available Thirteen patients exhibited a communicating hydrocephalus following subarachnoid hemorrhage secondary to ruptured intracranial aneurysms and were treated with shunt procedures. The interval between subarachnoid hemorrhage and surgery averaged 9 weeks. Seven of the patients showed improvement. The prognostic value for surgical management was evaluated on the basis of three different diagnostic examinations (computed tomography(CT, cisternography and constant infusion test. A correct diagnosis was obtained in 78 per cent in cisternography, and 63 per cent in infusion test and CT. All patients responding to surgery showed a typical pattern in cisternography, consisting of ventricular retention of radiopharmaceutical tracer for 48 h or longer in association with no radioactivity over the cerebral hemispheres. The constant infusion test correlated well with typical cisternographic patterns. CT is useful in demonstrating pathophysiological changes in hydrocephalus. Periventricular hypodensity was visible in patients with normal or slightly elevated intracranial pressure, accompanied by fairly rapid deterioration. All of them responded well to shunting. In most cases which benefited from the shunt, the postoperative CT showed not only normal-sized ventricles but also marked regression of the hypodensity over a short period.

  4. Hydrocephalus associated with subarachnoid hemorrhage. Clinical study by computed tomography, radioisotope cisternography and constant infusion test

    Energy Technology Data Exchange (ETDEWEB)

    Nosaka, Y. (Okayama Univ. (Japan). School of Medicine)

    1981-02-01

    Thirteen patients exhibited a communicating hydrocephalus following subarachnoid hemorrhage secondary to ruptured intracranial aneurysms and were treated with shunt procedures. The interval between subarachnoid hemorrhage and surgery averaged 9 weeks. Seven of the patients showed improvement. The prognostic value for surgical management was evaluated on the basis of three different diagnostic examinations (computed tomography (CT), cisternography and constant infusion test). A correct diagnosis was obtained in 78 per cent in cisternography, and 63 per cent in infusion test and CT. All patients responding to surgery showed a typical pattern in cisternography, consisting of ventricular retention of radiopharmaceutical tracer for 48 h or longer in association with no radioactivity over the cerebral hemispheres. The constant infusion test correlated well with typical cisternographic patterns. CT is useful in demonstrating pathophysiological changes in hydrocephalus. Periventricular hypodensity was visible in patients with normal or slightly elevated intracranial pressure, accompanied by fairly rapid deterioration. All of them responded well to shunting. In most cases which benefited from the shunt, the postoperative CT showed not only normal-sized ventricles but also marked regression of the hypodensity over a short period.

  5. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines.

    Science.gov (United States)

    Gansäuer, Andreas; Seddiqzai, Meriam; Dahmen, Tobias; Sure, Rebecca; Grimme, Stefan

    2013-01-01

    The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol(-1) and was therefore employed in further calculations. Corrections for intramolecular London dispersion and solvation effects in the quantum chemical treatment are essential to obtain consistent and accurate theoretical data. For the investigated radical addition reaction it turned out that the polarity of the molecules is important and that a combination of electrophilic radicals with preferably nucleophilic arenes results in the highest rate constants. This is opposite to the Minisci reaction where the radical acts as nucleophile and the arene as electrophile. The substitution at the N-atom of the aniline is crucial. Methyl substitution leads to slower addition than phenyl substitution. Carbamates as substituents are suitable only when the radical center is not too electrophilic. No correlations between free reaction barriers and energies (ΔG (‡) and ΔG R) are found. Addition reactions leading to indanes or dihydrobenzofurans are too slow to be useful synthetically. PMID:24062821

  6. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

    Directory of Open Access Journals (Sweden)

    Andreas Gansäuer

    2013-08-01

    Full Text Available The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol−1 and was therefore employed in further calculations. Corrections for intramolecular London dispersion and solvation effects in the quantum chemical treatment are essential to obtain consistent and accurate theoretical data. For the investigated radical addition reaction it turned out that the polarity of the molecules is important and that a combination of electrophilic radicals with preferably nucleophilic arenes results in the highest rate constants. This is opposite to the Minisci reaction where the radical acts as nucleophile and the arene as electrophile. The substitution at the N-atom of the aniline is crucial. Methyl substitution leads to slower addition than phenyl substitution. Carbamates as substituents are suitable only when the radical center is not too electrophilic. No correlations between free reaction barriers and energies (ΔG‡ and ΔGR are found. Addition reactions leading to indanes or dihydrobenzofurans are too slow to be useful synthetically.

  7. Studies of the silencing of Baculovirus DNA binding protein

    NARCIS (Netherlands)

    Quadt, I.; Lent, van J.W.M.; Knebel-Morsdorf, D.

    2007-01-01

    Baculovirus DNA binding protein (DBP) binds preferentially single-stranded DNA in vitro and colocalizes with viral DNA replication sites. Here, its putative role as viral replication factor has been addressed by RNA interference. Silencing of DBP in Autographa californica multiple nucleopolyhedrovir

  8. Study on Synthesis and Binding Ability of a New Anion Receptor Containing NH Binding Sites

    Institute of Scientific and Technical Information of China (English)

    QIAO,Yan-Hong; LIN,Hai; LIN,Hua-Kuan

    2007-01-01

    A new colorimetric recognition receptor 1 based on the dual capability containing NH binding sites of selectively sensing anionic guest species has been synthesized. Compared with other halide anions, its UV/Vis absorption spectrum in dimethyl sulfoxide showed the response toward the presence of fluoride anion with high selectivity,and also displayed dramatic color changes from colorless to yellow in the presence of TBAF (5 × 10-5 mol/L). The similar UV/Vis absorption spectrum change also occurred when 1 was treated with AcO- while a little change with H2PO-4 and OH-. Receptor 1 has almost not affinity abilities to Cl-, Br- and I-. The binding ability of receptor 1to fluoride with high selectivity over other halides contributes to the anion size and the ability of forming hydrogen bonding. While the different ability of binding with geometrically triangular (AcO-), tetrahedral (H2PO-4 ) and linear (OH-) anions maybe result from their geometry configuration.

  9. Interaction of zinc and cobalt with dipeptides and their DNA binding studies

    Indian Academy of Sciences (India)

    P Rabindra Reddy; M Radhika; K Srinivas Rao

    2004-06-01

    Interactions of zinc and cobalt with peptides cysteinylglycine and histidylglycine have been studied. The binding modes were identified and geometry assigned. Stabilities of these complexes and their ability to bind DNA have been investigated. It is demonstrated that only zinc complexes bind DNA as compared to cobalt complexes.

  10. Biomolecular interaction study of hydralazine with bovine serum albumin and effect of β-cyclodextrin on binding by fluorescence, 3D, synchronous, CD, and Raman spectroscopic methods.

    Science.gov (United States)

    Bolattin, Mallavva B; Nandibewoor, Sharanappa T; Chimatadar, Shivamurti A

    2016-07-01

    Spectrofluoremetric technique was employed to study the binding behavior of hydralazine with bovine serum albumin (BSA) at different temperatures. Binding study of bovine serum albumin with hydralazine has been studied by ultraviolet-visible spectroscopy, fluorescence spectroscopy and confirmed by three-dimensional, synchronous, circular dichroism, and Raman spectroscopic methods. Effect of β-cyclodextrin on binding was studied. The experimental results showed a static quenching mechanism in the interaction of hydralazine with bovine serum albumin. The binding constant and the number of binding sites are calculated according to Stern-Volmer equation. The thermodynamic parameters ∆H(o) , ∆G(o) , ∆S(o) at different temperatures were calculated. These indicated that the hydrogen bonding and weak van der Waals forces played an important role in the interaction. Based on the Förster's theory of non-radiation energy transfer, the binding average distance, r, between the donor (BSA) and acceptor (hydralazine) was evaluated and found to be 3.95 nm. Spectral results showed that the binding of hydralazine to BSA induced conformational changes in BSA. The effect of common ions on the binding of hydralazine to BSA was also examined. Copyright © 2016 John Wiley & Sons, Ltd.

  11. Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

    Directory of Open Access Journals (Sweden)

    Ronne Hans

    2008-11-01

    Full Text Available Abstract Background The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence is important for gene regulation. Results In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. Conclusion We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

  12. Study on Absorption Heat transfer of Two-Dimensionally Constant Curvature Surface Tubes-1

    Science.gov (United States)

    Ogawa, Kiyoshi; Isshiki, Naotsugu

    In order to get better heat transfer coefficient of absorption in actual apparatus, it is considered that the wettability of the surface should be high, and that the thickness of liquid film should not be too thin or too thick all over the surface. So, new conception of two-dimensionally constant curvature surface (CCS) for absorption heat transfer has been introduced for the first time by the authors. First, theoretical CCS section curves of CCS tubes were calculated, and some of them were manufactured for the test. The wettability of CCS is tested and compared to the other finned tubes (radial fin tubes of triangular and rectangular profiles). As may be seen from photographs and compared to the other finned tubes, on the CCS surface, the thickness of liquid has shown to be even all over the surface without creating paticulary thick or thin place, so that, liquid films are very wettable on the CCS surface.

  13. Study on the Binding Mode of a Co(Ⅱ) Complex with DNA

    Institute of Scientific and Technical Information of China (English)

    ZHOU Qing-Hua; YANG Pin

    2005-01-01

    The mode of binding of CoLCl2, here L=bis(2-benzimidazolylmethyl)amine, with calf thymus DNA has been investigated by fluorescence measurements, equilibrium dialysis, viscosity experiments and gel electrophoresis. The complex was found to bind but weakly to DNA, with binding constant of 1.96× 104 L/mol determind at 20 ℃ in a solution containing 5 mmol/L Tris-HCl (pH 7.1) and 50 mmol/L NaCl. Polyelectrolyte theory was applied to analyse these values. Viscosity experiments show that binding did not alter the relative viscosity of DNA with any complexes to an appreciable extent. Electrophoresis test displayed that the compound could not cleave the DNA.These results show that the complex is essentially electrostatically bound to DNA.

  14. Binding Interaction of Captopril with Metal Ions: A Fluorescence Quenching Study

    Institute of Scientific and Technical Information of China (English)

    SIDDIQI K.S.; BANO Shaista; MOHD Ayaz; KHAN Aslam Aftab Parwaz

    2009-01-01

    The binding interaction of captopril(CPL)with biologically active metal ions Mg2+,Ca2+,Mn2+,Co2+,Ni2+,Cu2+ and Zn2+ was investigated in an aqueous acidic medium by fluorescence spectroscopy.The experimental results showed that the metal ions quenched the intrinsic fluorescence of CPL by forming CPL-metal complexes.It was found that static quenching was the main reason for the fluorescence quenching.The quenching constant in the case of Cu2+ was highest among all quenchers,perhaps due to its high nuclear charge and small size.Quenching of CPL by metal ions follows the order Cu2+> Ni2+> Co2+> Ca2+>Zn2+ > Mn2+ > Mg2+.The quenching constant Ksv,bimolecular quenching constant Kq,binding constant K and the binding sites "n" were determined together with their thermodynamic parameters at 27 and 37℃.The positive entropy change indicated the gain in configurational entropy as a result of chelation.The process of interaction was spontaneous and mainly △S-driven.

  15. Surface induced constant composition crystal growth kinetics studies. The brushite gypsum system

    Science.gov (United States)

    Hina, A.; Nancollas, G. H.; Grynpas, M.

    2001-02-01

    The possible oriented growth of one crystalline phase on the surface of another is especially important in systems containing both phosphate and sulfate salts of calcium. Whether the overgrowth results from a true epitaxial relationship is dependent on factors such as the thermodynamic driving forces and the free energies of the surfaces. Despite the fact that calcium sulfate dihydrate (CSD, gypsum) and calcium hydrogen phosphate dihydrate (DCPD, brushite) show many crystallographic and structural analogies, their surface reactions are quite different. The nucleation and growth of gypsum on brushite surfaces has been investigated in supersaturated solutions of calcium sulfate dihydrate at 25.0°C using the constant composition (CC) method. During the kinetics experiments, the harvested solid phases were examined by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), transmission electron microscopy (TEM) and energy dispersive X-ray analysis (EDS). Induction periods, τ, preceding the initial formation of gypsum crystals at the brushite surfaces, varied markedly with relative supersaturation, σ. A thin layer wicking method was used to investigate the interfacial free energies of the growing phases, and these data were also calculated from the kinetics results. The interfacial free energy, γ, estimated from initial growth rates was 8.4 mJ m -2, while that calculated from the induction times was 8.9 mJ m -2. These values were in agreement with those determined directly using thin layer wicking.

  16. Experimental studies on the multistage constant modulus array for the estimation of directions-of-arrival

    Institute of Scientific and Technical Information of China (English)

    ZHUO Jie; SUN Chao

    2004-01-01

    The performance of the multistage Constant Modulus (CM) array, one of the most striking blind beamforming algorithms, for the source Directions-of-Arrival (DOA) estimation was analyzed via computer simulations and water tank experiments, and was compared to that of other DOA estimation algorithms including the ‘non-blind' and the ‘blind'. Firstly, a nominal array model and an array model with gain and phase perturbations were established,respectively. Secondly, the multistage CM array algorithm was described and computer simulations were conducted. Simulation results showed that the multistage CM array could correctly estimate the DOA at the same time when the sources were blindly recovered, and the angle separating ability of the algorithm was beyond the Rayleigh resolution limit. By changing the variance of the array model errors, it was also verified that the multistage CM array was more robust to the errors than some other algorithms mentioned in this paper. Finally, water tank experiments and data processing results were provided. Situations with different array sizes and source angular separations were considered. It was shown that the results were in good agreement with computer simulations. Results of computer simulations and water tank experiments verified that the DOAs of the multiple independent sources could be blindly and robustly estimated with the multistage CM array.

  17. Entrapment of alpha1-acid glycoprotein in high-performance affinity columns for drug-protein binding studies.

    Science.gov (United States)

    Bi, Cong; Jackson, Abby; Vargas-Badilla, John; Li, Rong; Rada, Giana; Anguizola, Jeanethe; Pfaunmiller, Erika; Hage, David S

    2016-05-15

    A slurry-based method was developed for the entrapment of alpha1-acid glycoprotein (AGP) for use in high-performance affinity chromatography to study drug interactions with this serum protein. Entrapment was achieved based on the physical containment of AGP in hydrazide-activated porous silica supports and by using mildly oxidized glycogen as a capping agent. The conditions needed for this process were examined and optimized. When this type of AGP column was used in binding studies, the association equilibrium constant (Ka) measured by frontal analysis at pH 7.4 and 37°C for carbamazepine with AGP was found to be 1.0 (±0.5)×10(5)M(-1), which agreed with a previously reported value of 1.0 (±0.1)×10(5)M(-1). Binding studies based on zonal elution were conducted for several other drugs with such columns, giving equilibrium constants that were consistent with literature values. An entrapped AGP column was also used in combination with a column containing entrapped HSA in a screening assay format to compare the binding of various drugs to AGP and HSA. These results also agreed with previous data that have been reported in literature for both of these proteins. The same entrapment method could be extended to other proteins and to the investigation of additional types of drug-protein interactions. Potential applications include the rapid quantitative analysis of biological interactions and the high-throughput screening of drug candidates for their binding to a given protein.

  18. A comparative study of constant-order and variable-order fractional models in characterizing memory property of systems

    Science.gov (United States)

    Sun, H. G.; Chen, W.; Wei, H.; Chen, Y. Q.

    2011-03-01

    How to characterize the memory property of systems is a challenging issue in the modeling and analysis of complex systems. This study makes a comparative investigation of integer-order derivative, constant-order fractional derivative and two types of variable-order fractional derivatives in characterizing the memory property of systems. The advantages and potential applications of two variable-order derivative definitions are highlighted through a comparative analysis of anomalous relaxation process.

  19. In Silico and in Vitro Study of Binding Affinity of Tripeptides to Amyloid β Fibrils: Implications for Alzheimer's Disease.

    Science.gov (United States)

    Viet, Man Hoang; Siposova, Katarina; Bednarikova, Zuzana; Antosova, Andrea; Nguyen, Truc Trang; Gazova, Zuzana; Li, Mai Suan

    2015-04-23

    Self-assembly of Aβ peptides into amyloid aggregates has been suggested as the major cause of Alzheimer's disease (AD). Nowadays, there is no medication for AD, but experimental data indicate that reversion of the process of amyloid aggregation reduces the symptoms of disease. In this paper, all 8000 tripeptides were studied for their ability to destroy Aβ fibrils. The docking method and the more sophisticated MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method were employed to calculate the binding affinity and mode of tripeptides to Aβ fibrils. The ability of these peptides to depolymerize Aβ fibrils was also investigated experimentally using atomic force microscopy and fluorescence spectroscopy (Thioflavin T assay). It was shown that tripeptides prefer to bind to hydrophobic regions of 6Aβ9-40 fibrils. Tripeptides WWW, WWP, WPW and PWW were found to be the most potent binders. In vitro experiments showed that tight-binding tripeptides have significant depolymerizing activities and their DC50 values determined from dose-response curves were in micromolar range. The ability of nonbinding (GAM, AAM) and weak-binding (IVL and VLA) tripeptides to destroy Aβ fibrils was negligible. In vitro data of tripeptide depolymerizing activities support the predictions obtained by molecular docking and all-atom simulation methods. Our results suggest that presence of multiple complexes of heterocycles forming by tryptophan and proline residues in tripeptides is crucial for their tight binding to Aβ fibrils as well as for extensive fibril depolymerization. We recommend PWW for further studies as it has the lowest experimental binding constant. PMID:25815792

  20. Elastic constants and Fermi surface topology change in Calaverite AuTe{sub 2}: A density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Gudelli, Vijay Kumar, E-mail: kanchana@iith.ac.in; Kanchana, V., E-mail: kanchana@iith.ac.in [Department of Physics, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram-502205, Andhra Pradesh (India)

    2014-04-24

    Structural, elastic, electronic and Fermi surface studies of AuTe{sub 2} have been carried out by means of first principles calculations based on density functional theory. The calculated ground state properties agree well with the experiment. Fermi surface and elastic constants are predicted for the first time and from the calculated elastic constants we find the compound to be mechanically stable satisfying the stability criteria of monoclinic structure. In addition, we also find the c-axis to be more compressible than the other two which is also speculated from the present work. The metallic behaviour of this compound is confirmed from the electronic band structure calculation as we find the bands to cross the Fermi level (E{sub F}). In addition, we also observe a FS topology change under pressure which is also explained in the present work.

  1. Biological cell morphology studies by scanning electrochemical microscopy imagery at constant height: Contrast enhancement using biocompatible conductive substrates

    International Nuclear Information System (INIS)

    Scanning ElectroChemical Microscopy (SECM) has emerged as a very attractive method to image living cells activity due to its non invasive character and to the possibility of concomitant electro- and physico-chemical measurements. One of the difficulties when studying morphology of living cells in real time by SECM, using classical constant height mode, is the low contrast of the obtained images due to the insulating character of both the cells and of the underlying substrates. We propose here a technical approach to improve the contrast of SECM imagery obtained at constant height in the feedback mode without the need of Faraday cage. To this aim, a piece of biocompatible transparent conductive substrate (indium tin oxide, ITO coated PET) was attached into the bottom of cell culture well over which the cells were cultured. The transparency of ITO is intended to perform simultaneously SECM and optical microscopy measurements. The concept was applied to the study of endothelial cells, EA.hy926, whose morphology may be altered via an antivascular treatment. Our results show that the differences in the conductivity of the substrate and of the cells enhance the contrast of SECM image in feedback mode at constant height using highly charged redox mediator. In addition, differences in cell morphology are significantly observed by SECM after cell treatment with Combretastatin A4 antivascular agent

  2. Insulin binding to plastic bags: a methodologic study.

    Science.gov (United States)

    Twardowski, Z J; Nolph, K D; McGary, T J; Moore, H L; Collin, P; Ausman, R K; Slimack, W S

    1983-04-01

    A radiotracer method to assess insulin binding to commercially available plastic peritoneal dialysis solution containers was developed. A peritoneal dialysis bag (bag 2) was emptied and attached to another full bag (bag 1) of the same kind. In the syringe-to-bag method, bag 1 was symmetrically injected through the bag wall with four syringes containing dialysis solution and radioactive insulin, with or without regular insulin. The radioactivity in each syringe was measured with a gamma counter before injection, and all of the samples were counted afterwards directly in the syringes. Using a bag-to-bag transfer method, bag 1 was agitated, eight samples were taken from different parts through the wall, and then the contents were transferred to bag 2. Bag 2 was then agitated and eight samples were taken and counted. In the bag-pieces method, pieces of bag wall were cut and the radioactivity on the walls was measured to determine the amount of binding. The syringe-to-bag method gave negative results, severely underestimating the amount of insulin binding. The bag-to-bag transfer method yielded positive results in all instances. Increasing the amounts of regular insulin had no demonstrable impact on percent of binding. When the bag-to-bag method was compared with the bag-pieces method, it gave only slightly higher values; however, the bag-to-bag method was considered more reliable because the counting can be controlled more effectively. A 15-minute delay in sampling was not found to influence insulin binding. A reliable method of assessing insulin binding must be based on the following two principles: (1) The transfer of samples to intermediate containers should be avoided, and (2) radiotracer concentrations in the samples should be similar. PMID:6342377

  3. EPSP synthase: binding studies using isothermal titration microcalorimetry and equilibrium dialysis and their implications for ligand recognition and kinetic mechanism.

    Science.gov (United States)

    Ream, J E; Yuen, H K; Frazier, R B; Sikorski, J A

    1992-06-23

    Isothermal titration calorimetry measurements are reported which give important new binding constant (Kd) information for various substrate and inhibitor complexes of Escherichia coli EPSP synthase (EPSPS). The validity of this technique was first verified by determining Kd's for the known binary complex with the substrate, shikimate 3-phosphate (S3P), as well as the herbicidal ternary complex with S3P and glyphosate (EPSPS.S3P.glyphosate). The observed Kd's agreed very well with those from previous independently determined kinetic and fluorescence binding measurements. Further applications unequivocally demonstrate for the first time a fairly tight interaction between phosphoenolpyruvate (PEP) and free enzyme (Kd = 390 microM) as well as a correspondingly weak affinity for glyphosate (Kd = 12 mM) alone with enzyme. The formation of the EPSPS.PEP binary complex was independently corroborated using equilibrium dialysis. These results strongly suggest that S3P synergizes glyphosate binding much more effectively than it does PEP binding. These observations add important new evidence to support the hypothesis that glyphosate acts as a transition-state analogue of PEP. However, the formation of a catalytically productive PEP binary complex is inconsistent with the previously reported compulsory binding order process required for catalysis and has led to new studies which completely revise the overall EPSPS kinetic mechanism. A previously postulated ternary complex between S3P and inorganic phosphate (EPSPS.S3P.Pi, Kd = 4 mM) was also detected for the first time. Quantitative binding enthalpies and entropies were also determined for each ligand complex from the microcalorimetry data. These values demonstrate a clear difference in thermodynamic parameters for recognition at the S3P site versus those observed for the PEP, Pi, and glyphosate sites.

  4. A study on linear and non-linear optical constants of Rhodamine B thin film deposited on FTO glass

    Science.gov (United States)

    Yahia, I. S.; Jilani, Asim; Abutalib, M. M.; AlFaify, S.; Shkir, M.; Abdel-wahab, M. Sh.; Al-Ghamdi, Attieh A.; El-Naggar, A. M.

    2016-06-01

    The aim of this research was to fabricate/deposit the good quality thin film of Rhodamine B dye on fluorine doped tin oxide glass substrate by the low cost spin coating technique and study their linear and nonlinear optical parameters. The thickness of the thin film was measured about 300 nm with alpha step system. The transmittance of the fabricated thin film was found to be above 75% corresponding to the fluorine doped tin oxide layer. The structural analysis was performed with X-rays diffraction spectroscopy. Atomic force microscope showed the topographic image of deposited thin film. Linear optical constant like absorption coefficient, band gap, and extinction index was calculated. The dielectric constant was calculated to know the optical response of Rhodamine B dye over fluorine doped tin oxide substrate. The nonlinear optical constant like linear optical susceptibility χ(1), nonlinear optical susceptibility χ(3), nonlinear refractive index (n2) were calculated by spectroscopic method. This method has advantage over the experimental method like Z-Scan for organic dye base semiconductors for future advance optoelectronics applications like dye synthesis solar cell.

  5. Vibrational study on the cobalt binding mode of Carnosine

    Science.gov (United States)

    Torreggiani, Armida; Taddei, Paola; Tinti, Anna; Fini, Giancarlo

    2002-10-01

    The Co(II)- L-Carnosine (Carnos) system was investigated at different pH and metal/ligand molar ratios by Raman and IR spectroscopy. Raman spectra present some marker bands yielding information on the ability of the Co(II)/Carnos system to bind molecular oxygen and to identify the metal co-ordination site of the imidazole ring (N π or N τ atom) of Carnos. The existence of different oxygenated species is greatly affected by pH and the structure of the predominant complexes depends on the available nitrogen atoms. Under basic conditions, binuclear complexes binding molecular oxygen are the predominant species and two forms (monobridged and dibridged) were identified by the Raman νO-O band (750-850 cm -1). Decreasing pH to 7, the species present in the system are less able to bind oxygen. Hydrogen peroxide and a Co(III) chelate not binding O 2, were formed with a significant conversion of peroxo into superoxo complexes. A slight excess of Carnos does not enhance metal chelation. In slightly acidic conditions, the formation of H 2O 2 and superoxo species is more enhanced than at pH 7 and another Co(III) chelate is probably formed.

  6. Glucagon and adenylate cyclase: binding studies and requirements for activation.

    Science.gov (United States)

    Levey, G S; Fletcher, M A; Klein, I

    1975-01-01

    Solubilization of myocardial adenylate cyclase abolished responsiveness to glucagon and catecholamines, two of the hormones which activate the membrane-bound enzyme. Adenylate cyclase freed of detergent by DEAE-cellulose chromatography continues to remain unresponsive to hormone stimulation. However, adding purified bovine brain phospholipids--phosphotidylserine and monophosphatidylinositol--restored responsiveness to glucagon and catecholamines, respectively. 125-i-glucagon binding appeared to be independent of phospholipid, since equal binding was observed in the presence or absence of detergent and in the presence or absence of phospholipids. Chromatography of the solubilized preparation on Sephadex G-100 WAS CHARACTERIZED BY 125-I-glucagon binding and fluoride-stimulatable adenylate cyclase activity appearing in the fractions consistent with the void volume, suggesting a molecular weight greater than 100,000 for the receptor-adenylate cyclase complex. Prior incubation of the binding peak with 125-I-glucagon and rechromatography of the bound glucagon on Sephadex G-100 shifted its elution to a later fraction consistent with a smaller-molecular-weight peak. The molecular weight of this material was 24,000 to 28,000, as determined by SDS polyacrylamide gel electrophoresis. The latter findings are consistent with a dissociable receptor site for glucagon on myocardial adenylate cyclase. PMID:165684

  7. Chronic insomnia and performance in a 24-h constant routine study.

    NARCIS (Netherlands)

    M. Varkevisser; G.A. Kerkhof

    2005-01-01

    Insomniacs report daytime functioning problems, but studies of neurobehavioral functioning in insomniacs have shown little objective evidence of impairment. In addition, very little is known about the influence of the circadian clock on performance in chronic insomniacs. In the present study, we inv

  8. Proton and metal ion binding to natural organic polyelectrolytes-I. Studies with synthetic model compounds

    Science.gov (United States)

    Marinsky, J.A.; Reddy, M.M.

    1984-01-01

    A unified physico-chemical model, based on a modified Henderson-Hasselbalch equation, for the analysis of ion complexation reactions involving charged polymeric systems is presented and verified. In this model pH = pKa+p(??Ka) + log(??/1 - ??) where Ka is the intrinsic acid dissociation constant of the ionizable functional groups on the polymer, ??Ka is the deviation of the intrinsic constant due to electrostatic interaction between the hydrogen ion and the polyanion, and alpha (??) is the polyacid degree of ionization. Using this approach pKa values for repeating acidic units of polyacrylic (PAA) and polymethacrylic (PMA) acids were found to be 4.25 ?? 0.03 and 4.8 ?? 0.1, respectively. The polyion electrostatic deviation term derived from the potentiometric titration data (i.e. p(??Ka)) is used to calculate metal ion concentration at the complexation site on the surface of the polyanion. Intrinsic cobalt-polycarboxylate binding constants (7.5 for PAA and 5.6 for PMA), obtained using this procedure, are consistent with the range of published binding constants for cobalt-monomer carboxylate complexes. In two phase systems incorporation of a Donnan membrane potential term allows determination of the intrinsic pKa of a cross-linked PMA gel, pKa = 4.83, in excellent agreement with the value obtained for the linear polyelectrolyte and the monomer. Similarly, the intrinsic stability constant for cobalt ion binding to a PMA-gel (??CoPMA+ = 11) was found to be in agreement with the linear polyelectrolyte analogue and the published data for cobalt-carboxylate monodentate complexes. ?? 1984.

  9. Binding of thiocyanate to lactoperoxidase: 1H and 15N nuclear magnetic resonance studies

    Energy Technology Data Exchange (ETDEWEB)

    Modi, S.; Behere, D.V.; Mitra, S. (Tata Institute of Fundamental Research, Bombay (India))

    1989-05-30

    The binding of thiocyanate to lactoperoxidase (LPO) has been investigated by 1H and 15N NMR spectroscopy. 1H NMR of LPO shows that the major broad heme methyl proton resonance at about 61 ppm is shifted upfield by addition of the thiocyanate, indicating binding of the thiocyanate to the enzyme. The pH dependence of line width of 15N resonance of SC15N- in the presence of the enzyme has revealed that the binding of the thiocyanate to the enzyme is facilitated by protonation of an ionizable group (with pKa of 6.4), which is presumably distal histidine. Dissociation constants (KD) of SC15N-/LPO, SC15N-/LPO/I-, and SC15N-/LPO/CN- equilibria have been determined by 15N T1 measurements and found to be 90 +/- 5, 173 +/- 20, and 83 +/- 6 mM, respectively. On the basis of these values of KD, it is suggested that the iodide ion inhibits the binding of the thiocyanate but cyanide ion does not. The thiocyanate is shown to bind at the same site of LPO as iodide does, but the binding is considerably weaker and is away from the ferric ion. The distance of 15N of the bound thiocyanate ion from the iron is determined to be 7.2 +/- 0.2 A from the 15N T1 measurements.

  10. Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate

    Science.gov (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Muhammad, Niaz; Shah, Naseer Ali; Sohail, Manzar; Pandarinathan, Vedapriya

    2015-08-01

    A new binuclear O-bridged Cu(II) complex with 4-chlorophenyl acetate and 2,2‧-bipyridine has been synthesized and characterized using FT-IR, powder and single crystal XRD and electrochemical solution studies. The results revealed that the two penta-coordinated Cu(II) centers are linked by two carboxylate ligands in end-on bonding fashion. The coordination geometry is slightly distorted square pyramidal (SP) with bridging oxygen atoms occupying the apical position and other ligands lying in the equatorial plane. The striking difference in Cu-O bond distance of the bridging oxygen atom in the complex may be responsible for the SP geometry of Cu(II) ion. The complex gave rise to metal centered irreversible electro-activity where one electron Cu(II)/Cu(III) oxidation process and a single step two electron Cu(II)/Cu(0) reduction process was observed. The redox processes were found predominantly adsorption controlled. The values of diffusion coefficient and heterogeneous rate constant for oxidation process were 6.98 × 10-7 cm2 s-1 and 4.60 × 10-5 cm s-1 while the corresponding values for reduction were 5.30 × 10-8 cm2 s-1 and 5.41 × 10-6 cm s-1, respectively. The formal potential and charge transfer coefficient were also calculated. The DNA-binding ability was explored through cyclic voltammetry and UV-Visible spectroscopy. Diminution in the value of Do for oxidation indicated the binding of the complex with DNA corresponding to Kb = 8.58 × 104 M-1. UV-Visible spectroscopy yielded ε = 49 L mol-1 cm-1 and Kb = 2.96 × 104 M-1. The data of both techniques support each other. The self-induced redox activation of the complex, as indicated by cyclic voltammetry heralds its potential applications in redox catalysis and anticancer activity.

  11. Comparative study of the binding of trypsin to caffeine and theophylline by spectrofluorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: wangry@zzu.edu.cn [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Kang, Xiaohui [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Wang, Ruiqiang [The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052 (China); Wang, Rui; Dou, Huanjing; Wu, Jing; Song, Chuanjun [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China)

    2013-06-15

    The interactions between trypsin and caffeine/theophylline were investigated by fluorescence spectroscopy, UV–visible absorption spectroscopy, resonance light scattering and synchronous fluorescence spectroscopy under mimic physiological conditions. The results revealed that the fluorescence quenching of trypsin by caffeine and theophylline was the result of the formed complex of caffeine–trypsin and theophylline–trypsin. The binding constants and thermodynamic parameters at three different temperatures were obtained. The hydrophobic interaction was the predominant intermolecular forces to stabilize the complex. Results showed that caffeine was the stronger quencher and bound to trypsin with higher affinity than theophylline. -- Highlights: ► The fluorescence of trypsin can be quenched by caffeine or theophylline via hydrophobic contacts. ► Caffeine binds to trypsin with higher affinity than theophylline. ► The influence of molecular structure on the binding aspects is reported.

  12. Studies on a Novel Minor-groove Targeting Artificial Nuclease: Synthesis and DNA Binding Behavior

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Nucleases play an important role in molecular biology, for example, in DNA sequencing. Synthetic polyamide conjugates can be considered as a novel tool for the selective inhibition of gene expressions and also as potential drugs in anticancer or antiviral chemotherapy. In this article, the synthesis of a novel minor-groove targeting artificial nuclease, an oligopyrrol-containing compound, has been reported. It was found that this novel compound can bind DNA in AT-rich minor groove with high affinity and site specificity. DNA binding behavior was determined by using UV-Vis and CD. It is indicated that compound 6 can enhance the Tm of DNA from 80. 4 C to 84. 4 ℃ and that it possesses a high binding constant value(Kb = 3.05×104 L/mol).

  13. DNA-binding studies and biological activities of new nitrosubstituted acyl thioureas

    Science.gov (United States)

    Tahir, Shaista; Badshah, Amin; Hussain, Raja Azadar; Tahir, Muhammad Nawaz; Tabassum, Saira; Patujo, Jahangir Ali; Rauf, Muhammad Khawar

    2015-11-01

    Four new nitrosubstituted acylthioureas i.e. 1-acetyl-3-(4-nitrophenyl)thiourea (TU1), 1-acetyl-3-(2-methyl-4-nitrophenyl)thiourea (TU2), 1-acetyl-3-(2-methoxy-4-nitrophenyl)thiourea (TU3) and 1-acetyl-3-(4-chloro-3-nitrophenyl)thiourea (TU4) have been synthesized and characterized (by C13 and H1 nuclear magnetic resonance, Fourier transform infrared spectroscopy and single crystal X-ray diffraction). As a preliminary investigation of the anti-cancer potencies of the said compounds, DNA interaction studies have been carried out using cyclic voltammetry and UV-vis spectroscopy along with verification from computational studies. The drug-DNA binding constants are found to be in the order, KTU3 9.04 × 106 M-1 > KTU4 8.57 × 106 M-1 > KTU2 6.05 × 106 M-1 > KTU1 1.16 × 106 M-1. Furthermore, the antioxidant, cytotoxic, antibacterial and antifungal activities have been carried out against DPPH (1,1-diphenyl-2-dipicrylhydrazyl), Brine shrimp eggs, gram positive (Micrococcus luteus, Staphylococcus aureus) and gram negative (Bordetella bronchiseptica, Salmonella typhimurium, Enterobacter aerogens) and fungal cultures (Aspergillus fumigatus, Mucor species, Aspergillus niger, Aspergillus flavus) respectively.

  14. Studies on folate binding and a radioassay for serum and whole blood folate using goat milk as binding agent

    International Nuclear Information System (INIS)

    Preparations of cow, goat, buffalo, and human milk in addition to pig plasma were tested for folate binding properties. Of these, only pig plasma and goat milk showed sufficient binding to enable use as binding agents in a radioassay for serum and whole blood folate. The binding of folate by cow mild preparations in particular was found to be very poor. (orig.)

  15. A methodology to study cyclic debond growth at constant mode-mixity and energy release rate

    DEFF Research Database (Denmark)

    Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

    2010-01-01

    It is well known that face/core debond crack propagation is governed by the critical energy release rate (fracture toughness) and mode-mixity at the crack tip. Thus, the current study focuses on the developing of a methodology to perform fatigue crack growth experiments of debonded sandwich...

  16. Study of Constant Voltage Control on Small Steam Generator Based on PID Algorithm

    Directory of Open Access Journals (Sweden)

    Yanjun Xiao

    2014-03-01

    Full Text Available The object of this study is a kind of 3 kW small steam generator, which can recover waste heat through making use of 0.1~0.3 MPa steam. This can exploit secondary energy efficiently. The electricity generated can be commonly used as factory lighting, heating, fan and emergency power supply. But the generation voltage of the existed steam turbine is instable, especially when the steam pressure and the load of the generator changes suddenly. This can pose a threat to electrical safety and greatly limit the market of small steam generator. In this study, PID control algorithm is used to control the amount of steam into the turbine of generator system. And the closed-loop control system can make a real-time feedback regulation to the steam, so that the generator voltage can be stable. The user's electrical safety requirements are satisfied as well.

  17. Thermodynamic dissociation constant studies of caffeine at different temperatures and in organic water solvent mixture.

    Science.gov (United States)

    Saeeduddin; Khanzada, A W K

    2004-01-01

    Thermodynamic dissociation studies have been carried out potentiometrically at various temperatures from 25 to 50 degrees C and in 10, 20, 30 and 40% v/v dioxane-water solvent mixture at 25 degrees C. The influence of temperature and nature of solvent on dissociation equilibria of caffeine is being investigated. A computer program in GW-BASIC has been used to calculate the pK values.

  18. Tamoxifen and curcumin binding to serum albumin. Spectroscopic study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Maliszewska, M.; Pożycka, J.; Równicka-Zubik, J.; Góra, A.; Sułkowska, A.

    2013-07-01

    Tamoxifen (TMX) is widely used for the breast cancer treatment and is known as chemopreventive agent. Curcumin (CUR) is natural phenolic compound with broad spectrum of biological activity e.g. anti-inflammatory, antimicrobial, antiviral, antifungal and chemopreventive. Combination of tamoxifen and curcumin could be more effective with lower toxicity than each agent alone in use for the treatment or chemoprevention of breast cancer. Binding of drugs to serum albumin is an important factor, which determines toxicity and therapeutic dosage of the drugs. When two drugs are administered together the competition between them for the binding site on albumin can result in a decrease in bound fraction and an increase in the concentration of free biologically active fraction of drug.

  19. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine-DNA adduct formation.

    Science.gov (United States)

    Agarwal, Shweta; Chadha, Deepti; Mehrotra, Ranjana

    2015-01-01

    Chloroethyl nitrosoureas constitute an important family of cancer chemotherapeutic agents, used in the treatment of various types of cancer. They exert antitumor activity by inducing DNA interstrand cross-links. Semustine, a chloroethyl nitrosourea, is a 4-methyl derivative of lomustine. There exist some interesting reports dealing with DNA-binding properties of chloroethyl nitrosoureas; however, underlying mechanism of cytotoxicity caused by semustine has not been precisely and completely delineated. The present work focuses on understanding semustine-DNA interaction to comprehend its anti-proliferative action at molecular level using various spectroscopic techniques. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy is used to determine the binding site of semustine on DNA. Conformational transition in DNA after semustine complexation is investigated using circular dichroism (CD) spectroscopy. Stability of semustine-DNA complexes is determined using absorption spectroscopy. Results of the present study demonstrate that semustine performs major-groove-directed DNA alkylation at guanine residues in an incubation-time-drug-concentration-dependent manner. CD spectral outcomes suggest partial transition of DNA from native B-conformation to C-form. Calculated binding constants (Ka) for semustine and lomustine interactions with DNA are 1.53 × 10(3) M(-1) and 8.12 × 10(3) M(-1), respectively. Moreover, molecular modeling simulation is performed to predict preferential binding orientation of semustine with DNA that corroborates well with spectral outcomes. Results based on comparative study of DNA-binding properties of semustine and lomustine, presented here, may establish a correlation between molecular structure and cytotoxicity of chloroethyl nitrosoureas that may be instrumental in the designing and synthesis of new nitrosourea therapeutics possessing better efficacy and fewer side effects. PMID:25350567

  20. Biophysical characterization and functional studies on calbindin-D28K: A vitamin D-induced calcium-binding protein

    International Nuclear Information System (INIS)

    Vitamin D dependent calcium binding protein, or calbindin-D, is the principal protein induced in the intestine in response to the steroid hormone 1,25(OH)2-vitamin D3. A definitive role for calbindin-D in vitamin D3 mediated biological responses remains unclear. Biophysical and functional studies on chick intestinal calbindin-D28K (CaBP) were initiated so that some insight might be gained into its relevance to the process of intestinal calcium transport. Calbindin-D belongs to a class of high affinity calcium binding proteins which includes calmodulin, parvalbumin and troponin C. The Ca 2+ binding stoichiometry and binding constants for calbindin-D28K were quantitated by Quin 2 titration analysis. The protein was found to bind 5-6 Ca 2+ ions with a KD on the order of 10-8, in agreement with the 6 domains identified from the amino acid sequence. A slow Ca 2+ exchange rate (80 s-1) as assessed by 43Ca NMR and extensive calcium dependent conformational changes in 1H NMR spectra were also observed. Functional studies on chick intestinal CaBP were carried out by two different methods. Interactions between CaBP and intestinal cellular components were assessed via photoaffinity labeling techniques. Specific calcium dependent complexes for CaBP were identified with bovine intestinal alkaline phosphatase and brush border membrane proteins of 60 and 150 kD. CaBP was also found to co-migrate with the alkaline phosphatase activity of chick intestinal brush border membranes as evaluated by gel filtration chromatography. The second procedure for evaluating CaBP functionality has involved the quantitation of CaBP association with vesicular transport components as assessed by ELISA. CaBP, immunoreactivity was observed in purified lysosomes, microsomes and microtubules

  1. Synthesis, biological investigation, calf thymus DNA binding and docking studies of the sulfonyl hydrazides and their derivatives

    Science.gov (United States)

    Murtaza, Shahzad; Shamim, Saima; Kousar, Naghmana; Tahir, Muhammad Nawaz; Sirajuddin, Muhammad; Rana, Usman Ali

    2016-03-01

    The present study describes the syntheses and biological investigations of sulfonyl hydrazides and their novel derivatives. The detailed investigations involved the characterization of the newly synthesized compounds using FTIR, NMR, mass spectrometry and by single crystal X-Ray diffraction (XRD) analysis techniques. The binding tendencies of these compounds with CT-DNA (calf thymus DNA) have been explored by electronic absorption (UV) spectroscopy and viscosity measurement. The binding constant (K) and Gibb's free energy (ΔG) values were also calculated accordingly. In addition, we also investigated the biological activities such as antioxidant, antibacterial, enzyme inhibition and DNA interactions. The antioxidant activity was assayed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, while antibacterial activity was investigated against four bacterial strains (viz. Escherichia coli, Crynibacteria bovius, Staphylococcus auras and Bacillus antherasis) by employing the common disc diffusion method. Enzyme inhibition activity of the synthesized compounds was examined against butyrylcholinestrase. The results of enzyme inhibition activity and the DNA binding interaction studies were also collected through molecular docking program using computational analysis. Our study reveals that the newly synthesized compounds possess moderate to good biological activities.

  2. EPR studies of cooperative binding of Cu (II) to hemoglobin

    International Nuclear Information System (INIS)

    The investigation of the relative affinities of the two pairs of hemoglobin copper sites by monitoring the EPR spectra of the complexes formed by the reaction of copper with deoxyhemoglobin is reported. A model in which two sites are assumed to accept copper ions in a noncooperative way is not able to predict the experimental results. Thus it is conclude that the binding of these ions to hemoglobin is a cooperative phenomenon. (Author)

  3. Numerical Study of Laminar Flow Forced Convection of Water-Al2O3 Nanofluids under Constant Wall Temperature Condition

    OpenAIRE

    Hsien-Hung Ting; Shuhn-Shyurng Hou

    2015-01-01

    This numerical study is aimed at investigating the forced convection heat transfer and flow characteristics of water-based Al2O3 nanofluids inside a horizontal circular tube in the laminar flow regime under the constant wall temperature boundary condition. Five volume concentrations of nanoparticle, 0.1, 0.5, 1, 1.5, and 2 vol.%, are used and diameter of nanoparticle is 40 nm. Characteristics of heat transfer coefficient, Nusselt number, and pressure drop are reported. The results show that h...

  4. Study of Constant Voltage Control on Small Steam Generator Based on PID Algorithm

    OpenAIRE

    Yanjun Xiao; Xuewei Ma; Wei Shao; Yuming Guan

    2014-01-01

    The object of this study is a kind of 3 kW small steam generator, which can recover waste heat through making use of 0.1~0.3 MPa steam. This can exploit secondary energy efficiently. The electricity generated can be commonly used as factory lighting, heating, fan and emergency power supply. But the generation voltage of the existed steam turbine is instable, especially when the steam pressure and the load of the generator changes suddenly. This can pose a threat to electrical safety and great...

  5. Experimental Study on Shock Wave Structures in Constant-area Passage of Cold Spray Nozzle

    Institute of Scientific and Technical Information of China (English)

    Hiroshi KATANODA; Takeshi MATSUOKA; Kazuyasu MATSUO

    2007-01-01

    Cold spray is a technique to make a coating on a wide variety of mechanical or electric parts by spraying solid particles accelerated through a high-speed gas flow in a converging-diverging nozzle. In this study, pseudo-shock waves in a modeled cold spray nozzle as well as high-speed gas jets are visualized by schlieren technique. The schlieren photographs reveals the supersonic flow with shock train in the nozzle. Static pressure along the barrel wall is also measured. The location of the head of pseudo-shock wave and its pressure distribution along the nozzle wall are analytically explained by using a formula of pseudo-shock wave. The analytical results show that the supersonic flow accompanying shock wave in the nozzle should be treated as pseudo-shock wave instead of normal shock wave.

  6. Theoretical study of the pressure dependent rate constants of the thermal decomposition of β-propiolactone

    Directory of Open Access Journals (Sweden)

    Abolfazl Shiroudi

    2015-09-01

    Full Text Available A theoretical study of the thermal decomposition of β-propiolactone is carried out using ab initio molecular orbital (MO methods at the MP2/6-311+G∗∗ level and Rice–Ramsperger–Kassel–Marcus (RRKM theory. The reported experimental results showed that decomposition of β-propiolactone occurred by three competing homogeneous and first order reactions. For the three reactions, the calculation was also performed at the MP2/6-311+G∗∗ level of theory, as well as by single-point calculations at the B3LYP/6-311+G∗∗//MP2/6-311+G∗∗, and MP4/6-311+G∗∗//MP2/6-311+G∗∗ levels of theory. The fall-off pressures for the decomposition in these reactions are found to be 2.415, 9.423 × 10−2 and 3.676 × 10−3 mmHg, respectively.

  7. Studies of (-)-pironetin binding to α-tubulin: conformation, docking, and molecular dynamics.

    Science.gov (United States)

    Bañuelos-Hernández, Angel E; Mendoza-Espinoza, José Alberto; Pereda-Miranda, Rogelio; Cerda-García-Rojas, Carlos M

    2014-05-01

    A comprehensive conformational analysis for the anticancer agent pironetin (1) was achieved by molecular modeling using density functional theory calculations at the B3PW91/DGTZVP level in combination with calculated and experimental (1)H-(1)H coupling constants comparison. Two solvent-dependent conformational families (L and M) were revealed for the optimum conformations. Docking studies of the pironetin-tubulin complex determined a quantitative model for the hydrogen-bond interactions of pironetin through the αAsn249, αAsn258, and αLys352 amino groups in α-tubulin, which supported the formation of a covalent adduct between the αLys352 and the β carbon atom of the α,β-unsaturated lactone. Saturation-transfer difference NMR spectroscopy confirmed that pironetin binds to tubulin, while molecular dynamics exposed a distortion of the tubulin secondary structure at the H8 and H10 α-helices as well as at the S9 β-sheet, where αLys352 is located. A large structural perturbation in the M-loop geometry between the αIle274 and αLeu285 residues, an essential region for molecular recognition between α-α and β-β units of protofilaments, was also identified and provided a rationale for the pironetin inhibitory activity. PMID:24761989

  8. A computational study of ligand binding affinities in iron(III) porphine and protoporphyrin IX complexes.

    Science.gov (United States)

    Durrant, Marcus C

    2014-07-01

    The search for novel anti-malarial drugs that can disrupt biomineralization of ferriprotoporphyrin IX to haemozoin requires an understanding of the fundamental chemistry of the porphyrin's iron(iii) centre at the water-lipid interface. Towards this end, the binding affinities for a diverse set of 31 small ligands with iron(iii) porphine have been calculated using density functional theory, in the gas phase and also with implicit solvent corrections for both water and n-octanol. In addition, the binding of hydroxide, chloride, acetate, methylamine and water to ferriprotoporphyrin IX has been studied, and very similar trends are observed for the smaller and larger models. Anionic ligands generally give stronger binding than neutral ones; the strongest binding is observed for RO(-) and OH(-) ligands, whilst acetate binds relatively weakly among the anions studied. Electron-rich nitrogen donors tend to bind more strongly than electron-deficient ones, and the weakest binding is found for neutral O and S donors such as oxazole and thiophene. In all cases, ligand binding is stronger in n-octanol than in water, and the differences in binding energies for the two solvents are greater for ionic ligands than for neutrals. Finally, dimerization of ferriprotoporphyrin IX by means of iron(iii)-carboxylate bond formation has been modelled. The results are discussed in terms of haemozoin crystal growth and its disruption by known anti-malarial drugs.

  9. Spectroscopic and molecular modelling studies of binding mechanism of metformin with bovine serum albumin

    Science.gov (United States)

    Sharma, Deepti; Ojha, Himanshu; Pathak, Mallika; Singh, Bhawna; Sharma, Navneet; Singh, Anju; Kakkar, Rita; Sharma, Rakesh K.

    2016-08-01

    Metformin is a biguanide class of drug used for the treatment of diabetes mellitus. It is well known that serum protein-ligand binding interaction significantly influence the biodistribution of a drug. Current study was performed to characterize the binding mechanism of metformin with serum albumin. The binding interaction of the metformin with bovine serum albumin (BSA) was examined using UV-Vis absorption spectroscopy, fluorescence, circular dichroism, density functional theory and molecular docking studies. Absorption spectra and fluorescence emission spectra pointed out the weak binding of metformin with BSA as was apparent from the slight change in absorbance and fluorescence intensity of BSA in presence of metformin. Circular dichroism study implied the significant change in the conformation of BSA upon binding with metformin. Density functional theory calculations showed that metformin has non-planar geometry and has two energy states. The docking studies evidently signified that metformin could bind significantly to the three binding sites in BSA via hydrophobic, hydrogen bonding and electrostatic interactions. The data suggested the existence of non-covalent specific binding interaction in the complexation of metformin with BSA. The present study will certainly contribute to the development of metformin as a therapeutic molecule.

  10. Atomic transition frequencies, isotope shifts, and sensitivity to variation of the fine structure constant for studies of quasar absorption spectra

    CERN Document Server

    Berengut, J C; Flambaum, V V; King, J A; Kozlov, M G; Murphy, M T; Webb, J K

    2010-01-01

    Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, alpha, could be detected via shifts in the frequencies of atomic transitions in quasar absorption systems. Recent studies using 140 absorption systems from the Keck telescope and 153 from the Very Large Telescope, suggest that alpha varies spatially. That is, in one direction on the sky alpha seems to have been smaller at the time of absorption, while in the opposite direction it seems to have been larger. To continue this study we need accurate laboratory measurements of atomic transition frequencies. The aim of this paper is to provide a compilation of transitions of importance to the search for alpha variation. They are E1 transitions to the ground state in several different atoms and ions, with wavelengths ranging from around 900 - 6000 A, and require an accuracy of better than 10^{-4} A. We discuss isotope shift measurements that are...

  11. Development and validation of a ReaxFF reactive force field for Fe/Al/Ni alloys: molecular dynamics study of elastic constants, diffusion, and segregation.

    Science.gov (United States)

    Shin, Yun Kyung; Kwak, Hyunwook; Zou, Chenyu; Vasenkov, Alex V; van Duin, Adri C T

    2012-12-13

    We have developed a ReaxFF force field for Fe/Al/Ni binary alloys based on quantum mechanical (QM) calculations. In addition to the various bulk phases of the binary alloys, the (100), (110) and (111) surface energies and adatom binding energies were included in the training set for the force field parametrization of the Fe/Al/Ni binary alloys. To validate these optimized force fields, we studied (i) elastic constants of the binary alloys at finite temperatures, (ii) diffusivity of alloy components in Al/Ni alloy, and (iii) segregation on the binary alloy surfaces. First, we calculated linear elastic constants of FeAl, FeNi(3), and Ni(3)Al in the temperature range 300 to 1100 K. The temperature dependences of the elastic constants of these three alloys, showing a decrease in C(11), C(12), and C(44) as temperature increases, were in good agreement with the experimental results. We also performed ReaxFF molecular dynamics (MD) simulations for Al or Ni diffusion in the system modeled as Al/Ni mixed layers with the linear composition gradients. At 1000 K, Al diffusivity at the pure Al end was 2 orders of magnitude larger than that in the Al trace layers, probably explaining the nature of different diffusion behavior between molten metals and alloys. However, the diffusivity of Ni at the pure Ni end was only slightly larger than that in the Ni trace layers at the system temperature much lower than the melting temperature of Ni. Third, we investigated the surface segregation in L1(2)-Fe(3)Al, Fe(3)Ni, and Ni(3)Al clusters at high temperature (2500 K). From the analysis of composition distribution of the alloy components from the bulk to the surface layer, it was found that the degree of segregation depended on the chemical composition of the alloy. Al surface segregation occurred most strongly in Fe(3)Al, whereas it occurred most weakly in Ni(3)Al. These results may support the segregation mechanism that surface segregation results from the interplay between the

  12. Study of Fluorine Addition Influence in the Dielectric Constant of Diamond-Like Carbon Thin Film Deposited by Reactive Sputtering

    Science.gov (United States)

    Trippe, S. C.; Mansano, R. D.

    The hydrogenated amorphous carbon films (a-C:H) or DLC (Diamond-Like Carbon) films are well known for exhibiting high electrical resistivity, low dielectric constant, high mechanical hardness, low friction coefficient, low superficial roughness and also for being inert. In this paper, we produced fluorinated DLC films (a-C:F), and studied the effect of adding CF4 on the above-mentioned properties of DLC films. These films were produced by a reactive RF magnetron sputtering system using a target of pure carbon in stable graphite allotrope. We performed measurements of electrical characteristic curves of capacitance as a function of applied tension (C-V) and current as a function of the applied tension (I-V). We showed the dielectric constant (k) and the resistivity (ρ) as functions of the CF4 concentration. On films with 65% CF4, we found that k = 2.7, and on films with 70% CF4, ρ = 12.3 × 1011 Ω cm. The value of the electrical breakdown field to films with 70% CF4 is 5.3 × 106 V/cm.

  13. Study of formation constant of molybdophosphate and it's application in the product of xenotime sand, tooth and bone

    International Nuclear Information System (INIS)

    The formation constant of molybdophosphate complex and it's application in the product of xenotime sand, tooth and bone have been studied by spectrophotometric method. The molybdophosphate complex were formed from reaction between phosphate and molybdate on several of pH in the strong acid condition (pH = 0.45 - 0.71) and several of phosphate mole fraction (0.01 - 0.08). The several of complex formation reactions were determined by matrix disintegration technique. Molybdophosphate complex were founded three forms i.e. (P2Mo18O62)6- or 9 MPA, (PMo11O39)7- or 11 MPA and (PMo12O40)3- or 12 MPA. The formation constant of (PMo12O40)3- complex was found β = 1046.95 ± 103.7, while for (P2Mo18O62)6- and (PMo11O39)7- were not detected. The application in samples were found the concentration of P in product of xenotime sand : 5.37±0.08 μg/ml, in canine-tooth: 10.40 - 19.49 % in cutting-tooth : 11.08 - 18.05 % and in bone 10.94 - 14.29 %. (author)

  14. 17O nuclear quadrupole coupling constants of water bound to a metal ion: A gadolinium(III) case study

    Science.gov (United States)

    Yazyev, Oleg V.; Helm, Lothar

    2006-08-01

    Rotational correlation times of metal ion aqua complexes can be determined from O17 NMR relaxation rates if the quadrupole coupling constant of the bound water oxygen-17 nucleus is known. The rotational correlation time is an important parameter for the efficiency of Gd3+ complexes as magnetic resonance imaging contrast agents. Using a combination of density functional theory with classical and Car-Parrinello molecular dynamics simulations we performed a computational study of the O17 quadrupole coupling constants in model aqua ions and the [Gd(DOTA)(H2O)]- complex used in clinical diagnostics. For the inner sphere water molecule in the [Gd(DOTA)(H2O)]- complex the determined quadrupole coupling parameter χ√1+η2/3 of 8.7MHz is very similar to that of the liquid water (9.0MHz ). Very close values were also predicted for the the homoleptic aqua ions of Gd3+ and Ca2+. We conclude that the O17 quadrupole coupling parameters of water molecules coordinated to closed shell and lanthanide metal ions are similar to water molecules in the liquid state.

  15. DNA- and BSA-binding studies and anticancer activity against human breast cancer cells (MCF-7) of the zinc(II) complex coordinated by 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine

    Science.gov (United States)

    Anjomshoa, Marzieh; Fatemi, Seyed Jamilaldin; Torkzadeh-Mahani, Masoud; Hadadzadeh, Hassan

    2014-06-01

    Binding studies of a mononuclear zinc(II) complex, [Zn(dppt)2Cl2] (dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), with DNA and bovine serum albumin (BSA) have been investigated under physiological conditions. The binding properties of the complex with fish sperm DNA (FS-DNA) have been investigated by UV-Vis absorption, thermal denaturation, competitive DNA-binding studies with ethidium bromide (EB) by fluorescence, and gel electrophoresis techniques. The competitive study with (EB) shows that the complex can displace EB from the DNA-EB system and compete for the DNA-binding sites with EB, which is usually characteristic of the intercalative interaction of compounds with DNA. The value of the fluorescence quenching constant (Ksv) was obtained as 3.1 × 104 M-1, indicating that this complex shows a high quenching efficiency and a significant degree of binding to DNA. Moreover, the intercalative binding mode has also been verified by the results of UV-Vis absorption, thermal denaturation and gel electrophoresis. The value of Kb at room temperature was calculated to be 1.97 × 105 M-1, indicating that the complex possesses strong tendency to bind with DNA. This value is very greater than to the values obtained for other zinc(II) complexes. The interaction of the complex with BSA has been studied by UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopic techniques. The results indicate that the complex has a quite strong ability to quench the fluorescence of BSA and the binding reaction is mainly a static quenching process. The quenching constants (KSV), the binding constants (Kb), the number of binding sites at different temperatures, the binding distance between BSA and the complex (r), and the thermodynamic parameters (ΔHo, ΔSo and ΔGo) between BSA and the complex were calculated. The complex exhibits good binding propensity to BSA showing relatively high binding constant values. The positive ΔHo and ΔSo values indicate that the

  16. DNA- and BSA-binding studies and anticancer activity against human breast cancer cells (MCF-7) of the zinc(II) complex coordinated by 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine.

    Science.gov (United States)

    Anjomshoa, Marzieh; Fatemi, Seyed Jamilaldin; Torkzadeh-Mahani, Masoud; Hadadzadeh, Hassan

    2014-06-01

    Binding studies of a mononuclear zinc(II) complex, [Zn(dppt)2Cl2] (dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), with DNA and bovine serum albumin (BSA) have been investigated under physiological conditions. The binding properties of the complex with fish sperm DNA (FS-DNA) have been investigated by UV-Vis absorption, thermal denaturation, competitive DNA-binding studies with ethidium bromide (EB) by fluorescence, and gel electrophoresis techniques. The competitive study with (EB) shows that the complex can displace EB from the DNA-EB system and compete for the DNA-binding sites with EB, which is usually characteristic of the intercalative interaction of compounds with DNA. The value of the fluorescence quenching constant (Ksv) was obtained as 3.1×10(4)M(-1), indicating that this complex shows a high quenching efficiency and a significant degree of binding to DNA. Moreover, the intercalative binding mode has also been verified by the results of UV-Vis absorption, thermal denaturation and gel electrophoresis. The value of Kb at room temperature was calculated to be 1.97×10(5)M(-1), indicating that the complex possesses strong tendency to bind with DNA. This value is very greater than to the values obtained for other zinc(II) complexes. The interaction of the complex with BSA has been studied by UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopic techniques. The results indicate that the complex has a quite strong ability to quench the fluorescence of BSA and the binding reaction is mainly a static quenching process. The quenching constants (KSV), the binding constants (Kb), the number of binding sites at different temperatures, the binding distance between BSA and the complex (r), and the thermodynamic parameters (ΔH(o), ΔS(o) and ΔG(o)) between BSA and the complex were calculated. The complex exhibits good binding propensity to BSA showing relatively high binding constant values. The positive ΔH(o) and ΔS(o) values indicate that

  17. Comparison of [11C]cocaine binding at tracer and pharmacological doses of baboon brain: A PET study

    Energy Technology Data Exchange (ETDEWEB)

    Volkow, N.D.; Fowler, J.S.; Logan, J. [Brookhaven National Lab., Upton, NY (United States)] [and others

    1994-05-01

    In vitro studies have shown that cocaine (C) binds to both high and low affinity sites on the dopamine transporter (DAT). We have previously characterized the binding of tracer doses of [{sup 11}C]cocaine (C*)to a high affinity site on the DAT. To assess if in vivo C also binds to low affinity sites we used PET to compare binding of tracer doses (17.8{plus_minus}12.2 {mu}g C) of C* to pharmacological doses (8 mg of C coadministered with C*). Sixteen paired studies were done to assess test/retest variability, specific versus non specific binding and to characterize binding profile. Dynamic scans were started immediately after injection of C* (5-8 mCi) for 50 min on the CTI-931 (6 x 6 x 6.5 mm FWHM). Time activity curves for tissue concentration and for unchanged tracer in plasma were used to calculate the transport constant between plasma and tissue (K1) and to obtain the distribution volume (DV). The ratio of the DV in striatum (ST) to that in cerebellum (CB) (which corresponds to Bmax/Kd-1) was used as model parameter. Peak brain uptake of C* was significantly higher for tracer than for pharmacological doses (0.041 versus 0.033 % dose/cc), as were the values for K1 (1.07{plus_minus}0.21 versus 0.68{plus_minus}0.26 (t=3.0 p<0.01)). Repeated measures were reproducible for tracer ({plus_minus}2%) and pharmacological doses of C* ({plus_minus}4%). Tracer dose C* showed highest binding and slowest clearance in ST which was reduced by C (0.5-2.0 mg/kg iv, -25 to -30%) and by drugs that inhibit DAT (2mg/kg nomifensine - 21%, 0.5 mg/kg methylphenidate -12%) and was increased by serotonin transporter inhibitors (5HT-Ti) (2 mg/kg citalopram +11%, 0.5 mg/kg fluoxetine +6%) and not changed by NE transporter inhibitors (0.5 mg/kg desipramine or 2 mg/kg tomoxetine). The increase with (5HT-Ti) may reflect neurotransmitter interactions or changes in bioavailability. At pharmacological doses C* showed homogeneous distribution and was not changed by C nor by any of the above drugs.

  18. Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.

    Science.gov (United States)

    Enlow, Mark A

    2012-03-01

    Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds.

  19. Full quantum mechanical study of binding of HIV-1 protease drugs

    Science.gov (United States)

    Zhang, Da W.; Zhang, John Z. H.

    Fully quantum mechanical studies of detailed binding interactions between HIV-1 protease and six FDA (Food and Drug Administration)-approved drugs (saquinavir, indinavir, ritonavir, nelfinavir, amprenavir, and lopinavir) are carried out using a recently developed MFCC (molecular fractionation with conjugate caps) method. The MFCC calculation produces a quantum mechanical interaction spectrum for any protease drug binding complex. Detailed quantitative analysis on binding of lopinavir to specific residues of the protease is given from the current study. The present calculation shows that the dominant binding of lopinavir to the protease is through the formation of a strong hydrogen bond between the central hydroxyl group of the drug to the aspartate oxygen of Asp25 in one of the two chains of the protease (A chain). This is closely followed by hydrogen binding of the drug to Asp29 in the B chain and somewhat weak hydrogen bonding to Asp30, Gly27, Gly48, and Ile50 in both chains. By partitioning all six drugs into four building blocks besides the central component containing the hydroxyl group, MFCC calculation finds that block III has essentially no binding interaction with the protease and the major binding interactions of these drugs are from blocks II and IV, in addition to the dominant central hydroxyl group. This detailed quantitative information on drug binding to the protease is very useful in rational design of new and improved inhibitors of HIV-1 protease and its mutants.

  20. A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

    Directory of Open Access Journals (Sweden)

    Xiongwu Wu

    2015-10-01

    Full Text Available Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66's pKa.

  1. Ligand binding studies in the mouse olfactory bulb: identification and characterisation of a L-[3H]carnosine binding site

    International Nuclear Information System (INIS)

    Binding sites for the dipeptide L-carnosine (β-alanyl-t-histidine) have been detected in membranes prepared from mouse olfactory bulbs. The binding of L-[3H]- carnosine was saturable, reversible and stereospecific and had a Ksub(d) of about 770 nM. The stereospecific binding of L-carnosine represented about 30% of the totoal binding at pH 6.8, and decreased markedly with increasing pH. Binding was stimulated by calcium, unaffected by zinc, magnesium or manganese and inhibted by sodium and potassium. Carnosine binding was sensitive to trypsin and phospholipases A and C, but not to neuraminidase. Nystatin and filipin, which interact with membrane lipids, also interfered with binding. Some peptide analogues of carnosine were potent inhibitors of binding, but a variety of drugs serving as potent inhibitors in other binding systems had no effect on carnosine binding. Carnosine binding to mouse olfactory bulb membranes was 15-fold higher than that seen in membranes prepared from cerebral hemispheres, 5-fold higher than in cerebellum membranes and 3-fold higher than in membranes from spinal medulla and the olfactory tubercle-lateral olfactory tract area. (Auth.)

  2. Experimental study and finite element analysis based on equivalent load method for laser ultrasonic measurement of elastic constants.

    Science.gov (United States)

    Zhan, Yu; Liu, Changsheng; Zhang, Fengpeng; Qiu, Zhaoguo

    2016-07-01

    The laser ultrasonic generation of Rayleigh surface wave and longitudinal wave in an elastic plate is studied by experiment and finite element method. In order to eliminate the measurement error and the time delay of the experimental system, the linear fitting method of experimental data is applied. The finite element analysis software ABAQUS is used to simulate the propagation of Rayleigh surface wave and longitudinal wave caused by laser excitation on a sheet metal sample surface. The equivalent load method is proposed and applied. The pulsed laser is equivalent to the surface load in time and space domain to meet the Gaussian profile. The relationship between the physical parameters of the laser and the load is established by the correction factor. The numerical solution is in good agreement with the experimental result. The simple and effective numerical and experimental methods for laser ultrasonic measurement of the elastic constants are demonstrated. PMID:27079489

  3. Metal ion binding sites of bacteriorhodopsin. Laser-induced lanthanide luminescence study

    International Nuclear Information System (INIS)

    Laser-excited luminescence lifetimes of lanthanide ions bound to bacteriorhodopsin have been measured in deionized membranes. The luminescence titration curve, as well as the binding curve of apomembrane (retinal-free) with Eu3+, has shown that the removal of the retinal does not significantly affect the affinity of Eu3+ for the two high affinity sites of bacteriorhodopsin. The D2O effects on decay rate constants indicate that Eu3+ bound to the high affinity sites of native membrane or apomembrane is coordinated by about six ligands in the first coordination sphere. Tb3+ is shown to be coordinated by four ligands. The data indicate that metal ions bind to the protein with a specific geometry. From intermetal energy transfer experiments using Eu3+-Pr3+, Tb3+-Ho3+, and Tb3+-Er3+, the distance between the two high affinity sites is estimated to be 7-8 A

  4. Affinity Capillary Electrophoresis:Study of the Binding of HIV-1 gp41 with a Membrane Protein (P45) on the Human B Cell Line,Raji

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Affinity capillary electrophoresis has been used to study the interaction between a membrane protein (P45) isolated from the Human B cell line, Raji, and rsgp41. P45, rsgp41 and the complexes were well resolved. The entire separation was achieved in less than 3min. Formations of two kinds of stable P45-rsgp41 complexes were confirmed based on migration time comparison; the binding equilibrium was achieved as soon as two proteins were mixed. The results indicate that the interaction between P45 and rsgp41 is strong with a fast association rate and a slow dissociation rate, and there are at least two kinds of binding sites with different binding constants between P45 and rsgp41.

  5. Studies on the Synthesis, Characterization, DNA Binding, Cytotoxicity and Antioxidant activity of 2-methyl-4-nitrophenylferrocene

    International Nuclear Information System (INIS)

    We report herein the synthesis, structural characterization, DNA binding, BamH1 digestion, cytotoxicity and antioxidant activity of 2-methyl-4-nitrophenylferrocene. Structural characterization is based on multinuclear (1H and 13C) NMR, FT-IR spectroscopy and elemental analysis. Interaction of 2-methyl-4-nitrophenylferrocene with pBR322 plasmid DNA shows noncovalent interactions however these noncovalent interactions reveal the prevention of BamH1 restriction site (g/ggtcc). In the voltammogram, a negative shift in peak potential has been observed on addition of increasing concentration of CT-DNA, which shows electrostatic interaction for 2-methyl-4-nitrophenylferro with negatively charged phosphate of DNA backbone. The binding ratio, binding constant, binding free energy and diffusion coefficient of free and bound drug were calculated to understand the mechanism. The high negative value of -delta G signifies the spontaneity and high conformational stability of 2-methyl-4-nitrophenylferro with CT-DNA. The compound has the ability to scavenge free radicals as have been revealed by DPPH findings. (author)

  6. QM/MM Molecular Dynamics Studies of Metal Binding Proteins

    Directory of Open Access Journals (Sweden)

    Pietro Vidossich

    2014-07-01

    Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

  7. Study on the thermodynamics of the binding of iminium and alkanolamine forms of the anticancer agent sanguinarine to human serum albumin

    International Nuclear Information System (INIS)

    Highlights: ► Energetics of sanguinarine–human serum albumin has been elucidated. ► The alkanolamine binds stronger than iminium. ► Enthalpy driven binding for iminium was revealed. ► Alkanolamine form binding was favored by negative enthalpy and entropy changes. ► Spectroscopic results support calorimetry data. - Abstract: Sanguinarine is an anticancer plant alkaloid that can exist in the charged iminium and neutral alkanolamine forms. The thermodynamics of the interaction of the two forms with human serum albumin was investigated using calorimetric techniques, and the data supplemented with circular dichroism and spectrofluorimetric studies. The thermodynamic results show that there is only one class of binding for sanguinarine on HSA. The equilibrium constant was four times higher for the alkanolamine (Ka = 2.18 · 105 M−1) than for iminium (Ka = 5.97 · 104 M−1). The binding was enthalpy driven for iminium and favoured by both a negative enthalpy and a stronger favourable entropy contribution for the alkanolamine. Temperature dependent calorimetric data yielded values of ΔCp∘ that are consistent with the involvement of different molecular forces in the complexation of the two forms of sanguinarine to HSA. The fluorescence quenching data suggest a static quenching mechanism. Synchronous fluorescence and circular dichroic data are consistent with a conformational change in the protein on binding that was also higher for the alkanolamine form.

  8. Systematic Study of Binding of μ-Conotoxins to the Sodium Channel NaV1.4

    Directory of Open Access Journals (Sweden)

    Somayeh Mahdavi

    2014-12-01

    Full Text Available Voltage-gated sodium channels (NaV are fundamental components of the nervous system. Their dysfunction is implicated in a number of neurological disorders, such as chronic pain, making them potential targets for the treatment of such disorders. The prominence of the NaV channels in the nervous system has been exploited by venomous animals for preying purposes, which have developed toxins that can block the NaV channels, thereby disabling their function. Because of their potency, such toxins could provide drug leads for the treatment of neurological disorders associated with NaV channels. However, most toxins lack selectivity for a given target NaV channel, and improving their selectivity profile among the NaV1 isoforms is essential for their development as drug leads. Computational methods will be very useful in the solution of such design problems, provided accurate models of the protein-ligand complex can be constructed. Using docking and molecular dynamics simulations, we have recently constructed a model for the NaV1.4-μ-conotoxin-GIIIA complex and validated it with the ample mutational data available for this complex. Here, we use the validated NaV1.4 model in a systematic study of binding other μ-conotoxins (PIIIA, KIIIA and BuIIIB to NaV1.4. The binding mode obtained for each complex is shown to be consistent with the available mutation data and binding constants. We compare the binding modes of PIIIA, KIIIA and BuIIIB to that of GIIIA and point out the similarities and differences among them. The detailed information about NaV1.4-μ-conotoxin interactions provided here will be useful in the design of new NaV channel blocking peptides.

  9. Experimental and computational studies on a steam jet refrigeration system with constant area and variable area ejectors

    International Nuclear Information System (INIS)

    Graphical abstract: The work aimed at studying the performance of a steam jet refrigeration system with (i) a constant area ejector and (ii) a variable area ejector under different operating conditions both experimentally and computationally. The boiler temperature was varied from 90 °C to 120 °C, the evaporator temperature was varied from 5 °C to 15 °C and the entertainment ratio, variation of Mach number along the ejector and the Coefficient of Performance were obtained. With proper design, the shock phenomenon in the variable area ejector was eliminated as shown in the left figure, which resulted in a better performance of the variable area ejector over a range of evaporator temperatures. The study also confirmed that the system can operate steadily at a boiler temperature of 90 °C which can be obtained from waste heat. - Highlights: • Experimental and computational studies on steam jet refrigeration system carried out. • Constant area and variable area ejectors were designed for low heat input. • Evaporator temperature was varied from 5 °C to 15 °C and the boiler temperature from 90 °C to 120 °C. • At the lower boiler temperature, no shock formed in the variable area ejector resulting in better performance. • A steam jet refrigeration system can operate steadily at boiler temperature of 90 °C. - Abstract: This paper first presents the results from an experimental study of a conventional steam jet ejector refrigeration system and compares the performance with the computational fluid dynamics (CFD) results of the same. Secondly, it describes a method of developing a variable area supersonic ejector and presents experimental results of the operating performance of the variable area ejector over the same operating conditions. The two ejectors were experimentally tested for boiler temperatures below 120 °C and an evaporator temperature below 15 °C. It was found that the steam jet refrigeration system can operate with stability at low boiler

  10. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Fagan, P A [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I{center_dot}C base pairs are functional analogs of A{center_dot}T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  11. NMR Studies of a New Binding Mode of the Amino Acid Esters by Porphyrinatozinc(Ⅱ)

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The binding mode of the amino acid ethyl esters(guest) by 5-(2-carboxylphenyl)-10,15,20-triphenylporphyrinatozinc(Ⅱ)(host 1) was studied by means of 1H NMR spectra. The binding mode is the hydrogen-bonding between the amino group of the guest and the carboxyl group of host 1 plus the coordination between the zinc atom of porphyrinatozinc(Ⅱ) and the carbonyl group of the guest. This is a novel binding mode of the metalloporphyrin to amino acid derivatives.

  12. Kinetic and equilibrium studies of acrylonitrile binding to cytochrome c peroxidase and oxidation of acrylonitrile by cytochrome c peroxidase compound I

    Energy Technology Data Exchange (ETDEWEB)

    Chinchilla, Diana, E-mail: Diana_Chinchilla@yahoo.com; Kilheeney, Heather, E-mail: raindropszoo@yahoo.com; Vitello, Lidia B., E-mail: lvitello@niu.edu; Erman, James E., E-mail: jerman@niu.edu

    2014-01-03

    Highlights: •Cytochrome c peroxidase (CcP) binds acrylonitrile in a pH-independent fashion. •The spectrum of the CcP/acrylonitrile complex is that of a 6c–ls ferric heme. •The acrylonitrile/CcP complex has a K{sub D} value of 1.1 ± 0.2 M. •CcP compound I oxidizes acrylonitrile with a maximum turnover rate of 0.61 min{sup −1}. -- Abstract: Ferric heme proteins bind weakly basic ligands and the binding affinity is often pH dependent due to protonation of the ligand as well as the protein. In an effort to find a small, neutral ligand without significant acid/base properties to probe ligand binding reactions in ferric heme proteins we were led to consider the organonitriles. Although organonitriles are known to bind to transition metals, we have been unable to find any prior studies of nitrile binding to heme proteins. In this communication we report on the equilibrium and kinetic properties of acrylonitrile binding to cytochrome c peroxidase (CcP) as well as the oxidation of acrylonitrile by CcP compound I. Acrylonitrile binding to CcP is independent of pH between pH 4 and 8. The association and dissociation rate constants are 0.32 ± 0.16 M{sup −1} s{sup −1} and 0.34 ± 0.15 s{sup −1}, respectively, and the independently measured equilibrium dissociation constant for the complex is 1.1 ± 0.2 M. We have demonstrated for the first time that acrylonitrile can bind to a ferric heme protein. The binding mechanism appears to be a simple, one-step association of the ligand with the heme iron. We have also demonstrated that CcP can catalyze the oxidation of acrylonitrile, most likely to 2-cyanoethylene oxide in a “peroxygenase”-type reaction, with rates that are similar to rat liver microsomal cytochrome P450-catalyzed oxidation of acrylonitrile in the monooxygenase reaction. CcP compound I oxidizes acrylonitrile with a maximum turnover number of 0.61 min{sup −1} at pH 6.0.

  13. Inclusion complex formation of ionic liquids with 4-sulfonatocalixarenes studied by competitive binding of berberine alkaloid fluorescent probe

    Science.gov (United States)

    Miskolczy, Zsombor; Biczók, László

    2009-07-01

    A clinically important natural isoquinoline alkaloid, berberine, was used as a fluorescent probe to study the encapsulation of 1-alkyl-3-methylimidazolium (C nMIm +) type ionic liquids in 4-sulfonato-substituted calix[4]arene (SCX4) and calix[6]arene (SCX6) at pH 2. Addition of ionic liquids to the aqueous solution of berberine-SCXn inclusion complexes brought about considerable fluorescence intensity diminution due to the extrusion of berberine from the macrocycle into the aqueous phase by the competitive inclusion of C nMIm + cation. The lengthening of the aliphatic side chain of the imidazolium moiety diminished the equilibrium constant of complexation with SCX4, but enhanced the stability of SCX6 complexes. Larger binding strength was found for SCX4.

  14. Study of the temperature and organic bindings effects in the dielectric and structural properties of the lithium ferrite ceramic matrix (LiFe{sub 5}O{sub 8})

    Energy Technology Data Exchange (ETDEWEB)

    Costa, M.M., E-mail: maurocosta@pq.cnpq.br [Telecommunications and Materials Science and Engineering Laboratory (LOCEM), Department of Physics, Federal University of Ceara, Campus do Pici, Postal Code 6030, 60455-760 Fortaleza, CE (Brazil); Department of Physics, Federal University of Mato Grosso - UFMT, 78060-900 Cuiaba, MT (Brazil); Sohn, R.S.T.M. [Telecommunications and Materials Science and Engineering Laboratory (LOCEM), Department of Physics, Federal University of Ceara, Campus do Pici, Postal Code 6030, 60455-760 Fortaleza, CE (Brazil); Department of Physics, Federal University of Ceara, Campus do Pici, Postal Code 6030, 60455-760 Fortaleza, CE (Brazil); Macedo, A.A.M.; Mazzetto, S.E. [Technology Products Laboratory (LPT), Northeast Network on Biotechnology (RENORBIO), Federal University of Ceara, Postal Code 6021, 60455-900 Fortaleza, CE (Brazil); Graca, M.P.F. [I3N - Aveiro, Physics Department, Aveiro University, Campus Universitario de Santiago, 3810-193, Aveiro (Portugal); Sombra, A.S.B. [Telecommunications and Materials Science and Engineering Laboratory (LOCEM), Department of Physics, Federal University of Ceara, Campus do Pici, Postal Code 6030, 60455-760 Fortaleza, CE (Brazil); Department of Physics, Federal University of Ceara, Campus do Pici, Postal Code 6030, 60455-760 Fortaleza, CE (Brazil)

    2011-09-29

    Highlights: > Organic bindings show that the bindings significantly alter the dielectric properties. - Abstract: In this study, the effects of the calcination temperature and of the organic bindings in the structural and dielectric properties of lithium ferrite (LiFe{sub 5}O{sub 8}) were investigated. The organic bindings used were glycerol, PVA (polyvinyl alcohol) and Galactomannan (Adenanthera pavonina). The investigated calcination temperature range was from 773 K to 1073 K. The structural properties were analyzed using differential scanning calorimetry, thermogravimetry, X-ray diffraction and infra-red spectroscopy. The electrical and magnetical properties were investigated using impedance dielectric spectroscopy and Moessbauer spectroscopy. The study of the structural and electrical properties of the lithium ferrites is an important issue in view to their attractive technological properties and low cost of fabrication. This work shows that the binding type, affects significantly the dielectric constant and loss of the LiFe{sub 5}O{sub 8} ceramics.

  15. Study of optical non-linear properties of a constant total effective length multiple quantum wells system

    Energy Technology Data Exchange (ETDEWEB)

    Solaimani, M.; Morteza, Izadifard [Faculty of Physics, Shahrood University of technology, Shahrood (Iran, Islamic Republic of); Arabshahi, H., E-mail: arabshahi@um.ac.ir [Department of Physics, Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Physics Department, Payame Noor University, P.O. Box 19395-3697, Tehran (Iran, Islamic Republic of); Reza, Sarkardehi Mohammad [Physics Department, Al-Zahra University, Vanak, Tehran (Iran, Islamic Republic of)

    2013-02-15

    In this work, we have studied the effect of the number of the wells, in a multiple quantum wells structure with constant total effective length, on the optical properties of multiple quantum wells like the absorption coefficient and the refractive index by means of compact density matrix approach. GaAs/Al{sub x}Ga{sub (1-x)}As multiple quantum wells systems was selected as an example. Besides, the effect of varying number of wells on the subband energies, wave functions, number of bound states, and the Fermi energy have been also investigated. Our calculation revealed that the number of wells in a multiple quantum well is a criterion with which we can control the amount of nonlinearity. This study showed that for the third order refractive index change there is two regimes of variations and the critical well number was six. In our calculations, we have used the same wells and barrier thicknesses to construct the multiple quantum wells system. - Highlights: Black-Right-Pointing-Pointer OptiOptical Non-Linear. Black-Right-Pointing-Pointer Total Effective Length. Black-Right-Pointing-Pointer Multiple Quantum Wells System - genetic algorithm Black-Right-Pointing-Pointer Schroedinger equation solution. Black-Right-Pointing-Pointer Nanostructure.

  16. Laminar flow heat transfer studies in a twisted square duct for constant wall heat flux boundary condition

    Indian Academy of Sciences (India)

    Rambir Bhadouriya; Amit Agrawal; S V Prabhu

    2015-04-01

    The problem of fluid flow and heat transfer was studied for flow inside twisted duct of square cross-section. Three-dimensional numerical solutions were obtained for steady fully developed laminar flow and for uniform wall heat flux boundary conditions using commercially available software. Reynolds number range considered was 100-3000. Twist ratio used are 2.5, 5, 10 and 20. Fluids considered are in Prandtl number range of 0.7-20. Product of friction factor and Reynolds number is found to be a function of Reynolds number and maximum values are observed for a twist ratio of 2.5 and Reynolds number of 3000. Maximum Nusselt number is observed for the same values along with Prandtl number of 20. Correlations for friction factor and Nusselt number are developed involving swirl parameter. Local distribution of friction factor ratio and Nusselt number across a cross-section is presented. Based on constant pumping power criteria, enhancement factor is defined to compare twisted ducts with straight ducts. Selection of twisted square duct is presented in terms of enhancement factor. It is found that twisted duct performs well in the laminar region for range of parameters studied. Heat transfer enhancement for Reynolds number of 3000 and Prandtl number of 0.7 for twist ratio of 2.5, 5, 10, and 20 is 20%, 17.8%, 16.1% and 13.7%, respectively. The results are significant because it will contribute to development of energy efficient compact size heat exchangers.

  17. Protein nanoparticle interaction: A spectrophotometric approach for adsorption kinetics and binding studies

    Science.gov (United States)

    Vaishanav, Sandeep K.; Chandraker, Kumudini; Korram, Jyoti; Nagwanshi, Rekha; Ghosh, Kallol K.; Satnami, Manmohan L.

    2016-08-01

    Investigating the protein nanoparticle interaction is crucial to understand how to control the biological interactions of nanoparticles. In this work, Model protein Bovine serum albumin (BSA) was used to evaluate the process of protein adsorption to the gold nanoparticles (GNPs) surface. The binding of a model protein (BSA) to GNPs was investigated through fluorescence quenching measurements. The strong affinities of BSA for GNPs were confirmed by the high value of binding constant (Ks) which was calculated to be 2.2 × 1011 L/mol. In this consequence, we also investigated the adsorption behavior of BSA on GNPs surface via UV-Vis spectroscopy. The effect of various operational parameters such as pH, contact time, initial BSA concentration, and temperature on adsorption of BSA was investigated using batch adsorption experiments. Kinetics of adsorption was found to follow the pseudo-second order rate equation. The suitability of Freundlich and Langmuir adsorption models to the equilibrium data was investigated. The equilibrium adsorption was well described by the Freundlich isotherm model. The maximum adsorption capacity for BSA adsorbed on GNPs was 58.71 mg/g and equilibrium constant was 0.0058 calculated by the Langmuir model at 298 K and pH = 11.0. Thermodynamic parameters showed that the adsorption of BSA onto GNPs was feasible, spontaneous, and exothermic.

  18. Study of the influence of actin-binding proteins using linear analyses of cell deformability.

    Science.gov (United States)

    Plaza, Gustavo R; Uyeda, Taro Q P; Mirzaei, Zahra; Simmons, Craig A

    2015-07-21

    The actin cytoskeleton plays a key role in the deformability of the cell and in mechanosensing. Here we analyze the contributions of three major actin cross-linking proteins, myosin II, α-actinin and filamin, to cell deformability, by using micropipette aspiration of Dictyostelium cells. We examine the applicability of three simple mechanical models: for small deformation, linear viscoelasticity and drop of liquid with a tense cortex; and for large deformation, a Newtonian viscous fluid. For these models, we have derived linearized equations and we provide a novel, straightforward methodology to analyze the experiments. This methodology allowed us to differentiate the effects of the cross-linking proteins in the different regimes of deformation. Our results confirm some previous observations and suggest important relations between the molecular characteristics of the actin-binding proteins and the cell behavior: the effect of myosin is explained in terms of the relation between the lifetime of the bond to actin and the resistive force; the presence of α-actinin obstructs the deformation of the cytoskeleton, presumably mainly due to the higher molecular stiffness and to the lower dissociation rate constants; and filamin contributes critically to the global connectivity of the network, possibly by rapidly turning over cross-links during the remodeling of the cytoskeletal network, thanks to the higher rate constants, flexibility and larger size. The results suggest a sophisticated relationship between the expression levels of actin-binding proteins, deformability and mechanosensing. PMID:26059185

  19. The Dynamic Pollen Tube Cytoskeleton: Live Cell Studies Using Actin-Binding and Microtubule-Binding Reporter Proteins

    Institute of Scientific and Technical Information of China (English)

    Alice Y. Cheung; Qiao-hong Duan; Silvia Santos Costa; Barend H.J.de Graaf; Veronica S.Di Stilio; Jose Feijo; Hen-Ming Wu

    2008-01-01

    Pollen tubes elongate within the pistil to transport sperm cells to the embryo sac for fertilization.Growth occurs exclusively at the tube apex,rendering pollen tube elongation a most dramatic polar cell growth process.A hall-mark pollen tube feature is its cytoskeleton,which comprises elaborately organized and dynamic actin microfilaments and microtubules.Pollen tube growth is dependent on the actin cytoskeleton;its organization and regulation have been exalined extensively by various approaches.including fluorescent protein labeled actin-binding proteins in live cell studies.Using the previously described GFP-NtADF1 and GFP-LIADF1, and a new actin reporter protein NtPLIM2b-GFP,we re-affirm that the predominant actin structures in elongating tobacco and lily pollen tubes are long,streaming actin cables along the pollen tube shank,and a subapical structure comprising shorter actin cables.The subapical collection of actin microfilaments undergoes dynamic changes,giving rise to the appearance of structures that range from basket-or funnel-shaped,mesh-like to a subtle ring.NtPLIM2b-GFP is used in combination with a guanine nucleotide exchange factor for the Rho GTPases,AtROP-GEF1,to illustrate the use of these actin reporter proteins to explore the linkage between the polar cell growth process and its actin cytoskeleton.Contrary to the actin cytoskeleton,microtubules appear not to play a direct role in supporting the polar cell growth process in angiosperm pollen tubes.Using a microtubule reporter protein based on the microtubule end-binding protein from Arabidopsis AtEB1,GFP-AtEB1,we show that the extensive microtubule network in elongating pollen tubes displays varying degrees of dynamics.These reporter proteins provide versatile tools to explore the functional connection between major structural and signaling components of the polar pollen tube growth process.

  20. Protein binding studies with radiolabeled compounds containing radiochemical impurities. Equilibrium dialysis versus dialysis rate determination

    DEFF Research Database (Denmark)

    Honoré, B

    1987-01-01

    The influence of radiochemical impurities in dialysis experiments with high-affinity ligands is investigated. Albumin binding of labeled decanoate (97% pure) is studied by two dialysis techniques. It is shown that equilibrium dialysis is very sensitive to the presence of impurities resulting...... in erroneously low estimates of the binding affinity and in inconsistent results at varying albumin concentrations. Dialysis rate determination (R. Brodersen et al. (1982) Anal. Biochem. 121, 395-408) is less sensitive to impurities. Udgivelsesdato: 1987-Apr...

  1. Binding of (/sup 125/I)-N-(p-aminophenethyl)spiroperidol to the D-2 dopamine receptor in the neurointermediate lobe of the rat pituitary gland: a thermodynamic study

    Energy Technology Data Exchange (ETDEWEB)

    Agui, T.; Amlaiky, N.; Caron, M.G.; Kebabian, J.W.

    1988-02-01

    The novel iodinated ligand (/sup 125/I)-N-(p-aminophenethyl)spiroperidol ((/sup 125/I)NAPS) was used to identify the D-2 dopamine receptor in the intermediate lobe of the rat pituitary gland. The binding of (/sup 125/I)NAPS was of high affinity and saturable, given that the dissociation constant and the maximal binding were 34.7 +/- 4.8 pM and 21.1 +/- 2.5 fmol/mg of protein, respectively. The ability of dopaminergic agonists and antagonists to compete with (/sup 125/I)NAPS varied markedly with incubation temperature. The marked decrease of the molar potency associated with increasing incubation temperature in the competitive displacement curve suggested that the binding of five agonists, dopamine, (-)-apomorphine, (-)-n-propylnorapomorphine, N-0434, and LY-171555, to the D-2 dopamine receptor was enthalpy-driven, with a negative change in entropy. In contrast, the binding of three antagonists, fluphenazine, (+)-butaclamol, and domperidone, was entropy-driven, with positive change in entropy, suggesting less temperature-sensitive change in the molar potency. Several molecules gave unanticipated results; the molar potency of two dopamine agonists, bromocriptine and lisuride, was much less temperature-sensitive than the other agonists used in this study. The thermodynamic parameters for the atypical agonists indicated entropy-driven binding. Conversely, the molar potency of (+)-apomorphine, a dopamine receptor antagonist, was markedly affected by incubation temperature, indicating enthalpy-driven binding. Another antagonist, YM-09151-2, was affected by the inclusion of sodium chloride in the assay system: in the absence of sodium chloride, the drug was relatively weak and displayed enthalpy-driven binding; in the presence of sodium chloride, its molar potency was increased and its binding manner turned into entropy-driven.

  2. Tritium from ecosystem to man. Study of mechanisms and constants controlling the equilibria and the different transfer pathways

    International Nuclear Information System (INIS)

    Tritium is the radioactive isotope of hydrogen. It can be integrated in most of the biological molecules. Even if its radiotoxicity is weak, effects of tritium could be increased if it can concentrate in some critical compartments of beings. In order to better understand the tritium circulation in the environment and highlight constants of transfer between compartments, we have studied the tritiation of different agricultural matrices chronically exposed to tritium. The first step of our study is the validation of the different techniques used to prepare our sample. We have also demonstrated that it was possible to store environmental samples in the Valduc centre and have underlined some biases due to the extraction of free water. Some ways of improvements are proposed. A hypothesis has also been formulated on the origin of an original isotopic fractionation effect during the extraction of the free water of milk. In the environmental study, the specific activities measured on plants confirm the importance of the atmospheric exposure on their tritiation. No difference in the tritiation has been measured between wheat, barley and colza. Some differences have been measured in the tritiation of some organic components of vegetal matrices. These results underline the interest of continuing this kind of study. We have also compared the tritiation of the main hydrogenated components of milk, first, component to component, then, sample to sample. Some origins of the measured differences have been shown. We have demonstrated the correlation between the specific activities of drinking water and the free water of milk as between the tritiations of dry matter of cattle's food and of the main organic components of milk. Our results show also the importance of the metabolism on the distribution of tritium in the different compartments. The overall synthesis of our results show the importance of the dilution of hydrogen in the considered environmental compartments, above the

  3. Measurement of the strong interaction coupling constant αs by jet study in the H1 experiment

    International Nuclear Information System (INIS)

    The H1 experiment allows to study hadronic jets produced in deep inelastic lepton (27.5 GeV) scattering off protons (820 GeV). The coupling constant of the strong interaction αs can be extracted from the measurement of the 2-jets rate in the final state. The use of the JADE algorithm is optimal for events with high energy transfer (100-4,000 GeV2), corresponding to the 1994 and 1995 data. The error on αs (MZ02) is dominated by the uncertainty from the hadronic energy measurement and the experimental resolution effects on jets. The theoretical error is dominated by the renormalization scale dependence. The final result is (MZ02) 0.118 -0.008+0.008. This analysis is extended to smaller momentum transfers (25-100 GeV 2) using the factorizable Kt algorithm, taking the transferred momentum as energy scale of the particle re-clustering. The result αs (MZ02) 0.117 -0.008+0.009 is compatible with the previous one. The precision of the measurement performed in this thesis is 7%. A precision of 4% could be achieved after progresses in the theoretical framework and/or after a significant increase of the luminosity. (author)

  4. An Experimental Study on the Macroscopic Spray Characteristics of Biodiesel and Diesel in a Constant Volume Chamber

    Directory of Open Access Journals (Sweden)

    Hongzhan Xie

    2015-06-01

    Full Text Available The objective of this study was to investigate the macroscopic spray characteristics of different 0%–100% blends of biodiesel derived from drainage oil and diesel (BD0, BD20, BD50, BD80, BD100, such as spray tip penetration, average tip velocity at penetration, spray angle, average spray angle, spray evolution process, spray area and spray volume under different injection pressures (60, 70, 80, 90, 100 MPa and ambient pressures (0.1, 0.3, 0.5, 0.7, 0.9 MPa using a common rail system equipped with a constant volume chamber. The characteristic data was extracted from spray images grabbed by a high speed visualization system. The results showed that the ambient pressure and injection pressure had significant effects on the spray characteristics. As the ambient pressure increased, the spray angle increased, while the spray tip penetration and the peak of average tip velocity decreased. As the injection pressure increased, the spray tip penetration, spray angle, spray area and spray volume increased. The increasing blend ratio of biodiesel brought about a shorter spray tip penetration and a smaller spray angle compared with those of diesel. This is due to the comparatively higher viscosity and surface tension of biodiesel, which enhanced the friction effect between fuel and the injector nozzle surface and inhibited the breakup of the liquid jet.

  5. Numerical Study of Laminar Flow Forced Convection of Water-Al2O3 Nanofluids under Constant Wall Temperature Condition

    Directory of Open Access Journals (Sweden)

    Hsien-Hung Ting

    2015-01-01

    Full Text Available This numerical study is aimed at investigating the forced convection heat transfer and flow characteristics of water-based Al2O3 nanofluids inside a horizontal circular tube in the laminar flow regime under the constant wall temperature boundary condition. Five volume concentrations of nanoparticle, 0.1, 0.5, 1, 1.5, and 2 vol.%, are used and diameter of nanoparticle is 40 nm. Characteristics of heat transfer coefficient, Nusselt number, and pressure drop are reported. The results show that heat transfer coefficient of nanofluids increases with increasing Reynolds number or particle volume concentration. The heat transfer coefficient of the water-based nanofluid with 2 vol.% Al2O3 nanoparticles is enhanced by 32% compared with that of pure water. Increasing particle volume concentration causes an increase in pressure drop. At 2 vol.% of particle concentration, the pressure drop reaches a maximum that is nearly 5.7 times compared with that of pure water. It is important to note that the numerical results are in good agreement with published experimental data.

  6. Atmospheric reaction of Cl + methacrolein: a theoretical study on the mechanism, and pressure- and temperature-dependent rate constants.

    Science.gov (United States)

    Sun, Cuihong; Xu, Baoen; Zhang, Shaowen

    2014-05-22

    Methacrolein is a major degradation product of isoprene, the reaction of methacrolein with Cl atoms may play some roles in the degradation of isoprene where these species are relatively abundant. However, the energetics and kinetics of this reaction, which govern the reaction branching, are still not well understood so far. In the present study, two-dimensional potential energy surfaces were constructed to analyze the minimum energy path of the barrierless addition process between Cl and the C═C double bond of methacrolein, which reveals that the terminal addition intermediate is directly formed from the addition reaction. The terminal addition intermediate can further yield different products among which the reaction paths abstracting the aldehyde hydrogen atom and the methyl hydrogen atom are dominant reaction exits. The minimum reaction path for the direct aldehydic hydrogen atom abstraction is also obtained. The reaction kinetics was calculated by the variational transition state theory in conjunction with the master equation method. From the theoretical model we predicted that the overall rate constant of the Cl + methacrolein reaction at 297 K and atmospheric pressure is koverall = 2.3× 10(-10) cm(3) molecule(-1) s(-1), and the branching ratio of the aldehydic hydrogen abstraction is about 12%. The reaction is pressure dependent at P pressure limit at about 100 Torr. The calculated results could well account for the experimental observations.

  7. Numerical Study of Laminar Flow and Convective Heat Transfer Utilizing Nanofluids in Equilateral Triangular Ducts with Constant Heat Flux

    Directory of Open Access Journals (Sweden)

    Hsien-Hung Ting

    2016-07-01

    Full Text Available This study numerically investigates heat transfer augmentation using water-based Al2O3 and CuO nanofluids flowing in a triangular cross-sectional duct under constant heat flux in laminar flow conditions. The Al2O3/water nanofluids with different volume fractions (0.1%, 0.5%, 1%, 1.5%, and 2% and CuO/water nanofluids with various volume fractions (0.05%, 0.16%, 0.36%, 0.5%, and 0.8% are employed, and Reynolds numbers in the range of 700 to 1900 in a laminar flow are considered. The heat transfer rate becomes more remarkable when employing nanofluids. As compared with pure water, at a Peclet number of 7000, a 35% enhancement in the convective heat transfer coefficient, is obtained for an Al2O3/water nanofluid with 2% particle volume fraction; at the same Peclet number, a 41% enhancement in the convective heat transfer coefficient is achieved for a CuO/water nanofluid with 0.8% particle volume concentration. Heat transfer enhancement increases with increases in particle volume concentration and Peclet number. Moreover, the numerical results are found to be in good agreement with published experimental data.

  8. Slow-binding and competitive inhibition of 8-amino-7-oxopelargonate synthase, a pyridoxal-5'-phosphate-dependent enzyme involved in biotin biosynthesis, by substrate and intermediate analogs. Kinetic and binding studies.

    Science.gov (United States)

    Ploux, O; Breyne, O; Carillon, S; Marquet, A

    1999-01-01

    8-Amino-7-oxopelargonate synthase catalyzes the first committed step of biotin biosynthesis in micro-organisms and plants. Because inhibitors of this pathway might lead to antibacterials or herbicides, we have undertaken an inhibition study on 8-amino-7-oxopelargonate synthase using six different compounds. d-Alanine, the enantiomer of the substrate of this pyridoxal-5'-phosphate-dependent enzyme was found to be a competitive inhibitor with respect to l-alanine with a Ki of 0.59 mm. The fact that this inhibition constant was four times lower than the Km for l-alanine was interpreted as the consequence of the inversion-retention stereochemistry of the catalyzed reaction. Schiff base formation between l or d-alanine and pyridoxal-5'-phosphate, in the active site of the enzyme, was studied using ultraviolet/visible spectroscopy. It was found that l and d-alanine form an external aldimine with equilibrium constants K = 4.1 mm and K = 37.8 mm, respectively. However, the equilibrium constant for d-alanine aldimine formation dramatically decreased to 1.3 mm in the presence of saturating concentration of pimeloyl-CoA, the second substrate. This result strongly suggests that the binding of pimeloyl-CoA induces a conformational change in the active site, and we propose that this new topology is complementary to d-alanine and to the putative reaction intermediate since they both have the same configuration. (+/-)-8-Amino-7-oxo-8-phosphonononaoic acid (1), the phosphonate derivative of the intermediate formed during the reaction, was our most potent inhibitor with a Ki of 7 microm. This compound behaved as a reversible slow-binding inhibitor, competitive with respect to l-alanine. Kinetic investigation showed that this slow process was best described by a one-step mechanism (mechanism A) with the following rate constants: k1 = 0.27 x 103 m-1.s-1, k2 = 1.8 s-1 and half-life for dissociation t1/2 = 6.3 min. The binding of compound 1 to the enzyme was also studied using

  9. Experimental and theoretical study on the binding of 2-mercaptothiazoline to bovine serum albumin

    International Nuclear Information System (INIS)

    2-Mercaptothiazoline (MTZ) is widely utilized as a brightening and stabilization agent, corrosion inhibitor and antifungal reagent. The residue of MTZ in the environment is potentially hazardous to human health. In this study, the binding mode of MTZ with bovine serum albumin (BSA) was investigated using spectroscopic and molecular docking methods under physiological conditions. MTZ could spontaneously bind with BSA through hydrogen bond and van der Waals interactions with one binding site. The site marker displacement experiments and the molecular docking revealed that MTZ bound into site II (subdomain IIIA) of BSA, which further resulted in some backbone structures and microenvironmental changes of BSA. This work is helpful for understanding the transportation, distribution and toxicity effects of MTZ in blood. - Highlights: • The mechanism was explored by multiple spectroscopic and molecular docking methods. • MTZ can spontaneously bind with BSA at subdomain IIIA (site II). • MTZ can lead to some conformational changes of BSA

  10. Experimental and theoretical study on the binding of 2-mercaptothiazoline to bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Teng, Yue, E-mail: tengyue@jiangnan.edu.cn; Wang, Xiang; Zou, Luyi; Huang, Ming; Du, Xianzheng

    2015-05-15

    2-Mercaptothiazoline (MTZ) is widely utilized as a brightening and stabilization agent, corrosion inhibitor and antifungal reagent. The residue of MTZ in the environment is potentially hazardous to human health. In this study, the binding mode of MTZ with bovine serum albumin (BSA) was investigated using spectroscopic and molecular docking methods under physiological conditions. MTZ could spontaneously bind with BSA through hydrogen bond and van der Waals interactions with one binding site. The site marker displacement experiments and the molecular docking revealed that MTZ bound into site II (subdomain IIIA) of BSA, which further resulted in some backbone structures and microenvironmental changes of BSA. This work is helpful for understanding the transportation, distribution and toxicity effects of MTZ in blood. - Highlights: • The mechanism was explored by multiple spectroscopic and molecular docking methods. • MTZ can spontaneously bind with BSA at subdomain IIIA (site II). • MTZ can lead to some conformational changes of BSA.

  11. Study on the characteristics of SOFC operating in constant fuel flow and constant fuel utilization%定燃料流量和定燃料利用率时SOFC发电系统特性研究

    Institute of Scientific and Technical Information of China (English)

    周念成; 李春艳; 王强钢; 邓浩

    2011-01-01

    The Solid Oxide Fuel Cell generation system model is established ,which operated in constant fuel flow and constant fuel utilization. The steady-state (V-I and P-I) characteristics of the SOFC stack model has been studied, and the effect of fuel flow on the characteristics of SOFC steady-state in constant fuel flow mode has been obtained. Then SOFC stack operated in two different typical modes are applied in the simulation of SOFC-based distributed generation system aiming at changing load and fault condition. By comparing the simulation results, the applicable application sphere of two operation mode are given.%在定燃料输入流量和定燃料利用率两种典型控制方式下,建立了固体氧化物燃料电池(SOFC)发电系统模型.研究了两种控制方式下的固体氧化物燃料电池堆的稳态特性,采用定燃料流量控制方式时考虑了燃料流量对SOFC稳态特性的影响.针对出现负荷改变和故障的情况,分别在两种典型控制模式下对SOFC发电系统进行了仿真,通过对仿真结果的比较,给出了两种控制方式的适用范围.

  12. Correlation study between sperm concentration, hyaluronic acid-binding capacity and sperm aneuploidy in Hungarian patients.

    Science.gov (United States)

    Mokánszki, Attila; Molnár, Zsuzsanna; Ujfalusi, Anikó; Balogh, Erzsébet; Bazsáné, Zsuzsa Kassai; Varga, Attila; Jakab, Attila; Oláh, Éva

    2012-12-01

    Infertile men with low sperm concentration and/or less motile spermatozoa have an increased risk of producing aneuploid spermatozoa. Selecting spermatozoa by hyaluronic acid (HA) binding may reduce genetic risks such as chromosomal rearrangements and numerical aberrations. Fluorescence in-situ hybridization (FISH) has been used to evaluate the presence of aneuploidies. This study examined spermatozoa of 10 oligozoospermic, 9 asthenozoospermic, 9 oligoasthenozoospermic and 17 normozoospermic men by HA binding and FISH. Mean percentage of HA-bound spermatozoa in the normozoospermic group was 81%, which was significantly higher than in the oligozoospermic (Psex chromosomes (P=0.014) and chromosome 17 (P=0.0019), diploidy (P=0.03) and estimated numerical chromosome aberrations (P=0.004) were significantly higher in the oligoasthenozoospermic group compared with the other groups. There were statistically significant relationships (Pchromosome aberrations (r=-0.668) and between HA binding and estimated numerical chromosome aberrations (r=-0.682). HA binding and aneuploidy studies of spermatozoa in individual cases allow prediction of reproductive prognosis and provision of appropriate genetic counselling. Infertile men with normal karyotypes and low sperm concentrations and/or less motile spermatozoa have significantly increased risks of producing aneuploid (diminished mature) spermatozoa. Selecting spermatozoa by hyaluronic acid (HA) binding, based on a binding between sperm receptors for zona pellucida and HA, may reduce the potential genetic risks such as chromosomal rearrangements and numerical aberrations. In the present study we examined sperm samples of 45 men with different sperm parameters by HA-binding assay and fluorescence in-situ hybridization (FISH). Mean percentage of HA-bound spermatozoa in the normozoospermic group was significantly higher than the oligozoospermic, the asthenozoospermic and the oligoasthenozoospermic groups. Using FISH, disomy of sex

  13. [Study of the binding characteristics of chlorophenoxyisobutyric acid to serum proteins in chronically uremic patients : influence of dialysis and heparine (author's transl)].

    Science.gov (United States)

    Lacour, B; Di Giulio, S; Nicolaï, A; Drüeke, T; Debray, M; Boulu, R G

    1982-01-01

    The binding characteristics of chlorophenoxyisobutyric acid (CPIB) to serum proteins has been studied in 10 chronically uremic patients and 9 healthy subjects using the technique of equilibrium dialysis. Scatchard analysis of the results indicated a significant decrease in association constants for low as well as for high affinity sites. The number of binding sites however was not diminished thus suggesting the presence of competitive inhibitors. Such inhibitors were dializable, at least in part, as demonstrated by in vivo-hemodialysis and in vitro-dialysis experiments. The in vivo administration of 50 mg heparin intravenously led to a striking increase in the unbound fraction of serum CPIB whereas the addition of 10 IU/ml heparin in vitro induced no change of protein binding which is in favor of only an indirect effect of heparin. In conclusion, CPIB binding to serum proteins of chronically uremic patients as compared to normal volunteers was decreased leading to an increase of its unbound circulating fraction. The observed change of protein binding appeared to be due to the presence of competitive inhibitors in uremic serum. PMID:7088259

  14. In vivo and in vitro studies of hafnium-binding to rat serum transferrin

    Energy Technology Data Exchange (ETDEWEB)

    Then, G.M.; Appel, H.; Duffield, J.; Taylor, D.M.; Thies, W.G.

    1986-08-01

    The binding of hafnium to rat serum transferrin was studied using the time differential perturbed angular correlation (TDPAC) technique. Hafnium is interesting as a toxic metal binding to transferrin because it behaves metabolically similarly to plutonium. The isotope 181Hf offers favorable access to the TDPAC-method. Samples were prepared in vivo by intravenous injection of Hf-NTA, Hf-citrate, and Hf-oxalate solutions, respectively, into Sprague-Dawley rats and in vitro by adding Hf-NTA solution to fresh rat serum. In both cases two specific electric quadrupole interactions were observed, which correspond to two well-defined binding configurations. They may be attributed to the N-terminal and the C-terminal binding site in the transferrin molecule. The 181Hf-distribution between these two binding states depends on pH, salt and hafnium concentrations, temperature, and incubation time. With a fast TDPAC-setup of four BaF2-detectors a time resolution of about 600 ps could be achieved. The specific binding configurations of 181Hf and the comparatively slow relaxation times lead to spectra of considerable accuracy.

  15. A comparative study of capillary zone electrophoresis and pH-potentiometry for determination of dissociation constants.

    Science.gov (United States)

    Andrasi, Melinda; Buglyo, Peter; Zekany, Laszlo; Gaspar, Attila

    2007-09-01

    Acidity constants of six cephalosporin antibiotics, cefalexin, cefaclor, cefadroxil, cefotaxim, cefoperazon and cefoxitin are determined using capillary zone electrophoresis (CZE) and pH-potentiometric titrations. Since CZE is a separation method, it is not necessary for the samples to be of high purity and known concentration because only mobilities are measured. The effect on determination of dissociation constants of different matrices (serum, 0.9% NaCl, fermentation matrix) was examined. The advantages of CZE can be utilized in those fields where potentiometry has limitations (sample quantity, solubility, purity, simultaneous determinations), although pK(a) values that are close to each other can be determined by potentiometry with more accuracy.

  16. Glycaemic responses to different types of bread in insulin-dependent diabetic subjects (IDDM): studies at constant insulinaemia.

    Science.gov (United States)

    Rasmussen, O; Winther, E; Hermansen, K

    1991-02-01

    To study the glycaemic effect of various Danish bread types in insulin-dependent diabetic subjects (IDDM) we looked at the incremental blood glucose areas after isocaloric meals of grained wholemeal rye bread, wholemeal bread (graham bread) and white bread in seven C-peptide negative diabetic subjects. Furthermore, we evaluated the glycaemic potency of dried fruits by exchanging 40 per cent of the starch of grained wholemeal rye bread as dried figs. Prior to the meal intake the patients had attained normoglycaemia and isoinsulinaemia by means of the artificial pancreas. The four test meals containing 50 g of available carbohydrate were taken in random order. The postprandial blood glucose response areas after whole-meal bread (1037 +/- 113 mM X 180 min) and white bread (1021 +/- 100 mM X 180 min) were significantly higher than that to grained wholemeal rye bread (786 +/- 66 mM X 180 min, P less than 0.05). Exchange of 40 per cent of the complex carbohydrate as grained wholemeal rye bread with simple sugars, such as figs, had no influence on the blood glucose response (786 +/- 66 mM X 180 min vs. 766 +/- 56 mM X 180 min). Constant and identical serum-free insulin levels at 30 mU/l and similar amounts of glucose lost in the urine were found after the four test meals. In conclusion, the difference in extraction rate of wheat in the form of white flour (0, 7) and wholemeal flour (1, 0) was not reflected in the glycaemic responses in IDDM subjects. Grained wholemeal rye bread is a fibre-rich, cheap nutrient which elicits a significantly lower glycaemic response compared to wholemeal and white bread and can be recommended to diabetic subjects.

  17. Interference of anaesthetics with radioligand binding in neuroreceptor studies

    Energy Technology Data Exchange (ETDEWEB)

    Elfving, Betina; Knudsen, Gitte Moos [Neurobiology Research Unit N9201, University hospital Rigshospitalet, 9 Blegdamsvej, 2100, Copenhagen (Denmark); Bjoernholm, Berith [Department of Computational Chemistry, H. Lundbeck A/S, Copenhagen-Valby (Denmark)

    2003-06-01

    Evaluations of new emission tomography ligands are usually carried out in animals. In order to keep the animals in a restricted position during the scan session, anaesthesia is almost inevitable. In ex vivo rat studies we investigated the interference of ketamine/xylazine, zoletile mixture, isoflurane and halothane with the serotonin re-uptake site, the serotonin{sub 2A} receptor and the dopamine re-uptake site by use of [{sup 3}H]-(S)-citalopram, [{sup 18}F]altanserin and [{sup 125}I]PE2I, respectively. Ketamine/xylazine decreased the target-to-background ratio (mean {+-} SD) of [{sup 3}H]-(S)-citalopram from 1.5{+-}0.19 to 0.81{+-}0.19 (P<0.05), whereas isoflurane and halothane increased the ratio from 1.5{+-}0.19 to 1.9{+-}0.24 and 2.1{+-}0.13 (P<0.05), respectively. Only with the zoletile mixture did the ratio remain unaltered. None of the tested anaesthetics affected the target-to-background ratio of [{sup 18}F]altanserin. The [{sup 125}I]PE2I target-to-background ratio decreased with both ketamine/xylazine (from 12.4{+-}0.81 to 10.1{+-}1.4, P<0.05) and isoflurane (from 12.4{+-}0.81 to 9.5{+-}1.1, P<0.05) treated rats, whereas treatment with zoletile mixture and halothane left the ratio unaltered. It is concluded that prior to performance of neuroreceptor radioligand studies, the possible interaction between radioligands and anaesthetics should be carefully evaluated. (orig.)

  18. Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst

    Science.gov (United States)

    Kundu, Partha P.; Kumari, Gayatri; Chittoory, Arjun K.; Rajaram, Sridhar; Narayana, Chandrabhas

    2015-12-01

    Bis-camphorsulfonyl urea, a newly developed hydrogen bonding catalyst, was evaluated in an enantioselective Friedel-Crafts reaction. We observed that complexation of the sulfonyl urea with a sodium cation enhanced the selectivity of reactions in comparison to reactions performed with urea alone. To understand the role of sodium cation, we performed Infrared and Raman spectroscopic studies. The detailed band assignment of the molecule was made by calculating spectra using Density Functional theory. Our studies suggest that the binding of the cation takes place through the oxygen atoms of carbonyl and sulfonyl groups. Natural Bond Orbital (NBO) analysis shows the expected charge distribution after sodium binding. The changes in the geometrical parameter and charge distribution are in line with the experimentally observed spectral changes. Based on these studies, we conclude that binding of the sodium cation changes the conformation of the sulfonyl urea to bring the chiral camphor groups closer to the incipient chiral center.

  19. Binding of an anticancer Rutaceae plant flavonoid glycoside with calf thymus DNA: Biophysical and electrochemical studies

    International Nuclear Information System (INIS)

    In the present work, we report the interaction of a bioactive Rutaceae plant flavonoid glycoside, diosmin (DIO) with calf thymus DNA employing ethidium bromide as a fluorescence probe. The mode of binding between DIO and DNA was investigated by UV absorption, fluorescence, 3D-fluorescence, fluorescence polarization, FT-IR, circular dichroism, melting temperature (Tm) measurements and differential pulse voltammogram studies. The results revealed the intercalative mode of binding between DIO and DNA. Further, the values of thermodynamic parameters, ∆H° (−388.32 kJ mol−1) and ∆S° (−1.22 kJ mol−1 K−1) indicated that the van der Waals forces and hydrogen bond played a major role in the binding of DIO to DNA. The observed negative ∆G° values revealed the spontaneity of interaction process. The binding of DIO to DNA–EB was found to be stronger in the presence of coexisting substances. -- Highlights: • Mechanism of interaction of diosmin with DNA was studied by spectroscopic methods. • Ethidium bromide was used as a fluorescence probe in the present study. • The van der Waals forces and hydrogen bond played a significant role in the interaction. • Intercalative mode of binding was proposed between DIO and DNA

  20. Intact brain cells: a novel model system for studying opioid receptor binding

    International Nuclear Information System (INIS)

    The use of a novel tissue preparation to study opioid receptor binding in viable, intact cells derived from whole brains of adult rats is presented. Mechanically dissociated and sieved cells, which were not homogenized at any stage of the experimental protocol, and iso-osmotic physiological buffer were used in these experiments. This system was adapted in order to avoid mechanical and chemical disruption of cell membranes, cytoskeletal ultrastructure or receptor topography by homogenization or by the use of nonphysiological buffers, and to mimic in vivo binding conditions as much as possible. Using [3H]naloxone as the radioligand, the studies showed saturable and stereospecific high-affinity binding of this opioid antagonist in intact cells, which in turn showed consistently high viability. [3H]Naloxone binding was also linear over a wide range of tissue concentrations. This technique provides a very promising model for future studies of the binding of opioids and of many other classes of drugs to brain tissue receptors in a more physiologically relevant system than those commonly used to date

  1. Binding of an anticancer Rutaceae plant flavonoid glycoside with calf thymus DNA: Biophysical and electrochemical studies

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishnan, Sandhya; Jaldappagari, Seetharamappa, E-mail: jseetharam@yahoo.com

    2013-10-15

    In the present work, we report the interaction of a bioactive Rutaceae plant flavonoid glycoside, diosmin (DIO) with calf thymus DNA employing ethidium bromide as a fluorescence probe. The mode of binding between DIO and DNA was investigated by UV absorption, fluorescence, 3D-fluorescence, fluorescence polarization, FT-IR, circular dichroism, melting temperature (T{sub m}) measurements and differential pulse voltammogram studies. The results revealed the intercalative mode of binding between DIO and DNA. Further, the values of thermodynamic parameters, ∆H° (−388.32 kJ mol{sup −1}) and ∆S° (−1.22 kJ mol{sup −1} K{sup −1}) indicated that the van der Waals forces and hydrogen bond played a major role in the binding of DIO to DNA. The observed negative ∆G° values revealed the spontaneity of interaction process. The binding of DIO to DNA–EB was found to be stronger in the presence of coexisting substances. -- Highlights: • Mechanism of interaction of diosmin with DNA was studied by spectroscopic methods. • Ethidium bromide was used as a fluorescence probe in the present study. • The van der Waals forces and hydrogen bond played a significant role in the interaction. • Intercalative mode of binding was proposed between DIO and DNA.

  2. Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites.

    Directory of Open Access Journals (Sweden)

    Anoop Narayanan

    Full Text Available Expression of KdpFABC, a K(+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC(BS via the winged helix-turn-helix type DNA binding domain (KdpE(DBD. Exploration of E. coli KdpE(DBD and kdpFABC(BS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpE(DBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpE(DBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpE(DBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.

  3. Nuclear binding energy using semi empirical mass formula

    Science.gov (United States)

    Ankita, Suthar, B.

    2016-05-01

    In the present communication, semi empirical mass formula using the liquid drop model has been presented. Nuclear binding energies are calculated using semi empirical mass formula with various constants given by different researchers. We also compare these calculated values with experimental data and comparative study for finding suitable constants is added using the error plot. The study is extended to find the more suitable constant to reduce the error.

  4. Cosmological Hubble constant and nuclear Hubble constant

    International Nuclear Information System (INIS)

    The evolution of the Universe after the Big Bang and the evolution of the dense and highly excited nuclear matter formed by relativistic nuclear collisions are investigated and compared. Values of the Hubble constants for cosmological and nuclear processes are obtained. For nucleus-nucleus collisions at high energies the nuclear Hubble constant is obtained in the frame of different models involving the hydrodynamic flow of the nuclear matter. Significant difference in the values of the two Hubble constant - cosmological and nuclear - is observed

  5. {\\it Ab initio} study of correlation and Gaunt interaction in ionization potentials and hyperfine constants of ground and first excited states of boron isoelectronic sequence

    CERN Document Server

    Dutta, Narendra Nath

    2011-01-01

    In this paper, we have studied correlation and Gaunt interaction effects in the ionization potentials (I.P.) and magnetic dipole hyperfine (A) constants of 2p$^2P_{1/2}$ and 2p$^2P_{3/2}$ states along with the fine structure separations between them for boron isoelectronic sequence by relativistic coupled-cluster (RCC) method. The range of Z has been taken from 8 to 21. Gaunt operator is reformulated explicitly both in Dirac-Fock (DF) and CC level. The I.P.'s and the fine structure splittings are compared with the results of National Institute of Standards and Technology (NIST). Important correlation contributions like core correlation, core polarisation, pair correlation etc. are studied for hyperfine A constants. Many distinct features of correlation and relativistic effects are observed in these studies. With best of our knowledge, except O IV, hyperfine A constants of all the other elements are reported for the first time in the literature.

  6. Pulsatile Support Mode of BJUT-II Ventricular Assist Device (VAD) has Better Hemodynamic Effects on the Aorta than Constant Speed Mode: A Primary Numerical Study.

    Science.gov (United States)

    Gu, Kaiyun; Gao, Bin; Chang, Yu; Zeng, Yi

    2016-01-01

    BACKGROUND BJUT-II VAD is a novel left ventricular assist device (LVADs), directly implanted into the ascending aorta. The pulsatile support mode is proposed to achieve better unloading performance than constant speed mode. However, the hemodynamic effects of this support mode on the aorta are still unclear. The aim of this study was to clarify the hemodynamic effects BJUT-II VAD under pulsatile support mode on the aorta. MATERIAL AND METHODS Computational fluid dynamics (CFD) studies, based on a patient-specific aortic geometric model, were conducted. Wall shear stress (WSS), averaged WSS (avWSS), oscillatory shear index (OSI), and averaged helicity density (Ha) were calculated to compare the differences in hemodynamic effects between pulsatile support mode and constant speed mode. RESULTS The results show that avWSS under pulsatile support mode is significantly higher than that under constant speed mode (0.955Pa vs. 0.675Pa). Similarly, the OSI value under pulsatile mode is higher than that under constant speed mode (0.104 vs. 0.057). In addition, Ha under pulsatile mode for all selected cross-sections is larger than that under constant mode. CONCLUSIONS BJUT-II VAD, under pulsatile control mode, may prevent atherosclerosis lesions and aortic remodeling. The precise effects of pulsatile support mode on atherosclerosis and aortic remodeling need to be further studied in animal experiments. PMID:27363758

  7. Study of the Impact of Non-linear Piezoelectric Constants on the Acoustic Wave Propagation on Lithium Niobate

    Directory of Open Access Journals (Sweden)

    C. Soumali

    2016-06-01

    Full Text Available Impact of nonlinear piezoelectric constants on surface acoustic wave propagation on a piezoelectric substrate is investigated in this work. Propagation of acoustic wave propagation under uniform stress is analyzed; the wave equation is obtained by incorporating the applied uniform stress in the equation of motion and taking account of the set of linear and nonlinear piezoelectric constants. A new method of separation between the different modes of propagation is proposed regarding the attenuation coefficients and not to the displacement vectors. Detail calculations and simulations have made for Lithium Niobate (LiNbO3; transformations between modes of propagation, under uniform stress, have been found. These results leads to conclusion that nonlinear terms affect the acoustic wave propagation and also we can make controllable acoustic devices.

  8. Interaction of hydrated electron with dietary flavonoids and phenolic acids. Rate constants and transient spectra studied by pulse radiolysis

    International Nuclear Information System (INIS)

    The reaction rate constants and transient spectra of 11 flavonoids and 4 phenolic acids reacting with eaq- at neutral pH were measured. The results suggest that C4 keto group is the active site for eaq- to attack on flavonoids and phenolic acids, while the o-dihydroxy structure in B-ring, the C2,3 double bond, the C3-OH group and glycosylation have little effects on the eaq- scavenging activities. (author)

  9. l-Tryptophan Radical Cation Electron Spin Resonance Studies: Connecting Solution-derived Hyperfine Coupling Constants with Protein Spectral Interpretations

    OpenAIRE

    Connor, Henry D.; Sturgeon, Bradley E.; Mottley, Carolyn; Sipe, Herbert J.; Mason, Ronald P.

    2008-01-01

    Fast-flow electron spin resonance (ESR) spectroscopy has been used to detect a free radical formed from the reaction of l-tryptophan with Ce4+ in an acidic aqueous environment. Computer simulations of the ESR spectra from l-tryptophan and several isotopically modified forms strongly support the conclusion that the l-tryptophan radical cation has been detected by ESR for the first time. The hyperfine coupling constants (HFCs) determined from the well-resolved isotropic ESR spectra support expe...

  10. Synthesis and spectroscopic studies of the aminoglycoside (neomycin)--perylene conjugate binding to human telomeric DNA.

    Science.gov (United States)

    Xue, Liang; Ranjan, Nihar; Arya, Dev P

    2011-04-12

    Synthesis of a novel perylene-neomycin conjugate (3) and the properties of its binding to human telomeric G-quadruplex DNA, 5'-d[AG3(T2AG3)3] (4), are reported. Various spectroscopic techniques were employed to characterize the binding of conjugate 3 to 4. A competition dialysis assay revealed that 3 preferentially binds to 4, in the presence of other nucleic acids, including DNA, RNA, DNA-RNA hybrids, and other higher-order structures (single strands, duplexes, triplexes, other G-quadruplexes, and the i-motif). UV thermal denaturation studies showed that thermal stabilization of 4 increases as a function of the increasing concentration of 3. The fluorescence intercalator displacement (FID) assay displayed a significantly tighter binding of 3 with 4 as compared to its parent constituents [220-fold stronger than neomycin (1) and 4.5-fold stronger than perylene diamine (2), respectively]. The binding of 3 with 4 resulted in pronounced changes in the molar ellipticity of the DNA absorption region as confirmed by circular dichroism. The UV-vis absorption studies of the binding of 3 to 4 resulted in a red shift in the spectrum of 3 as well as a marked hypochromic change in the perylene absorption region, suggesting that the ligand-quadruplex interaction involves stacking of the perylene moiety. Docking studies suggest that the perylene moiety serves as a bridge that end stacks on 4, making contacts with two thymine bases in the loop, while the two neomycin moieties branch into the grooves of 4.

  11. Light scattering study of the "pseudo-layer" compression elastic constant in a twist-bend nematic liquid crystal

    CERN Document Server

    Parsouzi, Z; Welch, C; Ahmed, Z; Mehl, G H; Baldwin, A R; Gleeson, J T; Lavrentovich, O D; Allender, D W; Selinger, J V; Jakli, A; Sprunt, S

    2016-01-01

    The nematic twist-bend (TB) phase, exhibited by certain achiral thermotropic liquid crystalline (LC) dimers, features a nanometer-scale, heliconical rotation of the average molecular long axis (director) with equally probable left- and right-handed domains. On meso to macroscopic scales, the TB phase may be considered as a stack of equivalent slabs or "pseudo-layers", each one helical pitch in thickness. The long wavelength fluctuation modes should then be analogous to those of a smectic-A phase, and in particular the hydrodynamic mode combining "layer" compression and bending ought to be characterized by an effective layer compression elastic constant $B_{eff}$ and average director splay constant $K_1^{eff}$. The magnitude of $K_1^{eff}$ is expected to be similar to the splay constant of an ordinary nematic LC, but due to the absence of a true mass density wave, $B_{eff}$ could differ substantially from the typical value of $\\sim 10^6$ Pa in a conventional smectic-A. Here we report the results of a dynamic l...

  12. Multi-scale molecular dynamics study of cholera pentamer binding to a GM1-phospholipid membrane.

    Science.gov (United States)

    Sridhar, Akshay; Kumar, Amit; Dasmahapatra, Ashok Kumar

    2016-07-01

    The AB5 type toxin produced by the Vibrio cholerae bacterium is the causative agent of the cholera disease. The cholera toxin (CT) has been shown to bind specifically to GM1 glycolipids on the membrane surface. This binding of CT to the membrane is the initial step in its endocytosis and has been postulated to cause significant disruption to the membrane structure. In this work, we have carried out a combination of coarse-grain and atomistic simulations to study the binding of CT to a membrane modelled as an asymmetrical GM1-DPPC bilayer. Simulation results indicate that the toxin binds to the membrane through only three of its five B subunits, in effect resulting in a tilted bound configuration. Additionally, the binding of the CT can increase the area per lipid of GM1 leaflet, which in turn can cause the membrane regions interacting with the bound subunits to experience significant bilayer thinning and lipid tail disorder across both the leaflets. PMID:27474868

  13. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

    Science.gov (United States)

    Ohno, Kazuki; Mitsui, Takashi; Tanida, Yoshiaki; Matsuura, Azuma; Fujitani, Hideaki; Niimi, Tatsuya; Orita, Masaya

    2011-02-01

    Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein/ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1)/inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects. PMID:20480380

  14. Cyanide binding to human plasma heme-hemopexin: A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Ascenzi, Paolo, E-mail: ascenzi@uniroma3.it [Laboratorio Interdipartimentale di Microscopia Elettronica, Universita Roma Tre, Roma (Italy); Istituto Nazionale di Biostrutture e Biosistemi, Roma (Italy); Leboffe, Loris [Istituto Nazionale di Biostrutture e Biosistemi, Roma (Italy); Polticelli, Fabio [Dipartimento di Biologia, Universita Roma Tre, Roma (Italy)

    2012-11-16

    Highlights: Black-Right-Pointing-Pointer Cyanide binding to ferric HHPX-heme-Fe. Black-Right-Pointing-Pointer Cyanide binding to ferrous HHPX-heme-Fe. Black-Right-Pointing-Pointer Dithionite-mediated reduction of ferric HHPX-heme-Fe-cyanide. Black-Right-Pointing-Pointer Cyanide binding to HHPX-heme-Fe is limited by ligand deprotonation. Black-Right-Pointing-Pointer Cyanide dissociation from HHPX-heme-Fe-cyanide is limited by ligand protonation. -- Abstract: Hemopexin (HPX) displays a pivotal role in heme scavenging and delivery to the liver. In turn, heme-Fe-hemopexin (HPX-heme-Fe) displays heme-based spectroscopic and reactivity properties. Here, kinetics and thermodynamics of cyanide binding to ferric and ferrous hexa-coordinate human plasma HPX-heme-Fe (HHPX-heme-Fe(III) and HHPX-heme-Fe(II), respectively), and for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex, at pH 7.4 and 20.0 Degree-Sign C, are reported. Values of thermodynamic and kinetic parameters for cyanide binding to HHPX-heme-Fe(III) and HHPX-heme-Fe(II) are K = (4.1 {+-} 0.4) Multiplication-Sign 10{sup -6} M, k{sub on} = (6.9 {+-} 0.5) Multiplication-Sign 10{sup 1} M{sup -1} s{sup -1}, and k{sub off} = 2.8 Multiplication-Sign 10{sup -4} s{sup -1}; and H = (6 {+-} 1) Multiplication-Sign 10{sup -1} M, h{sub on} = 1.2 Multiplication-Sign 10{sup -1} M{sup -1} s{sup -1}, and h{sub off} = (7.1 {+-} 0.8) Multiplication-Sign 10{sup -2} s{sup -1}, respectively. The value of the rate constant for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex is l = 8.9 {+-} 0.8 M{sup -1/2} s{sup -1}. HHPX-heme-Fe reactivity is modulated by proton acceptor/donor amino acid residue(s) (e.g., His236) assisting the deprotonation and protonation of the incoming and outgoing ligand, respectively.

  15. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

    Science.gov (United States)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

  16. Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study

    Energy Technology Data Exchange (ETDEWEB)

    Ramírez-Morales, A.; Martínez-Orozco, J. C.; Rodríguez-Vargas, I. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, Zac. (Mexico)

    2014-05-15

    The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented.

  17. Interaction of coumarin with calf thymus DNA: deciphering the mode of binding by in vitro studies.

    Science.gov (United States)

    Sarwar, Tarique; Rehman, Sayeed Ur; Husain, Mohammed Amir; Ishqi, Hassan Mubarak; Tabish, Mohammad

    2015-02-01

    DNA is the major target for a wide range of therapeutic substances. Thus, there has been considerable interest in the binding studies of small molecules with DNA. Interaction between small molecules and DNA provides a structural guideline in rational drug designing and in the synthesis of new and improved drugs with enhanced selective activity and greater clinical efficacy. Plant derived polyphenolic compounds have a large number of biological and pharmacological properties. Coumarin is a polyphenolic compound which has been extensively studied for its diverse pharmacological properties. However, its mode of interaction with DNA has not been elucidated. In the present study, we have attempted to ascertain the mode of binding of coumarin with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of UV-visible absorbance spectra and fluorescence spectra indicates the formation of complex between coumarin and Ct-DNA. Several other experiments such as effect of ionic strength, iodide induced quenching, competitive binding assay with ethidium bromide, acridine orange and Hoechst 33258 reflected that coumarin possibly binds to the minor groove of the Ct-DNA. These observations were further supported by CD spectral analysis, viscosity measurements, DNA melting studies and in silico molecular docking.

  18. Approximations to Euler's constant

    International Nuclear Information System (INIS)

    We study a problem of finding good approximations to Euler's constant γ=lim→∞ Sn, where Sn = Σk=Ln (1)/k-log(n+1), by linear forms in logarithms and harmonic numbers. In 1995, C. Elsner showed that slow convergence of the sequence Sn can be significantly improved if Sn is replaced by linear combinations of Sn with integer coefficients. In this paper, considering more general linear transformations of the sequence Sn we establish new accelerating convergence formulae for γ. Our estimates sharpen and generalize recent Elsner's, Rivoal's and author's results. (author)

  19. Synthesis, characterization, molecular docking, DNA binding, cytotoxicity and DFT studies of 1-(4-methoxyphenyl)-3-(pyridine-3-ylmethyl)thiourea

    Science.gov (United States)

    Mushtaque, Md; Jahan, Meriyam; Ali, Murtaza; Khan, Md Shahzad; Khan, Mohd Shahid; Sahay, Preeti; Kesarwani, Ashwani

    2016-10-01

    A new compound 1-(4-methoxyphenyl)-3-(pyridine-3-ylmethyl)thiourea was synthesized and structure of compound (3) was elucidated by FT-IR, 1H-NMR, and mass spectrophotometer. The computational quantum chemical studies of compound (3) like, IR, UV, NBO analysis were performed by DFT with B3LYP exchange-correlation functional in combination with 6-311++G(d, p) basis sets. The compound (3) adopted syn-anti-configuration around sulphur atom, possessing stablization relative energy -740715 kcal/mol. The chemical potential of compound (3) is -3.37 eV and chemical hardness is -2.33 eV. However, ionization and electron affinity of compound (3) are -5.70 eV and -1.04 eV. The compound (3) was docked with B-DNA (1BNA) and the binding energy was found to be -7.41 kcal/mol. The nitrogen atom of thiourea of compound (3) binds with O3 and O4 of cytosine of A strand of DNA having bond lengths (1.92 Å) and (1.74 Å) respectively Furthermore, DNA binding constant was performed by UV-visible spectrophotometer. The binding constant was found 3.71 × 106 Lmol-1. In order to assess cytotoxic nature of the lead compound, MTT-assay was performed against MCF-7 cell line and IC50 value of compound (3) was observed at 160.97 μ M. Theoretical studies revealed that they are good agreement with experimental results.

  20. Cosmological constant and curved 5D geometry

    CERN Document Server

    Ito, M

    2002-01-01

    We study the value of cosmological constant in de Sitter brane embedded in five dimensions with positive, vanishing and negative bulk cosmological constant. In the case of negative bulk cosmological constant, we show that not zero but tiny four-dimensional cosmological constant can be realized by tiny deviation from bulk curvature of the Randall-Sundrum model.

  1. Ion exchange equilibrium constants

    CERN Document Server

    Marcus, Y

    2013-01-01

    Ion Exchange Equilibrium Constants focuses on the test-compilation of equilibrium constants for ion exchange reactions. The book first underscores the scope of the compilation, equilibrium constants, symbols used, and arrangement of the table. The manuscript then presents the table of equilibrium constants, including polystyrene sulfonate cation exchanger, polyacrylate cation exchanger, polymethacrylate cation exchanger, polysterene phosphate cation exchanger, and zirconium phosphate cation exchanger. The text highlights zirconium oxide anion exchanger, zeolite type 13Y cation exchanger, and

  2. Photoelectron Spectroscopy and Theoretical Studies of Anion-pi Interactions: Binding Strength and Anion Specificity

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jian; Zhou, Bin; Sun, Zhenrong; Wang, Xue B.

    2015-01-01

    Proposed in theory and confirmed to exist, anion–π interactions have been recognized as new and important non-covalent binding forces. Despite extensive theoretical studies, numerous crystal structural identifications, and a plethora of solution phase investigations, intrinsic anion–π interaction strengths that are free from complications of condensed phases’ environments, have not been directly measured in the gas phase. Herein we present a joint photoelectron spectroscopic and theoretical study on this subject, in which tetraoxacalix[2]arene[2]triazine 1, an electron-deficient and cavity self-tunable macrocyclic was used as a charge-neutral molecular host to probe its interactions with a series of anions with distinctly different shapes and charge states (spherical halides Cl⁻, Br⁻, I⁻, linear thiocyanate SCN⁻, trigonal planar nitrate NO₃⁻, pyramidic iodate IO₃⁻, and tetrahedral sulfate SO₄²⁻). The binding energies of the resultant gaseous 1:1 complexes (1•Cl⁻,1•Br⁻, 1•I⁻, 1•SCN⁻, 1•NO₃⁻, 1•IO₃⁻ and 1•SO₄²⁻) were directly measured experimentally, exhibiting substantial non-covalent interactions with pronounced anion specific effects. The binding strengths of Cl⁻, NO₃⁻, IO₃⁻ with 1 are found to be strongest among all singly charged anions, amounting to ca. 30 kcal/mol, but only about 40% of that between 1 and SO₄²⁻. Quantum chemical calculations reveal that all anions reside in the center of the cavity of 1 with anion–π binding motif in the complexes’ optimized structures, where 1 is seen to be able to self-regulate its cavity structure to accommodate anions of different geometries and three-dimensional shapes. Electron density surface and natural bond orbital charge distribution analysis further support anion–π binding formation. The calculated binding energies of the anions and 1 nicely reproduce the experimentally estimated electron binding energy increase. This work

  3. Photoelectron spectroscopy and theoretical studies of anion-π interactions: binding strength and anion specificity.

    Science.gov (United States)

    Zhang, Jian; Zhou, Bin; Sun, Zhen-Rong; Wang, Xue-Bin

    2015-02-01

    Proposed in theory and then their existence confirmed, anion-π interactions have been recognized as new and important non-covalent binding forces. Despite extensive theoretical studies, numerous crystal structural identifications, and a plethora of solution phase investigations, anion-π interaction strengths that are free from complications of condensed-phase environments have not been directly measured in the gas phase. Herein we present a joint photoelectron spectroscopic and theoretical study on this subject, in which tetraoxacalix[2]arene[2]triazine 1, an electron-deficient and cavity self-tunable macrocyclic, was used as a charge-neutral molecular host to probe its interactions with a series of anions with distinctly different shapes and charge states (spherical halides Cl(-), Br(-), I(-), linear thiocyanate SCN(-), trigonal planar nitrate NO3(-), pyramidic iodate IO3(-), and tetrahedral sulfate SO4(2-)). The binding energies of the resultant gaseous 1 : 1 complexes (1·Cl(-), 1·Br(-), 1·I(-), 1·SCN(-), 1·NO3(-), 1·IO3(-) and 1·SO4(2-)) were directly measured experimentally, exhibiting substantial non-covalent interactions with pronounced anion-specific effects. The binding strengths of Cl(-), NO3(-), IO3(-) with 1 are found to be strongest among all singly charged anions, amounting to ca. 30 kcal mol(-1), but only about 40% of that between 1 and SO4(2-). Quantum chemical calculations reveal that all the anions reside in the center of the cavity of 1 with an anion-π binding motif in the complexes' optimized structures, where 1 is seen to be able to self-regulate its cavity structure to accommodate anions of different geometries and three-dimensional shapes. Electron density surface and charge distribution analyses further support anion-π binding formation. The calculated binding energies of the anions and 1 nicely reproduce the experimentally estimated electron binding energy increase. This work illustrates that size-selective photoelectron

  4. Synthesis, stability constants and electronic spectral studies of ternary complexes of Pr(III) with histidine and diols

    International Nuclear Information System (INIS)

    The mixed ligand complexes of the type MAB, MA2B and MaB2 where M = Pr(III), A = histidine and B = ethanediol, prop-1,2-diol, 2-butene-1, 4-diol, but-2,3-diol, pent-1,5-diol and hex-1,6-diol have been investigated by alkalimetric titrations. The overall stability constants have been evaluated at 30+1degC (μ = 0.2MKNO3). The absorption spectra of some praseodymium(III) ternary complexes in solution have been used to calculate energy interaction and intensity parameters. The low intensity of the pseudohypersensitive transition suggests higher coordination number. (author)

  5. Interaction of hydrated electron with dietary flavonoids and phenolic acids. Rate constants and transient spectra studied by pulse radiolysis

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Zhongli; Li, Xifeng; Katsumura, Yosuke [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab

    2000-03-01

    The reaction rate constants and transient spectra of 11 flavonoids and 4 phenolic acids reacting with e{sub aq}{sup -} at neutral pH were measured. The results suggest that C{sub 4} keto group is the active site for e{sub aq}{sup -} to attack on flavonoids and phenolic acids, while the o-dihydroxy structure in B-ring, the C{sub 2,3} double bond, the C{sub 3}-OH group and glycosylation have little effects on the e{sub aq}{sup -} scavenging activities. (author)

  6. Crossed laser and molecular beam study of multiphoton dissociation of C/sub 2/F/sub 5/Cl. [Rate constants, angular and velocity distributions

    Energy Technology Data Exchange (ETDEWEB)

    Krajnovich, D.J.; Giardini-Guidoni, A.; Sudboe, A.S.; Schulz, P.A.; Shen, Y.R.; Lee, Y.T.

    1978-09-01

    Rate constants for the photodissociation of C/sub 2/F/sub 5/Cl as well as the yield of C/sub 2/F/sub 4//sup +/ were measured. The dynamics of the two dissociation channels was studied by measuring the angular and velocity distributions of the products. 2 references. (JFP)

  7. Fluorescence Correlation Spectroscopy in Drug Discovery: Study of Alexa532-Endothelin 1 Binding to the Endothelin ETA Receptor to Describe the Pharmacological Profile of Natural Products

    Directory of Open Access Journals (Sweden)

    Catherina Caballero-George

    2012-01-01

    Full Text Available Fluorescence correlation spectroscopy and the newly synthesized Alexa532-ET1 were used to study the dynamics of the endothelin ETA receptor-ligand complex alone and under the influence of a semisynthetic selective antagonist and a fungal extract on living A10 cells. Dose-dependent increase of inositol phosphate production was seen for Alexa532-ET1, and its binding was reduced to 8% by the selective endothelin ETA antagonist BQ-123, confirming the specific binding of Alexa532-ET1 to the endothelin ETA receptor. Two different lateral mobilities of the receptor-ligand complexes within the cell membrane were found allowing the discrimination of different states for this complex. BQ-123 showed a strong binding affinity to the “inactive” receptor state characterized by the slow diffusion time constant. A similar effect was observed for the fungal extract, which completely displaced Alexa532-ET1 from its binding to the “inactive” receptor state. These findings suggest that both BQ-123 and the fungal extract act as inverse agonists.

  8. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    Science.gov (United States)

    Endres, Christopher J.; Hammoud, Dima A.; Pomper, Martin G.

    2011-04-01

    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [11C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (kr2) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BPND). Compared with standard SRTM, either coupling of kr2 across regions or constraining kr2 to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BPND between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining kr2 to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the variance of parameter estimates and may better discriminate between

  9. Studies of ruthenium(II) polypyridyl complexes on cytotoxicity in vitro, apoptosis, DNA-binding and antioxidant activity

    Science.gov (United States)

    Huang, Hong-Liang; Liu, Yun-Jun; Zeng, Cheng-Hui; Yao, Jun-Hua; Liang, Zhen-Hua; Li, Zheng-Zheng; Wu, Fu-Hai

    2010-03-01

    Two new ruthenium(II) polypyridyl complexes [Ru(dmb) 2(maip)](ClO 4) 21 (maip = 2-(3-aminophenyl)imizado[4,5-f][1,10]phenanthroline and [Ru(dmb) 2(maip)](ClO 4) 22 (paip = 2-(4-aminophenyl)imidazo[4,5-f][1,10]phenanthroline, dmb = 4,4'-dimethyl-2,2'-bipyridine) have been synthesized and characterized. The DNA-binding behaviors of complexes 1 and 2 were studied by viscosity measurements, thermal denaturation, photocleavage, absorption titration and luminescence spectra. The results show that the two complexes intercalate between the base pairs of DNA. The DNA-binding constants Kb for complexes 1 and 2 were determined to be 1.12 ± 0.11 × 10 5 M -1 ( s = 2.17) and 3.46 ± 0.59 × 10 5 M -1 ( s = 2.11) M -1. The studies on the mechanism of photocleavage demonstrate that superoxide anion radical (O 2rad - ) and singlet oxygen ( 1O 2) may play an important role. The cytotoxicity of these complexes has been evaluated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. The IC 50 values are 19.21, 33.15, 38.57 and 21.15 for complex 1 and 41.77, 123.58, 255.44 and 49.11 for complex 2 against BEL-7402, C-6, HepG-2 and MCF-7 cell lines, respectively. The apoptosis assay was carried out with acridine orange/ethidium bromide (AO/EB) staining methods and the results indicate that complexes can induce the apoptosis of BEL-7402 cells. The experiments on antioxidant activity show these complexes exhibit good antioxidant activity against hydroxyl radical (OH rad ).

  10. Insights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies.

    Science.gov (United States)

    Karthikeyan, Subramani; Bharanidharan, Ganesan; Kesherwani, Manish; Mani, Karthik Ananth; Srinivasan, Narasimhan; Velmurugan, Devadasan; Aruna, Prakasarao; Ganesan, Singaravelu

    2016-06-01

    4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl acetate [Ace semi],4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl propanoate [Pro semi] from the family of thiosemicarbazones derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and it is also less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiosemicarbazone derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance (r) between donor (HSA) and acceptor (thiosemicarbazone derivative) was estimated according to Forster's theory of non-radiative energy transfer using fluorescence spectroscopy. The binding dynamics has been elaborated using synchronous fluorescence spectroscopy, and the feature of thiosemicarbazone derivative induced structural changes of HSA has been studied by circular dichorism, Fourier transform infrared spectroscopy. Molecular modelling simulations explore the hydrophobic interaction and hydrogen bonding which stabilizes the interaction. PMID:26368536

  11. Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome.

    Science.gov (United States)

    Yue, Hongjun; Fang, He; Wei, Sijie; Hayes, Jeffrey J; Lee, Tae-Hee

    2016-04-12

    Linker histone H1 regulates chromatin structure and gene expression. Investigating the dynamics and stoichiometry of binding of H1 to DNA and the nucleosome is crucial to elucidating its functions. Because of the abundant positive charges and the strong self-affinity of H1, quantitative in vitro studies of its binding to DNA and the nucleosome have generated results that vary widely and, therefore, should be interpreted in a system specific manner. We sought to overcome this limitation by developing a specially passivated microscope slide surface to monitor binding of H1 to DNA and the nucleosome at a single-molecule level. According to our measurements, the stoichiometry of binding of H1 to DNA and the nucleosome is very heterogeneous with a wide distribution whose averages are in reasonable agreement with previously published values. Our study also revealed that H1 does not dissociate from DNA or the nucleosome on a time scale of tens of minutes. We found that histone chaperone Nap1 readily dissociates H1 from DNA and superstoichiometrically bound H1 from the nucleosome, supporting a hypothesis whereby histone chaperones contribute to the regulation of the H1 profile in chromatin.

  12. Relating age and micro-architecture with apparent-level elastic constants: a micro-finite element study of female cortical bone from the anterior femoral midshaft.

    Science.gov (United States)

    Donaldson, F E; Pankaj, P; Cooper, D M L; Thomas, C D L; Clement, J G; Simpson, A H R W

    2011-06-01

    Homogenized elastic properties are often assumed for macro-finite element (FE) models used in orthopaedic biomechanics. The accuracy of material property assignments may have a strong effect on the ability of these models to make accurate predictions. For cortical bone, most macro-scale FE models assume isotropic elastic material behaviour and do not include variation of material properties due to bone micro-architecture. The first aim of the present study was to evaluate the variation of apparent-level (homogenized) orthotropic elastic constants of cortical bone with age and indices of bone micro-architecture. Considerable age-dependent differences in porosity were noted across the cortical thickness in previous research. The second aim of the study was to quantify the resulting differences in elastic constants between the periosteum and endosteum. Specimens were taken from the anterior femoral midshaft of 27 female donors (age 53.4 +/- 23.6 years) and micro-FE (gFE) analysis was used to derive orthotropic elastic constants. The variation of orthotropic elastic constants (Young's moduli, shear moduli, and Poisson's ratios) with various cortical bone micro-architectural indices was investigated. The ratio of canal volume to tissue volume, Ca.V/TV, analogous to porosity, was found to be the strongest predictor (r2(ave) = 0.958) of the elastic constants. Age was less predictive (r2(ave) = 0.385) than Ca.V/TV. Elastic anisotropy increased with increasing Ca.V/TV, leading to lower elastic moduli in the transverse, typically less frequently loaded, directions. Increased Ca.V/TV led to a more substantial reduction in elastic constants at the endosteal aspect than at the periosteal aspect. The results are expected to be most applicable in similar midshaft locations of long bones; specific analysis of other sites would be necessary to evaluate elastic properties elsewhere. It was concluded that Ca.V/TV was the most predictive of cortical bone elastic constants and that

  13. Probing different conformational states of pregnancy-zone protein. Fluorescence studies utilizing the binding of 4,4'-bis(8-anilino-1-naphthalenesulphonate).

    Science.gov (United States)

    Arbelaez, L F; Jensen, P E; Shanbhag, V P; Stigbrand, T

    1993-12-01

    The binding of the fluorescence probe 4,4'-bis(8-anilino-1-naphthalenesulphonate) (bis-ANS) to the human proteinase inhibitor pregnancy-zone protein (PZP) and its complexes with methylamine and chymotrypsin were investigated. The existence of dimeric PZP-chymotrypsin complex was demonstrated and both the dimeric and the tetrameric PZP-chymotrypsin complexes could be studied separately. The fluorescence data indicate that bis-ANS binds to two different sites on PZP and its complexes. The values of the dissociation constant, Kd1, for the binding to the high-affinity site were determined to be 231 +/- 14, 220 +/- 28, 114 +/- 15 and 49 +/- 1 nM, for the binding to native PZP, PZP-methylamine and dimeric and tetrameric PZP-chymotrypsin, respectively. An 11-30-fold decrease was observed in the affinity for the second site, the corresponding values of the dissociation constant, Kd2, being 1.5-2.8 +/- 1.0 microM, which are not significantly different for PZP and its derivatives. The results suggest that the probe bis-ANS discriminates between the different conformational states of PZP and that while the conformation of the complex with methylamine does not differ much from that of the native protein, there is a significant change in conformation when chymotrypsin cleaves the bait region. This is substantiated by a 30%-45% decrease in the maximum enhancement of fluorescence intensity when PZP is treated with chymotrypsin. Although the dimeric and tetrameric forms of PZP-chymotrypsin complexes differ in Kd1 values, the difference in the maximum enhancement of the fluorescence of bis-ANS by the two forms is not significant. This indicates that dimer-dimer interaction in the tetrameric form does not involve hydrophobic sites. The necessity of bait-region cleavage for extensive conformational changes in PZP distinguishes it from alpha 2-macroglobulin, the other alpha-macroglobulin in human plasma.

  14. Buffer Interference with Protein Dynamics: A Case Study on Human Liver Fatty Acid Binding Protein

    OpenAIRE

    Long, Dong; Yang, Daiwen

    2009-01-01

    Selection of suitable buffer types is often a crucial step for generating appropriate protein samples for NMR and x-ray crystallographic studies. Although the possible interaction between MES buffer (2-(N-morpholino)ethanesulfonic acid) and proteins has been discussed previously, the interaction is usually thought to have no significant effects on the structures of proteins. In this study, we demonstrate the direct, albeit weak, interaction between MES and human liver fatty acid binding prote...

  15. Cosmological Constant, Fine Structure Constant and Beyond

    CERN Document Server

    Wei, Hao; Li, Hong-Yu; Xue, Dong-Ze

    2016-01-01

    In this work, we consider the cosmological constant model $\\Lambda\\propto\\alpha^{-6}$, which is well motivated from three independent approaches. As is well known, the evidence of varying fine structure constant $\\alpha$ was found in 1998. If $\\Lambda\\propto\\alpha^{-6}$ is right, it means that the cosmological constant $\\Lambda$ should be also varying. In this work, we try to develop a suitable framework to model this varying cosmological constant $\\Lambda\\propto\\alpha^{-6}$, in which we view it from an interacting vacuum energy perspective. We propose two types of models to describe the evolutions of $\\Lambda$ and $\\alpha$. Then, we consider the observational constraints on these models, by using the 293 $\\Delta\\alpha/\\alpha$ data from the absorption systems in the spectra of distant quasars, and the data of type Ia supernovae (SNIa), cosmic microwave background (CMB), baryon acoustic oscillation (BAO). We find that the model parameters can be tightly constrained to the narrow ranges of ${\\cal O}(10^{-5})$ t...

  16. Escherichia coli Single-Stranded DNA-Binding Protein: NanoESI-MS Studies of Salt-Modulated Subunit Exchange and DNA Binding Transactions

    Science.gov (United States)

    Mason, Claire E.; Jergic, Slobodan; Lo, Allen T. Y.; Wang, Yao; Dixon, Nicholas E.; Beck, Jennifer L.

    2013-02-01

    Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)70, one molecule of (dT)35, or two molecules of (dT)35] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.

  17. On-column entrapment of alpha1-acid glycoprotein for studies of drug-protein binding by high-performance affinity chromatography.

    Science.gov (United States)

    Anguizola, Jeanethe; Bi, Cong; Koke, Michelle; Jackson, Abby; Hage, David S

    2016-08-01

    An on-column approach for protein entrapment was developed to immobilize alpha1-acid glycoprotein (AGP) for drug-protein binding studies based on high-performance affinity chromatography. Soluble AGP was physically entrapped by using microcolumns that contained hydrazide-activated porous silica and by employing mildly oxidized glycogen as a capping agent. Three on-column entrapment methods were evaluated and compared to a previous slurry-based entrapment method. The final selected method was used to prepare 1.0 cm × 2.1 mm I.D. affinity microcolumns that contained up to 21 (±4) μg AGP and that could be used over the course of more than 150 sample applications. Frontal analysis and zonal elution studies were performed on these affinity microcolumns to examine the binding of various drugs with the entrapped AGP. Site-selective competition studies were also conducted for these drugs. The results showed good agreement with previous observations for these drug-protein systems and with binding constants that have been reported in the literature. The entrapment method developed in this study should be useful for future work in the area of personalized medicine and in the high-throughput screening of drug interactions with AGP or other proteins. Graphical abstract On-column protein entrapment using a hydrazide-activated support and oxidized glycogen as a capping agent.

  18. Human Islet Amyloid Polypeptide Fibril Binding to Catalase: A Transmission Electron Microscopy and Microplate Study

    Directory of Open Access Journals (Sweden)

    Nathaniel G. N. Milton

    2010-01-01

    Full Text Available The diabetes-associated human islet amyloid polypeptide (IAPP is a 37-amino-acid peptide that forms fibrils in vitro and in vivo. Human IAPP fibrils are toxic in a similar manner to Alzheimer's amyloid-β (Aβ and prion protein (PrP fibrils. Previous studies have shown that catalase binds to Aβ fibrils and appears to recognize a region containing the Gly-Ala-Ile-Ile sequence that is similar to the Gly-Ala-Ile-Leu sequence found in human IAPP residues 24-27. This study presents a transmission electron microscopy (TEM—based analysis of fibril formation and the binding of human erythrocyte catalase to IAPP fibrils. The results show that human IAPP 1-37, 8-37, and 20-29 peptides form fibrils with diverse and polymorphic structures. All three forms of IAPP bound catalase, and complexes of IAPP 1-37 or 8-37 with catalase were identified by immunoassay. The binding of biotinylated IAPP to catalase was high affinity with a KD of 0.77nM, and could be inhibited by either human or rat IAPP 1-37 and 8-37 forms. Fibrils formed by the PrP 118-135 peptide with a Gly-Ala-Val-Val sequence also bound catalase. These results suggest that catalase recognizes a Gly-Ala-Ile-Leu—like sequence in amyloid fibril-forming peptides. For IAPP 1-37 and 8-37, the catalase binding was primarily directed towards fibrillar rather than ribbon-like structures, suggesting differences in the accessibility of the human IAPP 24-27 Gly-Ala-Ile-Leu region. This suggests that catalase may be able to discriminate between different structural forms of IAPP fibrils. The ability of catalase to bind IAPP, Aβ, and PrP fibrils demonstrates the presence of similar accessible structural motifs that may be targets for antiamyloid therapeutic development.

  19. Analytical methods to determine the comparative DNA binding studies of curcumin-Cu(II) complexes

    Science.gov (United States)

    Rajesh, Jegathalaprathaban; Rajasekaran, Marichamy; Rajagopal, Gurusamy; Athappan, Periakaruppan

    2012-11-01

    DNA interaction studies of two mononuclear [1:1(1); 1:2(2)] copper(II) complexes of curcumin have been studied. The interaction of these complexes with CT-DNA has been explored by physical methods to propose modes of DNA binding of the complexes. Absorption spectral titrations of complex 1 with CT-DNA shows a red-shift of 3 nm with the DNA binding affinity of Kb, 5.21 × 104 M-1 that are higher than that obtained for 2 (red-shift, 2 nm; Kb, 1.73 × 104 M-1) reveal that the binding occurs in grooves as a result of the interaction is via exterior phosphates. The CD spectra of these Cu(II) complexes show a red shift of 3-10 nm in the positive band with increase in intensities. This spectral change of induced CD due to the hydrophobic interaction of copper complexes with DNA is the characteristic of B to A conformational change. The EB displacement assay also reveals the same trend as observed in UV-Vis spectral titration. The addition of complexes 1 and 2 to the DNA bound ethidium bromide (EB) solutions causes an obvious reduction in emission intensities indicating that these complexes competitively bind to DNA with EB. The positive shift of both the Epc and E0' accompanied by reduction of peak currents in differential pulse voltammogram (DPV), upon adding different concentrations of DNA to the metal complexes, are obviously in favor of strong binding to DNA. The super coiled plasmid pUC18 DNA cleavage ability of Cu(II) complexes in the presence of reducing agent reveals the single strand DNA cleavage (ssDNA) is observed. The hydroxyl radical (HOrad ) and the singlet oxygen are believed to be the reactive species responsible for the cleavage.

  20. Seasonal variations in the heterologous binding of viscacha spermatozoa. A scanning electron microscope study.

    Science.gov (United States)

    Merlo, Claudia Aguilera; Muñoz, Estela; Dominguez, Susana; Fóscolo, Mabel; Scardapane, Luis; de Rosas, Juan Carlos

    2005-12-01

    Seasonal changes in the reproductive activity of the adult male viscacha (Lagostomus maximus maximus) were investigated during the annual reproductive cycle. Assays of heterologous in vitro binding between compatible gametes were used to evaluate the ability of viscacha spermatozoa to achieve primary binding during its annual reproductive cycle. Sperm were collected by mincing cauda epididymis in HECM-3 medium and the sperm concentration and motility were evaluated. Cumulus-free and zona-free oocytes obtained from superovulated hamsters were inseminated in vitro with capacitated sperm suspensions, incubated at 37 degrees C, 5% CO2 for 3 h, and then processed for studies by scanning electronic microscopy. Statistical analysis was used to compare the quantitative differences. The number of spermatozoa significantly decreases during the regression period, while sperm motility was progressive speed in both periods. During the active period elevated sperm binding to cumulus-free and zona-free oocytes was observed, while the binding during the regression period decreased drastically. In both periods, oocyte microvilli covered sperm heads and tails. These results suggest that the ability of viscacha spermatozoa to participate in gamete recognition is profoundly affected. This would likely be related to different functional stages of the spermatozoa and their epididymal microenvironment during the annual reproductive cycle of viscacha. PMID:16524245

  1. The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.

    Science.gov (United States)

    Furukawa-Hagiya, Tomoka; Furuta, Tadaomi; Chiba, Shuntaro; Sohma, Yoshiro; Sakurai, Minoru

    2013-01-10

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a "closed-apo" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions. PMID:23214920

  2. Use of computational modeling approaches in studying the binding interactions of compounds with human estrogen receptors.

    Science.gov (United States)

    Wang, Pan; Dang, Li; Zhu, Bao-Ting

    2016-01-01

    Estrogens have a whole host of physiological functions in many human organs and systems, including the reproductive, cardiovascular, and central nervous systems. Many naturally-occurring compounds with estrogenic or antiestrogenic activity are present in our environment and food sources. Synthetic estrogens and antiestrogens are also important therapeutic agents. At the molecular level, estrogen receptors (ERs) mediate most of the well-known actions of estrogens. Given recent advances in computational modeling tools, it is now highly practical to use these tools to study the interaction of human ERs with various types of ligands. There are two common categories of modeling techniques: one is the quantitative structure activity relationship (QSAR) analysis, which uses the structural information of the interacting ligands to predict the binding site properties of a macromolecule, and the other one is molecular docking-based computational analysis, which uses the 3-dimensional structural information of both the ligands and the receptor to predict the binding interaction. In this review, we discuss recent results that employed these and other related computational modeling approaches to characterize the binding interaction of various estrogens and antiestrogens with the human ERs. These examples clearly demonstrate that the computational modeling approaches, when used in combination with other experimental methods, are powerful tools that can precisely predict the binding interaction of various estrogenic ligands and their derivatives with the human ERs.

  3. Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

    Institute of Scientific and Technical Information of China (English)

    HU; JianPing; CHANG; Shan; CHEN; WeiZu; WANG; CunXin

    2007-01-01

    Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

  4. Structural Studies of GABAA Receptor Binding Sites: Which Experimental Structure Tells us What?

    Science.gov (United States)

    Puthenkalam, Roshan; Hieckel, Marcel; Simeone, Xenia; Suwattanasophon, Chonticha; Feldbauer, Roman V; Ecker, Gerhard F; Ernst, Margot

    2016-01-01

    Atomic resolution structures of cys-loop receptors, including one of a γ-aminobutyric acid type A receptor (GABAA receptor) subtype, allow amazing insights into the structural features and conformational changes that these pentameric ligand-gated ion channels (pLGICs) display. Here we present a comprehensive analysis of more than 30 cys-loop receptor structures of homologous proteins that revealed several allosteric binding sites not previously described in GABAA receptors. These novel binding sites were examined in GABAA receptor homology models and assessed as putative candidate sites for allosteric ligands. Four so far undescribed putative ligand binding sites were proposed for follow up studies based on their presence in the GABAA receptor homology models. A comprehensive analysis of conserved structural features in GABAA and glycine receptors (GlyRs), the glutamate gated ion channel, the bacterial homologs Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus GLIC, and the serotonin type 3 (5-HT3) receptor was performed. The conserved features were integrated into a master alignment that led to improved homology models. The large fragment of the intracellular domain that is present in the structure of the 5-HT3 receptor was utilized to generate GABAA receptor models with a corresponding intracellular domain fragment. Results of mutational and photoaffinity ligand studies in GABAA receptors were analyzed in the light of the model structures. This led to an assignment of candidate ligands to two proposed novel pockets, candidate binding sites for furosemide and neurosteroids in the trans-membrane domain were identified. The homology models can serve as hypotheses generators, and some previously controversial structural interpretations of biochemical data can be resolved in the light of the presented multi-template approach to comparative modeling. Crystal and cryo-EM microscopic structures of the closest homologs that were solved in different conformational

  5. Conformational stability and aggregation of therapeutic monoclonal antibodies studied with ANS and Thioflavin T binding.

    Science.gov (United States)

    Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Helk, Bernhard; Trout, Bernhardt L

    2011-01-01

    Characterization of aggregation profiles of monoclonal antibodies (mAb) is gaining importance because an increasing number of mAb-based therapeutics are entering clinical studies and gaining marketing approval. To develop a successful formulation, it is imperative to identify the critical biochemical properties of each potential mAb drug candidate. We investigated the conformational change and aggregation of a human IgG1 using external dye-binding experiments with fluorescence spectroscopy and compared the aggregation profiles obtained to the results of size-exclusion chromatography. We show that using an appropriate dye at selected mAb concentration, unfolding or aggregation can be studied. In addition, dye-binding experiments may be used as conventional assays to study therapeutic mAb stability. PMID:21540645

  6. Study on spectroscopic parameters and molecular constants of HC1(X1Σ+) molecule by using multireference configuration interaction approach

    International Nuclear Information System (INIS)

    Equilibrium internuclear separations, harmonic frequencies and potential energy curves (PECs) of HC1(X1Σ+) molecule are investigated by using the highly accurate valence internally contracted multireference configuration interaction (MRCI) approach in combination with a series of correlation-consistent basis sets in the valence range. The PECs are all fitted to the Murrell–Sorbie function, and they are used to accurately derive the spectroscopic parameters (De, D0, ωeχe, αe and Be). Compared with the available measurements, the PEC obtained at the basis set, aug-cc-pV5Z, is selected to investigate the vibrational manifolds. The constants D0, De, Re, ωe, ωeχe, αe and Be at this basis set are 4.4006 eV, 4.5845 eV, 0.12757 nm, 2993.33 cm−1, 52.6273 cm−1, 0.2981 cm−1 and 10.5841 cm−1, respectively, which almost perfectly conform to the available experimental results. With the potential determined at the MRCI/aug-cc-pV5Z level of theory, by numerically solving the radial Schrödinger equation of nuclear motion in the adiabatic approximation, a total of 21 vibrational levels are predicted. Complete vibrational levels, classical turning points, inertial rotation and centrifugal distortion constants are reproduced, which are in excellent agreement with the available Rydberg–Klein–Rees data. Most of these theoretical vibrational manifolds are reported for the first time to the best of our knowledge. (atomic and molecular physics)

  7. Understanding binding affinity : A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

    NARCIS (Netherlands)

    Talhout, Reinskje; Villa, Alessandra; Mark, AE; Engberts, JBFN

    2003-01-01

    The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para p

  8. Improved assay for measuring heparin binding to bull sperm

    International Nuclear Information System (INIS)

    The binding of heparin to sperm has been used to study capacitation and to rank relative fertility of bulls. Previous binding assays were laborious, used 107 sperm per assay point, and required large amounts of radiolabeled heparin. A modified heparin-binding assay is described that used only 5 x 104 cells per incubation well and required reduced amounts of [3H] heparin. The assay was performed in 96-well Millititer plates, enabling easy incubation and filtering. Dissociation constants and concentrations of binding sites did not differ if analyzed by Scatchard plots, Woolf plots, or by log-logit transformed weighted nonlinear least squares regression, except in the case of outliers. In such cases, Scatchard analysis was more sensitive to outliers. Nonspecific binding was insignificant using nonlinear logistic fit regression and a proportion graph. The effects were tested of multiple free-thawing of sperm in either a commercial egg yolk extender, 40 mM Tris buffer with 8% glycerol, or 40 mM Tris buffer without glycerol. Freeze-thawing in extender did not affect the dissociation constant or the concentration of binding sites. However, freeze-thawing three times in 40 mM Tris reduced the concentration of binding sites and lowered the dissociation constant (raised the affinity). The inclusion of glycerol in the 40 mM Tris did not significantly affect the estimated dissociation constant or the concentration of binding sites as compared to 40 mM Tris without glycerol

  9. Study of dynamic properties for NaK binary liquid alloy using first principle and theoretical predictions of isothermal bulk modulus using elastic constants

    International Nuclear Information System (INIS)

    Study of atomic motions in the binary liquid alloys have been studied in terms of dynamical variables like velocity auto correlation, power spectrum and mean square displacement. Elastic constants and isothermal bulk modulus have been calculated to see the effeectiveness of ab-initio pseudopotentials which has been used in this paper. This appraoch is free from the fitting parameters and results obtained using this appraoch have been found very close to the average values

  10. Study of dynamic properties for NaK binary liquid alloy using first principle and theoretical predictions of isothermal bulk modulus using elastic constants

    Energy Technology Data Exchange (ETDEWEB)

    Thakur, Anil, E-mail: anil-t2001@yahoo.com; Kashyap, Rajinder [Department of Physics, Govt. P. G. College Solan-173212, Himachal Pradesh (India); Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University Shimla-171005, Himachal Pradesh (India)

    2014-04-24

    Study of atomic motions in the binary liquid alloys have been studied in terms of dynamical variables like velocity auto correlation, power spectrum and mean square displacement. Elastic constants and isothermal bulk modulus have been calculated to see the effeectiveness of ab-initio pseudopotentials which has been used in this paper. This appraoch is free from the fitting parameters and results obtained using this appraoch have been found very close to the average values.

  11. A comparative study of recombinant and native frutalin binding to human prostate tissues

    Directory of Open Access Journals (Sweden)

    Domingues Lucília

    2009-09-01

    Full Text Available Abstract Background Numerous studies indicate that cancer cells present an aberrant glycosylation pattern that can be detected by lectin histochemistry. Lectins have shown the ability to recognise these modifications in several carcinomas, namely in the prostate carcinoma, one of the most lethal diseases in man. Thus, the aim of this work was to investigate if the α-D-galactose-binding plant lectin frutalin is able to detect such changes in the referred carcinoma. Frutalin was obtained from different sources namely, its natural source (plant origin and a recombinant source (Pichia expression system. Finally, the results obtained with the two lectins were compared and their potential use as prostate tumour biomarkers was discussed. Results The binding of recombinant and native frutalin to specific glycoconjugates expressed in human prostate tissues was assessed by using an immuhistochemical technique. A total of 20 cases of prostate carcinoma and 25 cases of benign prostate hyperplasia were studied. Lectins bound directly to the tissues and anti-frutalin polyclonal antibody was used as the bridge to react with the complex biotinilated anti-rabbit IgG plus streptavidin-conjugated peroxidase. DAB was used as visual indicator to specifically localise the binding of the lectins to the tissues. Both lectins bound to the cells cytoplasm of the prostate carcinoma glands. The binding intensity of native frutalin was stronger in the neoplasic cells than in hyperplasic cells; however no significant statistical correlation could be found (P = 0.051. On the other hand, recombinant frutalin bound exclusively to the neoplasic cells and a significant positive statistical correlation was obtained (P Conclusion Native and recombinant frutalin yielded different binding responses in the prostate tissues due to their differences in carbohydrate-binding affinities. Also, this study shows that both lectins may be used as histochemical biomarkers for the prostate

  12. Variational implicit-solvent modeling of host-guest binding: A case study on cucurbit[7]uril

    OpenAIRE

    S. Zhou; Rogers, KE; De Oliveira, CAF; Baron, R; Cheng, LT; Dzubiella, J.; Li, B.; McCammon, JA

    2013-01-01

    The synthetic host cucurbit[7]uril (CB[7]) binds aromatic guests or metal complexes with ultrahigh affinity compared with that typically displayed in protein-ligand binding. Due to its small size, CB[7] serves as an ideal receptor-ligand system for developing computational methods for molecular recognition. Here, we apply the recently developed variational implicit-solvent model (VISM), numerically evaluated by the level-set method, to study hydration effects in the high-affinity binding of t...

  13. Binding studies of the antitumoral radiopharmaceutical 125I-Crotoxin to Ehrlich ascites tumor cells

    International Nuclear Information System (INIS)

    The development of tools for functional diagnostic imaging is mainly based on radiopharmaceuticals that specifically target membrane receptors. Crotoxin (Crtx), a polypeptide isolated from Crotalus durissus terrificus venom, has been shown to have an antitumoral activity and is a promising bioactive tracer for tumor detection. More specific radiopharmaceuticals are being studied to complement the techniques applied in the conventional medicine against breast cancer, the most frequent cause of death from malignant disease in women. Crtx's effect has been shown to be related with the overexpression of epidermal growth factor receptor (EGFR), present in high levels in 30 to 60% of breast tumor cells. Our objective was to evaluate Crtx as a tracer for cancer diagnosis, investigating its properties as an EGFR-targeting agent. Ehrlich ascites tumor cells (EAT cells) were used due to its origin and similar characteristics to breast tumor cells, specially the presence of EGFR. Crtx was labeled with 125I and binding experiments were performed. To evaluate the specific binding in vitro of Crtx, competition binding assay was carried out in the presence of increasing concentrations of non-labelled crotoxin and epidermal growth factor (EGF). Specific binding of 125I-Crtx to EAT cells was determined and the binding was considered saturable, with approximately 70% of specificity, high affinity (Kd = 19.7 nM) and IC50 = 1.6 x 10-11 M. Our results indicate that Crtx's interaction with EAT cells is partially related with EGFR and increases the biotechnological potential of Crtx as a template for radiopharmaceutical design for cancer diagnosis. (author)

  14. Binding study of tetracyclines to human serum albumin using difference spectrophotometry.

    Science.gov (United States)

    Zia, H; Price, J C

    1976-02-01

    The binding of several tetracyclines to human serum albumin was studied using difference spectrophotometry and a spectrophotometric probe, 2-(4'-hydroxybenzeneazo)benzoic acid. Difference spectra observed for the interaction between the probe and human serum albumin were similar to probe-bovine serum albumin spectra but were less intense for a given concentration of probe and did not reach saturation as quickly. Difference spectra for the tetracyclines were dependent on the characteristics of the ring substituents. More hydrophobic substituents on the D and C rings tended to give more intense difference spectra, but charge-transfer complexing may also have been involved since methacycline with a methylene group in the 6-position showed the most intense spectra of the compounds studied. Solvent perturbation, pH, and urea studies tended to confirm that something other than hydrophobic binding of the tetracyclines was involved. Drug-probe displacement studies showed that methacycline gave the greatest probe displacement followed by doxycycline, chlortetracycline, oxytetracycline, and tetracycline. This order of displacement of the anionic probe indicates that both hydrophobic and charge-transfer binding are involved. Experiments with calcium ion and ethylenediaminetetraacetic acid showed that the difference spectra obtained with the tetracyclines and human serum albumin were not the result of metallic bridge-chelate formation. PMID:3641

  15. Study of the Pion-Nucleon Coupling Constant Charge Dependence on the Basis of the Low-Energy Data on Nucleon-Nucleon Interaction

    CERN Document Server

    Babenko, V A

    2016-01-01

    We study relationship between the physical quantities that characterize pion-nucleon and nucleon-nucleon interaction on the basis of the fact that nuclear forces in the nucleon-nucleon system at low energies are mainly determined by the one-pion exchange mechanism. By making use of the recommended proton-proton low-energy scattering parameters, we obtain the following value for the charged pion-nucleon coupling constant g$_{\\pi ^{\\pm }}^{2}/4\\pi =14.55(13)$. Calculated value of this quantity is in excellent agreement with the experimental result g$_{\\pi ^{\\pm }}^{2}/4\\pi =14.52(26)$ of the Uppsala Neutron Research Group. At the same time, the obtained value of the charged pion-nucleon coupling constant differs markedly from the value of the neutral pion-nucleon coupling constant g$_{\\pi ^{0}}^{2}/4\\pi =13.55(13)$. Thus, our results show considerable charge splitting of the pion-nucleon coupling constant.

  16. Revisiting the streptavidin-biotin binding by using an aptamer and displacement isothermal calorimetry titration.

    Science.gov (United States)

    Kuo, Tai-Chih; Tsai, Ching-Wei; Lee, Peng-Chen; Chen, Wen-Yih

    2015-03-01

    The association constant of a well-known streptavidin-biotin binding has only been inferred from separately measured kinetic parameters. In a single experiment, we obtained Ka 1 × 10(12)  M(-1) by using a streptavidin-binding aptamer and ligand-displacement isothermal titration calorimetry. This study explores the challenges of determining thermodynamic parameters and the derived equilibrium binding affinity of tight ligand-receptor binding.

  17. Synthesis, characterization, DNA binding studies, photocleavage, cytotoxicity and docking studies of ruthenium(II) light switch complexes.

    Science.gov (United States)

    Gabra, Nazar Mohammed; Mustafa, Bakheit; Kumar, Yata Praveen; Devi, C Shobha; Srishailam, A; Reddy, P Venkat; Reddy, Kotha Laxma; Satyanarayana, S

    2014-01-01

    A new ligand 3-(1H-imidazo[4,5-f][1,10]phenanthrolin-2yl)phenylboronic acid and its (IPPBA) three ruthenium(II) complexes [Ru(phen)2(IPPBA)](ClO4)2 (1), [Ru(bpy)2(IPPBA)](ClO4)2 (2) and [Ru(dmb)2(IPPBA)](ClO4)2 (3) have been synthesized and characterized by elemental analysis, UV/VIS, IR, (1)H-NMR,(13)C-NMR and mass spectra. The binding behaviors of the three complexes to calf thymus DNA were investigated by absorption spectra, emission spectroscopy, viscosity measurements, thermal denaturation and photoactivated cleavage. The DNA-binding constants for complexes 1, 2 and 3 have been determined to be 7.9 × 10(5) M(-1), 6.7 × 10(5) M(-1) and 2.9 × 10(5) M(-1). The results suggest that these complexes bound to double-stranded DNA in an intercalation mode. Upon irradiation at 365 nm, three ruthenium complexes were found to promote the cleavage of plasmid pBR322 DNA from super coiled form І to nicked form ІІ. Further in the presence of Co(2+), the emission of DNA-Ru(ΙΙ) complexes can be quenched. And when EDTA was added, the emission was recovered. The experimental results show that all three complexes exhibited the "on-off-on" properties of molecular "light switch". The highest Cytotoxicity potential of the complex1 was observed on the Human alveolar adenocarcinoma (A549) cell line. Good agreement was generally found between the spectroscopic techniques and molecular docked model which provides further evidence of groove binding. PMID:23982735

  18. Comparative study on ChIP-seq data: normalization and binding pattern characterization

    OpenAIRE

    Taslim, Cenny; Wu, Jiejun; Yan, Pearlly; Singer, Greg; Parvin, Jeffrey; Huang, Tim; Lin, Shili; Huang, Kun

    2009-01-01

    Motivation: Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their ...

  19. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer.

    Science.gov (United States)

    Wu, Tsai-Chin; Vasudev, Milana; Dutta, Mitra; Stroscio, Michael A

    2013-06-01

    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.

  20. The Nucleotide-Free State of the Multidrug Resistance ABC Transporter LmrA: Sulfhydryl Cross-Linking Supports a Constant Contact, Head-to-Tail Configuration of the Nucleotide-Binding Domains.

    Directory of Open Access Journals (Sweden)

    Peter M Jones

    Full Text Available ABC transporters are integral membrane pumps that are responsible for the import or export of a diverse range of molecules across cell membranes. ABC transporters have been implicated in many phenomena of medical importance, including cystic fibrosis and multidrug resistance in humans. The molecular architecture of ABC transporters comprises two transmembrane domains and two ATP-binding cassettes, or nucleotide-binding domains (NBDs, which are highly conserved and contain motifs that are crucial to ATP binding and hydrolysis. Despite the improved clarity of recent structural, biophysical, and biochemical data, the seemingly simple process of ATP binding and hydrolysis remains controversial, with a major unresolved issue being whether the NBD protomers separate during the catalytic cycle. Here chemical cross-linking data is presented for the bacterial ABC multidrug resistance (MDR transporter LmrA. These indicate that in the absence of nucleotide or substrate, the NBDs come into contact to a significant extent, even at 4°C, where ATPase activity is abrogated. The data are clearly not in accord with an inward-closed conformation akin to that observed in a crystal structure of V. cholerae MsbA. Rather, they suggest a head-to-tail configuration 'sandwich' dimer similar to that observed in crystal structures of nucleotide-bound ABC NBDs. We argue the data are more readily reconciled with the notion that the NBDs are in proximity while undergoing intra-domain motions, than with an NBD 'Switch' mechanism in which the NBD monomers separate in between ATP hydrolysis cycles.

  1. Structural-functional insights and studies on saccharide binding of Sophora japonica seed lectin.

    Science.gov (United States)

    Yadav, Priya; Shahane, Ganesh; Ramasamy, Sureshkumar; Sengupta, Durba; Gaikwad, Sushama

    2016-10-01

    Functional and conformational transitions of the Sophora japonica seed lectin (SJL) were studied in detail using bioinformatics and biophysical tools. Homology model of the lectin displayed all the characteristics of the legume lectin monomer and the experimental observations correlated well with the structural information. In silico studies were performed by protein-ligand docking, calculating the respective binding energies and the residues involved in the interactions were derived from LigPlot(+) analysis. Fluorescence titrations showed three times higher affinity of T-antigen disaccharide than N-acetyl galactosamine (GalNAc) towards SJL indicating extended sugar binding site of the lectin. Thermodynamic parameters of T-antigen binding to SJL indicated the process to be endothermic and entropically driven while those of GalNAc showed biphasic process. SDS-PAGE showed post-translationally modified homotetrameric species of the lectin under native conditions. In presence of guanidine hydrochloride (0.5-5.0M), the tetramer first dissociated into dimers followed by unfolding of the protein as indicated by size exclusion chromatography, fluorescence and CD spectroscopy. Different structural rearrangements were observed during thermal denaturation of SJL at physiological pH 7.2, native pH 8.5 and molten globule inducing pH 1.0. Topological information revealed by solute quenching studies at respective pH indicated differential hydrophobic environment and charge density around tryptophan residues. PMID:27185070

  2. Study of low-modulus biomedical β Ti-Nb-Zr alloys based on single-crystal elastic constants modeling.

    Science.gov (United States)

    Wang, Xing; Zhang, Ligang; Guo, Ziyi; Jiang, Yun; Tao, Xiaoma; Liu, Libin

    2016-09-01

    CALPHAD-type modeling was used to describe the single-crystal elastic constants of the bcc solution phase in the ternary Ti-Nb-Zr system. The parameters in the model were evaluated based on the available experimental data and first-principle calculations. The composition-elastic properties of the full compositions were predicted and the results were in good agreement with the experimental data. It is found that the β phase can be divided into two regions which are separated by a critical dynamical stability composition line. The corresponding valence electron number per atom and the polycrystalline Young׳s modulus of the critical compositions are 4.04-4.17 and 30-40GPa respectively. Orientation dependencies of single-crystal Young׳s modulus show strong elastic anisotropy on the Ti-rich side. Alloys compositions with a Young׳s modulus along the direction matching that of bone were found. The current results present an effective strategy for designing low modulus biomedical alloys using computational modeling. PMID:27235781

  3. Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates.

    Science.gov (United States)

    Xue, Liang; Xi, Hongjuan; Kumar, Sunil; Gray, David; Davis, Erik; Hamilton, Paris; Skriba, Michael; Arya, Dev P

    2010-07-01

    Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA).2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1-4) stabilized poly(dA).2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (T(m3-->2)) at which poly(dA).2poly(dT) dissociated into poly(dA).poly(dT) and poly(dT) increased dramatically (>12 degrees C) in the presence of intercalator-neomycin conjugates (1-4) even at a very low concentration (2 muM). In contrast to intercalator-neomycin conjugates, the increment of T(m3-->2) of poly(dA).2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA).2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1-4 had slightly larger binding site size ( approximately 7-7.5) with poly(dA).2poly(dT) as compared to neomycin ( approximately 6.5). The thermodynamic parameters of these intercalator-neomycin conjugates with poly(dA).2poly(dT) were derived from an integrated van't Hoff equation using the T(m3-->2) values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA).2poly(dT) increased in the following order: neomycin neomycin. The binding of compounds 1-4 with poly(dA).2poly(dT) was mostly enthalpy

  4. Experimental study of laminar forced convective heat transfer of deionized water based copper (I) oxide nanofluids in a tube with constant wall heat flux

    Science.gov (United States)

    Umer, Asim; Naveed, Shahid; Ramzan, Naveed

    2016-10-01

    Nanofluids, having 1-100 nm size particles in any base fluid are promising fluid for heat transfer intensification due to their enhanced thermal conductivity as compared with the base fluid. The forced convection of nanofluids is the major practical application in heat transfer equipments. In this study, heat transfer enhancements at constant wall heat flux under laminar flow conditions were investigated. Nanofluids of different volume fractions (1, 2 and 4 %) of copper (I) oxide nanoparticles in deionized water were prepared using two step technique under mechanical mixing and ultrasonication. The results were investigated by increasing the Reynolds number of the nanofluids at constant heat flux. The trends of Nusselt number variation with dimensionless length (X/D) and Reynolds numbers were studied. It was observed that heat transfer coefficient increases with increases particles volume concentration and Reynolds number. The maximum enhancement in heat transfer coefficient of 61 % was observed with 4 % particle volume concentration at Reynolds number (Re ~ 605).

  5. Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an antiparallel folded human telomere sequence.

    Science.gov (United States)

    Wilson, Tom; Costa, Paulo J; Félix, Vítor; Williamson, Mike P; Thomas, Jim A

    2013-11-14

    We report DNA binding studies of the dinuclear ruthenium ligand [{Ru(phen)2}2tpphz](4+) in enantiomerically pure forms. As expected from previous studies of related complexes, both isomers bind with similar affinity to B-DNA and have enhanced luminescence. However, when tested against the G-quadruplex from human telomeres (which we show to form an antiparallel basket structure with a diagonal loop across one end), the ΛΛ isomer binds approximately 40 times more tightly than the ΔΔ, with a stronger luminescence. NMR studies show that the complex binds at both ends of the quadruplex. Modeling studies, based on experimentally derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz](4+), show that the ΛΛ isomer fits neatly under the diagonal loop, whereas the ΔΔ isomer is unable to bind here and binds at the lateral loop end. Molecular dynamics simulations show that the ΔΔ isomer is prevented from binding under the diagonal loop by the rigidity of the loop. We thus present a novel enantioselective binding substrate for antiparallel basket G-quadruplexes, with features that make it a useful tool for quadruplex studies.

  6. Studies on the effect of AgNP binding on α-amylase structure of porcine pancreas and Bacillus subtilis by multi-spectroscopic methods

    International Nuclear Information System (INIS)

    Functionalizing silver nanoparticles (AgNPs) with biomolecules have a number of applications in catalysis, sensing, pharmaceutics and therapy. For the first time, herein we report the interaction of amylase-AgNPs through various spectroscopic techniques. AgNPs are synthesized and characterized by UV–vis spectroscopy, transmission electron microscopy (TEM) and Dynamic Light Scattering (DLS). The binding of AgNPs to α-amylase are investigated by UV–vis, fluorescence, circular dichroism and FTIR spectroscopic techniques. Absorption intensity and Stern–Volmer plots confirmed the formation of the ground state complex with AgNPs. The quenching of the intrinsic protein fluorescence in the presence of different concentrations of AgNP was observed. The apparent binding constant (K) and number of binding sites (n) was calculated from the Stern–Volmer plot was found to be 4.92×103, 3.8×103 and 1.57, 1.3 for porcine pancreas and Bacillus subtilis α-amylase, respectively. Far-UV CD studies revealed the characteristic dichoric band at 222 nm for α-helical structure was shifted to 215 nm in porcine pancreatic α-amylase upon AgNP binding. Further, structural conformation change with peak shifts and the possible binding residues was confirmed through FTIR spectroscopy. -- Highlights: • AgNPs were synthesized using modified Creighton's method and characterized. • Structural changes analyzed by UV–vis, fluorescence spectroscopy. • CD and FTIR spectra reveal the secondary structure conformation change. • Potential application in food industry

  7. Studies on the effect of AgNP binding on α-amylase structure of porcine pancreas and Bacillus subtilis by multi-spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Ernest, Vinita; Sekar, Gajalakshmi; Mukherjee, Amitava; Chandrasekaran, N., E-mail: nchandrasekaran@vit.ac.in

    2014-02-15

    Functionalizing silver nanoparticles (AgNPs) with biomolecules have a number of applications in catalysis, sensing, pharmaceutics and therapy. For the first time, herein we report the interaction of amylase-AgNPs through various spectroscopic techniques. AgNPs are synthesized and characterized by UV–vis spectroscopy, transmission electron microscopy (TEM) and Dynamic Light Scattering (DLS). The binding of AgNPs to α-amylase are investigated by UV–vis, fluorescence, circular dichroism and FTIR spectroscopic techniques. Absorption intensity and Stern–Volmer plots confirmed the formation of the ground state complex with AgNPs. The quenching of the intrinsic protein fluorescence in the presence of different concentrations of AgNP was observed. The apparent binding constant (K) and number of binding sites (n) was calculated from the Stern–Volmer plot was found to be 4.92×10{sup 3}, 3.8×10{sup 3} and 1.57, 1.3 for porcine pancreas and Bacillus subtilis α-amylase, respectively. Far-UV CD studies revealed the characteristic dichoric band at 222 nm for α-helical structure was shifted to 215 nm in porcine pancreatic α-amylase upon AgNP binding. Further, structural conformation change with peak shifts and the possible binding residues was confirmed through FTIR spectroscopy. -- Highlights: • AgNPs were synthesized using modified Creighton's method and characterized. • Structural changes analyzed by UV–vis, fluorescence spectroscopy. • CD and FTIR spectra reveal the secondary structure conformation change. • Potential application in food industry.

  8. Capping of Silybin with β-Cyclodextrin Influences its Binding with Bovine Serum Albumin: A Study by Fluorescence Spectroscopy and Molecular Modeling

    International Nuclear Information System (INIS)

    The association of silybin with β-cyclodextrin and its influence on silybin's binding with bovine serum albumin are reported. The stoichiometry, binding constant, and the structure of silybin-β-cyclodextrin inclusion complex are reported. The titrations of silybin with bovine serum albumin in the absence and presence of β-cyclodextrin are carried out and the differences in binding strengths are discussed. Molecular modeling is used to optimize the sites and mode of binding of silybin with bovine serum albumin. Forster resonance energy transfer is calculated and the proximity of interacting molecules is reported in the presence and absence of β-cyclodextrin

  9. Capping of Silybin with β-Cyclodextrin Influences its Binding with Bovine Serum Albumin: A Study by Fluorescence Spectroscopy and Molecular Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Natesan, Sudha; Sowrirajan, Chandrasekaran; Dhanaraj, Premnath; Enoch, Israel V. M. V. [Karunya Univ., Tamil Nadu (India)

    2014-07-15

    The association of silybin with β-cyclodextrin and its influence on silybin's binding with bovine serum albumin are reported. The stoichiometry, binding constant, and the structure of silybin-β-cyclodextrin inclusion complex are reported. The titrations of silybin with bovine serum albumin in the absence and presence of β-cyclodextrin are carried out and the differences in binding strengths are discussed. Molecular modeling is used to optimize the sites and mode of binding of silybin with bovine serum albumin. Forster resonance energy transfer is calculated and the proximity of interacting molecules is reported in the presence and absence of β-cyclodextrin.

  10. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ruthenium-fluoroquinolone complexes

    Indian Academy of Sciences (India)

    Mohan N Patel; Hardik N Joshi; Chintan R Patel

    2014-05-01

    Six new Ru(II) and Ru(III) complexes have been synthesized and characterized by elemental analysis, LC-MS, electronic spectra, IR spectra and magnetic moment measurements. DNA-binding properties of Ru complexes have been studied by means of absorption spectrophotometry and viscosity measurements as well as their HS DNA cleavage properties by means of agarose gel electrophoresis. The experimental results show that all the complexes can bind to DNA via partial intercalative mode. The b values of complexes were found in the range 2.14 × 104 to 2.70 × 105 M-1. All the complexes show excellent efficiency of cleaving DNA than respective fluoroquinolones. Brine shrimp lethality bioassay has been performed to check the cytotoxic activity. The IC50 values of the complexes are in the range of 6.27 to 16.05 g mL-1.

  11. The Binding of Roxarsone at the Silica/Water Interface Studied with Second Harmonic Generation

    Science.gov (United States)

    Konek, Christopher; Ostrowski, David; Geiger, Franz

    2005-03-01

    Arsenic is a carcinogen that can also cause chronic poisoning when ingested via drinking water in quantities as low as 10 micrograms/L. In the US, organic arsenicals such as Roxarsone are commonly used as feed additives in the poultry industry. The use of poultry litter as fertilizer results in environmental arsenic deposition rates of up to 50 metric tons per year; the subsequent environmental fate of Roxarsone is unknown. We use second harmonic generation (SHG) to study the thermodynamics and kinetics of Roxarsone binding to environmentally relevant mineral oxide/water interfaces. Roxarsone binding to water/SiO2 interfaces is fully reversible, consistent with high Roxarsone mobility. Results from Langmuir isotherm measurements and surface SHG spectra are presented as well.

  12. A longitudinal study of serum cobalamins and its binding proteins in lactating women

    DEFF Research Database (Denmark)

    Mørkbak, A L; Ramlau-Hansen, C H; Møller, U K;

    2006-01-01

    were analysed. RESULTS: No significant differences were observed in serum cobalamins or its binding proteins related to supplementation with vitamin B12 or the duration of lactation. Serum cobalamins remained unchanged from 3 weeks to 9 months post-partum. Total TC (holoTC) (median+/-s.e. pmol...... in HC during a 9-month period post-partum. No differences were observed between the vitamin B12-supplemented and the unsupplemented groups. Thus, supplementation with vitamin B12 has no impact on the circulating level of serum cobalamins or its binding proteins in a Danish population of lactating......OBJECTIVE: To examine longitudinal changes in serum cobalamins, transcobalamin (TC) and haptocorrin (HC) during lactation and to investigate the influence of vitamin B12 supplementation on these parameters. DESIGN: A 9-month follow-up study. SUBJECTS AND METHODS: Lactating mothers (N=89) including...

  13. A path integral molecular dynamics study of the hyperfine coupling constants of the muoniated and hydrogenated acetone radicals

    Science.gov (United States)

    Oba, Yuki; Kawatsu, Tsutomu; Tachikawa, Masanori

    2016-08-01

    The on-the-fly ab initio density functional path integral molecular dynamics (PIMD) simulations, which can account for both the nuclear quantum effect and thermal effect, were carried out to evaluate the structures and "reduced" isotropic hyperfine coupling constants (HFCCs) for muoniated and hydrogenated acetone radicals (2-muoxy-2-propyl and 2-hydoxy-2-propyl) in vacuo. The reduced HFCC value from a simple geometry optimization calculation without both the nuclear quantum effect and thermal effect is -8.18 MHz, and that by standard ab initio molecular dynamics simulation with only the thermal effect and without the nuclear quantum effect is 0.33 MHz at 300 K, where these two methods cannot distinguish the difference between muoniated and hydrogenated acetone radicals. In contrast, the reduced HFCC value of the muoniated acetone radical by our PIMD simulation is 32.1 MHz, which is about 8 times larger than that for the hydrogenated radical of 3.97 MHz with the same level of calculation. We have found that the HFCC values are highly correlated with the local molecular structures; especially, the Mu—O bond length in the muoniated acetone radical is elongated due to the large nuclear quantum effect of the muon, which makes the expectation value of the HFCC larger. Although our PIMD result calculated in vacuo is about 4 times larger than the measured experimental value in aqueous solvent, the ratio of these HFCC values between muoniated and hydrogenated acetone radicals in vacuo is in reasonable agreement with the ratio of the experimental values in aqueous solvent (8.56 MHz and 0.9 MHz); the explicit presence of solvent molecules has a major effect on decreasing the reduced muon HFCC of in vacuo calculations for the quantitative reproduction.

  14. Temporal variation of coupling constants and nucleosynthesis

    CERN Document Server

    Oberhummer, Heinz; Fairbairn, M; Schlattl, H; Sharma, M M

    2003-01-01

    We investigate the triple-alpha process and the Oklo phenomenon to obtain constraints on possible cosmological time variations of fundamental constants. Specifically we study cosmological temporal constraints for the fine structure constant and nucleon and meson masses.

  15. Temporal variation of coupling constants and nucleosynthesis

    Science.gov (United States)

    Oberhummer, H.; Csótó, A.; Fairbairn, M.; Schlattl, H.; Sharma, M. M.

    2003-05-01

    We investigate the triple-alpha process and the Oklo phenomenon to obtain constraints on possible cosmological time variations of fundamental constants. Specifically we study cosmological temporal constraints for the fine structure constant and nucleon and meson masses.

  16. Surfaces of a Constant Negative Curvature

    Directory of Open Access Journals (Sweden)

    G. M. Gharib

    2012-01-01

    Full Text Available I study the geometric notion of a differential system describing surfaces of a constant negative curvature and describe a family of pseudospherical surfaces for the nonlinear partial differential equations with constant Gaussian curvature .

  17. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    Energy Technology Data Exchange (ETDEWEB)

    Endres, Christopher J; Pomper, Martin G [Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Hammoud, Dima A, E-mail: endres@jhmi.edu [Radiology and Imaging Sciences, National Institutes of Health/Clinical Center, Bethesda, MD (United States)

    2011-04-21

    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [{sup 11}C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (k{sup r}{sub 2}) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BP{sub ND}). Compared with standard SRTM, either coupling of k{sup r}{sub 2} across regions or constraining k{sup r}{sub 2} to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BP{sub ND} between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining k{sup r}{sub 2} to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the

  18. Free volume study on the origin of dielectric constant in a fluorine-containing polyimide blend: poly(vinylidene fluoride-co-hexafluoro propylene)/poly(ether imide).

    Science.gov (United States)

    Ramani, R; Das, V; Singh, A; Ramachandran, R; Amarendra, G; Alam, S

    2014-10-23

    The dielectric constant of fluorinated polymides, their blends, and composites is known to decrease with the increase in free volume due to a decrease in the number of polarizable groups per unit volume. Herein, we report an interesting finding on the origin of dielectric constant in a polymer blend prepared using a fluorine-containing polymer and a polyimide probed in terms of its available free volume, which is distinct from the generally observed behavior in fluorinated polyimides. For this study, a blend of poly(vinylidene fluoride-co-hexafluoro propylene) and poly(ether imide) was chosen and the interaction between them was studied using FTIR, XRD, TGA, and SEM. The blend was investigated by positron annihilation lifetime spectroscopy (PALS), Doppler broadening (DB), and dielectric analysis (DEA). With the increase in the free volume content in the blend, surprisingly, the dielectric constant also increases and is attributed to additional space available for the polarizable groups to orient themselves to the applied electric field. The results obtained would pave the way for more effective design of polymeric electrical charge storage devices.

  19. Binding of piano-stool Ru(II) complexes to DNA; QM/MM study.

    Science.gov (United States)

    Futera, Zdeněk; Platts, James A; Burda, Jaroslav V

    2012-10-01

    Ru(II) "piano-stool" complexes belong to group of biologically active metallocomplexes with promising anticancer activity. In this study, we investigate the reaction mechanism of [(η(6)-benzene)Ru(II)(en)(H(2)O)](2+) (en = ethylenediamine) complex binding to DNA by hybrid QM/MM computational techniques. The reaction when the Ru(II) complex is coordinated on N7-guanine from major groove is explored. Two reaction pathways, direct binding to N7 position and two-step mechanism passing through O6 position, are considered. It was found that the reaction is exothermic and the direct binding process is preferred kinetically. In analogy to cisplatin, we also explored the possibility of intrastrand cross-link formation where the Ru(II) complex makes a bridge between two adjacent guanines. Two different pathways were found, leading to a final structure with released benzene ligand. This process is exothermic; however, one pathway is blocked by relatively high initial activation barrier. Geometries, energies, and electronic properties analyzed by atoms in molecules and natural population analysis methods are discussed. PMID:22707416

  20. Synthesis and microarray-assisted binding studies of core xylose and fucose containing N-glycans.

    Science.gov (United States)

    Brzezicka, Katarzyna; Echeverria, Begoña; Serna, Sonia; van Diepen, Angela; Hokke, Cornelis H; Reichardt, Niels-Christian

    2015-05-15

    The synthesis of a collection of 33 xylosylated and core-fucosylated N-glycans found only in nonmammalian organisms such as plants and parasitic helminths has been achieved by employing a highly convergent chemo-enzymatic approach. The influence of these core modifications on the interaction with plant lectins, with the human lectin DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Nonintegrin), and with serum antibodies from schistosome-infected individuals was studied. Core xylosylation markedly reduced or completely abolished binding to several mannose-binding plant lectins and to DC-SIGN, a C-type lectin receptor present on antigen presenting cells. Employing the synthetic collection of core-fucosylated and core-xylosylated N-glycans in the context of a larger glycan array including structures lacking these core modifications, we were able to dissect core xylose and core fucose specific antiglycan antibody responses in S. mansoni infection sera, and we observed clear and immunologically relevant differences between children and adult groups infected with this parasite. The work presented here suggests that, quite similar to bisecting N-acetylglucosamine, core xylose distorts the conformation of the unsubstituted glycan, with important implications for the immunogenicity and protein binding properties of complex N-glycans.

  1. Europium chelate-loaded liposomes: a tool for the study of binding and integrity of liposomes.

    Science.gov (United States)

    Orellana, A; Laukkanen, M L; Keinänen, K

    1996-10-01

    Using the biotin-streptavidin interaction as a model, we investigated the suitability of lanthanide chelates as encapsulated liposomal labels in liposome-based binding assays. Large unilamellar phospholipid:cholesterol liposomes containing europium-DTPA chelate and biotinylated phosphatidylethanolamine were prepared by detergent dialysis. The resulting Eu-liposomes ([symbol: see text] 120 nm) bound specifically to streptavidin in microtiter wells as measured by time-resolved fluorometric assay (TRF). The intensity of fluorescence released from the bound liposomes was dependent on the concentration of biotin in the liposome membrane, the concentration of europium entrapped in the liposomes, the incubation time and the amount of liposomes used in the assay. The sensitivity of the TRF assay allowed the detection of binding of attomole quantities of liposomes. The streptavidin-immobilised liposomes subjected to porcine pancreatic phospholipase A2 (EC 3.1.1.4) and detergents displayed a dose-dependent release of the encapsulated europium. Lanthanide-chelate-liposomes should prove useful for studies addressing binding and stability of liposomes. PMID:8865811

  2. Resonance Raman study on indoleamine 2,3-dioxygenase: Control of reactivity by substrate-binding

    International Nuclear Information System (INIS)

    Highlights: • Indoleamine 2,3-dioygenase has been studied by resonance Raman spectroscopy. • Trp-binding to the enzyme induces high frequency shift of the Fe–His stretching mode. • Increased imidazolate character of histidine promotes the O–O bond cleavage step. • A fine-tuning of the reactivity of the O–O bond cleavage reaction is identified. • The results are consistent with the sequential oxygen-atom-transfer mechanism. - Abstract: Resonance Raman spectra of ligand-bound complexes including the 4-phenylimidazole complex and of free and L-Trp-bound forms of indoleamine 2, 3-dioxygenase in the ferric state were examined. Effects on the vinyl and propionate substituent groups of the heme were detected in a ligand-dependent fashion. The effects of phenyl group of 4-phenylimidazole on the vinyl and propionate Raman bands were evident when compared with the case of imidazole ligand. Substrate binding to the ferrous protein caused an upshift of the iron–histidine stretching mode by 3 cm−1, indicating an increase in negativity of the imidazole ring, which favors the O–O bond cleavage. The substrate binding event is likely to be communicated from the heme distal side to the iron–histidine bond through heme substituent groups and the hydrogen-bond network which includes water molecules, as identified in an X-ray structure of a 4-phenylimidazole complex. The results provide evidence for fine-tuning of the reactivity of O–O bond cleavage by the oxygenated heme upon binding of L-Trp

  3. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

    Directory of Open Access Journals (Sweden)

    Keskin Ozlem

    2007-05-01

    Full Text Available Abstract Background How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.

  4. (/sup 3/H)nitrobenzylthioinosine binding as a probe for the study of adenosine uptake sites in brain

    Energy Technology Data Exchange (ETDEWEB)

    Marangos, P.J.; Patel, J.; Clark-Rosenberg, R.; Martino, A.M.

    1982-07-01

    The binding of the potent adenosine uptake inhibitor (/sup 3/H)nitrobenzylthioinosine ((/sup 3/H)NBI) to brain membrane fractions was investigated. Reversible, saturable, specific, high-affinity binding was demonstrated in both rat and human brain. The KD in both was 0.15 nM with Bmax values of 140-200 fmol/mg protein. Linear Scatchard plots were routinely obtained, indicating a homogeneous population of binding sites in brain. The highest density of binding sites was found in the caudate and hypothalamus in both species. The binding site was heat labile and trypsin sensitive. Binding was also decreased by incubation of the membranes in 0.05% Triton X-100 and by treatment with dithiothreitol and iodoacetamide. Of the numerous salt and metal ions tested, only copper and zinc had significant effects on (/sup 3/H)NBI binding. The inhibitory potencies of copper and zinc were IC50 . 160 microM and 6 mM, respectively. Subcellular distribution studies revealed a high percentage of the (/sup 3/H)NBI binding sites on synaptosomes, indicating that these sites were present in the synaptic region. A study of the tissue distribution of the (/sup 3/H)NBI sites revealed very high densities of binding in erythrocyte, lung, and testis, with much lower binding densities in brain, kidney, liver, muscle, and heart. The binding affinity in the former group was approximately 1.5 nM, whereas that in the latter group was 0.15 nM, suggesting two types of binding sites. The pharmacologic profile of (/sup 3/H)NBI binding was consistent with its function as the adenosine transport site, distinct from the adenosine receptor, since thiopurines were very potent inhibitors of binding whereas adenosine receptor ligands, such as cyclohexyladenosine and 2-chloroadenosine, were three to four orders of magnitude less potent. (/sup 3/H)NBI binding in brain should provide a useful probe for the study of adenosine transport in the brain.

  5. Clicked bis-PEG-peptide conjugates for studying calmodulin-Kv7.2 channel binding

    OpenAIRE

    Bonache de Marcos, María Ángeles; Alaimo, Alessandro; Malo, Covadonga; Millet, Oscar; Villarroel, Alvaro; González-Muñiz, Rosario

    2014-01-01

    The recombinant Kv7.2 calmodulin (CaM) binding site (Q2AB CaMBD) shows a high tendency to aggregate, thus complicating biochemical and structural studies. To facilitate these studies we have conceived bis-PEG-peptide CaMBD-mimetics linking helices A and B in single, easy to handle molecules. Short PEG chains were selected as spacers between the two peptide molecules, and a Cu(i)-catalyzed cycloaddition (CuAAC) protocol was used to assemble the final bis-PEG-peptide conjugate, by the convenien...

  6. Cobalt(III), nickel(II) and ruthenium(II) complexes of 1,10-phenanthroline family of ligands: DNA binding and photocleavage studies

    Indian Academy of Sciences (India)

    S Arounaguiri; D Easwaramoorthy; A Ashokkumar; Aparna Dattagupta; Bhaskar G Maiya

    2000-02-01

    DNA binding and photocleavage characteristics of a series of mixedligand complexes of the type [M(phen)2LL]n+ (where M = Co(III), Ni(II) or Ru(II), LL = 1,10-phenanthroline (phen), phenanthroline-dione (phen-dione) or dipyridophenazine (dppz) and = 3 or 2) have been investigated in detail. Various physico-chemical and biochemical techniques including UV/Visible, fluorescence and viscometric titration, thermal denaturation, and differential pulse voltammetry have been employed to probe the details of DNA binding by these complexes; intrinsic binding constants () have been estimated under a similar set of experimental conditions. Analysis of the results suggests that intercalative ability of the coordinated ligands varies as dppz > phen < phen-dione in this series of complexes. While the Co(II) and Ru(II) complexes investigated in this study effect photocleavage of the supercoiled pBR 322 DNA, the corresponding Ni(II) complexes are found to be inactive under similar experimental conditions. Results of detailed investigations carried out inquiring into the mechanistic aspects of DNA photocleavage by [Co(phen)2 (dppz)]3+ have also been reported.

  7. Comparative thermodynamic studies on substrate and product binding of O-Acetylserine Sulfhydrylase reveals two different ligand recognition modes†

    Directory of Open Access Journals (Sweden)

    Kumaran Sangaralingam

    2011-06-01

    Full Text Available Abstract Background The importance of understanding the detailed mechanism of cysteine biosynthesis in bacteria is underscored by the fact that cysteine is the only sulfur donor for all cellular components containing reduced sulfur. O-acetylserine sulfhydrylase (OASS catalyzes this crucial last step in the cysteine biosynthesis and has been recognized as an important gene for the survival and virulence of pathogenic bacteria. Structural and kinetic studies have contributed to the understanding of mechanistic aspects of OASS, but details of ligand recognition features of OASS are not available. In the absence of any detailed study on the energetics of ligand binding, we have studied the thermodynamics of OASS from Salmonella typhimurium (StOASS, Haemophilus influenzae (HiOASS, and Mycobacterium tuberculosis (MtOASS binding to their substrate O-acetylserine (OAS, substrate analogue (methionine, and product (cysteine. Results Ligand binding properties of three OASS enzymes are studied under defined solution conditions. Both substrate and product binding is an exothermic reaction, but their thermodynamic signatures are very different. Cysteine binding to OASS shows that both enthalpy and entropy contribute significantly to the binding free energy at all temperatures (10-30°C examined. The analyses of interaction between OASS with OAS (substrate or methionine (substrate analogue revealed a completely different mode of binding. Binding of both OAS and methionine to OASS is dominated by a favorable entropy change, with minor contribution from enthalpy change (ΔHSt-Met = -1.5 ± 0.1 kJ/mol; TΔSSt-Met = 8.2 kJ/mol at 20°C. Our salt dependent ligand binding studies indicate that methionine binding affinity is more sensitive to [NaCl] as compared to cysteine affinity. Conclusions We show that OASS from three different pathogenic bacteria bind substrate and product through two different mechanisms. Results indicate that predominantly entropy driven

  8. Application of the novel bioluminescent ligand-receptor binding assay to relaxin-RXFP1 system for interaction studies.

    Science.gov (United States)

    Wu, Qing-Ping; Zhang, Lei; Shao, Xiao-Xia; Wang, Jia-Hui; Gao, Yu; Xu, Zeng-Guang; Liu, Ya-Li; Guo, Zhan-Yun

    2016-04-01

    Relaxin is a prototype of the relaxin family peptide hormones and plays important biological functions by binding and activating the G protein-coupled receptor RXFP1. To study their interactions, in the present work, we applied the newly developed bioluminescent ligand-receptor binding assay to the relaxin-RXFP1 system. First, a fully active easily labeled relaxin, in which three Lys residues of human relaxin-2 were replaced by Arg, was prepared through overexpression of a single-chain precursor in Pichia pastoris and in vitro enzymatic maturation. Thereafter, the B-chain N-terminus of the easily labeled relaxin was chemically cross-linked with a C-terminal cysteine residue of an engineered NanoLuc through a disulfide linkage. Receptor-binding assays demonstrated that the NanoLuc-conjugated relaxin retained high binding affinity with the receptor RXFP1 (K d = 1.11 ± 0.08 nM, n = 3) and was able to sensitively monitor binding of a variety of ligands with RXFP1. Using the novel bioluminescent binding assay, we demonstrated that three highly conserved B-chain Arg residues of relaxin-3 had distinct contributions to binding of the receptor RXFP1. In summary, our present work provides a novel bioluminescent ligand-receptor binding assay for the relaxin-RXFP1 system to facilitate their interaction studies, such as characterization of relaxin analogues or screening novel agonists or antagonists of RXFP1. PMID:26767372

  9. The screening and functional study of proteins binding with the BmNPV polyhedrin promoter

    Directory of Open Access Journals (Sweden)

    Yu Wei

    2012-05-01

    Full Text Available Abstract Background The polyhedrin gene promoter has an essential role in regulating foreign gene expression in baculovirus expression vector systems (BEVS; however, the high-level transcription mechanism is still unknown. One-hybrid screening in yeast is a powerful way of identifying rapidly heterologous transcription factors that can interact with the polyhedrin promoter DNA sequence. In the current study, total RNA was extracted from the fat bodies of fifth-instar silkworm larvae that had been infected with Bombyx mori nuclear polyhedrosis virus (BmNPV for 5 days; complementary DNA (cDNA was then generated using reverse-transcription (RT-PCR to construct a silkworm gene expression library. Key polyhedrin promoter bait sequences were synthesized to generate a bait yeast strain, which was used to screen the one-hybrid cDNA library. Results In total, 12 positive yeast colonies were obtained from the SD/-Leu/AbA plates; sequencing analysis showed that they belong to two different protein cDNA colonies. Positive colonies underwent bioinformatics analysis, which revealed one colony to be ribosomal proteins [B. mori ribosomal protein SA (BmRPSA] and the other to be NPV DNA-binding proteins (DBP. To further verify the regulatory function of these two protein groups, transient expression vectors (pSK-IE-dbp and pSK-IE-BmRPSA were constructed. The recombinant plasmids were then transfected into cultured B. mori N (BmN cells, which had been infected with a recombinant bacmid containing the gene encoding luciferase (luc. The results showed that overexpression of either dbp or BmRPSA upregulated the polh promoter-driven transcription of luc in BmN cells. In addition, dbp or BmRPSA RNA interference (RNAi resulted in the downregulation of luciferase reporter expression in BmN cells, demonstrating that DBP and BmRPSA are important for luc transcription. EMSA results further confirmed that DBP could directly bind to the conserved single-stranded polh

  10. Study in static mode of a photovoltaic cell bi facial to crystalline silicon under electric polarization and constant multispectral illumination

    International Nuclear Information System (INIS)

    The theoretical study in static mode of a photovoltaic cell bi facial to silicon under electric polarization and multispectral illumination is presented. Through this study, various expressions of the parameters of recombination have been established as well for an illumination by the face before an illumination by the back face. Curves of variation of the densities of carriers, densities of photocurrent, speeds of recombinations and photo tensions have been traced for the two modes of illumination

  11. Phenanthrene binding by humic acid–protein complexes as studied by passive dosing technique

    International Nuclear Information System (INIS)

    This work investigated the binding behavior of phenanthrene by humic acids (HA-2 and HA-5), proteins (bovine serum albumin (BSA)), lysozyme and pepsin), and their complexes using a passive dosing technique. All sorption isotherms were fitted well with Freundlich model and the binding capability followed an order of HA-5 > HA-2 > BSA > pepsin > lysozyme. In NaCl solution, phenanthrene binding to HA-BSA complexes was much higher than the sum of binding to individual HA and BSA, while there was no enhancement for HA-pepsin. Positively charged lysozyme slightly lowered phenanthrene binding on both HAs due to strong aggregation of HA-lysozyme complexes, leading to reduction in the number of binding sites. The binding enhancement by HA-BSA was observed under all tested ion species and ionic strengths. This enhancement can be explained by unfolding of protein, reduction of aggregate size and formation of HA-BSA complexes with favorable conformations for binding phenanthrene. Highlights: • Phenanthrene binding capability followed an order: HA-5>HA-2>BSA>pepsin>lysozyme. • Phenanthrene binding to HA-BSA was enhanced relative to individual HA and BSA. • Binding enhancement to HA-BSA was observed under all tested solution conditions. • The enhancement is related to BSA unfolding, size reduction and HA-BSA complexation. -- Phenanthrene binding to HA-BSA complexes is much higher than the sum to individual HA and BSA while there was no binding enhancement to HA-pepsin or HA-lysozyme

  12. Structural Studies of the Alzheimer's Amyloid Precursor Protein Copper-Binding Domain Reveal How It Binds Copper Ions

    Energy Technology Data Exchange (ETDEWEB)

    Kong, G.K.-W.; Adams, J.J.; Harris, H.H.; Boas, J.F.; Curtain, C.C.; Galatis, D.; Master, C.L.; Barnham, K.J.; McKinstry, W.J.; Cappai, R.; Parker, M.W.; /Sydney U.

    2007-07-09

    Alzheimer's disease (AD) is the major cause of dementia. Amyloid {beta} peptide (A {beta}), generated by proteolytic cleavage of the amyloid precursor protein (APP), is central to AD pathogenesis. APP can function as a metalloprotein and modulate copper (Cu) transport, presumably via its extracellular Cu-binding domain (CuBD). Cu binding to the CuBD reduces A{beta} levels, suggesting that a Cu mimetic may have therapeutic potential. We describe here the atomic structures of apo CuBD from three crystal forms and found they have identical Cu-binding sites despite the different crystal lattices. The structure of Cu[2+]-bound CuBD reveals that the metal ligands are His147, His151, Tyrl68 and two water molecules, which are arranged in a square pyramidal geometry. The site resembles a Type 2 non-blue Cu center and is supported by electron paramagnetic resonance and extended X-ray absorption fine structure studies. A previous study suggested that Met170 might be a ligand but we suggest that this residue plays a critical role as an electron donor in CuBDs ability to reduce Cu ions. The structure of Cu[+]-bound CuBD is almost identical to the Cu[2+]-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavorable for Cu[+], thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins.

  13. radiochemical studies on the binding of humic materials with toxic elements and compounds

    International Nuclear Information System (INIS)

    industrial nations produce several billion tons of waste every year . this figure will increase as both population and industrial growth increase. there are many kinds of waste, including refinery waste, which consists of hydrocarbons, heavy metals, metal catalysts and caustic solution; dredge spoils, some of which are highly polluted and cntains substances potentially hazardous to human health or the marine ecosystem; chemical waste such as insecticides, pesticides, other complex chemicals and heavy metals; radioactive waste and agricultural waste, anmd most of them are extremely hazardous and harmful to the marine ecosystem and its inhabitants.the aim of this thesis is to study the binding of humic materials with toxic elements and compounds

  14. A Study on Solubilization of Poorly Soluble Drugs by Cyclodextrins and Micelles: Complexation and Binding Characteristics of Sulfamethoxazole and Trimethoprim

    Directory of Open Access Journals (Sweden)

    Sinem Göktürk

    2012-01-01

    > α-CD. With taking into consideration of solubilization capacity of SDS micelles, it has been found that the solubility enhancement of TMP is much higher than that of SMX in the presence of SDS micelles. The binding constants of SMX and TMP obtained from the Benesi-Hildebrand equation are also confirmed by the estimated surface properties of SDS, employing the surface tension measurements. In order to elucidate the solubilization characteristics the surface tension measurements were also performed for nonionic surfactant Triton X-100. Polarity of the microenvironment and probable location of SMX and TMP were also discussed in the presence of various organic solvents.

  15. Binding hot-spots in an antibody-ssDNA interface: a molecular dynamics study.

    Science.gov (United States)

    Wang, Yeng-Tseng; Lee, Wen-Jay

    2012-10-30

    Simulating antigen-antibody interactions is essential for elucidating antigen-antibody mechanics. Proteins interactions are vital for elucidating antibody-ssDNA associations in immunology. Therefore, this study investigated the dissociation of the human systemic lupus erythematosus antibody-ssDNA complex structure. Dissociation (i.e. the distance between the center of mass of the ssDNA and the antibody) is also studied using the potential of mean force calculations based on molecular dynamics and the explicit water model. The MM-PBSA method is also used to prove our dissociation simulations. With 605 nanosecond molecular dynamics simulations, the results indicate that the 8 residues (i.e. Gly44 (HCDR2), Asn54 (HCDR2), Arg98 (HCDR3), Tyr100 (HCDR3), Asp101 (HCDR3), Tyr32 (LCDR1), Tyr49 (LCDR2) and Asn50 (LCDR2)), and the five inter-protein molecular hydrogen bonds may profoundly impact the antibody-ssDNA interaction, a finding which may be useful for protein engineering of this antibody-ssDNA structure. Experimental binding affinity of this antibody-ssDNA complex equals 7.00 kcal mol(-1). Our dissociation binding affinity is 7.96 ± 0.33 kcal mol(-1) and MM-PBSA binding affinity is 9.12 ± 1.65 kcal mol(-1), which is close to the experimental value. Additionally, the 8 residues Gly44 (HCDR2), Asn54 (HCDR2), Arg98 (HCDR3), Tyr100 (HCDR3), Asp101 (HCDR3), Tyr32 (LCDR1), Tyr49 (LCDR2) and Asn50 (LCDR2) may play a more significant role in developing bioactive antibody analogues. PMID:23079742

  16. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Univ. of California, Berkeley, CA (United States)

    2015-01-21

    The uranyl cation (UO₂²⁺) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  17. Mineralocorticoid specificity of renal type I receptors: in vivo binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Sheppard, K.; Funder, J.W.

    1987-02-01

    The authors have injected rats with (TH)aldosterone or (TH) corticosterone, plus 100-fold excess of the highly specific glucocorticoid RU 28362, with or without excess unlabeled aldosterone or corticosterone and compared type I receptor occupancy in kidney and hippocampus. Thirty minutes after subcutaneous injection (TH)aldosterone was well retained in renal papilla-inner medulla, renal cortex-outer medulla, and hippocampus; in contrast, (TH)corticosterone was well retained only in hippocampus. Competition studies for (TH)aldosterone binding sites showed corticosterone to be a poor competitor in the kidney compared with hippocampus. Time-course studies, with rats killed 10-180 min after tracer administration, showed very low uptake/retention of (TH)corticosterone by kidney; in hippocampus (TH)corticosterone retention was similar to that of (TH)aldosterone in kidney, and retention of (TH)aldosterone by hippocampus was much more prolonged than of either tracer in any other tissue. Studies in 10-day-old rats, with very low levels of corticosteroid binding globulin (CBG), showed a high degree of aldosterone selectivity in both zones of the kidney, whereas 9TH)aldosterone and (TH)corticosterone were equivalently bound in hippocampus. They interpret these data as evidenced for a mechanism unrelated to extravascular CBG conferring mineralocorticoid specificity on renal type I receptors and propose two models derived from their findings consistent with such differential selectivity.

  18. Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch

    Directory of Open Access Journals (Sweden)

    Herman O. Sintim

    2012-11-01

    Full Text Available C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues. We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering. Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.

  19. Endo-S-c-di-GMP analogues-polymorphism and binding studies with class I riboswitch.

    Science.gov (United States)

    Zhou, Jie; Sayre, David A; Wang, Jingxin; Pahadi, Nirmal; Sintim, Herman O

    2012-01-01

    C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch. PMID:23143150

  20. Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO.

    Science.gov (United States)

    Raghavendra, S; Aditya Rao, S J; Kumar, Vadlapudi; Ramesh, C K

    2015-12-01

    Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the protein Polyphenoloxidase (PPO). The protein was isolated from Mucuna pruriens and confirmed as tyrosinases involved in L-DOPA production. The activity was measured using different inhibitors at different concentrations taking catechol as substrate. A high-throughput binding study was conducted to compare the binding orientations of individual ligands and multiple ligands employing Autodock 4.2. The results of single substrate docking showed a better binding of urea with the binding energy of -3.48 kJ mol(-1) and inter molecular energy of -3.48 kJ mol(-1) while the results of MLSD revealed that ascorbic acid combined with the substrate showed better inhibition with a decreased binding energy of -2.37 kJ mol(-1). PMID:26414950

  1. Structural studies of nucleoside analog and feedback inhibitor binding to Drosophila melanogaster multisubstrate deoxyribonucleoside kinase

    DEFF Research Database (Denmark)

    Mikkelsen, Niels Egil; Munch-Petersen, Birgitte; Eklund, Hans

    2008-01-01

    relate them to the binding of substrate and feedback inhibitors. dCTP and dGTP binds similarly as the feedback inhibitor dTTP with the base in the substrate site. All investigated nucleoside analogs bind similarly as the pyrimidine substrates with many interactions in common. In contrast, the base of d...

  2. An Experimental Study on the Macroscopic Spray Characteristics of Biodiesel and Diesel in a Constant Volume Chamber

    OpenAIRE

    Xie, Hongzhan; Song, Lanbo; Xie, Yizhi; Pi, Dong; Shao, Chunyu; Lin, Qizhao

    2015-01-01

    The objective of this study was to investigate the macroscopic spray characteristics of different 0%–100% blends of biodiesel derived from drainage oil and diesel (BD0, BD20, BD50, BD80, BD100), such as spray tip penetration, average tip velocity at penetration, spray angle, average spray angle, spray evolution process, spray area and spray volume under different injection pressures (60, 70, 80, 90, 100 MPa) and ambient pressures (0.1, 0.3, 0.5, 0.7, 0.9 MPa) using a common rail system equipp...

  3. An Experimental Study on the Macroscopic Spray Characteristics of Biodiesel and Diesel in a Constant Volume Chamber

    OpenAIRE

    Hongzhan Xie; Lanbo Song; Yizhi Xie; Dong Pi; Chunyu Shao; Qizhao Lin

    2015-01-01

    The objective of this study was to investigate the macroscopic spray characteristics of different 0%–100% blends of biodiesel derived from drainage oil and diesel (BD0, BD20, BD50, BD80, BD100), such as spray tip penetration, average tip velocity at penetration, spray angle, average spray angle, spray evolution process, spray area and spray volume under different injection pressures (60, 70, 80, 90, 100 MPa) and ambient pressures (0.1, 0.3, 0.5, 0.7, 0.9 MPa) using a common rail system equi...

  4. Variation of Fundamental Constants

    Science.gov (United States)

    Flambaum, V. V.

    2006-11-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. The spatial variation can explain a fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence. We present a review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra. Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance.

  5. Binding Studies of Natural Product Berberine with DNA G-Quadruplex

    Directory of Open Access Journals (Sweden)

    Nagendra K. Sharma

    2011-01-01

    Full Text Available Problem statement: The ends of chromosome had highly repetitive short G and C-rich sequences of DNA. These sequences were known to form stable tetraplex type of secondary structures which help to maintain gene integratity after cell divison. Approach: Any reagent which controls the random cell division would be useful to design anticancer drugs. Therefore a many natural and synthesized molecules which stabilized tetraplex structures are targeted as anticancer drug entities. Results: Among them, Berberine hydrochloride natural product and its analogues are well studies as G-quadruplex stabilizing agent. In this report, DNA sequence 5’-G3-C5-G3-3’ has been designed which has probability to form i-motif and G-qua druplex types of secondary structures. Herein we studied the interaction between this DNA strands and Berberine hydrochloride by 1H-NMR techniques and UV in two different PH (4.7 and 7.4 conditions. Conclusion/Recommendations: Our preliminary results showed that Berberine bind with this DNA strand in both pH conditions which is further supported by UV melting experiments. In future this sequence can be used as probe to screen out tetraplex binding natural products which help to generate new anticancer drugs.

  6. Structural, vibrational, NMR, quantum chemical, DNA binding and protein docking studies of two flexible imine oximes

    Indian Academy of Sciences (India)

    YUNUS KAYA

    2016-09-01

    Two flexible imine oxime molecules, namely, 3-(pyridin-2-ylmethylimino)-butan-2-one oxime (HL¹) and 3-(pyridin-2-ylmethylimino)-pentan-2-one oxime (HL²) have been synthesized and characterized by elemental analysis, IR and NMR techniques. The conformational behavior was investigated using the density functional theory (DFT) with the B3LYP method combined with the 6-311++G(d,p) basis set. As a result of the conformational studies, three stable molecules and the most stable conformer were determined for the both imine oximes. The spectroscopic properties such as vibrational and NMR were calculated for the most stable conformer of the HL¹ and HL². The calculation results were applied to simulate infrared spectra of the title compounds, which show good agreement with observed spectra. In addition, the stable three molecules of the both imine oximes have been used to carry out DNA binding and protein docking studies with DNA and protein structures (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligands inside the DNA and protein cavity.

  7. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhongshan [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom); College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Xiang, Quanju [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Department of Microbiology, College of Resource and Environment Science, Sichuan Agriculture University, Yaan 625000 (China); Zhu, Xiaofeng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Dong, Haohao [Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); He, Chuan [School of Electronics and Information, Wuhan Technical College of Communications, No. 6 Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065 (China); Wang, Haiyan; Zhang, Yizheng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Wang, Wenjian, E-mail: Wenjian166@gmail.com [Laboratory of Department of Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080 (China); Dong, Changjiang, E-mail: C.Dong@uea.ac.uk [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom)

    2014-09-26

    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.

  8. Elastic constants for 8-OCB

    Science.gov (United States)

    Czechowski, Grzegorz; Zywucki, B.; Jadzyn, Jan

    1993-10-01

    The Frederiks transitions for the n-octyloxycyanobiphenyl (8-OCB) placed in the external magnetic and electric field as a function of the temperature have been studied. On the basis of threshold values Bc and Uc, the elastic constants for splay, bend and twist modes are determined. The magnetic anisotropy of 8-OCB as a function of temperature has been determined. The K11 and K33 elastic constants show the pretransitional nematic- smectic A effect. The values of critical exponents obtained from the temperature dependence of K11 and K33 in the vicinity of N-SA phase transition are discussed.

  9. Radiographic constant exposure technique

    DEFF Research Database (Denmark)

    Domanus, Joseph Czeslaw

    1985-01-01

    The constant exposure technique has been applied to assess various industrial radiographic systems. Different X-ray films and radiographic papers of two producers were compared. Special attention was given to fast film and paper used with fluorometallic screens. Radiographic image quality...... was tested by the use of ISO wire IQI's and ASTM penetrameters used on Al and Fe test plates. Relative speed and reduction of kilovoltage obtained with the constant exposure technique were calculated. The advantages of fast radiographic systems are pointed out...

  10. Algorithm for structure constants

    CERN Document Server

    Paiva, F M

    2011-01-01

    In a $n$-dimensional Lie algebra, random numerical values are assigned by computer to $n(n-1)$ especially selected structure constants. An algorithm is then created, which calculates without ambiguity the remaining constants, obeying the Jacobi conditions. Differently from others, this algorithm is suitable even for poor personal computer. ------------- En $n$-dimensia algebro de Lie, hazardaj numeraj valoroj estas asignitaj per komputilo al $n(n-1)$ speciale elektitaj konstantoj de strukturo. Tiam algoritmo estas kreita, kalkulante senambigue la ceterajn konstantojn, obeante kondicxojn de Jacobi. Malsimile al aliaj algoritmoj, tiu cxi tauxgas ecx por malpotenca komputilo.

  11. The Hubble constant

    Science.gov (United States)

    Huchra, John P.

    1992-01-01

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy radial velocities and distances. Although there has been considerable progress in the development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution.

  12. Multi-wavelength spectrophotometric determination of the protolytic constants of tetracycline hydrochloride in some nonaqueous-water mixed solvents: A solvatochromism study

    Science.gov (United States)

    Ghasemi, Jahan B.; Jalalvand, Ali R.

    2011-01-01

    Annihilation of the contribution of one chemical component from the original data matrix is a general method in rank annihilation factor analysis (RAFA). However, RAFA is not applicable for studying the protonation equilibria of multiprotic acids but in this study two-rank annihilation factor analysis (TRAFA) was used as an efficient chemometrics algorithm for determination of the protolytic constants (p Ka) of tetracycline hydrochloride (TCHC) in some nonaqueous-water mixed solvents such as acetonitrile (AN)-water and methanol (MeOH)-water from the spectral pH-absorbance data. The spectral data was obtained from spectrophotometric acid-base titrations of different solutions of TCHC at (25.0 ± 0.10) °C and an ionic strength of 0.10 M. In TRAFA algorithm the p Ka values were obtained with relationship between residual standard deviation (R.S.D.) and hypothetical p Ka values. In the case of TCHC, the spectra were divided in two consecutive subdivisions according to their pH range having two p Ka and TRAFA was run twice. The validity of the obtained p Ka values was checked with well-known chemometrics algorithms such as DATAN, EQUSPEC, SPECFIT/32 and SQUAD. The effects of changing solvent composition on the protolytic constants were explained by linear solvation energy relationships (LSER) utilizing solvatochromic parameters.

  13. Origin of giant dielectric constant and magnetodielectric study in Ba(Fe{sub 0.5}Nb{sub 0.5})O{sub 3} nanoceramics

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Piyush Kumar [Department of Physics, Indian Institute of Technology Roorkee, Roorkee 247667 (India); Yadav, K.L., E-mail: klyadav35@yahoo.com [Department of Physics, Indian Institute of Technology Roorkee, Roorkee 247667 (India); Singh, Harishchandra [Indus Synchrotrons Utilization Division, Raja Ramanna Center for Advanced Technology, Indore 452013 (India); Yadav, A.K. [Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai 400088 (India)

    2014-04-05

    Highlights: • High dielectric constant (∼33,000) with low loss (∼0.45) was found at room temperature. • Cole–Cole plot analysis confirmed the formation of barrier layers on grain–grain boundary interfaces. • XANES study confirms the mixed valence state of Fe ion. • Reporting first time about presence of magnetocapacitance (∼3.4%) in the system. -- Abstract: Lead free Ba(Fe{sub 0.5}Nb{sub 0.5})O{sub 3} (BFN) ceramics were synthesized by sol–gel method. X-ray diffraction pattern of the samples at room temperature shows a monoclinic structure. The influence of sintering temperature on microstructure and dielectric properties of BFN ceramics were analysed. Microstructure analysis shows well-grown and dense microstructure in 1200 °C sintered sample exhibiting enhanced dielectric and magnetodielectric properties. We report a very high dielectric constant (∼33,000) with low dielectric loss (∼0.45) at room temperature for 1200 °C sintered sample at 100 Hz frequency. Cole–Cole plot shows that the grain boundary effect (barrier layer formation) is responsible for such a high value of dielectric constant. The sample was also analyzed by Fe K-edge X-ray absorption near-edge structure spectroscopy to obtain the Fe oxidation state. This analysis confirms that Fe ions in BFN ceramics are in mixed valance state (Fe{sup 2+}/Fe{sup 3+}). Another interesting feature of BFN ceramics is the appearance of room temperature high magnetodielectric response (3.8%) at 7 kOe magnetic field and 100 Hz frequency.

  14. Study of Binding Interaction between Pif80 Protein Fragment and Aragonite

    Science.gov (United States)

    Du, Yuan-Peng; Chang, Hsun-Hui; Yang, Sheng-Yu; Huang, Shing-Jong; Tsai, Yu-Ju; Huang, Joseph Jen-Tse; Chan, Jerry Chun Chung

    2016-08-01

    Pif is a crucial protein for the formation of the nacreous layer in Pinctada fucata. Three non-acidic peptide fragments of the aragonite-binding domain (Pif80) are selected, which contain multiple copies of the repeat sequence DDRK, to study the interaction between non-acidic peptides and aragonite. The polypeptides DDRKDDRKGGK (Pif80-11) and DDRKDDRKGGKDDRKDDRKGGK (Pif80-22) have similar binding affinity to aragonite. Solid-state NMR data indicate that the backbones of Pif80-11 and Pif80-22 peptides bound on aragonite adopt a random-coil conformation. Pif80-11 is a lot more effective than Pif80-22 in promoting the nucleation of aragonite on the substrate of β-chitin. Our results suggest that the structural arrangement at a protein-mineral interface depends on the surface structure of the mineral substrate and the protein sequence. The side chains of the basic residues, which function as anchors to the aragonite surface, have uniform structures. The role of basic residues as anchors in protein-mineral interaction may play an important role in biomineralization.

  15. Study of Binding Interaction between Pif80 Protein Fragment and Aragonite.

    Science.gov (United States)

    Du, Yuan-Peng; Chang, Hsun-Hui; Yang, Sheng-Yu; Huang, Shing-Jong; Tsai, Yu-Ju; Huang, Joseph Jen-Tse; Chan, Jerry Chun Chung

    2016-01-01

    Pif is a crucial protein for the formation of the nacreous layer in Pinctada fucata. Three non-acidic peptide fragments of the aragonite-binding domain (Pif80) are selected, which contain multiple copies of the repeat sequence DDRK, to study the interaction between non-acidic peptides and aragonite. The polypeptides DDRKDDRKGGK (Pif80-11) and DDRKDDRKGGKDDRKDDRKGGK (Pif80-22) have similar binding affinity to aragonite. Solid-state NMR data indicate that the backbones of Pif80-11 and Pif80-22 peptides bound on aragonite adopt a random-coil conformation. Pif80-11 is a lot more effective than Pif80-22 in promoting the nucleation of aragonite on the substrate of β-chitin. Our results suggest that the structural arrangement at a protein-mineral interface depends on the surface structure of the mineral substrate and the protein sequence. The side chains of the basic residues, which function as anchors to the aragonite surface, have uniform structures. The role of basic residues as anchors in protein-mineral interaction may play an important role in biomineralization. PMID:27484975

  16. In vitro RNA-binding assay for studying trans-factors for RNA editing in chloroplasts.

    Science.gov (United States)

    Shikanai, Toshiharu; Okuda, Kenji

    2011-01-01

    In plant organelles, specific C residues are modified to U by RNA editing. Short RNA sequences surrounding the target site (i.e., cis-elements) are recognized by trans-factors, which were recently shown to be pentatricopeptide repeat (PPR) proteins. PPR proteins consist of tandem arrays of a highly degenerate unit of 35 (pentatrico) amino acids, and PPR motifs are believed to recognize specific RNA sequences. In Arabidopsis thaliana, more than 450 sites are edited in mitochondria and plastids, and a similar number of PPR proteins are encoded in the nuclear genome. To study how the tandem array of a PPR motif facilitates the recognition of RNA sequences, an efficient biochemical strategy is an in vitro binding assay of recombinant PPR proteins with target RNA. This analysis is especially powerful with a combination of in vivo analyses based on the phenotypes of mutants and transgenic plants. In this chapter, we describe methods for the expression of recombinant PPR proteins in Escherichia coli, preparation of probe RNAs, and RNA gel shift assays. These methods can also be utilized for other RNA-binding proteins.

  17. DNA binding studies of 3, 5, 6-trichloro-2-pyridinol pesticide metabolite.

    Science.gov (United States)

    Kashanian, Soheila; Shariati, Zohreh; Roshanfekr, Hamideh; Ghobadi, Sirous

    2012-07-01

    3, 5, 6-Trichloro-2-pyridinol (TCP) is a stable metabolite of two major pesticides, Chlopyrifos insecticide and Triclopyr herbicide, which are widely used in the world. The potential health hazard associated with TCP is identified due to its high affinity to the DNA molecule. Therefore, in this study, the interaction of native calf thymus DNA with TCP has been investigated using spectrophotometric, circular dichroism (CD), spectrofluorometric, viscometric and voltametric techniques. It was found that TCP molecules could interact with DNA via a groove-binding mode, as evidenced by hyperchromism, with no red shift in the UV absorption band of TCP, no changes in K(b) values in the presence of salt, no significant changes in the specific viscosity and CD spectra of DNA, and a decrease in peak currents with no shift in the voltamogram. In addition, TCP is able to release Hoechst 33258, a strong groove binder, in the DNA solutions. The results are indicative of the groove-binding mode of TCP to DNA. PMID:22519761

  18. Interaction of Sodium Hyaluronate with a Biocompatible Cationic Surfactant from Lysine: A Binding Study.

    Science.gov (United States)

    Bračič, Matej; Hansson, Per; Pérez, Lourdes; Zemljič, Lidija F; Kogej, Ksenija

    2015-11-10

    Mixtures of natural and biodegradable surfactants and ionic polysaccharides have attracted considerable research interest in recent years because they prosper as antimicrobial materials for medical applications. In the present work, interactions between the lysine-derived biocompatible cationic surfactant N(ε)-myristoyl-lysine methyl ester, abbreviated as MKM, and the sodium salt of hyaluronic acid (NaHA) are investigated in aqueous media by potentiometric titrations using the surfactant-sensitive electrode and pyrene-based fluorescence spectroscopy. The critical micelle concentration in pure surfactant solutions and the critical association concentration in the presence of NaHA are determined based on their dependence on the added electrolyte (NaCl) concentration. The equilibrium between the protonated (charged) and deprotonated (neutral) forms of MKM is proposed to explain the anomalous binding isotherms observed in the presence of the polyelectrolyte. The explanation is supported by theoretical model calculations of the mixed-micelle equilibrium and the competitive binding of the two MKM forms to the surface of the electrode membrane. It is suggested that the presence of even small amounts of the deprotonated form can strongly influence the measured electrode response. Such ionic-nonionic surfactant mixtures are a special case of mixed surfactant systems where the amount of the nonionic component cannot be varied independently as was the case for some of the earlier studies.

  19. Dehydrogenation Kinetics and Modeling Studies of MgH2 Enhanced by Transition Metal Oxide Catalysts Using Constant Pressure Thermodynamic Driving Forces

    Directory of Open Access Journals (Sweden)

    Saidi Temitope Sabitu

    2012-06-01

    Full Text Available The influence of transition metal oxide catalysts (ZrO2, CeO2, Fe3O4 and Nb2O5 on the hydrogen desorption kinetics of MgH2 was investigated using constant pressure thermodynamic driving forces in which the ratio of the equilibrium plateau pressure (pm to the opposing plateau (pop was the same in all the reactions studied. The results showed Nb2O5 to be vastly superior to other catalysts for improving the thermodynamics and kinetics of MgH2. The modeling studies showed reaction at the phase boundary to be likely process controlling the reaction rates of all the systems studied.

  20. Tight-binding study of hydrogen adsorption on palladium decorated graphene and carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Corral, I.; German, E.; Brizuela, G.P.; Juan, A. [Departamento de Fisica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina); Volpe, M.A. [Planta Piloto de Ingenieria Quimica, Universidad Nacional del Sur-CONICET, camino de La Carrindanga Km. 7, 8000 Bahia Blanca (Argentina)

    2010-03-15

    In this work we report a theoretical study on the atomic and molecular hydrogen adsorption onto Pd-decorated graphene monolayer and carbon nanotubes by a semi-empirical tight-binding method. We first investigated the preferential adsorption geometry, considering different adsorption sites on the carbon surface, and then studied the evolution of the chemical bonding by evaluation of the overlap population (OP) and crystal orbital overlap population (COOP). Our results show that strong C-Pd and H-Pd bonds are formed during atomic hydrogen adsorption, with an important role in the bonding of C 2p{sub z} and Pd 5s, 5p{sub z} and 4d{sub z}{sup 2} orbitals. The hydrogen storage mechanism in Pd-doped carbon-based materials seems to involve the dissociation of H{sub 2} molecule on the decoration points and the bonding between resultant atomic hydrogen and the carbon surface. (author)

  1. Estimation of association constants between oral malodor components and various native and derivatized cyclodextrins

    Energy Technology Data Exchange (ETDEWEB)

    Lantz, Andrew W. [Department of Chemistry, Iowa State University, Ames, IA 50011-3111 (United States); Rodriguez, Michael A. [Department of Chemistry, Iowa State University, Ames, IA 50011-3111 (United States); Wetterer, Sean M. [GlaxoSmithKline, Parsippany, NJ 07054 (United States); Armstrong, Daniel W. [Department of Chemistry, Iowa State University, Ames, IA 50011-3111 (United States)]. E-mail: sec4dwa@iastate.edu

    2006-01-31

    The association constants of 33 oral malodorous compounds and odor precursors (9 organic acids, 7 amine-containing bases, 11 organic neutral and aromatic compounds, and 6 amino acids) with native and derivatized cyclodextrins were measured using one or more of a variety of techniques including affinity capillary electrophoresis, nuclear magnetic resonance titrations, and head-space gas chromatography. With the exception of formic acid and urea, which had binding constants that were too small to measure, all analytes showed significant binding to at least one of the cyclodextrins studied. In most cases, the native cyclodextrins exhibited the most stable complexes with these analytes. However, with cationic analytes under acidic conditions, the negatively charged sulfated and carboxymethyl cyclodextrins had higher association constants. The six amino acid precursor molecules only bound significantly with the sulfated cyclodextrins. In addition, several analyte-cyclodextrin combinations were observed to form insoluble complexes, indicating that these cyclodextrins are particularly effective at extracting these compounds from aqueous solution.

  2. Compassion is a constant.

    Science.gov (United States)

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands.

  3. Variation of fundamental constants: theory

    Science.gov (United States)

    Flambaum, Victor

    2008-05-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. There are some hints for the variation of different fundamental constants in quasar absorption spectra and Big Bang nucleosynthesis data. A large number of publications (including atomic clocks) report limits on the variations. We want to study the variation of the main dimensionless parameters of the Standard Model: 1. Fine structure constant alpha (combination of speed of light, electron charge and Plank constant). 2. Ratio of the strong interaction scale (LambdaQCD) to a fundamental mass like electron mass or quark mass which are proportional to Higgs vacuum expectation value. The proton mass is propotional to LambdaQCD, therefore, the proton-to-electron mass ratio comes into this second category. We performed necessary atomic, nuclear and QCD calculations needed to study variation of the fundamental constants using the Big Bang Nucleosynthsis, quasar spectra, Oklo natural nuclear reactor and atomic clock data. The relative effects of the variation may be enhanced in transitions between narrow close levels in atoms, molecules and nuclei. If one will study an enhanced effect, the relative value of systematic effects (which are not enhanced) may be much smaller. Note also that the absolute magnitude of the variation effects in nuclei (e.g. in very narrow 7 eV transition in 229Th) may be 5 orders of magnitude larger than in atoms. A different possibility of enhancement comes from the inversion transitions in molecules where splitting between the levels is due to the quantum tunneling amplitude which has strong, exponential dependence on the electron to proton mass ratio. Our study of NH3 quasar spectra has already given the best limit on the variation of electron to proton mass ratio.

  4. In vitro study of the binding between chlorpyrfos and sex hormones using headspace solid-phase microextraction combined with high-performance liquid chromatography: A new aspect of pesticides and breast cancer risk.

    Science.gov (United States)

    Farhadi, K; Tahmasebi, R; Biparva, P; Maleki, R

    2015-08-01

    Endocrine-disrupting chemicals are compounds that alter the normal functioning of the endocrine system. Organophosphorus insecticides, as chlorpyrifos (CPS), receive an increasing consideration as potential endocrine disrupters. Physiological estrogens, including estrone (E1), 17β-estradiol (E2), and diethylstilbestrol (DES) fluctuate with life stage, suggesting specific roles for them in biological and disease processes. There has been great interest in whether certain organophosphorus pesticides can affect the risk of breast cancer. An understanding of the interaction processes is the key to describe the fate of CPS in biological media. The objectives of this study were to evaluate total, bound, and freely dissolved amount of CPS in the presence of three estrogenic sex hormones (ESHs). In vitro experiments were conducted utilizing a headspace solid phase microextraction (HS-SPME) combined with high-performance liquid chromatography (HPLC) method. The obtained Scatchard plot based on the proposed SPME-HPLC method was employed to determine CPS-ESHs binding constant and the number of binding sites as well as binding percentage of each hormone to CPS. The number of binding sites per studied hormone molecule was 1.10, 1, and 0.81 for E1, E2, and DES, respectively. The obtained results confirmed that CPS bound to one class of binding sites on sex hormones.

  5. Study of Randomness in AES Ciphertexts Produced by Randomly Generated S-Boxes and S-Boxes with Various Modulus and Additive Constant Polynomials

    Science.gov (United States)

    Das, Suman; Sadique Uz Zaman, J. K. M.; Ghosh, Ranjan

    2016-06-01

    In Advanced Encryption Standard (AES), the standard S-Box is conventionally generated by using a particular irreducible polynomial {11B} in GF(28) as the modulus and a particular additive constant polynomial {63} in GF(2), though it can be generated by many other polynomials. In this paper, it has been shown that it is possible to generate secured AES S-Boxes by using some other selected modulus and additive polynomials and also can be generated randomly, using a PRNG like BBS. A comparative study has been made on the randomness of corresponding AES ciphertexts generated, using these S-Boxes, by the NIST Test Suite coded for this paper. It has been found that besides using the standard one, other moduli and additive constants are also able to generate equally or better random ciphertexts; the same is true for random S-Boxes also. As these new types of S-Boxes are user-defined, hence unknown, they are able to prevent linear and differential cryptanalysis. Moreover, they act as additional key-inputs to AES, thus increasing the key-space.

  6. Inhibition of [(11)C]mirtazapine binding by alpha(2)-adrenoceptor antagonists studied by positron emission tomography in living porcine brain

    DEFF Research Database (Denmark)

    Smith, Donald F.; Dyve, Suzan; Minuzzi, Luciano;

    2006-01-01

    We have developed [(11)C]mirtazapine as a ligand for PET studies of antidepressant binding in living brain. However, previous studies have determined neither optimal methods for quantification of [(11)C]mirtazapine binding nor the pharmacological identity of this binding. To obtain that informati...... brain. Synapse 59:463-471, 2006. (c) 2006 Wiley-Liss, Inc....

  7. Thermodynamics of binding of a sulfonamide inhibitor to metal-mutated carbonic anhydrase as studied by affinity capillary electrophoresis.

    Science.gov (United States)

    Sato, Yosuke; Hoshino, Hitoshi; Iki, Nobuhiko

    2015-09-01

    By affinity capillary electrophoresis (ACE), the thermodynamic binding constants of a sulfonamide (SA) inhibitor to bovine carbonic anhydrase II (CA) and metal mutated variants (M-CAs) were evaluated. 1-(4-Aminosulfonylphenylazo)-2-naphthol-6,8-disulfonate was used as the SA in the electrophoretic buffer for ACE. The Scatchard analysis of the dependence of the electrophoretic mobility of native CA on the SA concentration provided the binding constant to be Kb=(2.29±0.05)×10(6) M(-1) (at pH8.4, 25°C). On the other hand, apoCA showed far smaller value [Kb=(3.76±0.14)×10(2) M(-1)], suggesting that the coordination of SA to the Zn(II) center controlled the binding thermodynamics. The ACE of M-CAs showed the same behaviors as native CA but with different Kb values. For example, Co-CA adopting the same tetrahedral coordination geometry as native CA exhibited the largest Kb value [(2.55±0.05)×10(6) M(-1)] among the M-CAs. In contrast, Mn- and Ni-CA, which adopted the octahedral coordination geometry, had Kb values that were about two orders of magnitude lower. Because the hydrophobic cavity of CA around the active center pre-organized the orientation of SA, thereby fixing the ligating NH(-) moiety to the apex of the tetrahedron supported by three basal His3 of CA, metals such as Zn and Co at the center of M-CA gave the most stable CA-SA complex. However, pre-organization was not favored for octahedral geometry. Thus, pre-organization of SA was the key to facilitating the tetrahedral coordination geometry of the Zn(II) active center of CA.

  8. Frequency Dependence of Attenuation Constant of Dielectric Materials

    Directory of Open Access Journals (Sweden)

    A. S. Zadgaonkar

    1975-01-01

    Full Text Available Different dielectric materials have been studied for frequency dependence of attenuation constant. The sensitive cathode ray oscillograph method has been used to evaluate to the dielectric constant and loss factor, and from these attenuation constants have been calculated. The temperature remaining constant, a regular increase has been observed in attenuation constant, at higher frequencies of electro-magnetic propagating wave.

  9. DNA-binding studies of the natural β-carboline eudistomin U.

    Science.gov (United States)

    Giulietti, Jennifer M; Tate, Patrick M; Cai, Ang; Cho, Bongsup; Mulcahy, Seann P

    2016-10-01

    Eudistomin U is a member of the β-carboline class of heterocyclic amine-containing molecules that are capable of binding to DNA. The structure of eudistomin U is unique since it contains an indole ring at the 1-position of the pyridine ring. While simple β-carbolines are reported to intercalate DNA, an examination of the mode of binding of eudistomin U has been lacking. We report preliminary spectroscopic (UV-Vis, thermal denaturation, CD) and calorimetric (DSC) data on the binding of eudistomin U to DNA, which suggest that eudistomin U binds weakly according to a mechanism that is more complicated than other members of its class. PMID:27567367

  10. Synthesis of Cyclic Porphyrin Trimers through Alkyne Metathesis Cyclooligomerization and Their Host–Guest Binding Study

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Chao; Long, Hai; Jin, Yinghua; Zhang, Wei

    2016-06-17

    Cyclic porphyrin trimers were synthesized through one-step cyclooligomerization via alkyne metathesis from diyne monomers. These macrocycles show interesting host-guest binding interactions with fullerenes, selectively binding C70 (6 x 103 M-1) over C60 and C84 (no binding observed). The fullerene-encapsulated host-guest complex can undergo guest or host exchange in the presence of another guest (2,4,6-tri(4-pyridyl)-1,3,5-triazine) or host (cage COP5) molecule with higher binding affinity.

  11. Synthesis of Cyclic Porphyrin Trimers through Alkyne Metathesis Cyclooligomerization and Their Host-Guest Binding Study.

    Science.gov (United States)

    Yu, Chao; Long, Hai; Jin, Yinghua; Zhang, Wei

    2016-06-17

    Cyclic porphyrin trimers were synthesized through one-step cyclooligomerization via alkyne metathesis from diyne monomers. These macrocycles show interesting host-guest binding interactions with fullerenes, selectively binding C70 (6 × 10(3) M(-1)) over C60 and C84 (no binding observed). The fullerene-encapsulated host-guest complex can undergo guest or host exchange in the presence of another guest (2,4,6-tri(4-pyridyl)-1,3,5-triazine) or host (cage COP5) molecule with higher binding affinity. PMID:27267936

  12. Elevated serotonin transporter binding in depressed patients with Parkinson's disease: a preliminary PET study with [11C]DASB.

    Science.gov (United States)

    Boileau, Isabelle; Warsh, Jerry J; Guttman, Mark; Saint-Cyr, Jean A; McCluskey, Tina; Rusjan, Pablo; Houle, Sylvain; Wilson, Alan A; Meyer, Jeffrey H; Kish, Stephen J

    2008-09-15

    This study investigated whether abnormalities in serotonin transporter binding occur in Parkinson's disease (PD) patients with concurrent depression. We estimated serotonin transporter levels in seven clinically depressed early-stage PD patients and in seven healthy matched-control subjects during a single positron emission tomography (PET) scan with the serotonin transporter radioligand, [(11)C]DASB. Depressed PD patients displayed a wide-spread increase (8-68%) in [(11)C]DASB specific binding outside of the striatum, which was significant in dorsolateral (37%) and prefrontal (68%) cortices. Elevated [(11)C]DASB binding was positively correlated with depressive symptoms but not with disease severity or duration. Compatible with recent PET/[(11)C]DASB findings in major depression, the present preliminary data suggest that increased [(11)C]DASB binding, possibly reflecting greater serotonin transporter density (up-regulation), might be a pathological feature of depression in Parkinson's disease-and possibly a characteristic of depressive illness in general.

  13. Beyond the Hubble Constant

    Science.gov (United States)

    1995-08-01

    about the distances to galaxies and thereby about the expansion rate of the Universe. A simple way to determine the distance to a remote galaxy is by measuring its redshift, calculate its velocity from the redshift and divide this by the Hubble constant, H0. For instance, the measured redshift of the parent galaxy of SN 1995K (0.478) yields a velocity of 116,000 km/sec, somewhat more than one-third of the speed of light (300,000 km/sec). From the universal expansion rate, described by the Hubble constant (H0 = 20 km/sec per million lightyears as found by some studies), this velocity would indicate a distance to the supernova and its parent galaxy of about 5,800 million lightyears. The explosion of the supernova would thus have taken place 5,800 million years ago, i.e. about 1,000 million years before the solar system was formed. However, such a simple calculation works only for relatively ``nearby'' objects, perhaps out to some hundred million lightyears. When we look much further into space, we also look far back in time and it is not excluded that the universal expansion rate, i.e. the Hubble constant, may have been different at earlier epochs. This means that unless we know the change of the Hubble constant with time, we cannot determine reliable distances of distant galaxies from their measured redshifts and velocities. At the same time, knowledge about such change or lack of the same will provide unique information about the time elapsed since the Universe began to expand (the ``Big Bang''), that is, the age of the Universe and also its ultimate fate. The Deceleration Parameter q0 Cosmologists are therefore eager to determine not only the current expansion rate (i.e., the Hubble constant, H0) but also its possible change with time (known as the deceleration parameter, q0). Although a highly accurate value of H0 has still not become available, increasing attention is now given to the observational determination of the second parameter, cf. also the Appendix at the

  14. The Binding of Iron to Perineuronal Nets: A Combined Nuclear Microscopy and Moessbauer Study

    Energy Technology Data Exchange (ETDEWEB)

    Morawski, M. [Universitaet Leipzig, Paul Flechsig Institute fuer Hirnforschung (Germany); Reinert, T. [Universitaet Leipzig, Fakultaet fuer Physik und Geowissenschaften (Germany); Brueckner, G. [Universitaet Leipzig, Paul Flechsig Institute fuer Hirnforschung (Germany); Wagner, F. E. [Technische Universitaet Muenchen, Physik-Department E15 (Germany); Arendt, T. H. [Universitaet Leipzig, Paul Flechsig Institute fuer Hirnforschung (Germany); Troeger, W., E-mail: troeger@physik.uni-leipzig.de [Universitaet Leipzig, Fakultaet fuer Physik und Geowissenschaften (Germany)

    2004-12-15

    A specialized form of extracellular matrix (ECM) surrounds subpopulations of neurons termed 'perineuronal nets' (PNs). These PNs form highly anionic charged structures in the direct microenvironment of neurons, assumed to be involved in local ion homeostasis since they are able to scavenge and bind redox-active iron ions. The quantity and distribution of iron-charged PNs of the extracellular matrix in the rat brain areas of the cortex and the red nucleus was investigated using the powerful combination of Particle-Induced X-ray Emission (PIXE) and Moessbauer spectroscopy. These studies reveal that the iron is bound to the PNs as Fe(III). PNs in both brain regions accumulate up to three to five times more Fe{sup 3+} than any other tissue structure in dependency on the applied Fe concentration with local amount maximums of 480 mmol/l Fe at PNs.

  15. The Binding of Iron to Perineuronal Nets: A Combined Nuclear Microscopy and Moessbauer Study

    International Nuclear Information System (INIS)

    A specialized form of extracellular matrix (ECM) surrounds subpopulations of neurons termed 'perineuronal nets' (PNs). These PNs form highly anionic charged structures in the direct microenvironment of neurons, assumed to be involved in local ion homeostasis since they are able to scavenge and bind redox-active iron ions. The quantity and distribution of iron-charged PNs of the extracellular matrix in the rat brain areas of the cortex and the red nucleus was investigated using the powerful combination of Particle-Induced X-ray Emission (PIXE) and Moessbauer spectroscopy. These studies reveal that the iron is bound to the PNs as Fe(III). PNs in both brain regions accumulate up to three to five times more Fe3+ than any other tissue structure in dependency on the applied Fe concentration with local amount maximums of 480 mmol/l Fe at PNs.

  16. Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1982-01-01

    ., & Garrett, R. A. (1981) Biochemistry 20, 7301--7307], reveal an extensive interaction site for protein L18 and a more localized one for L25. Generally comparable results, with a few important differences, were obtained in a study of the binding sites of the two E. coli proteins on Bacillus...... experiments were performed for both RNAs. The effects of the bound proteins on the ribonuclease digestion of the RNAs could generally be correlated with the results obtained with the E. coli proteins L18 and L25, although there was evidence for an additional protein-induced conformational change in the B...... stearothermophilus 5S RNA. Several protein-induced changes in the RNA structures were identified; some are possibly allosteric in nature. The two prokaryotic 5S RNAs were also incubated with total 50S subunit proteins from E. coli and B. stearothermophilus ribosomes. Homologous and heterologous reconstitution...

  17. Binding of chrysoidine to catalase: spectroscopy, isothermal titration calorimetry and molecular docking studies.

    Science.gov (United States)

    Yang, Bingjun; Hao, Fang; Li, Jiarong; Chen, Dongliang; Liu, Rutao

    2013-11-01

    Chrysoidine is an industrial azo dye and the presence of chrysoidine in water and food has become an environmental concern due to its negative effects on human beings. In this work, the interactions between chrysoidine and bovine liver catalase (BLC) were explored. Obvious loss in catalytic activity was observed after incubation of BLC with chrysoidine, and the inhibition effect of BLC was found to be of the non-competitive type. No profound conformational change of BLC occurs in the presence of chrysoidine as revealed by UV-vis absorption, circular dichroism and fluorescence spectroscopy studies. Isothermal titration calorimetry results indicate that catalase has two sets of binding sites for chrysoidine. Further, molecular docking simulations show that chrysoidine is located within the bottleneck in the main channel of the substrate to the active site of BLC, which explain the activity inhibition of BLC by chrysoidine.

  18. Good use of fruit wastes: eco-friendly synthesis of silver nanoparticles, characterization, BSA protein binding studies.

    Science.gov (United States)

    Sreekanth, T V M; Ravikumar, Sambandam; Lee, Yong Rok

    2016-06-01

    A simple and eco-friendly methodology for the green synthesis of silver nanoparticles (AgNPs) using a mango seed extract was evaluated. The AgNPs were characterized by ultraviolet-visible spectrophotometry, Fourier transform infrared spectroscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, and X-ray diffraction. The interaction between the green synthesized AgNPs and bovine serum albumin (BSA) in an aqueous solution at physiological pH was examined by fluorescence spectroscopy. The results confirmed that the AgNPs quenched the fluorophore of BSA by forming a ground state complex in aqueous solution. This fluorescence quenching data were also used to determine the binding sites and binding constants at different temperatures. The calculated thermodynamic parameters (ΔG°, ΔH° and ΔS°) suggest that the binding process occurs spontaneously through the involvement of electrostatic interactions. The synchronous fluorescence spectra showed a blue shift, indicating increasing hydrophobicity. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26644144

  19. Biochemical studies of olfaction: binding specificity of odorants to a cilia preparation from rainbow trout olfactory rosettes

    Energy Technology Data Exchange (ETDEWEB)

    Rhein, L.D.; Cagan, R.H.

    1983-08-01

    Cilia isolated from the olfactory epithelium (olfactory rosettes) of rainbow trout (Salmo gairdneri) bind amino acids, which are odor stimuli to this species. We demonstrate that L-threonine, L-serine, and L-alanine bind to a common site, TSA, in the cilia preparation. All possible mixtures of two of the amino acids as competitors, with the third as the /sup 3/H-labeled ligand, were studied. The effect of two combined (unlabeled) competitors was always substantially less than additive compared with their actions singly. Along with additional inhibition studies using mixtures of inhibitors, the data show that the three odorants must interact with at least one common binding site, TSA. Binding of L-(/sup 3/H)lysine to site L was unaffected by addition of L-threonine, L-serine, or L-alanine, establishing its independence from site TSA. L-Arginine inhibited binding of L-(/sup 3/H)lysine, showing that both of these basic amino acids interact with site L. The data establish the presence, in trout olfactory cilia, of at least two separate and noninteracting populations of odorant binding sites, TSA and L.

  20. Studies on the hyaluronate binding properties of newly synthesized proteoglycans purified from articular chondrocyte cultures

    Energy Technology Data Exchange (ETDEWEB)

    Sandy, J.D.; Plaas, A.H.

    1989-06-01

    Primary cultures of rabbit articular chondrocytes have been maintained for 10 days and labeled with (35S)sulfate, (3H)leucine, and (35S)cysteine in pulse-chase protocols to study the structure and hyaluronate binding properties of newly synthesized proteoglycan monomers. Radiolabeled monomers were purified from medium and cell-layer fractions by dissociative CsCl gradient centrifugation with bovine carrier monomer, and analyzed for hyaluronate binding affinity on Sepharose CL-2B in 0.5 M Na acetate, 0.1% Triton X-100, pH 6.8. Detergent was necessary to prevent self-association of newly synthesized monomers during chromatography. Monomers secreted during a 30-min pulse labeling with (35S)sulfate had a low affinity relative to carrier. Those molecules released into the medium during the first 12 h of chase remained in the low affinity form whereas those retained by the cell layer rapidly acquired high affinity. In cultures where more than 90% of the preformed cell-layer proteoglycan was removed by hyaluronidase digestion before radiolabeling the newly synthesized low affinity monomers also rapidly acquired high affinity if retained in the cell layer. Cultures labeled with amino acid precursors were used to establish the purity of monomer preparations and to isolate core proteins for study. Leucine- or cysteine-labeled core proteins derived from either low or high affinity monomer preparations migrated as a single major species on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with electrophoretic mobility very similar to that of core protein derived from extracted proteoglycan monomer. Purified low affinity monomers were converted to the high affinity form by treatment at pH 8.6; however, this change was prevented by guanidinium-HCl at concentrations above 0.8 M.

  1. Effect of tetrahydrocurcumin on insulin receptor status in type 2 diabetic rats: studies on insulin binding to erythrocytes

    Indian Academy of Sciences (India)

    Pidaran Murugan; Leelavinothan Pari; Chippada Appa Rao

    2008-03-01

    Curcumin is the most active component of turmeric. It is believed that curcumin is a potent antioxidant and anti-inflammatory agent. Tetrahydrocurcumin (THC) is one of the major metabolites of curcumin, and exhibits many of the same physiological and pharmacological activities as curcumin and, in some systems, may exert greater antioxidant activity than curcumin. Using circulating erythrocytes as the cellular mode, the insulin-binding effect of THC and curcumin was investigated. Streptozotocin (STZ)–nicotinamide-induced male Wistar rats were used as the experimental models. THC (80 mg/kg body weight) was administered orally for 45 days. The effect of THC on blood glucose, plasma insulin and insulin binding to its receptor on the cell membrane of erythrocytes were studied. Mean specific binding of insulin was significantly lowered in diabetic rats with a decrease in plasma insulin. This was due to a significant decrease in mean insulin receptors. Erythrocytes from diabetic rats showed a decreased ability for insulin–receptor binding when compared with THC-treated diabetic rats. Scatchard analysis demonstrated that the decrease in insulin binding was accounted for by a decrease in insulin receptor sites per cell, with erythrocytes of diabetic rats having less insulin receptor sites per cell than THC-treated rats. High affinity (Kd1), low affinity (Kd2) and kinetic analyses revealed an increase in the average receptor affinity of erythrocytes from THC-treated rats compared with those of diabetic rats. These results suggest that acute alteration of the insulin receptor on the membranes of erythrocytes occurred in diabetic rats. Treatment with THC significantly improved specific insulin binding to the receptors, with receptor numbers and affinity binding reaching near-normal levels. Our study suggests the mechanism by which THC increases the number of total cellular insulin binding sites resulting in a significant increase in plasma insulin. The effect of THC is

  2. Variation of fundamental constants

    CERN Document Server

    Flambaum, V V

    2006-01-01

    We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

  3. Lysine-functionalized nanodiamonds: synthesis, physiochemical characterization, and nucleic acid binding studies

    Directory of Open Access Journals (Sweden)

    Kaur R

    2012-07-01

    . These modified NDs formed highly stable aqueous dispersions with a zeta potential of 49 mV and particle size of approximately 20 nm. The functionalized NDs were found to be able to bind plasmid DNA and small interfering RNA by forming nanosized "diamoplexes".Conclusion: The lysine-substituted ND particles generated in this study exhibit stable aqueous formulations and show potential for use as carriers for genetic materials.Keywords: disaggregation, spectroscopy, dispersion, electrophoresis, size, zeta potential

  4. Melting Heat Transfer Characteristics of Latent Heat Microcapsule-Water Mixed Slurry Flowing in a Pipe with Constant Wall Heat Flux (Experimental Study)

    Science.gov (United States)

    Inaba, Hideo; Kim, Myoung-Jun; Horibe, Akihiko

    The present experiments have been performed for obtaining the melting heat transfer characteristics of micro-encapsulated solid-liquid phase change material and water mixed slurry flow in a circular tube heated with constant wall heat flux. The phase change material having a low melting point was selected for a domestic cooling system in the present study. The governing parameters were found to be latent heat material concentration,heat,flux,and the slurry velocity. The experimental results revealed that the mean heat transfer coefficient of latent microcapsule slurry was about l.3~l.8 times greater than that of the single phase of water. Moreover the effectiveness of heat transfer coefficient to friction factor had a maximum at latent heat material concentration of 25%.

  5. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila.

    Science.gov (United States)

    Ruiz, Mario; Ganfornina, Maria D; Correnti, Colin; Strong, Roland K; Sanchez, Diego

    2014-04-01

    Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.

  6. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun

    2015-06-11

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  7. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray.

    Science.gov (United States)

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

    2016-01-01

    Transcription factor binding sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k = 8∼10). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build TFBS (also known as DNA motif) models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement if choosing di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  8. NMr studies of the AMP binding site and mechanism of adenylate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Kuby, S.A.; Fry, D.C.; Mildvan, A.S.

    1986-05-01

    The authors recently located by NMR the MgATP binding site on adenylate kinase correcting the proposed location for this site based on X-ray studies of the binding of salicylate. To determine the conformation and location of the other substrate, they have determined distances from Cr/sup 3 +/ AMPPCP to 6 protons and to the phosphorus atom of AMP on adenylate kinase using the paramagnetic-probe-T/sub 1/ method. They have also used time-dependent NOEs to measure five interproton distances on AMP, permitting evaluation of the conformation of enzyme-bound AMP and its position with respect to metal-ATP. Enzyme-bound AMP exhibits a high-anti glycosyl torsional angle (X = 110/sup 0/), a 3'-endo sugar pucker (delta = 105/sup 0/), and a gauche-trans orientation about the C/sub 4/'-C/sub 5/' bond (..gamma.. = 180/sup 0/). The distance from Cr/sup 3 +/ to the phosphorus of AMP is 6.4 +/- 0.3 A, indicating a reaction coordinate distance of greater than or equal to A which is consistent with an associative SN2 mechanism for the phosphoryl transfer. Ten intermolecular NOEs, from protons of the enzyme to those of AMP were detected. These constraints, together with the conformation of AMP and the X-ray structure of the enzyme, suggest proximity (less than or equal to A) of AMP to leu 116, arg 171, val 173, gln 185, thr 188, and asp 191.

  9. The vibrational spectrum and rotational constants of difluoroethyne FC 3/4 CF. Matrix and high resolution infrared studies and ab initio calculations

    Science.gov (United States)

    Bürger, H.; Schneider, W.; Sommer, S.; Thiel, W.; Willner, H.

    1991-10-01

    Infrared spectra of the short-lived difluoroethyne molecule have been recorded in neon and argon matrices between 200 and 5000 cm-1. Fourier transform infrared spectra with a resolution of 0.004 cm-1 have been measured in the gas phase around 1350 cm-1 (ν3, ν2+ν4+ν5, hot bands) and 2150 cm-1 (ν2+ν3, ν1-ν5, hot bands). The high resolution study yields rotational parameters of the ground and all singly excited vibrational states. The interpretation of the experimental data has been guided by ab initio calculations at the SCF (self-consistent-field) level and the correlated MP2 level (Moller-Plesset second order perturbation theory) employing three different large basis sets. The theoretical calculations provide the SCF and MP2 harmonic fields as well as the SCF anharmonic force field of FCCF. The agreement between the available theoretical and experimental results is generally quite good, with the exception of the spectroscopic constants involving the trans-bending mode ν4 where more theoretical work is required. The combined use of theoretical and experimental information leads to an estimate of the equilibrium structure [D∞h, re(CC)=1.1865 Å, re(CF)=1.2832 Å] and to recommended ``best'' values for the wave numbers of all fundamental vibrations based on the matrix and high resolution infrared data and some ab initio anharmonicity constants. The present study demonstrates the advantages of a combined theoretical and experimental approach to the spectroscopy of short-lived molecules.

  10. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies.

    Science.gov (United States)

    Yang, Zhiwei; Wu, Fei; Yuan, Xiaohui; Zhang, Lei; Zhang, Shengli

    2016-04-01

    Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs. PMID:26905206

  11. Studies on Interactions of Antibiotics with Serum Albumin by Surface Plasmon Resonance Biosensor

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Characterizing how chemical compounds binding to serum albumin is essential in evaluating drug candidates and is the focus of this study. A surface plasmon resonance biosensor developed in this laboratory was used to determine the binding constants of antibiotics with serum albumin. The binding constants of five antibiotics(azithromycin, spectinomycin, gentamycin, metacycline and kanamycin) with serum albumins were obtained.

  12. Multispectroscopic studies of paeoniflorin binding to calf thymus DNA in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guowen, E-mail: gwzhang@ncu.edu.cn [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China); Fu, Peng; Pan, Junhui [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China)

    2013-02-15

    The mechanism of paeoniflorin binding to calf thymus DNA in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and DNA melting techniques. The results suggested that paeoniflorin molecules could bind to DNA via groove binding mode as evidenced by no significant change in iodide quenching effect, increase in single-stranded DNA (ssDNA) quenching effect, and almost unchanged relative viscosity and melting temperature of DNA. The observed changes in CD signals revealed that DNA remains in the B-conformation. Further, the displacement experiments with Hoechst 33258 probe and the results of FT-IR spectra indicated that paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. The thermodynamic parameters, enthalpy change ({Delta}H Degree-Sign ) and entropy change ({Delta}S Degree-Sign ) were calculated to be -30.09{+-}0.18 kJ mol{sup -1} and -14.07{+-}0.61 J mol{sup -1} K{sup -1} by the van't Hoff equation, suggesting that hydrogen bond and van der Waals forces play a predominant role in the binding of paeoniflorin to DNA. - Highlights: Black-Right-Pointing-Pointer The binding mode of paeoniflorin to calf thymus DNA is the minor groove binding. Black-Right-Pointing-Pointer Paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. Black-Right-Pointing-Pointer The binding does not alter the native B-conformation of DNA. Black-Right-Pointing-Pointer The binding is driven mainly by hydrogen bonds and van der Waals forces.

  13. Electrostatic interactions in the binding pathway of a transient protein complex studied by NMR and isothermal titration calorimetry.

    Science.gov (United States)

    Meneses, Erick; Mittermaier, Anthony

    2014-10-01

    Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr-Purcell-Meiboom-Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes.

  14. Determination of paralytic shellfish toxins in shellfish by receptor binding assay: collaborative study.

    Science.gov (United States)

    Van Dolah, Frances M; Fire, Spencer E; Leighfield, Tod A; Mikulski, Christina M; Doucette, Gregory J

    2012-01-01

    A collaborative study was conducted on a microplate format receptor binding assay (RBA) for paralytic e shellfish toxins (PST). The assay quantifies the composite PST toxicity in shellfish samples based on the ability of sample extracts to compete with (3)H saxitoxin (STX) diHCl for binding to voltage-gated sodium channels in a rat brain membrane preparation. Quantification of binding can be carried out using either a microplate or traditional scintillation counter; both end points were included in this study. Nine laboratories from six countries completed the study. One laboratory analyzed the samples using the precolumn oxidation HPLC method (AOAC Method 2005.06) to determine the STX congener composition. Three laboratories performed the mouse bioassay (AOAC Method 959.08). The study focused on the ability of the assay to measure the PST toxicity of samples below, near, or slightly above the regulatory limit of 800 (microg STX diHCl equiv./kg). A total of 21 shellfish homogenates were extracted in 0.1 M HCl, and the extracts were analyzed by RBA in three assays on separate days. Samples included naturally contaminated shellfish samples of different species collected from several geographic regions, which contained varying STX congener profiles due to their exposure to different PST-producing dinoflagellate species or differences in toxin metabolism: blue mussel (Mytilus edulis) from the U.S. east and west coasts, California mussel (Mytilus californianus) from the U.S. west coast, chorito mussel (Mytilus chiliensis) from Chile, green mussel (Perna canaliculus) from New Zealand, Atlantic surf clam (Spisula solidissima) from the U.S. east coast, butter clam (Saxidomus gigantea) from the west coast of the United States, almeja clam (Venus antiqua) from Chile, and Atlantic sea scallop (Plactopecten magellanicus) from the U.S. east coast. All samples were provided as whole animal homogenates, except Atlantic sea scallop and green mussel, from which only the

  15. The Hubble Constant

    Directory of Open Access Journals (Sweden)

    Neal Jackson

    2015-09-01

    Full Text Available I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give H_0 values of around 72–74 km s^–1 Mpc^–1, with typical errors of 2–3 km s^–1 Mpc^–1. This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67–68 km s^–1 Mpc^–1 and typical errors of 1–2 km s^–1 Mpc^–1. The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.

  16. Molecular docking study investigating the possible mode of binding of C.I. Acid Red 73 with DNA.

    Science.gov (United States)

    Guo, Yumei; Yue, Qinyan; Gao, Baoyu

    2011-07-01

    C.I. Acid Red 73 is a reactive azo dye with a variable potential carcinogenicity. The mechanism mediating interactions that occur between the dye and DNA have not been completely understood thus far. In this study, molecular docking techniques were applied to describe the most probable mode of DNA binding as well as the sequence selectivity of the C.I. Acid Red 73 dye. These docking experiments revealed that the dye is capable of interacting with the minor groove of the DNA on the basis of its curved shape, which fits well with the topology of double-stranded DNA. In addition, the dye can bind selectively to the minor groove of the DNA by applying CGT sequence selectivity. Further, the minor groove can be recognized although DNA targets present intercalation gaps. However, intercalative binding can also occur when the DNA target possesses an appropriate intercalation gap. Compared with the other eight DNA sequences that were studied, the DNA dodecamer d(CGCGATATCGCG)(2) (PDB ID: 1DNE) presents a very favorable target for the binding of C.I. Acid Red 73 to the minor groove, with the lowest binding free energy -9.19 kcal/mol. Results reported from this study are expected to provide useful information for research involving further simulations of molecular dynamics and toxicology investigations of the dye.

  17. Cosmological Constant and Axions in String Theory

    Energy Technology Data Exchange (ETDEWEB)

    Svrcek, Peter; /Stanford U., Phys. Dept. /SLAC

    2006-08-18

    String theory axions appear to be promising candidates for explaining cosmological constant via quintessence. In this paper, we study conditions on the string compactifications under which axion quintessence can happen. For sufficiently large number of axions, cosmological constant can be accounted for as the potential energy of axions that have not yet relaxed to their minima. In compactifications that incorporate unified models of particle physics, the height of the axion potential can naturally fall close to the observed value of cosmological constant.

  18. Bubble Universes With Different Gravitational Constants

    OpenAIRE

    Takamizu, Yu-ichi; Maeda, Kei-ichi

    2015-01-01

    We argue a scenario motivated by the context of string landscape, where our universe is produced by a new vacuum bubble embedded in an old bubble and these bubble universes have not only different cosmological constants, but also their own different gravitational constants. We study these effects on the primordial curvature perturbations. In order to construct a model of varying gravitational constants, we use the Jordan-Brans-Dicke (JBD) theory where different expectation values of scalar fi...

  19. Radiolabelling of phoneutria nigriventer spider toxin (Tx1): a tool to study its binding site

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Raquel Gouvea dos [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, MG (Brazil); Diniz, Carlos Roberto; Nascimento, Marta Cordeiro [FUNED, Belo Horizonte, MG (Brazil); Lima, Maria Elena de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Bioquimica e Imunologia

    1996-07-01

    The neurotoxin Tx1, isolated from the venom of the South American spider Phoneutria nigriventer produces tail elevation and spastic paralysis of posterior limbs after intracerebral ventricular injection in mice. Tx1 also produces ileum contraction in bioassay. We have investigated the binding of radioiodinated-Tx1 ({sup 125} I-Tx1) on the preparation of myenteric plexus-longitudinal muscle membrane from guinea pig ileum (MPLM) as a tool to characterize the interaction of this neurotoxin with its site. The neurotoxin Tx1 was radioiodinated with Na{sup 125} I by the lactoperoxidase method. {sup 125} I-Tx1 specifically binds to a single class of noninteracting binding sites of high affinity (Kd= 3.5 x 10{sup -10} M) and low capacity (1.2 pmol/mg protein). The specific binding increased in parallel with the protein concentration. In competition experiments the ligands of ionic channels used (sodium, potassium and calcium) did not affect the binding of {sup 125} I-Tx1 to MPLM neither did the cholinergic ligands (hemicholinium-3, hexamethonium, d-tubocurarine and atropine). Another neurotoxin (Tx2-6, one of the isoforms of Tx2 pool) decreased toxin with MPLM and showed that toxin has a specific and saturable binding site in guinea pig ileum and this binding site appears to be related to the Tx2 site. (author)

  20. Significance of mannose-binding lectin deficiency and nucleotide-binding oligomerization domain 2 polymorphisms in Staphylococcus aureus bloodstream infections: a case-control study.

    Directory of Open Access Journals (Sweden)

    Michael Osthoff

    Full Text Available BACKGROUND: Pathways coordinated by innate pattern recognition receptors like mannose-binding lectin (MBL and nucleotide-binding oligomerization domain 2 (NOD2 are among the first immune responses to Staphylococcus aureus (S. aureus bloodstream infections (BSI in animal models, but human data are limited. Here, we investigated the role of MBL deficiency and NOD2 mutations in the predisposition to and severity of S. aureus BSI. PATIENTS AND METHODS: A matched case-control study was undertaken involving 70 patients with S. aureus BSI and 70 age- and sex-matched hospitalized controls. MBL levels, MBL2 and NOD2 polymorphisms were analyzed. RESULTS: After adjusting for potential confounders, MBL deficiency (<0.5 µg/ml was found less frequently in cases than controls (26 vs. 41%, OR 0.4, 95% confidence interval (CI 0.20-0.95, p=0.04 as were low producing MBL genotypes (11 vs. 23%, OR 0.2, 95% CI 0.08-0.75, p=0.01, whereas NOD2 polymorphisms were similarly distributed. Cases with NOD2 polymorphisms had less organ dysfunction as shown by a lower SOFA score (median 2.5 vs. 4.5, p=0.02, whereas only severe MBL deficiency (<0.1 µg/ml was associated with life-threatening S. aureus BSI (OR 5.6, 95% CI 1.25-24.85, p=0.02. CONCLUSIONS: Contrary to animal model data, our study suggests MBL deficiency may confer protection against acquiring S. aureus BSI. NOD2 mutations were less frequently associated with multi-organ dysfunction. Further human studies of the innate immune response in S. aureus BSI are needed to identify suitable host targets in sepsis treatment.

  1. Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA

    Directory of Open Access Journals (Sweden)

    Patricia Saenz-Méndez

    2007-01-01

    Full Text Available Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5′-TpA in (ATn sequences.

  2. Binding kinetics of magnetic nanoparticles on latex beads and yeast cells studied by magnetorelaxometry

    International Nuclear Information System (INIS)

    The ion exchange mediated binding of magnetic nanoparticles (MNP) to modified latex spheres and yeast cells was quantified using magnetorelaxometry. By fitting subsequently recorded relaxation curves, the kinetics of the binding reactions was extracted. The signal of MNP with weak ion exchanger groups bound to latex and yeast cells scales linearly with the concentration of latex beads or yeast cells whereas that of MNP with strong ion exchanger groups is proportional to the square root of concentration. The binding of the latter leads to a much stronger aggregation of yeast cells than the former MNP

  3. Klebsiella 'modifying factor': binding studies with HLA-B27+ and B27- lymphocytes.

    OpenAIRE

    Trapani, J A; McKenzie, I. F.

    1985-01-01

    On the basis that extracts of some klebsiella organisms bind selectively to the lymphocytes of HLA-B27+ individuals and induce the appearance of new antigens, attempts were made to detect the binding of klebsiella products to HLA-B27+ and B27- lymphocytes by a number of different techniques. Firstly, blocking of the binding of two different HLA-B27 specific monoclonal antibodies to HLA-B27+ lymphocytes has been examined following exposure of the lymphocytes to a cell-free culture filtrate fro...

  4. Yeast hexokinase. A fluorescence temperature-jump study of the kinetics of the binding of glucose to the monomer forms of hexokinases P-I and P-II.

    Science.gov (United States)

    Hoggett, J G; Kellett, G L

    1976-09-15

    The binding of glucose to the monomeric forms of hexokinases P-I and P-II in Tris and phosphate buffers at pH 8.0 in the presence of 1 mol l-1 KCl has been studied using the fluorescence temperature-jump technique. For both isozymes only one relaxation time was observed; values of tau-1 increased linearly with increasing concentration of free reacting partners. The apparent second-order rate constant for association was about 2 X 10(6) 1 mol-1 s-1 for both isozymes; the differences in the stabilities of the complexes with P-I and P-II are entirely attributable to the fact that glucose dissociates more slowly from its complex with P-I than P-II (approximately 300 s-1 and 1100 s-1 respectively). Although the kinetic data are compatible with a single-step mechanism for glucose binding the association rate constant was much lower than that expected for a diffusion-limited rate of encounter. Other mechanisms for describing an induced-fit are discussed. It is shown that the data are incompatible with a slow 'prior-isomerization' pathway of substrate binding, but are consistent with a 'substrate-guided' pathway involving isomerization of the enzyme-substrate complex. PMID:789076

  5. A comparative study of density functional and density functional tight binding calculations of defects in graphene

    Energy Technology Data Exchange (ETDEWEB)

    Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

    2012-02-15

    The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. 1HNMR study of methotrexate serum albumin (MTX SA) binding in rheumatoid arthritis

    Science.gov (United States)

    Sułkowska, A.; Maciążek-Jurczyk, M.; Bojko, B.; Równicka, J.; Sułkowski, W. W.

    2008-11-01

    Rheumatoid arthritis (RA) is an immunologically depended disease. It is characterized by a chronic, progressive inflammatory process. Methotrexate (4-amino-10-methylfolic acid, MTX) is the modifying drug used to treat RA. The aim of the presented studies is to determine the low affinity binding site of MTX in bovine (BSA) and human (HSA) serum albumin with the use of proton nuclear magnetic resonance ( 1HNMR) spectroscopy. The analysis of 1HNMR spectra of MTX in the presence of serum albumin (SA) allows us to observe the interactions between aromatic rings of the drug and the rings of amino acids located in the hydrophobic subdomains of the protein. On the basis of the chemical shifts σ [ppm] and the relaxation times T1 [s] of drug protons the hydrophobic interaction between MTX-SA and the stoichiometric molar ratio of the complex was evaluated. This work is a part of a spectroscopic study on MTX-SA interactions [A. Sułkowska, M. Maciążek, J. Równicka, B. Bojko, D. Pentak, W.W. Sułkowski, J. Mol. Struct. 834-836 (2007) 162-169].

  7. RNA targeting by small molecule alkaloids: Studies on the binding of berberine and palmatine to polyribonucleotides and comparison to ethidium

    Science.gov (United States)

    Islam, Md. Maidul; Suresh Kumar, Gopinatha

    2008-03-01

    The binding affinity, energetics and conformational aspects of the interaction of isoquinoline alkaloids berberine and palmatine to four single stranded polyribonucleotides polyguanylic acid [poly(G)], polyinosinic acid [poly(I)], polycytidylic acid [poly(C)] and polyuridylic acid [poly(U)] were studied by absorption, fluorescence, isothermal titration calorimetry and circular dichroism spectroscopy and compared with ethidium. Berberine, palmatine and ethidium binds strongly with poly(G) and poly(I) with affinity in the order 10 5 M -1 while their binding to poly(C) and poly(U) were very weak or practically nil. The same conclusions have also emerged from isothermal titration calorimetric studies. The binding of all the three compounds to poly(C) and poly(I) was exothermic and favored by both negative enthalpy change and positive entropy change. Conformational change in the polymer associated with the binding was observed in poly(I) with all the three molecules and poly(U) with ethidium but not in poly(G) and poly(C) revealing differences in the orientation of the bound molecules in the hitherto different helical organization of these polymers. These fundamental results may be useful and serve as database for the development of futuristic RNA based small molecule therapeutics.

  8. Synthesis, characterization and DNA-binding studies of 2-carboxybenzaldehydeisonicotinoylhydrazone and its La(III), Sm(III) and Eu(III) complexes

    Science.gov (United States)

    Wang, Yuan; Wang, Yan; Yang, Zheng-Yin

    2007-02-01

    2-Carboxybenzaldehydeisonicotinoylhydrazone (HL), and its three lanthanide complexes, LnL 3·4H 2O [Ln = La( 1), Sm( 2), Eu( 3)], have been synthesized and characterized on the basis of elemental analyses, molar conductivities, IR spectra and thermal analyses. In addition, the DNA-binding properties of the ligand and its complexes have been investigated by absorption, fluorescence and viscosity measurements. The experimental results indicated that the complexes ( 2) and ( 3) can bind to DNA, but the ligand and the complex ( 1) cannot; the binding affinity of the complex ( 3) is higher than that of the complex ( 2) and the intrinsic binding constant Kb of the complex ( 3) is 7.86 × 10 4 M -1.

  9. STD NMR spectroscopy: a case study of fosfomycin binding interactions in living bacterial cells

    Energy Technology Data Exchange (ETDEWEB)

    Milagre, Cintia D.F.; Cabeca, Luis Fernando; Martins, Lucas G.; Marsaioli, Anita J., E-mail: anita@iq [Universidade Estadual de Campinas (IQ/UNICAMP), SP (Brazil). Inst. de Quimica

    2011-07-01

    A saturation transfer difference (STD) NMR experiment was successfully employed to observe the binding interactions of fosfomycin resistant and non-resistant bacterial strains using living cell suspensions, without the need for isotopic labelling of the ligand or receptor. (author)

  10. Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.

    Science.gov (United States)

    Du, Juan; Wang, Xue; Dong, Chun-Hai; Yang, Jian Ming; Yao, Xiao Jun

    2016-01-01

    Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1-actin complex, we constructed a homology model of the AtADF1-actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson-Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin. PMID:27414648

  11. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties. PMID:27444879

  12. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties.

  13. Geometry, Energy, and Some Electronic Properties of Carbon Polyprismanes: Ab Initio and Tight-Binding Study

    OpenAIRE

    Konstantin P. Katin; Shostachenko, Stanislav A.; Avkhadieva, Alina I.; Mikhail M. Maslov

    2015-01-01

    We report geometry, energy, and some electronic properties of [n,4]- and [n,5]prismanes (polyprismanes): a special type of carbon nanotubes constructed from dehydrogenated cycloalkane C4- and C5-rings, respectively. Binding energies, interatomic bonds, and the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) have been calculated using density functional approach and nonorthogonal tight-binding model for the systems up to thir...

  14. Crystallographic studies on B12 binding proteins in eukaryotes and prokaryotes

    OpenAIRE

    Sukumar, Narayanasami

    2013-01-01

    The x-ray crystal structures of several important vitamin B12 binding proteins that have been solved in recent years have enhanced our current understanding in the vitamin B12 field. These structurally diverse groups of B12 binding proteins perform various important biological activities, both by transporting B12 as well as catalyzing various biological reactions. An in-depth comparative analysis of these structures was carried out using PDB coordinates of a carefully chosen database of B12 b...

  15. A Study on the Presence of Ferritin-binding Proteins in Fetal Horse Plasma

    OpenAIRE

    Hashimoto, Masafumi; NAMBO, Yasuo; Kondo, Takashi; Watanabe, Kiyotaka; Orino, Koichi

    2011-01-01

    In mammal circulation, ferritin-binding proteins (FBPs) are thought to be involved in clearance of circulating ferritin after complex formation with it through receptor-mediated uptake. However, there is no report on fetal FBP in fetal circulation. Although iron concentrations of fetal horse plasma were higher than those of adult horse plasma, plasma ferritin concentrations and ferritin-binding activities were found to be significantly lower in fetus than in adult. FBPs were purified from fet...

  16. Crystallization and preliminary structural studies of champedak galactose-binding lectin.

    Science.gov (United States)

    Gabrielsen, Mads; Riboldi-Tunnicliffe, Alan; Abdul-Rahman, Puteri Shafinaz; Mohamed, Emida; Ibrahim, Wan Izlina Wan; Hashim, Onn Haji; Isaacs, Neil W; Cogdell, Richard J

    2009-09-01

    Galactose-binding lectin from champedak (Artocarpus integer) consists of two chains: alpha and beta (133 and 21 amino acids, respectively). It has been shown to recognize and bind to carbohydrates involved in IgA and C1 inhibitor molecules. The protein was purified and crystallized at 293 K. Crystals were observed in two space groups, P2(1) and P2(1)2(1)2, and diffracted to 1.65 and 2.6 A, respectively.

  17. Computational study of the binding modes of caffeine to the adenosine A2A receptor.

    Science.gov (United States)

    Liu, Yuli; Burger, Steven K; Ayers, Paul W; Vöhringer-Martinez, Esteban

    2011-12-01

    Using the recently solved crystal structure of the human adenosine A(2A) receptor, we applied MM/PBSA to compare the binding modes of caffeine with those of the high-affinity selective antagonist ZM241385. MD simulations were performed in the environment of the lipid membrane bilayer. Four low-energy binding modes of caffeine-A(2A) were found, all of which had similar energies. Assuming an equal contribution of each binding mode of caffeine, the computed binding free energy difference between caffeine and ZM241385 is -2.4 kcal/mol, which compares favorably with the experimental value, -3.6 kcal/mol. The configurational entropy contribution of -0.9 kcal/mol from multiple binding modes of caffeine helps explain how a small molecule like caffeine can compete with a significantly larger molecule, ZM241385, which can form many more interactions with the receptor. We also performed residue-wise energy decomposition and found that Phe168, Leu249, and Ile274 contribute most significantly to the binding modes of caffeine and ZM241385. PMID:21970461

  18. Binding of 2',3'-cyclic nucleotide 3'-phosphodiesterase to myelin: an in vitro study.

    Science.gov (United States)

    De Angelis, D A; Braun, P E

    1996-06-01

    The binding of 2', 3'-cyclic nucleotide 3'-phosphodiesterase isoform 1 (CNP1) to myelin and its association with cytoskeletal elements of the sheath have been characterized with in vitro synthesized polypeptides and purified myelin. We have previously shown that the cysteine residue present in the carboxy-terminal CXXX box of CNP1 is isoprenylated, and that both C15 farnesyl and C20 geranylgeranyl isoprenoids can serve as substrates for the modification. Here, we have mutated the CXXX box to obtain selectively farnesylated CNP1 or geranyl- geranylated CNP1 and found that these two modified forms of CNP1 behave identically in all of the assays performed. Isoprenylation is essential but not sufficient for the binding of in vitro synthesized CNP1 to purified myelin, because a control nonmyelin protein is isoprenylated, yet unable to bind to myelin. In our assay, membrane-bound CNP1 partitions quantitatively into the nonionic detergent-insoluble phase of myelin, suggesting that CNP1 binds to cytoskeletal elements within myelin. However, isoprenylated CNP1 fails to bind to the cytoskeletal matrix isolated from myelin by detergent treatment, implying that both detergent-soluble and insoluble myelin components are involved in the binding of CNP1. A model for the interactions between CNP1 and myelin is presented, consistent with models proposed for other isoprenylated proteins. PMID:8632178

  19. Biologically active monoiodinated alpha-MSH derivatives for receptor binding studies using human melanoma cells

    International Nuclear Information System (INIS)

    Three different monoiodinated radioligands of alpha-MSH (alpha-melanocyte-stimulating hormone) were compared in a binding assay with human D10 melanoma cells: [Tyr(125I)2]-alpha-MSH, [Tyr(125I)2,NIe4]-alpha-MSH, and [Tyr(125I)2,NIe4,D-Phe7]-alpha-MSH. They were prepared either by the classical chloramine T method or by the Enzymobead method. A simple and rapid purification scheme was developed consisting of a primary separation on reversed-phase C18 silica cartridges immediately after the iodination, followed by HPLC purification before each binding experiment. Biological testing of the three radioligands showed that they all retained high melanotropic activity in the B16 melanin assay and the Anolis melanophore assay. However, in human D10 melanoma cells, [Tyr(125I)2,NIe4]-alpha-MSH led to a high degree of non-specific binding to the cells which could not be displaced by excess alpha-MSH and only partially by [NIe4]-alpha-MSH. The [Tyr(125I)2,NIe4,D-Phe7]-alpha-MSH tracer gave similar results but with a much lower proportion of non-specific binding. On the other hand, [Tyr(125I)2]-alpha-MSH proved to be an excellent radioligand whose non-specific binding to the D10 cells was not higher than 20% of the total binding

  20. Decay constants in geochronology

    Institute of Scientific and Technical Information of China (English)

    IgorM.Villa; PaulR.Renne

    2005-01-01

    Geologic time is fundamental to the Earth Sciences, and progress in many disciplines depends critically on our ability to measure time with increasing accuracy and precision. Isotopic geochronology makes use of the decay of radioactive nuclides as a help to quantify the histories of rock, minerals, and other materials. Both accuracy and precision of radioisotopic ages are, at present, limited by those of radioactive decay constants. Modem mass spectrometers can measure isotope ratios with a precision of 10-4 or better. On the other hand, the uncertainties associated with direct half-life determinations are, in most cases, still at the percent level. The present short note briefly summarizes progress and problems that have been encountered during the Working Group's activity.

  1. Characterization of histamine receptors in isolated pig basilar artery by functional and radioligand binding studies

    International Nuclear Information System (INIS)

    Histamine receptors in pig basilar arteries were investigated in vitro by radioligand binding assays and by measuring the contractile and relaxant responses to histamine. Histamine and 2-pyridyethylamine (H1-agonist) induced concentration-dependent contractions, whereas impromidine (H2-agonist) induced concentration-dependent relaxations. These responses were independent of the presence of endothelial cells. Diphenhydramine (H1-antagonist) partially reversed the histamine-induced contractions to relaxations. Cimetidine (Hα2-antagonist) potentiated the contraction in a concentration-dependent manner. In the presence of cimetidine, the pEC50 value of histamine for the contraction was 6.30, and diphenhydramine competitively antagonized the histamine-induced contractions (pA2, 7.77). In the presence of diphenhydramine, the pEC50 value of histamine for the relaxation was 5.93, and cimetidine competitively antagonized the histamine-induced relaxations (pA2, 6.62). In the binding studies, the Kd value of [3H]mepyramine was 2.1 nM and the Bmax value was 95.6 fmol/mg protein. A competition experiment with diphenhydramine showed that the pKi value (7.51) was similar to the pA2 value. The Kd value for [3H]cimetidine was 126.0 nM and the Bmax value was 459.8 fmol/mg protein. The pKd (6.90) for [3H]cimetidine was similar to the pA2 for cimetidine. The Hill coefficients for these experiments were not significantly different from unity. The present findings indicate that the number of H1-receptors, in terms of the Bmax value for [3H]mepyramine, is smaller than that of H2-receptors, in terms of the Bmax value for [3H]cimetidine. However, the contractile response to histamine is predominantly mediated through stimulation of H1-receptors on vascular smooth muscle cells in pig basilar artery

  2. Preparation of 99Tcm-Annexin V and in vitro study of its binding characteristics in dopaminergic apoptotic neurons

    International Nuclear Information System (INIS)

    Objective: The aims of this study were two. One was to find out an optimal method for 99Tcm-Annexin V preparation and the other was to investigate the binding characteristics of 99Tcm-Annexin V in dopaminergic apoptotic neurons in vitro. Methods: For 99Tcm-Annexin V preparation, hydrazine nicotinamide (HYNIC), a bifunctional chelating agent was used. Product was purified by Sephadex G-25 column chromatography and analyzed with instant thin layer chromatography (ITLC). To test the binding characteristics in dopaminergic apoptotic neurons in vitro, a rat pheoehromocytoma cell line (PC12) treated with l-methyl-4-phenylpyridinium (MPP+) was used. Tests including time-temperature binding, saturable bind- ing, competition binding between dopaminergic apoptotic neurons and 99Tcm-HYNIC-Annexin V and dose- dependent MPP+ studies were performed and evaluated. Results: The labeling rate of 99Tcm was (64.56 ± 6.23)%. The specific activity of 99Tcm-HYNIC-Annexin V was (3.7-74)xl05 kBq/mg protein. The radiochemical purity was (93.6±2.48)% and was >90% after 4 hours storage at room temperature. Seat- chard plotting suggested that the concentrations of Kd was (7.16±1.78) nmol/L, and Bmax was (178.73± 32.62) fmoL/106 ceils. Conclusions: The preliminary results show that an optimal 99Tcm-HYNIC-Annexin V preparation method can be provided. The 99Tcm-HYNIC-Annexin V prepared in our laboratory has good receptor-binding activity and may possibly be a potential drug in studying the apoptotic phenomenon in Parkin- son's disease at early stage in an animal model. (authors)

  3. Stability, protein binding and clearance studies of [99mTc]DTPA. Evaluation of a commercially available dry-kit

    DEFF Research Database (Denmark)

    Rehling, M

    1988-01-01

    the quality of a commercial [99mTc]DTPA preparation (C.I.S., France) with reference to stability, protein binding and accuracy of the determined plasma clearance values as a measure of GFR. The stability of the preparations was studied by thin-layer chromatography, the in vitro protein binding by Sephadex...... filtration after incubation with human serum albumin and in vivo protein binding by filtration of human plasma. The accuracy of the plasma clearance values was investigated by comparison with the simultaneously measured plasma clearance of [51Cr]EDTA. There was no detectable free pertechnetate or hydrolysed...... reduced technetium in eight vials five and six hours after the preparation. The in vitro protein binding 10 (20), 120 and 300 min after the preparation of eight vials was 2.3% (0.8%), 0.2% and 0.1%, respectively. The in vivo protein binding in 12 patients 5, 90 and 180 min after the injection was 0.3%, 0...

  4. Kinetics and thermodynamics of glycans and glycoproteins binding to Holothuria scabra lectin: a fluorescence and surface plasmon resonance spectroscopic study.

    Science.gov (United States)

    Gowda, Nagaraj M; Gaikwad, Sushama M; Khan, M Islam

    2013-11-01

    Holothuria scabra produces a monomeric lectin (HSL) of 182 kDa. HSL showed strong antibacterial activity and induced bacterial agglutination under in vitro conditions, indicating its role in animals' innate immune responses. Very few lectins have been reported from echinoderms and none of these lectins have been explored in detail for their sugar-binding kinetics. Affinity, kinetics and thermodynamic analysis of glycans and glycoproteins binding to HSL were studied by fluorescence and surface plasmon resonance spectroscopy. Lectin binds with higher affinity to O-linked than N-linked asialo glycans, and the affinities were relatively higher than that for sialated glycans and glycoproteins. T-antigen α-methyl glycoside was the most potent ligand having the highest affinity (Ka 8.32 ×10(7) M(-1)). Thermodynamic and kinetic analysis indicated that the binding of galactosyl Tn-antigen and asialo glycans is accompanied by an enthalpic contribution in addition to higher association rate coupled by low activation energy for the association process. Presence of sialic acid or protein matrix inhibits binding. Higher affinity of HSL for O-glycans than N-glycans had biological implications; since HSL specifically recognizes bacteria, which have mucin or O-glycan cognate on their cell surfaces and play a major role in animal innate immunity. Since, HSL had higher affinity to T-antigen, makes it a useful tool for cancer diagnostic purpose. PMID:23736907

  5. A structure-activity-relationship (SAR) study of somatostatin receptor-binding peptides radiolabeled with Tc-99m

    Energy Technology Data Exchange (ETDEWEB)

    Lister-James, J.; McBride, W.J.; Moyer, B.R. [Diatech, Inc, Londonderry, NH (United States)] [and others

    1994-05-01

    Somatostatin receptor (SSTR)-expressing tumors can be detected with high accuracy using In-111-[DTPA]octreotide. We sought a high-affinity SSTR-binding peptide labeled with the preferred radioisotope Tc-99m. We have prepared over 120 SSTR-binding peptides each containing a (N{sub 3}S or N{sub 2}S{sub 2}) chelator for Tc-99m in a SAR study in which peptide structure was systematically altered to optimize SSTR-binding affinity, in vivo rumor uptake and favorable biodistribution and pharmacokinetics. The HPLC-purified (>90% purity), chelator-containing peptides were characterized by FAB/ESMS and assayed in vitro for SSTR binding affinity by a competition assay (I-125 somatostatin-14 tracer and AR42J rat pancreatic tumor cell membranes). The oxo-rhenium complexes of the peptides were prepared by ligand exchange, characterized by FAB or ESMS and assayed for SSTR binding affinity as surrogates for the Tc-99m complexes. The Tc-99m complexes of peptides giving high-affinity oxo-rhenium complexes were also prepared by ligand exchange with specific activities of approx 300 mCi/mmol and examined in vivo for biodistribution and tumor uptake characteristics in CA20948 tumor-bearing rats.

  6. Atomic hydrogen and fundamental physical constants

    International Nuclear Information System (INIS)

    Techniques are described which allow the study, in undergraduate laboratories, of the spectrum of atomic hydrogen. The Rydberg constant, the electron-proton mass ratio, and the fine-structure constant are evaluated from the measurements. The key to the series of experiments is a discharge tube in which atomic lines dominate over the molecular lines. (author)

  7. Modulation of the antioxidant activity of HO* scavengers by albumin binding: a 19F-NMR study.

    Science.gov (United States)

    Aime, Silvio; Digilio, Giuseppe; Bruno, Erik; Mainero, Valentina; Baroni, Simona; Fasano, Mauro

    2003-08-01

    The interaction between different HO(z.rad;) radical scavengers in a three-component antioxidant system has been investigated by means of 19F-NMR spectroscopy. This system is composed of bovine serum albumin (BSA), trolox, and N-(4-hydroxyphenyl)-trifluoroacetamide (CF(3)PAF). The antioxidant capacity of BSA and trolox has been assessed by measuring the amount of trifluoroacetamide (TFAM) arising from the radical mediated decomposition of CF(3)PAF. When assayed separately, both trolox and BSA behaved as antioxidants, as they were effective to protect CF(3)PAF from HO* radical-mediated decomposition. By contrast, trolox enhanced the production of TFAM in the presence of BSA, thus behaving as a pro-oxidant. Urate, carnosine, glucose, and propylgallate showed antioxidant properties both with or without BSA. CF(3)PAF and trolox were found to bind to BSA with association constants in the order of 5 x 10(3)M(-1) and to compete for the same binding sites. These results have been discussed in terms of BSA-catalysed cross-reactions between trolox-derived secondary radicals and CF(3)PAF. PMID:12878205

  8. A sensitive flow cytometric methodology for studying the binding of L. chagasi to canine peritoneal macrophages

    Directory of Open Access Journals (Sweden)

    Mosser David M

    2005-05-01

    Full Text Available Abstract Background The Leishmania promastigote-macrophage interaction occurs through the association of multiple receptors on the biological membrane surfaces. The success of the parasite infection is dramatically dependent on this early interaction in the vertebrate host, which permits or not the development of the disease. In this study we propose a novel methodology using flow cytometry to study this interaction, and compare it with a previously described "in vitro" binding assay. Methods To study parasite-macrophage interaction, peritoneal macrophages were obtained from 4 dogs and adjusted to 3 × 106 cells/mL. Leishmania (Leishmania chagasi parasites (stationary-phase were adjusted to 5 × 107 cells/mL. The interaction between CFSE-stained Leishmania chagasi and canine peritoneal macrophages was performed in polypropylene tubes to avoid macrophage adhesion. We carried out assays in the presence or absence of normal serum or in the presence of a final concentration of 5% of C5 deficient (serum from AKR/J mice mouse serum. Then, the number of infected macrophages was counted in an optical microscope, as well as by flow citometry. Macrophages obtained were stained with anti-CR3 (CD11b/CD18 antibodies and analyzed by flow citometry. Results Our results have shown that the interaction between Leishmania and macrophages can be measured by flow cytometry using the fluorescent dye CFSE to identify the Leishmania, and measuring simultaneously the expression of an important integrin involved in this interaction: the CD11b/CD18 (CR3 or Mac-1 β2 integrin. Conclusion Flow cytometry offers rapid, reliable and sensitive measurements of single cell interactions with Leishmania in unstained or phenotypically defined cell populations following staining with one or more fluorochromes.

  9. Docking Studies of Binding of Ethambutol to the C-Terminal Domain of the Arabinosyltransferase from Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Guillermo Salgado-Moran

    2013-01-01

    Full Text Available The binding of ethambutol to the C-terminal domain of the arabinosyltransferase from Mycobacterium tuberculosis was studied. The analysis was performed using an in silico approach in order to find out, by docking calculations and energy descriptors, the conformer of Ethambutol that forms the most stable complex with the C-terminal domain of arabinosyltransferase. The complex shows that location of the Ethambutol coincides with the cocrystallization ligand position and that amino acid residues ASH1051, ASN740, ASP1052, and ARG1055 should be critical in the binding of Ethambutol to C-terminal domain EmbC.

  10. Reductions in [3H]nicotinic acetylcholine binding in Alzheimer's disease and Parkinson's disease: an autoradiographic study

    International Nuclear Information System (INIS)

    In Alzheimer's disease (AD) and Parkinson's disease (PD), dysfunction in the basal forebrain cholinergic system is accompanied by a consistent loss of presynaptic cholinergic markers in cortex, but changes in cholinergic receptor binding sites are poorly understood. In the present study, we used receptor autoradiography to map the distribution of nicotinic [3H]acetylcholine binding sites in cortices of individuals with AD and PD and matched control subjects. In both diseases, a profound loss of nicotinic receptors occurs in all cortical layers, particularly the deepest layers

  11. Application of a simple calorimetric data analysis on the binding study of cyanide ions by Jack bean urease

    Institute of Scientific and Technical Information of China (English)

    G.Rezaei; Behbehani; A.A.Saboury; M.Mohebbian; S.Ghammamy

    2010-01-01

    Cyanide ion was studied as an effector of Jack bean urease(JBU) at 300 K in 30 mmol/LTris buffer,pH 7 by isothermal titration calorimetry(ITC).The simple novel model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the simple novel model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a noncooperative inhibitor of JBU,and there is a set of 12 identical and independent binding sites for CN~- ions.The...

  12. Structural and thermodynamic analysis of the binding of tRNA(phe) by the putative anticancer alkaloid chelerythrine: Spectroscopy, calorimetry and molecular docking studies.

    Science.gov (United States)

    Basu, Pritha; Payghan, Pavan V; Ghoshal, Nanda; Suresh Kumar, Gopinatha

    2016-08-01

    The interaction of the putative anticancer alkaloid chelerythrine with tRNA(phe) was characterized by spectroscopy, calorimetry and molecular docking studies. The charged iminium form of chelerythrine binds with tRNA(phe) in a cooperative mode with a binding affinity value of (4.06±0.01)×10(5)M(-1). The neutral alkanolamine form does not bind to tRNA(phe) but in the presence of high concentration of tRNA(phe) this form gets converted to the iminium form and then binds with tRNA(phe). The partial intercalative mode of binding of chelerythrine to the tRNA(phe) was characterized from the steady state anisotropy, iodide ion-induced fluorescence quenching and viscosity measurements. Chelerythrine binding induced conformational perturbations in tRNA(phe) as observed from the circular dichroism spectroscopy. The strong binding was also supported by the ethidium bromide displacement assay. The binding was favoured by both enthalpy and entropy contributions. Although the binding was dependent on the [Na(+)], non-electrostatic forces contributed predominantly to the Gibbs energy change. The negative value of the heat capacity change proposed the involvement of hydrophobic forces in the binding. Molecular docking study was carried out to decipher the details of the recognition of tRNA(phe) by chelerythrine. The study provided insights about the chelerythrine binding pockets on tRNA(phe) and marked the necessary interactions for binding of chelerythrine molecule. Partially intercalative mode of the alkaloid binding was supported by docking studies. In total, docking studies corroborated well with our experiential observations. The structural and thermodynamic results of chelerythrine binding to tRNA(phe) may be helpful to develop new RNA therapeutic agents. PMID:27289446

  13. Structural and functional studies of a large winged Z-DNA-binding domain of Danio rerio protein kinase PKZ.

    Science.gov (United States)

    Subramani, Vinod Kumar; Kim, Doyoun; Yun, Kyunghee; Kim, Kyeong Kyu

    2016-07-01

    The Z-DNA-binding domain of PKZ from zebrafish (Danio rerio; drZαPKZ ) contains the largest β-wing among known Z-DNA-binding domains. To elucidate the functional implication of the β-wing, we solved the crystal structure of apo-drZαPKZ . Structural comparison with its Z-DNA-bound form revealed a large conformational change within the β-wing during Z-DNA binding. Biochemical studies of protein mutants revealed that two basic residues in the β-wing are responsible for Z-DNA recognition as well as fast B-Z transition. Therefore, the extra basic residues in the β-wing of drZαPKZ are necessary for the fast B-Z transition activity. PMID:27265117

  14. Investigation of three flavonoids binding to bovine serum albumin using molecular fluorescence technique

    International Nuclear Information System (INIS)

    The three flavonoids including naringenin, hesperetin and apigenin binding to bovine serum albumin (BSA) at pH 7.4 was studied by fluorescence quenching, synchronous fluorescence and UV-vis absorption spectroscopic techniques. The results obtained revealed that naringenin, hesperetin and apigenin strongly quenched the intrinsic fluorescence of BSA. The Stern-Volmer curves suggested that these quenching processes were all static quenching processes. At 291 K, the value and the order of the binding constant were KAnaringenin)=4.08x104A(hesperetin)=5.40x104∼KA(apigenin)=5.32x104 L mol-1. The main binding force between the flavonoid and BSA was hydrophobic and electrostatic force. According to the Foerster theory of non-radiation energy transfer, the binding distances (r0) were obtained as 3.36, 3.47 and 3.30 nm for naringenin-BSA, hesperetin-BSA and apigenin-BSA, respectively. The effect of some common ions such as Fe3+, Cu2+, Mg2+, Mn2+, Zn2+ and Ca2+ on the binding was also studied in detail. The competition binding was also performed. The apparent binding constant (K'A) obtained suggested that one flavonoid had an obvious effect on the binding of another flavonoid to protein when they coexisted in BSA solution. - Highlights: → Quenchings of BSA fluorescence by the flavonoids was all static quenchings. → Synchronous fluorescence was applied to study the structural change of BSA. → Binding constant, binding site and binding force were determined. → Competition binding experiments were performed. → One flavonoid had an obvious effect on the binding of another one to BSA.

  15. Growth hormone-binding protein: II. Studies in pygmies and normal statured subjects.

    Science.gov (United States)

    Merimee, T J; Baumann, G; Daughaday, W

    1990-11-01

    The serum concentrations of a specific GH-binding protein, derived from the GH receptor, were assayed in sera from 62 African pygmies and 101 normal statured controls. Samples were assayed in the absence and presence of excess GH using 2 separatory procedures. Interassay variability for samples was corrected by a standard reference pool of sera from adults assayed with all unknown samples. Results were expressed as specific binding relative to this standard. The mean percent relative specific binding for GH increased with age in normal-statured controls throughout childhood and adolescence. Relative specific binding for GH was 37.0 +/- 2.0% (mean +/- SEM) in control subjects between the ages of 1-5 yr (mean age, 2.9 yr) and increased progressively to 93.0 +/- 7.0% in young adults (mean age, 23 yr). The relative specific binding of GH by serum from pygmies did not exceed 30.1 +/- 3.4% of the control adult standard at any age period (P less than 0.001), and there was no progressive age-related increase in binding. The decrease from normal binding was minimal in pygmies during childhood (29%), but the decrease from normal was 60-70% in adolescents and adults. Thus, short stature in pygmies probably results not from an absolute deficiency of GH receptors per se, as in Laron dwarfism, but from a failure of cellular GH receptors to increase in a normal manner. This is most compatible with a change in regulating expression of the GH receptor gene, rather than a structural defect in the coding sequence of the GH receptor gene.

  16. Molecular modeling study on the allosteric inhibition mechanism of HIV-1 integrase by LEDGF/p75 binding site inhibitors.

    Directory of Open Access Journals (Sweden)

    Weiwei Xue

    Full Text Available HIV-1 integrase (IN is essential for the integration of viral DNA into the host genome and an attractive therapeutic target for developing antiretroviral inhibitors. LEDGINs are a class of allosteric inhibitors targeting LEDGF/p75 binding site of HIV-1 IN. Yet, the detailed binding mode and allosteric inhibition mechanism of LEDGINs to HIV-1 IN is only partially understood, which hinders the structure-based design of more potent anti-HIV agents. A molecular modeling study combining molecular docking, molecular dynamics simulation, and binding free energy calculation were performed to investigate the interaction details of HIV-1 IN catalytic core domain (CCD with two recently discovered LEDGINs BI-1001 and CX14442, as well as the LEDGF/p75 protein. Simulation results demonstrated the hydrophobic domain of BI-1001 and CX14442 engages one subunit of HIV-1 IN CCD dimer through hydrophobic interactions, and the hydrophilic group forms hydrogen bonds with HIV-1 IN CCD residues from other subunit. CX14442 has a larger tert-butyl group than the methyl of BI-1001, and forms better interactions with the highly hydrophobic binding pocket of HIV-1 IN CCD dimer interface, which can explain the stronger affinity of CX14442 than BI-1001. Analysis of the binding mode of LEDGF/p75 with HIV-1 IN CCD reveals that the LEDGF/p75 integrase binding domain residues Ile365, Asp366, Phe406 and Val408 have significant contributions to the binding of the LEDGF/p75 to HIV1-IN. Remarkably, we found that binding of BI-1001 and CX14442 to HIV-1 IN CCD induced the structural rearrangements of the 140 s loop and oration displacements of the side chains of the three conserved catalytic residues Asp64, Asp116, and Glu152 located at the active site. These results we obtained will be valuable not only for understanding the allosteric inhibition mechanism of LEDGINs but also for the rational design of allosteric inhibitors of HIV-1 IN targeting LEDGF/p75 binding site.

  17. Metal-ligand binding affinity vs reactivity: qualitative studies in Rh(I)-catalyzed asymmetric ring-opening reactions.

    Science.gov (United States)

    Tsui, Gavin Chit; Dougan, Patrick; Lautens, Mark

    2013-06-01

    Rh(I)-catalyzed asymmetric ring opening (ARO) of oxabenzonorbornadiene is used as a model system to qualitatively study reactions involving multiple metal-ligand interactions. The key feature of this approach is the use of product ee as an indicator to quickly gain important information such as the relative ligand binding affinity and relative reactivity of catalysts.

  18. Interaction of phenylbutazone and colchicine in binding to serum albumin in rheumatoid therapy: 1H NMR study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Sułkowska, A.; Bojko, B.; Równicka-Zubik, J.; Sułkowski, W. W.

    2009-09-01

    The monitoring of drug concentration in blood serum is necessary in multi-drug therapy. Mechanism of drug binding with serum albumin (SA) is one of the most important factors which determine drug concentration and its transport to the destination tissues. In rheumatoid diseases drugs which can induce various adverse effects are commonly used in combination therapy. Such proceeding may result in the enhancement of those side effects due to drug interaction. Interaction of phenylbutazone and colchicine in binding to serum albumin and competition between them in gout has been studied by proton nuclear magnetic resonance ( 1H NMR) technique. The aim of the study was to determine the low affinity binding sites, the strength and kind of interaction between serum albumin and drugs used in combination therapy. The study of competition between phenylbutazone and colchicine in binding to serum albumin points to the change of their affinity to serum albumin in the ternary systems. This should be taken into account in multi-drug therapy. This work is a subsequent part of the spectroscopic study on Phe-COL-SA interactions [A. Sułkowska, et al., J. Mol. Struct. 881 (2008) 97-106].

  19. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    Energy Technology Data Exchange (ETDEWEB)

    Bijari, Nooshin [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Shokoohinia, Yalda [Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza; Ranjbar, Samira; Parvaneh, Shahram [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Moieni-Arya, Maryam [Student Research Committee, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: rkhodarahmi@mbrc.ac.ir [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2013-11-15

    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp{sub 214} residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes.

  20. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    International Nuclear Information System (INIS)

    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp214 residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes

  1. Theoretical studies on the binding energy of β-sheet models

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper,B3LYP and MP2 methods are used to investigate the binding energy of seventeen antiparallel and parallel β-sheet models. The results indicate that the binding energy obtained from B3LYP calculations is weaker than that obtained from MP2 calculations but the relative binding energy yielded by B3LYP is almost the same as that by MP2. For the antiparallel β-sheets in which two N―H···O═C hydrogen bonds can form either a large hydrogen-bonded ring or a small hydrogen-bonded ring,the binding energy increases obviously when one large ring unit is added,whereas it only changes slightly when one small ring unit is added because of the secondary electrostatic repulsive interaction existing in the small ring unit which is estimated to be about 20 kJ/mol. For the parallel β-sheet models,the binding energy increases almost exactly linearly with the increase of the chain length.

  2. Comparative analysis of Vening-Meinesz Moritz isostatic models using the constant and variable crust-mantle density contrast – a case study of Zealandia

    Indian Academy of Sciences (India)

    Mohammad Bagherbandi; Robert Tenzer

    2013-04-01

    We compare three different numerical schemes of treating the Moho density contrast in gravimetric inverse problems for finding the Moho depths. The results are validated using the global crustal model CRUST2.0, which is determined based purely on seismic data. Firstly, the gravimetric recovery of the Moho depths is realized by solving Moritz’s generalization of the Vening-Meinesz inverse problem of isostasy while the constant Moho density contrast is adopted. The Pratt-Hayford isostatic model is then facilitated to estimate the variable Moho density contrast. This variable Moho density contrast is subsequently used to determine the Moho depths. Finally, the combined least-squares approach is applied to estimate jointly the Moho depths and density contract based on a priori error model. The EGM2008 global gravity model and the DTM2006.0 global topographic/bathymetric model are used to generate the isostatic gravity anomalies. The comparison of numerical results reveals that the optimal isostatic inverse scheme should take into consideration both the variable depth and density of compensation. This is achieved by applying the combined least-squares approach for a simultaneous estimation of both Moho parameters. We demonstrate that the result obtained using this method has the best agreement with the CRUST2.0 Moho depths. The numerical experiments are conducted at the regional study area of New Zealand’s continental shelf.

  3. Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study.

    Science.gov (United States)

    Carvalheda, Catarina A; Campos, Sara R R; Machuqueiro, Miguel; Baptista, António M

    2013-11-25

    The pulmonary surfactant protein C (SP-C) is a small highly hydrophobic protein that adopts a mainly helical structure while associated with the membrane but misfolds into a β-rich metastable structure upon deacylation, membrane dissociation, and exposure to the neutral pH of the aqueous alveolar subphase, eventually leading to the formation of amyloid aggregates associated with pulmonary alveolar proteinosis. The present constant-pH MD study of the acylated and deacylated isoforms of SP-C in a chloroform/methanol/water mixture, often used to mimic the membrane environment, shows that the loss of the acyl groups has a structural destabilizing effect and that the increase of pH promotes intraprotein contacts which contribute to the loss of helical structure in solution. These contacts result from the poor solvation of charged groups by the solvent mixture, which exhibits a limited membrane-mimetic character. Although a single SP-C molecule was used in the simulations, we propose that analogous intermolecular interactions may play a role in the early stages of the protein misfolding and aggregation in this mixture.

  4. The potentiometric and laser RAMAN study of the hydrolysis of uranyl chloride under physiological conditions and the effect of systematic and random errors on the hydrolysis constants

    International Nuclear Information System (INIS)

    The hydrolysis of uranyl ions in 0.15 mol/L (Na)C1 solution at 37 degrees Celsius has been studied by potentiometric titration. The results were consistent with the formation of (UO2)2(OH)2, (UO2)3(OH)4, (UO2)3(OH)5 and (UO2)4(OH)7. The stability constants, which were evaluated using a version of MINIQUAD, were found to be: log β22 = -5.693 ± 0.007, log β34 = -11.499 ± 0.024, log β35 = -16.001 ± 0.050, log β47 = -21.027 ± 0.051. Laser Raman spectroscopy has been used to identify the products including (UO2)4(OH)7 species. The difficulties in identifying the chemical species in solution and the effect of small errors on this selection has also been investigated by computer simulation. The results clearly indicate that small errors can lead to the selection of species that may not exist

  5. A study of the importance of the cell geometry in non-Faradaic systems. A new definition of the cell constant for conductivity measurement

    International Nuclear Information System (INIS)

    A new definition for the electrochemical cell constant in conductivity measurements is presented in this paper. Electrochemical Impedance Spectroscopy and DC pulses measurements have been carried out in non-Faradaic conditions in order to evaluate the effects of the cell geometry. The results obtained demonstrate that conductivity measurements are affected not only by the electrodes surface and separation but also by the cross section of the electrochemical cell. In order to obtain a linear behavior of the resistance versus the distance between electrodes, the cross section of the cell should be equal to the electrodes surface. Differences between the cell cross section and the electrodes surface produce a heterogeneous distribution of the electric field that causes the non-linear behavior for low values of the electrodes separation. This study shows that the reproducibility in electronic tongue and humid electronic nose measurements can be improved by designing an electrochemical cell structure that warrants a homogeneous distribution of the electrical field, which results in a reduction of the detection threshold in these types of system

  6. Numerical Study of Laminar Forced Convection of Water/Al2o3 Nanofluid in an Annulus with Constant Wall Temperature

    Directory of Open Access Journals (Sweden)

    Amin Kashani

    2013-04-01

    Full Text Available Laminar forced convection of a nanofluid consisting of water and Al2O3 in a horizontal annulus has been studied numerically. Two-phase mixture model has been used to investigate thermal behaviors of the nanofluid over constant temperature thermal boundary condition and with different volume concentration of nanoparticles. Comparisons with previously published experimental and analytical works on flow behavior in horizontal annulus show good agreements between the results as volume fraction is zero. In general convective heat transfer coefficient increases with nanoparticle concentration. ABSTRAK: Kertaskerja ini mengkaji secara numerik olakan paksa bendalir lamina yang menganduangi air dan Al2O3 didalam anulus mendatar. Model campuran dua fasa digunakan bagi mengkaji tingkah laku haba bendalir nano pada keadaan suhu malar dengan kepekatan nanopartikel berbeza. Perbandingan dengan karya eksperimen dan analitikal yang telah diterbitkan menunjukkan bahawa kelakuan aliran didalm anulus mendatar adalah baik apabila pecahan isipadu adalah sifar. Pada amnya, pekali pemindahan haba olakan meningkat dengan kepekatan nanopartikel. KEYWORDS: nanofluid; volume concentration; heat transfer enhancement; laminar flow convection; annulus

  7. Study of pK values and effective dielectric constants of ionizable residues in pentapeptides and in staphylococcal nuclease (SNase) using a mean-field approach.

    Science.gov (United States)

    Bossa, Guilherme Volpe; Fahr, Alfred; Pereira de Souza, Tereza

    2014-04-17

    The determination of pK values of amino acid residues as a function of temperature and ionic concentration is crucial to understanding the dynamics of various biological processes such as adsorption of peptides and their interactions with active sites of enzymes. In this study we developed a mean-field model to calculate the position-dependent dielectric constants of ionizable groups and the mean electrostatic potential on the surface. Such potential, which takes into account the contributions exerted by neighboring groups and ions in solution, is responsible for the fine-tuning of the pK value of each residue. The proposed model was applied to the amino acids Asp, Glu, Lys, His, Tyr, and Cys, and since the results were consistent with experimentally obtained values, the model was extended and applied to computation of pK values of Gly and Ala pentapeptides and of ionizable residues of the enzyme staphylococcal nuclease (SNase). In this latter case, we used an approach similar to a first-neighbors approximation, and the results turned out to be in good agreement with previously reported data when considering only the interactions of charged groups located at distances of maximally 20 Å. These considerations and the little computational cost involved turn the suggested approach into a promising tool for the modeling of force fields in computational simulations.

  8. Combined spectroscopy and molecular modeling studies on the binding of galbanic acid and MMP9.

    Science.gov (United States)

    Kiani, Amir; Almasi, Khadijeh; Shokoohinia, Yalda; Sadrjavadi, Komail; Nowroozi, Amin; Shahlaei, Mohsen

    2015-11-01

    The molecular mechanism of galbanic acid (GBA) binding to matrix metalloproteinase 9 (MMP9) was investigated by fluorescence quenching, absorption spectroscopy, FT-IR, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of MMP9 was quenched by GBA. The titration of MMP9 by various amount of GBA was also followed by UV-Vis absorption spectroscopy. The results revealed that GBA, as a biologically active sesquiterpene coumarin derivative, has an ability to bind strongly to MMP9. Molecular docking results indicated that the main active binding site for GBA has been located in a hydrophobic cavity in the vicinity of Zn atom. Moreover, MD simulation results suggested that GBA as a coumarin derivative can interact with MMP9, without affecting the secondary structure of MMP9. MD simulations, molecular docking as computational methods from one hand and experimental data from other hand reciprocally supported each other.

  9. RNA and DNA binding properties of HIV-1 Vif protein: a fluorescence study.

    Science.gov (United States)

    Bernacchi, Serena; Henriet, Simon; Dumas, Philippe; Paillart, Jean-Christophe; Marquet, Roland

    2007-09-01

    The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Some "non-permissive" cell lines cannot sustain replication of Vif(-) HIV-1 virions. In these cells, Vif counteracts the natural antiretroviral activity of the DNA-editing enzymes APOBEC3G/3F. Moreover, Vif is packaged into viral particles through a strong interaction with genomic RNA in viral nucleoprotein complexes. To gain insights into determinants of this binding process, we performed the first characterization of Vif/nucleic acid interactions using Vif intrinsic fluorescence. We determined the affinity of Vif for RNA fragments corresponding to various regions of the HIV-1 genome. Our results demonstrated preferential and moderately cooperative binding for RNAs corresponding to the 5'-untranslated region of HIV-1 (5'-untranslated region) and gag (cooperativity parameter omega approximately 65-80, and K(d) = 45-55 nM). In addition, fluorescence spectroscopy allowed us to point out the TAR apical loop and a short region in gag as primary strong affinity binding sites (K(d) = 9.5-14 nM). Interestingly, beside its RNA binding properties, the Vif protein can also bind the corresponding DNA oligonucleotides and their complementary counterparts with an affinity similar to the one observed for the RNA sequences, while other DNA sequences displayed reduced affinity. Taken together, our results suggest that Vif binding to RNA and DNA offers several non-exclusive ways to counteract APOBEC3G/3F factors, in addition to the well documented Vif-induced degradation by the proteasome and to the Vif-mediated repression of translation of these antiviral factors. PMID:17609216

  10. 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 BACKGROUND: 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. METHODOLOGY: 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. CONCLUSIONS: 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. AVAILABILITY: We provide a web server for our three-phase approach: http://hybsvm.gdcb.iastate.edu.

  11. Membrane orientation and binding determinants of G protein-coupled receptor kinase 5 as assessed by combined vibrational spectroscopic studies.

    Directory of Open Access Journals (Sweden)

    Pei Yang

    Full Text Available G-protein coupled receptors (GPCRs are integral membrane proteins involved in a wide variety of biological processes in eukaryotic cells, and are targeted by a large fraction of marketed drugs. GPCR kinases (GRKs play important roles in feedback regulation of GPCRs, such as of β-adrenergic receptors in the heart, where GRK2 and GRK5 are the major isoforms expressed. Membrane targeting is essential for GRK function in cells. Whereas GRK2 is recruited to the membrane by heterotrimeric Gβγ subunits, the mechanism of membrane binding by GRK5 is not fully understood. It has been proposed that GRK5 is constitutively associated with membranes through elements located at its N-terminus, its C-terminus, or both. The membrane orientation of GRK5 is also a matter of speculation. In this work, we combined sum frequency generation (SFG vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR to help determine the membrane orientation of GRK5 and a C-terminally truncated mutant (GRK51-531 on membrane lipid bilayers. It was found that GRK5 and GRK51-531 adopt a similar orientation on model cell membranes in the presence of PIP2 that is similar to that predicted for GRK2 in prior studies. Mutation of the N-terminal membrane binding site of GRK5 did not eliminate membrane binding, but prevented observation of this discrete orientation. The C-terminus of GRK5 does not have substantial impact on either membrane binding or orientation in this model system. Thus, the C-terminus of GRK5 may drive membrane binding in cells via interactions with other proteins at the plasma membrane or bind in an unstructured manner to negatively charged membranes.

  12. A preliminary MTD-PLS study for androgen receptor binding of steroid compounds

    Science.gov (United States)

    Bora, Alina; Seclaman, E.; Kurunczi, L.; Funar-Timofei, Simona

    The relative binding affinities (RBA) of a series of 30 steroids for Human Androgen Receptor (AR) were used to initiate a MTD-PLS study. The 3D structures of all the compounds were obtained through geometry optimization in the framework of AM1 semiempirical quantum chemical method. The MTD hypermolecule (HM) was constructed, superposing these structures on the AR-bonded dihydrotestosterone (DHT) skeleton obtained from PDB (AR complex, ID 1I37). The parameters characterizing the HM vertices were collected using: AM1 charges, XlogP fragmental values, calculated fragmental polarizabilities (from refractivities), volumes, and H-bond parameters (Raevsky's thermodynamic originated scale). The resulted QSAR data matrix was submitted to PCA (Principal Component Analysis) and PLS (Projections in Latent Structures) procedure (SIMCA P 9.0); five compounds were selected as test set, and the remaining 25 molecules were used as training set. In the PLS procedure supplementary chemical information was introduced, i.e. the steric effect was always considered detrimental, and the hydrophobic and van der Waals interactions were imposed to be beneficial. The initial PLS model using the entire training set has the following characteristics: R2Y = 0.584, Q2 = 0.344. Based on distances to the model criterions (DMODX and DMODY), five compounds were eliminated and the obtained final model had the following characteristics: R2Y D 0.891, Q2 D 0.591. For this the external predictivity on the test set was unsatisfactory. A tentative explanation for these behaviors is the weak information content of the input QSAR matrix for the present series comparatively with other successful MTD-PLS modeling published elsewhere.

  13. Kinetic study of coniferyl alcohol radical binding to the (+)-pinoresinol forming dirigent protein.

    Science.gov (United States)

    Halls, Steven C; Davin, Laurence B; Kramer, David M; Lewis, Norman G

    2004-03-01

    An essential step in lignan and lignin formation in planta is one electron oxidation of (E)-coniferyl alcohol (CA) to generate the radical intermediate (CA(*)), which can then undergo directed radical-radical couplings in vivo. For lignan formation in vitro and in vivo, stereoselective coupling of CA(*) only occurs to afford (+)-pinoresinol in the additional presence of (+)-pinoresinol forming dirigent protein (DP). Presented herein is a kinetic and thermodynamic study which reveals the central mechanistic details of the coupling process involved in DP-mediated coupling. DP activity was maximal between pH 4.25 and pH 6.0, with activity being maintained at temperatures below 33 degrees C. Equilibrium binding assays revealed that coniferyl alcohol was only weakly bound to the DP, with a K(D) of 370 +/- 65 microM. On the other hand, the enantiomeric excess of (+)-pinoresinol formed was dependent on both DP concentration and rate of CA oxidation and, thus, on apparent steady-state [CA(*)]. The data obtained could best be explained using a kinetic model where radical-radical coupling via DP competes with that occurring in open solution. Using this model, an apparent K(M) of about 10 nM was estimated from the saturation behavior of (+)-pinoresinol formation with respect to apparent steady-state [CA(*)]. These data strongly suggest that CA(*), rather than CA, is the substrate for DP, in agreement with earlier predictions. A mechanism of directed radical-radical coupling, where two coniferyl alcohol radical substrates are bound per protein dimer, is proposed.

  14. Mechanical properties of phosphorene nanotubes: a density functional tight-binding study.

    Science.gov (United States)

    Sorkin, V; Zhang, Y W

    2016-09-30

    Using the density functional tight-binding method, we studied the elastic properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) under uniaxial tensile strain. We found that the deformation and failure of PNTs are very much anisotropic. For ZZ PNTs, three deformation phases are recognized: the primary linear elastic phase-which is associated with interactions between neighboring puckers, succeeded by the bond rotation phase-where the puckered configuration of phosphorene is smoothed via bond rotation, and lastly the bond elongation phase-where the P-P bonds are directly stretched up to the maximally allowed limit and failure is initiated by the rupture of the most stretched bonds. For AC PNTs, the applied strain stretches the bonds up to the maximally allowed limit, causing their ultimate failure. For both AC and ZZ PNTs, their failure strain and failure stress are sensitive- while the Young's modulus, flexural rigidity, radial Poisson's ratio and thickness Poisson's ratio are relatively insensitive-to the tube diameter. More specifically, for AC PNTs, the failure strain decreases from 0.40 to 0.25 and the failure stress increases from 13 GPa to 21 GPa when the tube diameter increases from 13.3 Å to 32.8 Å; while for ZZ PNTs, the failure strain decreases from 0.66 to 0.55 and the failure stress increases from 4 GPa to 9 GPa when the tube diameter increases from 13.2 Å to 31.1 Å. The Young's modulus, flexural rigidity, radial and thickness Poisson ratios are 114.2 GPa, 0.019 eV · nm(2), 0.47 and 0.11 for AC PNTs, and 49.2 GPa, 0.071 eV · nm(2), 0.07 and 0.21 for ZZ PNTs, respectively. The present findings provide valuable references for the design and application of PNTs as device elements. PMID:27535543

  15. Theory of dielectric loss in Graphene-on-substrate: A tight- binding model study

    Science.gov (United States)

    Sahu, Sivabrata; Panda, S. K.; Rout, G. C.

    2016-09-01

    Graphene-on-substrate exhibits interesting dielectric behaviour due to screening of coulomb interaction induced by many body effects. In this communication we attempt to study the dielectric loss property of graphene within tight-binding model approach. The Hamiltonian consisting of electron hopping upto third-nearest-neighbour's with impurities in two in equivalent sub-lattices. The graphene-on-substrate raises the energy +Δ at one sub lattice and reduces energy -Δ at other sub lattice. Further we introduced coulomb interaction between π - electrons at the two sub lattices separately with the same effective coulomb interaction. We calculate polarization function Π(q, ω) which is a two particle Green's function arising due to charge-charge correlation by using Zubarev's Green's function technique. Finally we calculate dielectric function of graphene i.e. ε(q, ω) =1+Π(q,ω) at arbitrary wave vector q and frequency ra. The dielectric loss in graphene calculated from the imaginary part of dielectric function which is a measure of absorption spectrum. Only a few Fragmentary theoretical attempts have been made to utilize the full frequency and wave vector dependent dielectric function. We compute numerically the frequency dependent dielectric loss function for 100x100 momentum grid points. We observe a low energy Plasmon resonance peak and a high energy flat peak arising due to absorption of optical energy at substrate induced gap. With increase of small Plasmon wave vector, both low and high energy peaks approach each other. The dielectric loss at low energies exhibits a parabolic curve, but it exhibit a clear peak on introduction of higher order electron hopping's. The Coulomb interaction suppresses induced gap in graphene and decreases the optical energy absorption spectra. The increase of substrate induced gap shifts the high energy flat peak to higher energies and enhances the dielectric loss throughout the frequency range. Finally the effect of doping on

  16. Apoferritin-based nanomedicine platform for drug delivery: equilibrium binding study of daunomycin with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Ma Ham, Aihui; Wu, Hong J.; Wang, Jun; Kang, Xinhuang; Zhang, Youyu; Lin, Yuehe

    2011-05-11

    Apoferritin is a nanostructured material with a uniform size and spherical structure, and it has excellent bio-compatibility. In this work, we report the use of apoferritin as a novel and biocompatible carrier for stabilizing enzymes and their activities. We used glucose oxidase (GOx) as a model enzyme. GOx was immobilized on the surface of the apoferritin through a green synthetic approach taking advantage of bioaffinity binding between streptavidin and biotin. As a result, a glucose oxidase-biotin/streptavidin/biotin-apoferritin conjugate (Apo-GOx) was prepared using streptavidin as a bridge. The synthesized Apo-GOx was characterized with transmission electron microscopy, ultraviolet, and fluorescence spectroscopy. The activity and stability of GOx on the surface of the apoferritin were studied in different environments, such as temperature, chemicals, and pH, in comparison with the biotinylated GOx (B-GOx). The results showed that the activity of GOx on the apoferritin surface was significantly enhanced. The thermal and chemical stability of the GOx on the apoferritin was also greatly improved compared to free B-GOx in a solution. It was found that the activity of the GOx on the apoferritin only lost 30% in comparison to a 70% loss of free B-GOx after a 2-hr incubation at 50oC. There was almost no decrease in activity for the GOx on the apoferritin as compared to an 80% activity decrease for free B-GOx after 30 minutes of incubation in a 5 M urea solution. The GOx immobilized apoferritin nanoparticles exhibited high sensitivity for glucose detection with a detection limit of 3 nM glucose. This work offers a novel approach for immobilizing enzymes with enhanced stability and activity, and this method may find a number of applications, such as in catalysis and bioassys/biosensors.

  17. The Interacting and Non-constant Cosmological Constant

    CERN Document Server

    Verma, Murli Manohar

    2009-01-01

    We propose a time-varying cosmological constant with a fixed equation of state, which evolves mainly through its interaction with the background during most of the long history of the universe. However, such interaction does not exist in the very early and the late-time universe and produces the acceleration during these eras when it becomes very nearly a constant. It is found that after the initial inflationary phase, the cosmological constant, that we call as lambda parameter, rolls down from a large constant value to another but very small constant value and further dominates the present epoch showing up in form of the dark energy driving the acceleration.

  18. Adelic Universe and Cosmological Constant

    OpenAIRE

    Makhaldiani, Nugzar

    2003-01-01

    In the quantum adelic field (string) theory models, vacuum energy -- cosmological constant vanish. The other (alternative ?) mechanism is given by supersymmetric theories. Some observations on prime numbers, zeta -- function and fine structure constant are also considered.

  19. Quantum Theory without Planck's Constant

    CERN Document Server

    Ralston, John P

    2012-01-01

    Planck's constant was introduced as a fundamental scale in the early history of quantum mechanics. We find a modern approach where Planck's constant is absent: it is unobservable except as a constant of human convention. Despite long reference to experiment, review shows that Planck's constant cannot be obtained from the data of Ryberg, Davisson and Germer, Compton, or that used by Planck himself. In the new approach Planck's constant is tied to macroscopic conventions of Newtonian origin, which are dispensable. The precision of other fundamental constants is substantially improved by eliminating Planck's constant. The electron mass is determined about 67 times more precisely, and the unit of electric charge determined 139 times more precisely. Improvement in the experimental value of the fine structure constant allows new types of experiment to be compared towards finding "new physics." The long-standing goal of eliminating reliance on the artifact known as the International Prototype Kilogram can be accompl...

  20. A first-principles study of cementite (Fe{sub 3}C) and its alloyed counterparts: Elastic constants, elastic anisotropies, and isotropic elastic moduli

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, G., E-mail: g-ghosh@northwestern.edu [Department of Materials Science and Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, 2220 Campus Drive, Evanston, IL 60208-3108 (United States)

    2015-08-15

    A comprehensive computational study of elastic properties of cementite (Fe{sub 3}C) and its alloyed counterparts (M{sub 3}C (M = Al, Co, Cr, Cu, Fe, Hf, Mn, Mo, Nb, Ni, Si, Ta, Ti, V, W, Zr, Cr{sub 2}FeC and CrFe{sub 2}C) having the crystal structure of Fe{sub 3}C is carried out employing electronic density-functional theory (DFT), all-electron PAW pseudopotentials and the generalized gradient approximation for the exchange-correlation energy (GGA). Specifically, as a part of our systematic study of cohesive properties of solids and in the spirit of materials genome, following properties are calculated: (i) single-crystal elastic constants, C{sub ij}, of above M{sub 3}Cs; (ii) anisotropies of bulk, Young’s and shear moduli, and Poisson’s ratio based on calculated C{sub ij}s, demonstrating their extreme anisotropies; (iii) isotropic (polycrystalline) elastic moduli (bulk, shear, Young’s moduli and Poisson’s ratio) of M{sub 3}Cs by homogenization of calculated C{sub ij}s; and (iv) acoustic Debye temperature, θ{sub D}, of M{sub 3}Cs based on calculated C{sub ij}s. We provide a critical appraisal of available data of polycrystalline elastic properties of alloyed cementite. Calculated single crystal properties may be incorporated in anisotropic constitutive models to develop and test microstructure-processing-property-performance links in multi-phase materials where cementite is a constituent phase.

  1. Characterization of 6-mercaptopurine binding to bovine serum albumin and its displacement from the binding sites by quercetin and rutin

    International Nuclear Information System (INIS)

    Binding of a drug to the serum albumins as major serum transport proteins can be influenced by other ligands leading to alteration of its pharmacological properties. In the present study, binding characteristics of 6-mercaptopurine (6-MP) with bovine serum albumin (BSA) together with its displacement from its binding site by quercetin and rutin have been investigated by the spectroscopic method. According to the binding parameters, a static quenching component in overall dynamic quenching process is operative in the interaction between 6-MP and BSA. The binding of 6-MP to BSA occurred spontaneously due to entropy-driven hydrophobic interactions. The synchronous fluorescence spectroscopy study revealed that the secondary structure of BSA is changed in the presence of 6-MP and both Tyr and Trp residues participate in the interaction between 6-MP and BSA with the later one being more dominant. The binding constant value of 6-MP–BSA in the presence of quercetin and rutin increased. 6-MP was displaced by ibuprofen indicating that the binding site of 6-MP on albumin is site II. Therefore, the change of the pharmacokinetic and pharmacodynamic properties of 6-MP by quercetin and rutin through alteration of binding capacity of 6-MP to the serum albumin cannot be ruled out. In addition, the displacement study showed that 6-MP is located in site II of BSA. - Highlights: ► Participation of both Tyr and particularly Trp residues in the interaction between 6-MP and BSA. ► Involvement of a static quenching component in an overall dynamic quenching process. ► Ability of quercetin and rutin to change the binding constants of 6-MP–BSA complex. ► Binding of 6-MP to BSA through entropy-driven hydrophobic interactions

  2. Characterization of 6-mercaptopurine binding to bovine serum albumin and its displacement from the binding sites by quercetin and rutin

    Energy Technology Data Exchange (ETDEWEB)

    Ehteshami, Mehdi [Nutrition Research Center, School of Health and Nutrition, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Rasoulzadeh, Farzaneh [Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Mahboob, Soltanali [Nutrition Research Center, School of Health and Nutrition, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Rashidi, Mohammad-Reza, E-mail: rashidi@tbzmed.ac.ir [Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of)

    2013-03-15

    Binding of a drug to the serum albumins as major serum transport proteins can be influenced by other ligands leading to alteration of its pharmacological properties. In the present study, binding characteristics of 6-mercaptopurine (6-MP) with bovine serum albumin (BSA) together with its displacement from its binding site by quercetin and rutin have been investigated by the spectroscopic method. According to the binding parameters, a static quenching component in overall dynamic quenching process is operative in the interaction between 6-MP and BSA. The binding of 6-MP to BSA occurred spontaneously due to entropy-driven hydrophobic interactions. The synchronous fluorescence spectroscopy study revealed that the secondary structure of BSA is changed in the presence of 6-MP and both Tyr and Trp residues participate in the interaction between 6-MP and BSA with the later one being more dominant. The binding constant value of 6-MP-BSA in the presence of quercetin and rutin increased. 6-MP was displaced by ibuprofen indicating that the binding site of 6-MP on albumin is site II. Therefore, the change of the pharmacokinetic and pharmacodynamic properties of 6-MP by quercetin and rutin through alteration of binding capacity of 6-MP to the serum albumin cannot be ruled out. In addition, the displacement study showed that 6-MP is located in site II of BSA. - Highlights: Black-Right-Pointing-Pointer Participation of both Tyr and particularly Trp residues in the interaction between 6-MP and BSA. Black-Right-Pointing-Pointer Involvement of a static quenching component in an overall dynamic quenching process. Black-Right-Pointing-Pointer Ability of quercetin and rutin to change the binding constants of 6-MP-BSA complex. Black-Right-Pointing-Pointer Binding of 6-MP to BSA through entropy-driven hydrophobic interactions.

  3. Binding mode of inhibitors and Cryptosporidium parvum IMP dehydrogenase: A combined ligand- and receptor-based study.

    Science.gov (United States)

    Li, R-J; Wang, Y-L; Wang, Q-H; Huang, W-X; Wang, J; Cheng, M-S

    2015-01-01

    A combined ligand- and target-based approach was used to analyse the interaction models of Cryptosporidium parvum inosine 5'-monophosphate dehydrogenase (CpIMPDH) with selective inhibitors. First, a ligand-based pharmacophore model was generated from 20 NAD(+) competitive CpIMPDH inhibitors with the HipHop module. The characteristic of the NAD(+) binding site of CpIMPDH was then described, and the binding modes of the representative inhibitors were studied by molecular docking. The combination of the pharmacophore model and the docking results allowed us to evaluate the pharmacophore features and structural information of the NAD(+) binding site of CpIMPDH. This research supports the proposal of an interaction model inside the NAD(+) binding site of CpIMPDH, consisting of four key interaction points: two hydrophobic-aromatic groups, a hydrophobic-aliphatic group and a hydrogen bond donor. This study also provides guidance for the design of more potent CpIMPDH inhibitors for the treatment of Cryptosporidium infections. PMID:25978645

  4. Studies on the binding of 5-N-methylated quindoline derivative to human telomeric G-quadruplex

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Wei; Tan, Jia-Heng; Chen, Shuo-Bin; Hou, Jin-Qiang; Li, Ding [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China); Huang, Zhi-Shu, E-mail: ceshzs@mail.sysu.edu.cn [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China); Gu, Lian-Quan, E-mail: cesglq@mail.sysu.edu.cn [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China)

    2011-03-18

    Research highlights: {yields} Hydrophobic interaction provided an important driving force for the interaction between ligand and G-quadruplex. {yields} Constrained water molecules were released from surface of G-tetrad upon the formation of the complex. {yields} The end-stacking mode for quindoline derivative was validated through UV-vis, ITC, steady-state, and time-resolved fluorescence experiment. {yields} The binding of compound 1 to quadruplex was found to be a temperature-dependent and enthalpy-entropy compensation process. -- Abstract: Quindoline derivatives as telomeric quadruplex ligands have shown good biological activity for telomerase inhibition. In the present study, we used spectroscopic and calorimetric methods to investigate the interactions between a quindoline derivative (5-methyl-11-(2-morpholinoethylamino)-10-H-indolo-[3,2-b]quinolin-5-ium iodide, compound 1) and human telomeric G-quadruplex. The thermodynamic studies using isothermal titration calorimetry (ITC) indicated that their binding process was temperature-dependent and enthalpy-entropy co-driven. The significant negative heat capacity was obtained experimentally from the temperature dependence of enthalpy changes, which was consistent with that from theoretical calculation, and all suggesting significant hydrophobic contribution to the molecular recognition process. Based on the results from UV-vis, ITC, steady-state and time-resolved fluorescence, their binding mode was determined as two ligand molecules stacking on the quartets on both ends of the quadruplex. These results shed light on rational design and development of quindoline derivatives as G-quadruplex binding ligands.

  5. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  6. Probing the human estrogen receptor-α binding requirements for phenolic mono- and di-hydroxyl compounds: a combined synthesis, binding and docking study.

    Science.gov (United States)

    McCullough, Christopher; Neumann, Terrence S; Gone, Jayapal Reddy; He, Zhengjie; Herrild, Christian; Wondergem Nee Lukesh, Julie; Pandey, Rajesh K; Donaldson, William A; Sem, Daniel S

    2014-01-01

    Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. Di-hydroxyl compounds were predicted to bind with their aliphatic hydroxyl group interacting with His524 in ERα. One nonsteroid-based dihdroxyl compound was 1000-fold specific for ERβ over ERα, and was also 25-fold specific for agonist ERβ versus antagonist activity. Docking predictions suggest this specificity may be due to interaction of the aliphatic hydroxyl with His475 in the agonist form of ERβ, versus with Thr299 in the antagonist form. But, the presence of this aliphatic hydroxyl is not required in all compounds, since mono-hydroxyl (phenolic) compounds bind ERα with high affinity, via hydroxyl hydrogen bonding interactions with the ERα Arg394/Glu353/water triad, and van der Waals interactions with the rest of the molecule.

  7. In silico studies on structure-function of DNA GCC- box binding domain of brassica napus DREB1 protein

    International Nuclear Information System (INIS)

    DREB1 is a transcriptional factor, which selectively binds with the promoters of the genes involved in stress response in the plants. Homology of DREB protein and its binding element have been detected in the genome of many plants. However, only a few reports exist that discusses the binding properties of this protein with the gene (s) promoter. In the present study, we have undertaken studies exploring the structure-function relationship of Brassica napus DREB1. Multiple sequence alignment, protein homology modeling and intermolecular docking of GCC-box binding domain (GBD) of the said protein was carried out using atomic coordinates of GBD from Arabdiopsis thaliana and GCC-box containing DNA respectively. Similarities and/or identities in multiple, sequence alignment, particularly at the functionally important amino acids, strongly suggested the binding specificity of B. napus DREB1 to GCC-box. Similarly, despite 56% sequence homology, tertiary structures of both template and modeled protein were found to be extremely similar as indicated by root mean square deviation of 0.34 A. More similarities were established between GBD of both A. thaliana and B. napus DREB1 by conducting protein docking with the DNA containing GCC-box. It appears that both proteins interact through their beta-sheet with the major DNA groove including both nitrogen bases and phosphate and sugar moieties. Additionally, in most cases the interacting residues were also found to be identical. Briefly, this study attempts to elucidate the molecular basis of DREB1 interaction with its target sequence in the promoter. (author)

  8. Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study.

    Directory of Open Access Journals (Sweden)

    Gugan Kothandan

    Full Text Available Chemokine receptors are G protein-coupled receptors that contain seven transmembrane domains. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, and furthermore, targeting both CCR2 and CCR5 can be a useful strategy. Owing to the importance of these receptors, information regarding the binding site is of prime importance. Structural studies have been hampered due to the lack of X-ray crystal structures, and templates with close homologs for comparative modeling. Most of the previous models were based on the bovine rhodopsin and β2-adrenergic receptor. In this study, based on a closer homolog with higher resolution (CXCR4, PDB code: 3ODU 2.5 Å, we constructed three-dimensional models. The main aim of this study was to provide relevant information on binding sites of these receptors. Molecular dynamics simulation was done to refine the homology models and PROCHECK results indicated that the models were reasonable. Here, binding poses were checked with some established inhibitors of high pharmaceutical importance against the modeled receptors. Analysis of interaction modes gave an integrated interpretation with detailed structural information. The binding poses confirmed that the acidic residues Glu291 (CCR2 and Glu283 (CCR5 are important, and we also found some additional residues. Comparisons of binding sites of CCR2/CCR5 were done sequentially and also by docking a potent dual antagonist. Our results can be a starting point for further structure-based drug design.

  9. Comparative study of heparin-binding proteins profile of Murrah buffalo (Bubalus bubalis semen

    Directory of Open Access Journals (Sweden)

    S. S. Ramteke

    2014-09-01

    Full Text Available Aim: The experiment was conducted to study the total seminal plasma protein (TSPP and heparin-binding proteins (HBPs in relation to initial semen quality of buffalo bull. Materials and Methods: Semen from two Murrah buffalo bulls (bull no. 605 and 790 with mass motility of ≥3+ were used for the study and categorized into three groups (Group I- Mass motility 3+, Group II- Mass motility 4+ and Group III- Mass motility 5+. Seminal plasma from semen was separated by centrifugation. HBPs was isolated and purified from heparin-agarose affinity column by modified elution buffer. TSPP and isolated HBPs concentration was estimated by Lowry’s method. The purified HBPs were resolved on Sodium dodecyl sulfate polyacrylamide gel electrophoresis to check the protein profile of two bulls. Results: The mean values of TSPP concentrations in bull no. 605 and 790 in Group I, II and III were 30.64±0.12, 31.66±0.09, 32.53±0.19 and 28.51±0.09, 29.49±0.15, 30.45±0.17 mg/mL, respectively. The mean values of HBPs concentrations in bull no. 605 and 790 in Group I, II and III were 3.11±0.07, 3.32±0.06, 3.46±0.08 and 2.51±0.08, 2.91±0.05, 3.10±0.03 mg/mL, respectively. Both the values of TSPP and HBPs were significantly higher (p<0.01 in bull no. 605 when compared to 790 in all the three groups. 31 kDa HBP was more intensely present in bull no. 605, thus may indicate its superiority over bull no. 790 in relation to fertility potential. Conclusion: TSPP and HBPs shows variation in concentration with respect to initial semen quality. Furthermore, presence of fertility related 31 kDa HBPs in one of the bull may be an indication of high fertility of a bull. In future, in-vivo and in-vitro correlative study on larger basis is needed for the establishment of fertility-related HBPs in semen which might establish criteria for selection of buffalo bull with high fertility potential.

  10. Studies on ATP-diphosphohydrolase nucleotide-binding sites by intrinsic fluorescence

    Directory of Open Access Journals (Sweden)

    A.M. Kettlun

    2000-07-01

    Full Text Available Potato apyrase, a soluble ATP-diphosphohydrolase, was purified to homogeneity from several clonal varieties of Solanum tuberosum. Depending on the source of the enzyme, differences in kinetic and physicochemical properties have been described, which cannot be explained by the amino acid residues present in the active site. In order to understand the different kinetic behavior of the Pimpernel (ATPase/ADPase = 10 and Desirée (ATPase/ADPase = 1 isoenzymes, the nucleotide-binding site of these apyrases was explored using the intrinsic fluorescence of tryptophan. The intrinsic fluorescence of the two apyrases was slightly different. The maximum emission wavelengths of the Desirée and Pimpernel enzymes were 336 and 340 nm, respectively, suggesting small differences in the microenvironment of Trp residues. The Pimpernel enzyme emitted more fluorescence than the Desirée apyrase at the same concentration although both enzymes have the same number of Trp residues. The binding of the nonhydrolyzable substrate analogs decreased the fluorescence emission of both apyrases, indicating the presence of conformational changes in the neighborhood of Trp residues. Experiments with quenchers of different polarities, such as acrylamide, Cs+ and I- indicated the existence of differences in the nucleotide-binding site, as further shown by quenching experiments in the presence of nonhydrolyzable substrate analogs. Differences in the nucleotide-binding site may explain, at least in part, the kinetic differences of the Pimpernel and Desirée isoapyrases.

  11. Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

    Institute of Scientific and Technical Information of China (English)

    HE Wenying; YAO Xiaojun; LIU Pengjun; GAO Zhenxia; HU Zhide

    2006-01-01

    The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immunoglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change -H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol(1 and 132.95 J·mol(1·K(1 according to the Vant' Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient F-rster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein's secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.

  12. Spectroscopic Studies on Binding of Porphyrin-Phenazine Conjugate to Four-Stranded Poly(G).

    Science.gov (United States)

    Ryazanova, Olga; Zozulya, Victor; Voloshin, Igor; Dubey, Larysa; Dubey, Igor; Karachevtsev, Victor

    2015-07-01

    Binding of a novel cationic porphyrin-imidazophenazine conjugate, TMPyP(3+)-ImPzn, to four-stranded poly(G) was investigated in aqueous solutions of neutral pH under near physiological ionic conditions using absorption, polarized fluorescent spectroscopy and fluorescence titration techniques. In absence of the polymer the conjugate folds into stable internal heterodimer with stacking between the porphyrin and phenazine chromophores. Binding of TMPyP(3+)-ImPzn to poly(G) is realized by two competing ways. At low polymer-to-dye ratio (P/D self-stacking is predominant. It is accompanied by heterodimer dissociation and distancing of phenazine moieties from the polymer. This binding mode is characterized by strong quenching of the conjugate fluorescence. Increase of P/D results in the disintegration of the porphyrin stacks and redistribution of the bound conjugate molecules along the polymer chain. At P/D > 10 another binding mode becomes dominant, embedding of TMPyP(3+)-ImPzn heterodimers into poly(G) groove as a whole is occurred. PMID:26076929

  13. TIGHT-BINDING MOLECULAR DYNAMICS STUDY OF C60-GRAPHITE COLLISIONS

    Institute of Scientific and Technical Information of China (English)

    Fang Yun-tuan; Luo Cheng-lin

    2000-01-01

    We report the tight-binding molecular dynamics simulations of C60 impacting on a graphite (0001) surface with different incident energy. The simulations provide detailed characterizations of the microscopic processes occurring during the collisions and show insight into the deposition mechanisms of C60 on semiconductor substrate.

  14. NMR studies of the GTP/GDP binding domain of translation initiation factor IF2

    NARCIS (Netherlands)

    Tishchenko, Evgeny Vladimirovich

    2005-01-01

    Translation Initiation Factor 2 (IF2) plays an important role in the initiation stage of bacterial protein biosynthesis. This protein binds both fMet-tRNA and 30S ribosomal subunit in the presence of GTP, and it stimulates the formation of the 70S initiation complex. The NMR samples of the 15N-, 15N

  15. AN EXPERIMENTAL STUDY FOR HEAT TRANSFER ENHANCEMENT BY LAMINAR FORCED CONVECTION FROM HORIZONTAL AND INCLINED TUBE HEATED WITH CONSTANT HEAT FLUX, USING TWO TYPES OF POROUS MEDIA

    Directory of Open Access Journals (Sweden)

    Thamir K. Jassem

    2013-05-01

    Full Text Available An experimental forced laminar study was presented in this research for an air flowing through a circular channel for different angles ( ,30o,45o,60o, the channel was heated at constant heat flux , the channel also was packed with steel and glass spheres respectively . The tests were done for three values of Peclets number (2111.71,3945.42,4575.47 with changing the heat flux for each case and five times for each number.The results showed that the dimensionless temperature distribution  will decrease with increasing the dimensionless channel length for all cases with changing Peclet number, heat flux and inclination angles, and its lowest value will be for glass spheres at highest flux, while at lower flux for , and the decreasing in dimensionless temperature was closed for both types of packed at other inclination angles.The study declared that the local Nusselt number decreases with increasing the dimensionless length of the channel for both packeds and for different applied heat flux, also through this study it was declared that the average Nusselt increases as Peclet number increases for both packed. Its value for the glass spheres is greater than the steel spheres with percentage (98.3% at small Peclet, and percentage (97.2% at large Peclet number for the horizontal tube, and (98.3% at small Peclet number and (97.8% at large Peclet number at  .Through this study its was found that average Nusselt number increases along the channel as the heat flux increases, because the bulk temperature will increase as the flow proceeds toward the end of the channel , so the heat transfer coefficient will increase.  It was declared from this study that in the case of the steel packed the heat transfer will occur mainly by conduction, while in the case of glass packed the heat transfer will occur mainly by laminar forced convection, where the lowest Nusselt number (Nu=3.8 was found when the pipe is horizontal and lowest heat flux and lowest Peclet number.  

  16. Bubble Universes With Different Gravitational Constants

    CERN Document Server

    Takamizu, Yu-ichi

    2015-01-01

    We argue a scenario motivated by the context of string landscape, where our universe is produced by a new vacuum bubble embedded in an old bubble and these bubble universes have not only different cosmological constants, but also their own different gravitational constants. We study these effects on the primordial curvature perturbations. In order to construct a model of varying gravitational constants, we use the Jordan-Brans-Dicke (JBD) theory where different expectation values of scalar fields produce difference of constants. In this system, we investigate the nucleation of bubble universe and dynamics of the wall separating two spacetimes. In particular, the primordial curvature perturbation on superhorizon scales can be affected by the wall trajectory as the boundary effect. We show the effect of gravitational constant in the exterior bubble universe can provide a peak like a bump feature at a large scale in a modulation of power spectrum.

  17. Comparison of crystal and solution hemoglobin binding of selected antigelling agents and allosteric modifiers

    Energy Technology Data Exchange (ETDEWEB)

    Mehanna, A.S.; Abraham, D.J. (Virginia Commonwealth Univ., Richmond (USA))

    1990-04-24

    This paper details comprehensive binding studies (solution and X-ray) of human hemoglobin A with a group of halogenated carboxylic acids that were investigated as potential antisickling agents. It is, to our knowledge, the first study to compare solution and crystal binding for a series of compounds under similar high-salt conditions used for cocrystallization. The compounds include ((3,4-dichlorobenzyl)oxy)acetic acid, ((p-bromobenzyl)oxy)acetic acid, clofibric acid, and bezafibrate. The location and stereochemistry of binding sites have been established by X-ray crystallography, while the number of binding sites and affinity constants were measured by using equilibrium dialysis. The observed crystal structures are consistent with the binding observed in solution and that the number of binding sites is independent of salt concentration, while the binding constant increases with increasing salt concentration. The studies also reveal that relatively small changes in the chemical structure of a drug molecule can result in entirely different binding sites on the protein. Moreover, the X-ray studies provide a possible explanation for the multiplicity in function exhibited by these compounds as allosteric modulators and/or antisickling agents. Finally, the studies indicate that these compounds bind differently to the R and T states of hemoglobin, and observation of special significance to the original design of these agents.

  18. Acetaminophen structure-toxicity studies: In vivo covalent binding of a nonhepatotoxic analog, 3-hydroxyacetanilide

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, S.A.; Price, V.F.; Jollow, D.J. (Medical Univ. of South Carolina, Charleston (USA))

    1990-09-01

    High doses of 3-hydroxyacetanilide (3HAA), a structural isomer of acetaminophen, do not produce hepatocellular necrosis in normal male hamsters or in those sensitized to acetaminophen-induced liver damage by pretreatment with a combination of 3-methylcholanthrene, borneol, and diethyl maleate. Although 3HAA was not hepatotoxic, the administration of acetyl-labeled (3H or 14C)3HAA (400 mg/kg, ip) produced levels of covalently bound radiolabel that were similar to those observed after an equimolar, hepatotoxic dose of (G-3H)acetaminophen. The covalent nature of 3HAA binding was demonstrated by retention of the binding after repetitive organic solvent extraction following protease digestion. Hepatic and renal covalent binding after 3HAA was approximately linear with both dose and time. In addition, 3HAA produced only a modest depletion of hepatic glutathione, suggesting the lack of a glutathione threshold. 3-Methylcholanthrene pretreatment increased and pretreatment with cobalt chloride and piperonyl butoxide decreased the hepatic covalent binding of 3HAA, indicating the involvement of cytochrome P450 in the formation of the 3HAA reactive metabolite. The administration of multiple doses or a single dose of (ring-3H)3HAA to hamsters pretreated with a combination of 3-methylcholanthrene, borneol, and diethyl maleate produced hepatic levels of 3HAA covalent binding that were in excess of those observed after a single, hepatotoxic acetaminophen dose. These data suggest that the nature and/or the intracellular processing of the reactive metabolites of acetaminophen and 3HAA are different. These data also demonstrate that absolute levels of covalently bound xenobiotic metabolites cannot be utilized as absolute predictors of cytotoxic potential.

  19. Competitive binding of phenylbutazone and colchicine to serum albumin in multidrug therapy: A spectroscopic study

    Science.gov (United States)

    Sułkowska, A.; Maciążek-Jurczyk, M.; Bojko, B.; Równicka, J.; Zubik-Skupień, I.; Temba, E.; Pentak, D.; Sułkowski, W. W.

    2008-06-01

    The binding sites for phenylbutazone and colchicine were identified in tertiary structure of bovine and human serum albumin with the use of spectrofluorescence analysis. It was found that phenylbutazone has two binding sites in both sera albumins (HSA and BSA), while colchicine has one binding site in BSA as well as in HSA. The comparison of the quenching effect of BSA and HSA fluorescence by phenylbutazone and colchicine allows us to identify subdomain IIA in protein as the binding site for these two drugs. In this subdomain tryptophan 214 is located. The participation of tyrosyl and tryptophanyl residues of protein was also estimated in the drug-albumin complex. The comparison of quenching of fluorescence of HSA and BSA excited at 280 nm with that at 295 nm allowed us to state that the participation of tyrosyl residues of albumin in the phenylbutazone-serum albumin interaction is significant. The analysis of quenching of fluorescence of BSA in the binary and ternary systems showed that phenylbutazone does not affect the complex formed between colchicine and BSA. Similarly, colchicine has no effect on the Phe-BSA complex. However marked differences were observed for the complex with HSA. On the basis of Ka and KQ values it was concluded that colchicine may probably cause displacement of phenylbutazone from its complex with serum albumin (SA). Static and dynamic quenching for the binary and ternary systems is also discussed. The competition of phenylbutazone and colchicine in binding to serum albumin should be taken into account in the multi-drug therapy.

  20. A comparative study of low dielectric constant barrier layer, etch stop and hardmask films of hydrogenated amorphous Si-(C, O, N)

    International Nuclear Information System (INIS)

    New barrier layer, etch stop and hardmask films, including hydrogenated amorphous a-SiCx:H (SiC), a-SiCxOy:H (SiCO), and a-SiCxNy:H (SiCN) films with a dielectric constant (k) approximately 4.3, are produced using the plasma-enhanced chemical vapor deposition technique. The chemical and structural nature, and mechanical properties of these films are characterized using X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and nano-indentation. The leakage current density and breakdown electric field are investigated by a mercury probe on a metal-insulator-semiconductor structure. The properties of the studied films indicate that they are potential candidates as barrier layer, etch stop and hardmask films for the advanced interconnect technology. The SiC film shows a high leakage current density (1.3x10-7 A/cm2 at 1.0 MV/cm) and low breakdown field (1.2 MV/cm at 1.0x10-6 A/cm2). Considering the mechanical and electrical properties requirements of the interconnect process, SiCN might be a good choice, but the N content may result in via poison problem. The low leakage current (1.2x10-9 A/cm2 at 1.0 MV/cm), high breakdown field (3.1 MV/cm at 1.0x10-6 A/cm2), and relative high hardness (5.7 GPa) of the SiCO film indicates a good candidate as a barrier layer, etch stop, or hardmask

  1. Circadian Melatonin and Temperature Taus in Delayed Sleep-wake Phase Disorder and Non-24-hour Sleep-wake Rhythm Disorder Patients: An Ultradian Constant Routine Study.

    Science.gov (United States)

    Micic, Gorica; Lovato, Nicole; Gradisar, Michael; Burgess, Helen J; Ferguson, Sally A; Lack, Leon

    2016-08-01

    Our objectives were to investigate the period lengths (i.e., taus) of the endogenous core body temperature rhythm and melatonin rhythm in delayed sleep-wake phase disorder patients (DSWPD) and non-24-h sleep-wake rhythm disorder patients (N24SWD) compared with normally entrained individuals. Circadian rhythms were measured during an 80-h ultradian modified constant routine consisting of 80 ultrashort 1-h "days" in which participants had 20-min sleep opportunities alternating with 40 min of enforced wakefulness. We recruited a community-based sample of 26 DSWPD patients who met diagnostic criteria (17 males, 9 females; age, 21.85 ± 4.97 years) and 18 healthy controls (10 males, 8 females; age, 23.72 ± 5.10 years). Additionally, 4 full-sighted patients (3 males, 1 female; age, 25.75 ± 4.99 years) were diagnosed with N24SWD and included as a discrete study group. Ingestible core temperature capsules were used to record minute temperatures that were averaged to obtain 80 hourly data points. Salivary melatonin concentration was assessed every half-hour to determine time of dim light melatonin onset at the beginning and end of the 80-h protocol. DSWPD patients had significantly longer melatonin rhythm taus (24 h 34 min ± 17 min) than controls (24 h 22 min ± 15 min, p = 0.03, d = 0.70). These results were further supported by longer temperature rhythm taus in DSWPD patients (24 h 34 min ± 26 min) relative to controls (24 h 13 min ± 15 min, p = 0.01, d = 0.80). N24SWD patients had even longer melatonin (25 h ± 19 min) and temperature (24 h 52 min ± 17 min) taus than both DSWPD (p = 0.007, p = 0.06) and control participants (p disorders. PMID:27312974

  2. Theoretical Study of Molecular Determinants Involved in Signal Binding to the TraR Protein of Agrobacterium tumefaciens

    Directory of Open Access Journals (Sweden)

    N. Kumar

    2005-10-01

    Full Text Available N-acylated homoserine lactone (AHL mediated cell-cell communication in bacteria is dependent on the recognition of the cognate signal by its receptor. This interaction allows the receptor-ligand complex to act as a transcriptional activator, controlling the expression of a range of bacterial phenotypes, including virulence factor expression and biofilm formation. One approach to determine the key features of signal- binding is to model the intermolecular interactions between the receptor and ligand using computational-based modeling software (LigandFit. In this communication, we have modeled the crystal structure of the AHL receptor protein TraR and its AHL signal N-(3- oxooctanoyl-homoserine lactone from Agrobacterium tumefaciens and compared it to the previously reported antagonist behaviour of a number of AHL analogues, in an attempt to determine structural constraints for ligand binding. We conclude that (i a common conformation of the AHL in the hydrophobic and hydrophilic region exists for ligand-binding, (ii a tail chain length threshold of 8 carbons is most favourable for ligand-binding affinity, (iii the positive correlation in the docking studies could be used a virtual screening tool.

  3. Black holes with constant topological Euler density

    CERN Document Server

    Bargueño, Pedro

    2016-01-01

    A class of four dimensional spherically symmetric and static geometries with constant topological Euler density is studied. These geometries are shown to solve the coupled Einstein-Maxwell system when non-linear Born-Infeld-like electrodynamics is employed.

  4. Synthesis, characterization, crystal structure, DNA- and HSA-binding studies of a dinuclear Schiff base Zn(II) complex derived from 2-hydroxynaphtaldehyde and 2-picolylamine

    Science.gov (United States)

    Kazemi, Zahra; Rudbari, Hadi Amiri; Mirkhani, Valiollah; Sahihi, Mehdi; Moghadam, Majid; Tangestaninejad, Sharam; Mohammadpoor-Baltork, Iraj

    2015-09-01

    A tridentate Schiff base ligand NNO donor (HL: 1-((E)-((pyridin-2-yl)methylimino)methyl)naphthalen-2-ol was synthesized from condensation of 2-hydroxynaphtaldehyde and 2-picolylamine. Zinc complex, Zn2L2(NO3)2, was prepared from reaction of Zn(NO3)2 and HL at ambient temperature. The ligand and complex were characterized by FT-IR, 1H NMR, 13C NMR and elemental analysis (CHN). Furthermore, the structure of dinuclear Zn(II) complex was determined by single crystal X-ray analysis. The complex, Zn2L2(NO3)2, is centrosymmetric dimer in which deprotonated phenolates bridge the two Zn(II) atoms and link the two halves of the dimer. In the structure, Zinc(II) ions have a highly distorted six-coordinate structure bonded to two oxygen atoms from a bidentate nitrate group, the pyridine nitrogen, an amine nitrogen and phenolate oxygens. The interaction of dinuclear Zn(II) complex with fish sperm DNA (FS-DNA) and HSA was investigated under physiological conditions using fluorescence quenching, UV-Vis spectroscopy, molecular dynamics simulation and molecular docking methods. The estimated binding constants for the DNA-complex and HSA-complex were (3.60 ± 0.18) × 104 M-1 and (1.35 ± 0.24) × 104 M-1, respectively. The distance between dinuclear Zn(II) complex and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Molecular docking studies revealed the binding of dinuclear Zn(II) complex to the major groove of FS-DNA and IIA site of protein by formation of hydrogen bond, π-cation and hydrophobic interactions.

  5. Ethanol intake and sup 3 H-serotonin uptake II: A study in alcoholic patients using platelets sup 3 H-paroxetine binding

    Energy Technology Data Exchange (ETDEWEB)

    Daoust, M.; Boucly, P. (U.F.R. de Medecine et Pharmacie, Saint Etienne du Rouvrary (France)); Ernouf, D. (Institut du Medicament, Tours (France)); Breton, P. (Centre National de Transfusion Sanguine de Rouen (France)); Lhuintre, J.P.

    1991-01-01

    The kinetic parameters of {sup 3}H-paroxetine binding and {sup 3}H-serotonin uptake were studied in platelets of alcoholic patients. There was no difference between alcoholic and non alcoholic subjects in {sup 3}H-paroxetine binding. When binding and {sup 3}H-serotonin uptake were studied, in the same plasma of the same subjects, the Vmax of serotonin uptake was increased in alcoholics. The data confirm the involvement of serotonin uptake system in alcohol dependance and suggest that serotonin uptake and paroxetine binding sites may be regulated independently in this pathology.

  6. In vitro auxin binding to cellular membranes of cucumber fruits.

    Science.gov (United States)

    Narayanan, K R; Mudge, K W; Poovaiah, B W

    1981-04-01

    Specific binding of 1-naphthaleneacetic acid (NAA) to crude membrane preparations from cucumber (Cucumis sativus L.) was demonstrated. This in vitro binding had a pH optimum of 3.75 and an equilibrium dissociation constant of 10 to 20 micromolar with 1250 picomoles binding sites per gram fresh weight. The NAA-binding sites were pronase sensitive. The supernatant from the fruit partially inhibited the in vitro NAA binding to fruit membranes. NAA, 2-naphthoxyacetic acid, 3-indoleacetic acid, 2-4-dichlorophenoxyacetic acid, and 2,3,5-triiodobenzoic acid, which are reported to be very good inducers of parthenocarpy in cucumber, showed a high degree of specific binding to cucumber fruit membranes. In comparison, 2-naphthaleneacetic acid and indolepropionic acid, which are reported to be very weak auxins in corn coleoptile, pea stem, and strawberry fruit growth bioassays, did not bind efficiently to cucumber fruit membranes. In vitro binding studies with fruit membranes suggest that auxin stimulated fruit growth may be mediated by membrane-associated, auxin-binding protein(s). PMID:16661764

  7. Binding interactions of pefloxacin mesylate with bovine lactoferrin and human serum albumin

    Institute of Scientific and Technical Information of China (English)

    FAN Ji-cai; CHEN Xiang; WANG Yun; FAN Cheng-ping; SHANG Zhi-cai

    2006-01-01

    The binding of pefloxacin mesylate (PFLX) to bovine lactoferrin (BLf) and human serum albumin (HSA) in dilute aqueous solution was studied using fluorescence spectra and absorbance spectra. The binding constant K and the binding sites n were obtained by fluorescence quenching method. The binding distance r and energy-transfer efficiency E between pefloxacin mesylate and bovine lactoferrin as well as human serum albumin were also obtained according to the mechanism of Forster-type dipole-dipole nonradiative energy-transfer. The effects of pefloxacin mesylate on the conformations of bovine lactoferrin and human serum albumin were also analyzed using synchronous fluorescence spectroscopy.

  8. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study.

    Science.gov (United States)

    Zhu, Shun; Travis, Sue M; Elcock, Adrian H

    2013-07-01

    A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant

  9. Mechanical properties of phosphorene nanotubes: a density functional tight-binding study

    Science.gov (United States)

    Sorkin, V.; Zhang, Y. W.

    2016-09-01

    Using the density functional tight-binding method, we studied the elastic properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) under uniaxial tensile strain. We found that the deformation and failure of PNTs are very much anisotropic. For ZZ PNTs, three deformation phases are recognized: the primary linear elastic phase—which is associated with interactions between neighboring puckers, succeeded by the bond rotation phase—where the puckered configuration of phosphorene is smoothed via bond rotation, and lastly the bond elongation phase—where the P–P bonds are directly stretched up to the maximally allowed limit and failure is initiated by the rupture of the most stretched bonds. For AC PNTs, the applied strain stretches the bonds up to the maximally allowed limit, causing their ultimate failure. For both AC and ZZ PNTs, their failure strain and failure stress are sensitive— while the Young’s modulus, flexural rigidity, radial Poisson’s ratio and thickness Poisson’s ratio are relatively insensitive—to the tube diameter. More specifically, for AC PNTs, the failure strain decreases from 0.40 to 0.25 and the failure stress increases from 13 GPa to 21 GPa when the tube diameter increases from 13.3 Å to 32.8 Å while for ZZ PNTs, the failure strain decreases from 0.66 to 0.55 and the failure stress increases from 4 GPa to 9 GPa when the tube diameter increases from 13.2 Å to 31.1 Å. The Young’s modulus, flexural rigidity, radial and thickness Poisson ratios are 114.2 GPa, 0.019 eV · nm2, 0.47 and 0.11 for AC PNTs, and 49.2 GPa, 0.071 eV · nm2, 0.07 and 0.21 for ZZ PNTs, respectively. The present findings provide valuable references for the design and application of PNTs as device elements.

  10. Lectin binding studies on a glycopolymer brush flow-through biosensor by localized surface plasmon resonance.

    Science.gov (United States)

    Rosencrantz, Ruben R; Nguyen, Vu Hoa; Park, Hyunji; Schulte, Christine; Böker, Alexander; Schnakenberg, Uwe; Elling, Lothar

    2016-08-01

    A localized surface plasmon resonance biosensor in a flow-through configuration was applied for investigating kinetics of lectin binding to surface-grafted glycopolymer brushes. Polycarbonate filter membranes with pore sizes of 400 nm were coated with a 114-nm thick gold layer and used as substrate for surface-initiated atom-transfer radical polymerization of a glycomonomer. These grafted from glycopolymer brushes were further modified with two subsequent enzymatic reactions on the surface to yield an immobilized trisaccharide presenting brush. Specific binding of lectins including Clostridium difficile toxin A receptor domain to the glycopolymer brush surface could be investigated in a microfluidic setup with flow-through of the analytes and transmission surface plasmon resonance spectroscopy. Graphical abstract Glycopolymer brushes serve as high affinity ligands for lectin and toxin interactions in a sensitive, disposable flow-through LSPR biosensor. PMID:27277814

  11. Binding of Breviscapine Toward Serum Albumin Studied by Spectroscopic and Electrochemical Techniques.

    Science.gov (United States)

    Liu, Wei; Chen, Yaqing; Chen, Hui; Zhang, Ying

    2016-09-01

    Breviscapine, a cerebrovascular drugs extracted from the Chinese herb Erigeron breviscapinus, has been frequently used to clinically treat cerebrovascular diseases such as cerebral thrombosis, cerebral infarction, and cerebral circulation insufficiency. In order to understand its pharmacology or toxicity, the binding mechanism of breviscapine to a model protein, human serum albumin (HSA), was probed by fluorescence, circular dichroism, Fourier transform infrared spectroscopy (FTIR), and electrochemical impedance spectroscopy approaches. The binding affinities and number of the drug with HSA were about 1.73 × 10(4)  M(-1) and 0.99 at 293 K, respectively. The conformation of the protein was slightly altered after interacting with breviscapine. The drug-protein complex was mainly stabilized by electrostatic forces.

  12. Emotional valence, sense of agency and responsibility: A study using intentional binding.

    Science.gov (United States)

    Christensen, J F; Yoshie, M; Di Costa, S; Haggard, P

    2016-07-01

    We investigated how the emotional valence of an action outcome influences the experience of control, in an intentional binding experiment. Voluntary actions were followed by emotionally positive or negative human vocalisations, or by neutral tones. We used mental chronometry to measure a retrospective component of sense of agency (SoA), triggered by the occurrence of the action outcome, and a prospective component, driven by the expectation that the outcome will occur. Positive outcomes enhanced the retrospective component of SoA, but only when both occurrence and the valence of the outcome were unexpected. When the valence of outcomes was blocked - and therefore predictable - we found a prospective component of SoA when neutral tones were expected but did not actually occur. This prospective binding was absent, and reversed, for positive and negative expected outcomes. Emotional expectation counteracts the prospective component of SoA, suggesting a distancing effect. PMID:27174794

  13. Kepler's Constant and WDS Orbit

    CERN Document Server

    Siregar, S

    2012-01-01

    The aim of this work are to find a Kepler's constant by using polynomial regression of the angular separation \\rho = \\rho(t) and the position angle \\theta = \\theta(t). The Kepler's constant obtained is used to derive the element of orbit. As a case study the angular separation and the position angle of the WDS 00063 +5826 and the WDS 04403-5857 were investigated. For calculating the element of orbit the Thiele-Innes van den Bos method is used. The rough data of the angular separation \\rho(t) and the position angle \\theta(t) are taken from the US Naval Observatory, Washington. This work also presents the masses and absolute bolometric magnitudes of each star.These stars include into the main-sequence stars with the spectral class G5V for WDS04403-5857and the type of spectrum G3V for WDS 00063+5826. The life time of the primary star and the secondary star of WDS 04403-5857 nearly equal to 20 Gyr. The life time of the primary star and the secondary star of WDS 00063+5826 are 20 Gyr and 19 Gyr, respectively.

  14. Preliminary Crystallographic Study of Streptomyces coelicolor Single-stranded DNA-binding Protein

    OpenAIRE

    Štefanić, Zoran; Vujaklija, Dušica; Andrišić, Luka; Mikleušević, Goran; Andrejašič, Miha; Turk, Dušan; Luić, Marija

    2007-01-01

    Single-stranded DNA-binding proteins (SSBs) play a crucial role in DNA processing such as replication, repair and recombination in all organisms, from bacteria to human. Streptomyces coelicolor ssb gene was overexpressed in a heterologous host, Escherichia coli NM522. 15 mg of purified protein from 1 dm(3) of culture was obtained in one-step procedure applying Ni2+ chelating chromatography. Among bacterial SSBs with the solved crystal structure, the S. coelicolor SSB displayed significant seq...

  15. Minor Groove Binding between Norfloxacin and DNA Duplexes in Solution: A Molecular Dynamics Study

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Molecular dynamics were used to investigate the interaction between norfloxacin and DNA duplex. The results showed that norfloxacin was situated in the minor groove of DNA,binding to the TCGA region of d [ATATCGATAT] 2. Specific hydrogen bonds were formed between norfloxacin and guanine base of DNA during the 2 ns MD, which may be the reason for the preferentiality of quinolone antibacterial towards the guanine base of DNA duplex.

  16. A Study on Efficient Mobile IPv6 Fast Handover Scheme Using Reverse Binding Mechanism

    Science.gov (United States)

    Tolentino, Randy S.; Lee, Kijeong; Kim, Sung-Gyu; Kim, Miso; Park, Byungjoo

    This paper proposes a solution for solving the packet handover issues of MIPv6. We propose an efficient scheme that can support fast handover effectively in standard Mobile IPv6 (MIPv6) by optimizing the associated data and the flow of signal during handover. A new signaling message Reverse Packet Binding Mechanism is defined and utilized to hasten the handover procedure by adding a buffer in access point (AP) and home agent (HA).

  17. Chandra Independently Determines Hubble Constant

    Science.gov (United States)

    2006-08-01

    A critically important number that specifies the expansion rate of the Universe, the so-called Hubble constant, has been independently determined using NASA's Chandra X-ray Observatory. This new value matches recent measurements using other methods and extends their validity to greater distances, thus allowing astronomers to probe earlier epochs in the evolution of the Universe. "The reason this result is so significant is that we need the Hubble constant to tell us the size of the Universe, its age, and how much matter it contains," said Max Bonamente from the University of Alabama in Huntsville and NASA's Marshall Space Flight Center (MSFC) in Huntsville, Ala., lead author on the paper describing the results. "Astronomers absolutely need to trust this number because we use it for countless calculations." Illustration of Sunyaev-Zeldovich Effect Illustration of Sunyaev-Zeldovich Effect The Hubble constant is calculated by measuring the speed at which objects are moving away from us and dividing by their distance. Most of the previous attempts to determine the Hubble constant have involved using a multi-step, or distance ladder, approach in which the distance to nearby galaxies is used as the basis for determining greater distances. The most common approach has been to use a well-studied type of pulsating star known as a Cepheid variable, in conjunction with more distant supernovae to trace distances across the Universe. Scientists using this method and observations from the Hubble Space Telescope were able to measure the Hubble constant to within 10%. However, only independent checks would give them the confidence they desired, considering that much of our understanding of the Universe hangs in the balance. Chandra X-ray Image of MACS J1149.5+223 Chandra X-ray Image of MACS J1149.5+223 By combining X-ray data from Chandra with radio observations of galaxy clusters, the team determined the distances to 38 galaxy clusters ranging from 1.4 billion to 9.3 billion

  18. Interaction study on bovine serum albumin physically binding to silver nanoparticles: Evolution from discrete conjugates to protein coronas

    Science.gov (United States)

    Guo, Jun; Zhong, Ruibo; Li, Wanrong; Liu, Yushuang; Bai, Zhijun; Yin, Jun; Liu, Jingran; Gong, Pei; Zhao, Xinmin; Zhang, Feng

    2015-12-01

    The nanostructures formed by inorganic nanoparticles together with organic molecules especially biomolecules have attracted increasing attention from both industries and researching fields due to their unique hybrid properties. In this paper, we systemically studied the interactions between amphiphilic polymer coated silver nanoparticles and bovine serum albumins by employing the fluorescence quenching approach in combination with the Stern-Volmer and Hill equations. The binding affinity was determined to 1.30 × 107 M-1 and the interaction was spontaneously driven by mainly the van der Waals force and hydrogen-bond mediated interactions, and negatively cooperative from the point of view of thermodynamics. With the non-uniform coating of amphiphilic polymer, the silver nanoparticles can form protein coronas which can become discrete protein-nanoparticle conjugates when controlling their molar ratios of mixing. The protein's conformational changes upon binding nanoparticles was also studied by using the three-dimensional fluorescence spectroscopy.

  19. Pilot study on binding of bovine salivary proteins to grit silicates and plant phytoliths

    Institute of Scientific and Technical Information of China (English)

    Marcus MAU; Thomas M.KAISER; Karl-Heinz S(U)DEKUM

    2013-01-01

    Mostly fed with grass in fresh or conserved form,cattle and other livestock have to cope with silicate defence bodies from plants (phytoliths) and environmental silicates (grit),which abrade tooth enamel and could additionally interact with various salivary proteins.To detect potential candidates for silicate-binding proteins,bovine whole saliva was incubated with grass-derived phytoliths and silicates.Interactions of salivary proteins with pulverized bovine dental enamel and dentine were additionally analysed.After intense washing,the powder fractions were loaded onto 1D-polyacrylamide gels,most prominent adhesive protein bands were cut out and proteins were identified by mass spectrometry within three independent replicates.All materials were mainly bound by bovine odorant-binding protein,bovine salivary protein 30× 103 and carbonic anhydrase VI.The phytolith/silicate fraction showed additional stronger interaction with haemoglobin β and lactoperoxidase.Conceivably,the binding of these proteins to the surfaces may contribute to biological processes occurring on them.

  20. Fluorescence Quenching and Binding Interaction of l0-Methylacridinium Iodide to Nucleic Acids

    Institute of Scientific and Technical Information of China (English)

    孙险峰; 江致勤; 丁兵林

    2003-01-01

    Interaction of 10-methylacridinium iodide (MAI) as fluorescence probe with nucleobases, nucleosides and nucleic acids has been studied by UV-visible absorption and fluorescence spectroscopy. It was found that fluorescence of MAI is strongly quenched by the nucleobases, nucleosides and nucleic acids, respectively. The quenching follows the Stern-Volmer linear equation. The fluorescence quenching rate constant (kq) was measured to be 109-1010 (L/mol)/s within the range of diffusion-controlled rate limit, indicating that the interaction between MAI and nucleic acid and their precursors is characteristic of electron transfer mechanism. In addition, the binding interaction model of MAI to calf thymus DNA (ct-DNA) was further investigated. Apparent hypochromism in the absorption spectra of MAI was observed when MAI binds to ct-DNA.Three spectroscopic methods, which include (1) UV spectroscopy, (2) fluorescence quenching of MAI, (3) competitive dual-probe method of MAI and ethidium bromide (EB), were utilized to determine the affinity binding constants (K)of MAI and ct-DNA. The binding constants K obtained from the above methods gave consistent data in the same range (1.0-5.5) ×104 L/mol, which lend credibility to these measurements. The binding site number was determined to be 1.9. The influence of thermal denaturation and phosphate concentration on the binding was examined. The binding model of MAI to ct-DNA including intercalation and outside binding was investigated.