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Sample records for wall protein dynamics

  1. Arabidopsis Regenerating Protoplast: A Powerful Model System for Combining the Proteomics of Cell Wall Proteins and the Visualization of Cell Wall Dynamics

    OpenAIRE

    Ryusuke Yokoyama; Hiroaki Kuki; Takeshi Kuroha; Kazuhiko Nishitani

    2016-01-01

    The development of a range of sub-proteomic approaches to the plant cell wall has identified many of the cell wall proteins. However, it remains difficult to elucidate the precise biological role of each protein and the cell wall dynamics driven by their actions. The plant protoplast provides an excellent means not only for characterizing cell wall proteins, but also for visualizing the dynamics of cell wall regeneration, during which cell wall proteins are secreted. It therefore offers a uni...

  2. Arabidopsis Regenerating Protoplast: A Powerful Model System for Combining the Proteomics of Cell Wall Proteins and the Visualization of Cell Wall Dynamics

    Directory of Open Access Journals (Sweden)

    Ryusuke Yokoyama

    2016-11-01

    Full Text Available The development of a range of sub-proteomic approaches to the plant cell wall has identified many of the cell wall proteins. However, it remains difficult to elucidate the precise biological role of each protein and the cell wall dynamics driven by their actions. The plant protoplast provides an excellent means not only for characterizing cell wall proteins, but also for visualizing the dynamics of cell wall regeneration, during which cell wall proteins are secreted. It therefore offers a unique opportunity to investigate the de novo construction process of the cell wall. This review deals with sub-proteomic approaches to the plant cell wall through the use of protoplasts, a methodology that will provide the basis for further exploration of cell wall proteins and cell wall dynamics.

  3. A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers

    Directory of Open Access Journals (Sweden)

    Jamet Elisabeth

    2008-09-01

    Full Text Available Abstract Background Cell elongation in plants requires addition and re-arrangements of cell wall components. Even if some protein families have been shown to play roles in these events, a global picture of proteins present in cell walls of elongating cells is still missing. A proteomic study was performed on etiolated hypocotyls of Arabidopsis used as model of cells undergoing elongation followed by growth arrest within a short time. Results Two developmental stages (active growth and after growth arrest were compared. A new strategy consisting of high performance cation exchange chromatography and mono-dimensional electrophoresis was established for separation of cell wall proteins. This work allowed identification of 137 predicted secreted proteins, among which 51 had not been identified previously. Apart from expected proteins known to be involved in cell wall extension such as xyloglucan endotransglucosylase-hydrolases, expansins, polygalacturonases, pectin methylesterases and peroxidases, new proteins were identified such as proteases, proteins related to lipid metabolism and proteins of unknown function. Conclusion This work highlights the CWP dynamics that takes place between the two developmental stages. The presence of proteins known to be related to cell wall extension after growth arrest showed that these proteins may play other roles in cell walls. Finally, putative regulatory mechanisms of protein biological activity are discussed from this global view of cell wall proteins.

  4. Dynamic Response of Wall Backfill Retaining System

    Directory of Open Access Journals (Sweden)

    Sreenivas Alampalli

    1997-01-01

    Full Text Available An in situ full-scale test is conducted to measure the dynamic response of a long cantilever wall that retains backfill soil. The recorded modal parameters of this retaining wall exhibited significant similarity to those of a clamped cantilever plate (rather than those of a cantilever beam or plane-strain analysis. Such a three-dimensional (3-D response pattern is not accounted for by current analysis procedures. A simple 3-D finite element model is employed to further analyze the observed resonant configurations. The results indicate that such configurations play an important role in the seismic response of wall backfill soil systems of variable height, such as wing walls supporting highway approach ramps.

  5. Domain wall dynamics of magnetically bistable microwires

    Directory of Open Access Journals (Sweden)

    Ipatov M.

    2012-06-01

    Full Text Available We studied domain wall propagation of magnetically-bistable Fe- Co-rich microwires paying attention on effect of applied and internal stresses. We measured hysteresis loops and domain wall propagation in various magnetic Fe- Co-rich amorphous microwires with metallic nucleus diameters (from 12 □m till 22 □m using Sixtus Tonks-like experiments. Application of tensile stresses results in decreasing of domain wall velocity. We discussed magnetoelastic contribution in dynamics of domain wall propagation. We observed, that microwires with different geometries exhibit v(H dependences with different slopes. Application of stresses resulted in decrease of DW velocity, v, and DW mobility S. Quite fast DW propagation (v till 2500 m/s at H about 30 A/m has been observed in low magnetostrictive magnetically bistable Co56Fe8Ni10Si110B16 microwires. Consequently, we can assume that generally magnetoelastic energy affects DW dynamics: decreasing magnetoelastic energy, Kme, DW velocity increases.

  6. CELL-WALL GROWTH AND PROTEIN SECRETION IN FUNGI

    NARCIS (Netherlands)

    SIETSMA, JH; WOSTEN, HAB; WESSELS, JGH

    1995-01-01

    Secretion of proteins is a vital process in fungi. Because hyphal walls form a diffusion barrier for proteins, a mechanism different from diffusion probably exist to transport proteins across the wall. In Schizophyllum commune, evidence has been obtained for synthesis at the hyphal apex of wall

  7. PREFACE: Domain wall dynamics in nanostructures Domain wall dynamics in nanostructures

    Science.gov (United States)

    Marrows, C. H.; Meier, G.

    2012-01-01

    Domain structures in magnetic materials are ubiquitous and have been studied for decades. The walls that separate them are topological defects in the magnetic order parameter and have a wide variety of complex forms. In general, their investigation is difficult in bulk materials since only the domain structure on the surface of a specimen is visible. Cutting the sample to reveal the interior causes a rearrangement of the domains into a new form. As with many other areas of magnetism, the study of domain wall physics has been revitalised by the advent of nanotechnology. The ability to fabricate nanoscale structures has permitted the formation of simplified and controlled domain patterns; the development of advanced microscopy methods has permitted them to be imaged and then modelled; subjecting them to ultrashort field and current pulses has permitted their dynamics to be explored. The latest results from all of these advances are described in this special issue. Not only has this led to results of great scientific beauty, but also to concepts of great applicability to future information technologies. In this issue the reader will find the latest results for these domain wall dynamics and the high-speed processes of topological structures such as domain walls and magnetic vortices. These dynamics can be driven by the application of magnetic fields, or by flowing currents through spintronic devices using the novel physics of spin-transfer torque. This complexity has been studied using a wide variety of experimental techniques at the edge of the spatial and temporal resolution currently available, and can be described using sophisticated analytical theory and computational modelling. As a result, the dynamics can be engineered to give rise to finely controlled memory and logic devices with new functionality. Moreover, the field is moving to study not only the conventional transition metal ferromagnets, but also complex heterostructures, novel magnets and even other

  8. Two endogenous proteins that induce cell wall extension in plants

    Science.gov (United States)

    McQueen-Mason, S.; Durachko, D. M.; Cosgrove, D. J.

    1992-01-01

    Plant cell enlargement is regulated by wall relaxation and yielding, which is thought to be catalyzed by elusive "wall-loosening" enzymes. By employing a reconstitution approach, we found that a crude protein extract from the cell walls of growing cucumber seedlings possessed the ability to induce the extension of isolated cell walls. This activity was restricted to the growing region of the stem and could induce the extension of isolated cell walls from various dicot stems and the leaves of amaryllidaceous monocots, but was less effective on grass coleoptile walls. Endogenous and reconstituted wall extension activities showed similar sensitivities to pH, metal ions, thiol reducing agents, proteases, and boiling in methanol or water. Sequential HPLC fractionation of the active wall extract revealed two proteins with molecular masses of 29 and 30 kD associated with the activity. Each protein, by itself, could induce wall extension without detectable hydrolytic breakdown of the wall. These proteins appear to mediate "acid growth" responses of isolated walls and may catalyze plant cell wall extension by a novel biochemical mechanism.

  9. Fast domain wall dynamics in amorphous and nanocrystalline magnetic microwires

    Energy Technology Data Exchange (ETDEWEB)

    Varga, R., E-mail: rvarga@upjs.sk [Institute of Physics, Faculty of Science, UPJS, Park Angelinum 9, 041 54, Kosice (Slovakia); Klein, P.; Richter, K. [Institute of Physics, Faculty of Science, UPJS, Park Angelinum 9, 041 54, Kosice (Slovakia); Zhukov, A. [Dept. Fisica de Materiales, Fac. Quimica, UPV/EHU, San Sebastian (Spain); Vazquez, M. [Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Ines de la Cruz 3, 28049 Cantoblanco, Madrid (Spain)

    2012-10-15

    We have studied the effect of thermal treatment on the domain wall dynamics of FeSiB and FeCoMoB microwires. It was shown that annealing in transversal magnetic field increases the domain wall mobility as well as the domain wall velocity. Annealing under the tensile stress hinders the appearance of the monodomain structure but application of tensile stress leads to the magnetic bistability having the domain wall mobility twice higher that in as-cast state. Further increase of the tensile stress reduces the domain wall mobility but the domain wall velocity increases as a result of the decrease of critical propagation field. Annealing of the FeCoMoB microwire by Joule heating leads to introduction of the circular anisotropy that favors the vortex domain wall. Such treatment increases the domain wall mobility as well as the maximum domain wall velocity.

  10. Domain-wall dynamics near a quantum critical point

    NARCIS (Netherlands)

    Yuan, Shengjun; De Raedt, Hans; Miyashita, Seiji

    We study the real-time domain-wall dynamics near a quantum critical point of the one-dimensional anisotropic ferromagnetic spin 1/2 chain. By numerical simulation, we find that the domain wall is dynamically stable in the Heisenberg-Ising model. Near the quantum critical point, the width of the

  11. Effects of wall condition on flow distributions in arterial modeling: comparison of rigid, dynamic, and compliant walls

    Energy Technology Data Exchange (ETDEWEB)

    He, Fan [Beijing University of Civil Engineering and Architecture, Beijing (China); Hua, Lu; Gao, Li jian [Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China)

    2016-03-15

    Blood flow distributions were evaluated using various computational strategies. Three commonly used wall conditions in arterial modeling were employed, namely rigid, dynamic and compliant walls. The results show that the velocity distributions are similar under rigid and dynamic walls, developing into the Poiseuille flow, but they are blunt under compliant walls. The peak pressure under rigid walls is highest, but the model of dynamic walls has a good approximation of pressure against the model of compliant walls. The results indicate that a model of compliant walls appears to be a computationally and reasonably accurate approximation of blood velocity distributions compared with the analysis under rigid or dynamic walls. Introducing fluid-structure interaction into arterial modeling is necessary to ensure reliable results and information. However, a model of dynamic walls seems to be a computationally inexpensive yet reasonably accurate approximation for pressure.

  12. Nonlinear dynamics of domain walls with cross-ties

    Energy Technology Data Exchange (ETDEWEB)

    Dubovik, M. N., E-mail: dubovik@imp.uran.ru [Russian Academy of Sciences, Institute of Metal Physics, Ural Branch (Russian Federation); Zverev, V. V. [Ural Federal University (Russian Federation); Filippov, B. N. [Russian Academy of Sciences, Institute of Metal Physics, Ural Branch (Russian Federation)

    2016-07-15

    The dynamic behavior of a domain wall with cross-ties is analyzed on the basis of micromagnetic simulation with exact allowance for all main (exchange, magnetoanisotropic, and magnetostatic) interactions in thin magnetically uniaxial ferromagnetic films with planar anisotropy. It is found that the peculiarities of motion of such domain walls are closely related to the behavior of topological defects in the magnetization distribution (generation, motion, and annihilation of vortex–antivortex pairs on the film surface and Bloch points). We observe three different regimes of motion (stationary, periodic, and turbulent regimes), each of which is realized in a certain range of fields oriented along the easy magnetization axis. It is shown that the experimentally observed dynamic bends of the walls with cross-ties are determined by the type of motion of vortices and antivortices. The velocities of domain walls in different regimes are calculated, and the dynamic configurations of the magnetization and existing dynamic transitions between them are investigated.

  13. Dynamic Stiffness Analysis of Curved Thin-Walled Beams

    Directory of Open Access Journals (Sweden)

    A.Y.T. Leung

    1993-01-01

    Full Text Available The natural vibration problem of curved thin-walled beams is solved by the dynamic stiffness method. The dynamic stiffness of a curved open thin-walled beam is given. The computed natural frequencies of the beam are compared with those obtained by a completely analytical method to show the high accuracy of the present method. The interaction of in-plane and out-of-plane modes is emphasized.

  14. Dynamic dependence to domain wall propagation through artificial spin ice

    Science.gov (United States)

    Burn, D. M.; Chadha, M.; Branford, W. R.

    2017-03-01

    Domain wall propagation dynamics has been studied in nanostructured artificial kagome spin-ice structures. A stripline circuit has been used to provide localized pulsed magnetic fields within the artificial spin-ice (ASI) structure. This provides control of the system through electrically assisted domain wall nucleation events. Synchronization of the pulsed fields with additional global magnetic fields and the use of a focused magneto-optical Kerr effect magnetometer allows our experiments to probe the domain wall transit through an extended ASI structure. We find that the propagation distance depends on the driving field revealing field-driven properties of domain walls below their intrinsic nucleation field.

  15. Dynamic characteristics of multi-walled carbon nanotubes under a ...

    Indian Academy of Sciences (India)

    Dynamic characteristics; multi-walled carbon nanotubes; transverse magnetic field; van der Waals force. ... Couple dynamic equations of MWNTs subjected to a transverse magnetic field are derived and solved by considering the Lorentz magnetic forces induced by a transverse magnetic field exerted on MWCNTs. Results ...

  16. Nonlinear dynamic behavior of microscopic bubbles near a rigid wall

    Science.gov (United States)

    Suslov, Sergey A.; Ooi, Andrew; Manasseh, Richard

    2012-06-01

    The nonlinear dynamic behavior of microscopic bubbles near a rigid wall is investigated. Oscillations are driven by the ultrasonic pressure field that arises in various biomedical applications such as ultrasound imaging or targeted drug delivery. It is known that, when bubbles approach a blood-vessel wall, their linear dynamic response is modified. This modification may be very useful for real-time detection of bubbles that have found targets; in future therapeutic technologies, it may be useful for controlled release of medical agents encapsulating microbubbles. In this paper, the nonlinear response of microbubbles near a wall is studied. The Keller-Miksis-Parlitz equation is adopted, but modified to account for the presence of a rigid wall. This base model describes the time evolution of the bubble surface, which is assumed to remain spherical, and accounts for the effect of acoustic radiation losses owing to liquid compressibility in the momentum conservation. Two situations are considered: the base case of an isolated bubble in an unbounded medium, and a bubble near a rigid wall. In the latter case, the wall influence is modeled by including a symmetrically oscillating image bubble. The bubble dynamics is traced using a numerical solution of the model equation. Subsequently, Floquet theory is used to accurately detect the bifurcation point where bubble oscillations stop following the driving ultrasound frequency and undergo period-changing bifurcations. Of particular interest is the detection of the subcritical period-tripling and -quadrupling transition. The parametric bifurcation maps are obtained as functions of nondimensional parameters representing the bubble radius, the frequency and pressure amplitude of the driving ultrasound field, and the distance from the wall. It is shown that the presence of the wall generally stabilises the bubble dynamics, so that much larger values of the pressure amplitude are needed to generate nonlinear responses. Thus, a

  17. Walled Carotid Bifurcation Phantoms for Imaging Investigations of Vessel Wall Motion and Blood Flow Dynamics.

    Science.gov (United States)

    Chee, Adrian J Y; Ho, Chung Kit; Yiu, Billy Y S; Yu, Alfred C H

    2016-07-18

    As a major application domain of vascular ultrasound, the carotid artery has long been the subject of anthropomorphic phantom design. It is nevertheless not trivial to develop walled carotid phantoms that are compatible for use in integrative imaging of carotid wall motion and flow dynamics. In this paper, we present a novel phantom design protocol that can enable efficient fabrication of walled carotid bifurcation phantoms with: (i) high acoustic compatibility, (ii) artery-like vessel elasticity, and (iii) stenotic narrowing feature. Our protocol first involved direct fabrication of the vessel core and an outer mold using computer-aided design tools and 3-D printing technology; these built parts were then used to construct an elastic vessel tube through investment casting of a polyvinyl alcohol containing mixture, and an agar-gelatin tissue mimicking slab was formed around the vessel tube. For demonstration, we applied our protocol to develop a set of healthy and stenosed (25%, 50%, 75%) carotid bifurcation phantoms. Plane wave imaging experiments were performed on these phantoms using an ultrasound scanner with channel-level configurability. Results show that the wall motion dynamics of our phantoms agreed with pulse wave propagation in an elastic vessel (pulse wave velocity of 4.67±0.71 m/s measured at the common carotid artery), and their flow dynamics matched the expected ones in healthy and stenosed bifurcation (recirculation and flow jet formation observed). Integrative imaging of vessel wall motion and blood flow dynamics in our phantoms was also demonstrated, from which we observed fluid-structure interaction differences between healthy and diseased bifurcation phantoms. These findings show that the walled bifurcation phantoms developed with our new protocol are useful in vascular imaging studies that individually or jointly assess wall motion and flow dynamics.

  18. Dynamics of cell wall assembly during early embryogenesis in the brown alga Fucus.

    Science.gov (United States)

    Torode, Thomas A; Siméon, Amandine; Marcus, Susan E; Jam, Murielle; Le Moigne, Marie-Anne; Duffieux, Delphine; Knox, J Paul; Hervé, Cécile

    2016-11-01

    Zygotes from Fucus species have been used extensively to study cell polarization and rhizoid outgrowth, and in this model system cell wall deposition aligns with the establishment of polarity. Monoclonal antibodies are essential tools for the in situ analysis of cell wall glycans, and here we report the characteristics of six monoclonal antibodies to alginates (BAM6-BAM11). The use of these, in conjunction with monoclonal antibodies to brown algal sulfated fucans, has enabled the study of the developmental dynamics of the Fucus zygote cell walls. Young zygotes are spherical and all alginate epitopes are deposited uniformly following cellulose deposition. At germination, sulfated fucans are secreted in the growing rhizoid wall. The redistribution of cell wall epitopes was investigated during treatments that cause reorientation of the growth axis (change in light direction) or disrupt rhizoid development (arabinogalactan-protein-reactive Yariv reagent). Alginate modeling was drastically impaired in the latter, and both treatments cause a redistribution of highly sulfated fucan epitopes. The dynamics of cell wall glycans in this system have been visualized in situ for the first time, leading to an enhanced understanding of the early developmental mechanisms of Fucus species. These sets of monoclonal antibodies significantly extend the available molecular tools for brown algal cell wall studies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  19. Delayed dynamic abdominal wall closure following multi-visceral transplantation.

    Science.gov (United States)

    Iype, Satheesh; Butler, Andrew; Jamieson, Neville; Middleton, Stephen; Jah, Asif

    2014-01-01

    Primary closure of the abdominal wall following intestinal transplantation or multivisceral transplantation could become a challenging problem in a significant number of patients. A 38-year-old woman with familial adenomatous polyposis (FAP) underwent a multi-visceral transplantation for short gut syndrome. She subsequently developed acute graft rejection that proved resistant to conventional treatment. She was relisted and underwent re-transplantation along with kidney transplantation. Abdominal wall closure could not be achieved because of the large size of the graft and bowel oedema. The wound was initially managed with laparostomy followed by insertion of the delayed dynamic abdominal closure (DDAC) device (Abdominal Retraction Anchor - ABRA(®) system). Continuous dynamic traction to the wound edges resulted in gradual approximation and complete closure of the abdominal wound was achieved within 3 weeks. Successful abdominal closure after multivisceral transplantation or isolated intestinal transplantation often requires biological mesh, vascularised flaps or abdominal wall transplantation. DDAC eliminated the need for a prosthetic mesh or skin graft and provided an excellent cosmetic result. Adjustment of the dynamic traction at the bedside minimised the need for multiple returns to the operating theatre. It resulted in a well-healed linear scar without a hernia. Dynamic traction allows delayed closure of laparotomy resulting in strong and cosmetically sound wound healing with native tissue. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. ESSENTIAL DYNAMICS OF PROTEINS

    NARCIS (Netherlands)

    AMADEI, A; LINSSEN, ABM; BERENDSEN, HJC

    1993-01-01

    Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an ''essential'' subspace containing only a few degrees of freedom in which anharmonic motion occurs that

  1. Novel current driven domain wall dynamics in synthetic antiferromagnets

    Science.gov (United States)

    Yang, See-Hun

    It was reported that the domain walls in nanowires can be moved efficiently by electrical currents by a new type of torque, chiral spin torque (CST), the combination of spin Hall effect and Dzyaloshinskii-Moriya interaction. Recently we domonstrated that ns-long current pulses can move domain walls at extraordinarily high speeds (up to ~750 m s -1) in synthetic antiferromagnetic (SAF) nanowires that have almost zero net magnetization, which is much more efficient compared with similar nanowires in which the sub-layers are coupled ferromagnetically (SF). This high speed is found to be due to a new type of powerful torque, exchange coupling torque (ECT) that is directly proportional to the strength of the antiferromagnetic exchange coupling between the two sub-layers, showing that the ECT is effective only in SAF not in SF. Moreover, it is found that the dependence of the wall velocity on the magnetic field applied along the nanowire is non-monotonic. Most recently we predict an Walker-breakdown-like domain wall precession in SAF nanowires in the presence of in-plane field based on the model we develop, and this extraordinary precession has been observed. In this talk I will discuss this in details by showing a unique characteristics of SAF sublayers' DW boost-and-drag mechanism along with CST and ECT. Novel current driven domain wall dynamics in synthetic antiferromagnets.

  2. Localization of vector field on dynamical domain wall

    Directory of Open Access Journals (Sweden)

    Masafumi Higuchi

    2017-03-01

    Full Text Available In the previous works (arXiv:1202.5375 and arXiv:1402.1346, the dynamical domain wall, where the four dimensional FRW universe is embedded in the five dimensional space–time, has been realized by using two scalar fields. In this paper, we consider the localization of vector field in three formulations. The first formulation was investigated in the previous paper (arXiv:1510.01099 for the U(1 gauge field. In the second formulation, we investigate the Dvali–Shifman mechanism (arXiv:hep-th/9612128, where the non-abelian gauge field is confined in the bulk but the gauge symmetry is spontaneously broken on the domain wall. In the third formulation, we investigate the Kaluza–Klein modes coming from the five dimensional graviton. In the Randall–Sundrum model, the graviton was localized on the brane. We show that the (5,μ components (μ=0,1,2,3 of the graviton are also localized on the domain wall and can be regarded as the vector field on the domain wall. There are, however, some corrections coming from the bulk extra dimension if the domain wall universe is expanding.

  3. A statistical state dynamics approach to wall turbulence.

    Science.gov (United States)

    Farrell, B F; Gayme, D F; Ioannou, P J

    2017-03-13

    This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation-perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or 'band-limiting' can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence.This article is part of the themed issue 'Toward the development of high-fidelity models of wall turbulence at large Reynolds number'. © 2017 The Author(s).

  4. Fetal fluid and protein dynamics

    NARCIS (Netherlands)

    Pasman, Suzanne

    2010-01-01

    In this thesis fetal fluid and protein dynamics are investigated to gain insight in fetal (patho-)physiology. Studies were performed in fetuses with severe anemia and/or hydrops fetalis. Measurements were performed in fetal blood or amniotic fluid, obtained before or during intrauterine

  5. A statistical state dynamics approach to wall turbulence

    Science.gov (United States)

    Farrell, B. F.; Gayme, D. F.; Ioannou, P. J.

    2017-03-01

    This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation-perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or `band-limiting' can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence.

  6. Domain-Wall Spin Dynamics in Kagome Antiferromagnets

    Science.gov (United States)

    Lhotel, E.; Simonet, V.; Ortloff, J.; Canals, B.; Paulsen, C.; Suard, E.; Hansen, T.; Price, D. J.; Wood, P. T.; Powell, A. K.; Ballou, R.

    2011-12-01

    We report magnetization and neutron scattering measurements down to 60 mK on a new family of Fe based kagome antiferromagnets, in which a strong local spin anisotropy combined with a low exchange path network connectivity lead to domain walls intersecting the kagome planes through strings of free spins. These produce unfamiliar slow spin dynamics in the ordered phase, evolving from exchange-released spin flips towards a cooperative behavior on decreasing the temperature, probably due to the onset of long-range dipolar interaction. A domain structure of independent magnetic grains is obtained that could be generic to other frustrated magnets.

  7. The Dynamic Similitude Design Method of Thin Walled Structures and Experimental Validation

    Directory of Open Access Journals (Sweden)

    Zhong Luo

    2016-01-01

    Full Text Available For the applicability of dynamic similitude models of thin walled structures, such as engine blades, turbine discs, and cylindrical shells, the dynamic similitude design of typical thin walled structures is investigated. The governing equation of typical thin walled structures is firstly unified, which guides to establishing dynamic scaling laws of typical thin walled structures. Based on the governing equation, geometrically complete scaling law of the typical thin walled structure is derived. In order to determine accurate distorted scaling laws of typical thin walled structures, three principles are proposed and theoretically proved by combining the sensitivity analysis and governing equation. Taking the thin walled annular plate as an example, geometrically complete and distorted scaling laws can be obtained based on the principles of determining dynamic scaling laws. Furthermore, the previous five orders’ accurate distorted scaling laws of thin walled annular plates are presented and numerically validated. Finally, the effectiveness of the similitude design method is validated by experimental annular plates.

  8. Protein kinesis: The dynamics of protein trafficking and stability

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  9. Spatiotemporal Patterns in Ultraslow Domain Wall Creep Dynamics.

    Science.gov (United States)

    Ferrero, Ezequiel E; Foini, Laura; Giamarchi, Thierry; Kolton, Alejandro B; Rosso, Alberto

    2017-04-07

    In the presence of impurities, ferromagnetic and ferroelectric domain walls slide only above a finite external field. Close to this depinning threshold, they proceed by large and abrupt jumps called avalanches, while, at much smaller fields, these interfaces creep by thermal activation. In this Letter, we develop a novel numerical technique that captures the ultraslow creep regime over huge time scales. We point out the existence of activated events that involve collective reorganizations similar to avalanches, but, at variance with them, display correlated spatiotemporal patterns that resemble the complex sequence of aftershocks observed after a large earthquake. Remarkably, we show that events assemble in independent clusters that display at large scales the same statistics as critical depinning avalanches. We foresee these correlated dynamics being experimentally accessible by magnetooptical imaging of ferromagnetic films.

  10. Interplay between Penicillin-binding proteins and SEDS proteins promotes bacterial cell wall synthesis

    NARCIS (Netherlands)

    Leclercq, Sophie; Derouaux, Adeline; Olatunji, Samir; Fraipont, Claudine; Egan, Alexander J F; Vollmer, Waldemar; Breukink, Eefjan|info:eu-repo/dai/nl/120305100; Terrak, Mohammed

    2017-01-01

    Bacteria utilize specialized multi-protein machineries to synthesize the essential peptidoglycan (PG) cell wall during growth and division. The divisome controls septal PG synthesis and separation of daughter cells. In E. coli, the lipid II transporter candidate FtsW is thought to work in concert

  11. The Role of Plant Cell Wall Proteins in Response to Salt Stress

    Directory of Open Access Journals (Sweden)

    Lyuben Zagorchev

    2014-01-01

    Full Text Available Contemporary agriculture is facing new challenges with the increasing population and demand for food on Earth and the decrease in crop productivity due to abiotic stresses such as water deficit, high salinity, and extreme fluctuations of temperatures. The knowledge of plant stress responses, though widely extended in recent years, is still unable to provide efficient strategies for improvement of agriculture. The focus of study has been shifted to the plant cell wall as a dynamic and crucial component of the plant cell that could immediately respond to changes in the environment. The investigation of plant cell wall proteins, especially in commercially important monocot crops revealed the high involvement of this compartment in plants stress responses, but there is still much more to be comprehended. The aim of this review is to summarize the available data on this issue and to point out the future areas of interest that should be studied in detail.

  12. Cell wall proteins of Sporothrix schenckii as immunoprotective agents.

    Science.gov (United States)

    Alba-Fierro, Carlos A; Pérez-Torres, Armando; López-Romero, Everardo; Cuéllar-Cruz, Mayra; Ruiz-Baca, Estela

    2014-01-01

    Sporothrix schenckii is the etiological agent of sporotrichosis, an endemic subcutaneous mycosis in Latin America. Cell wall (CW) proteins located on the cell surface are inducers of cellular and humoral immune responses, potential candidates for diagnosis purposes and to generate vaccines to prevent fungal infections. This mini-review emphasizes the potential use of S. schenckii CW proteins as protective and therapeutic immune response inducers against sporotrichosis. A number of pathogenic fungi display CW components that have been characterized as inducers of protective cellular and humoral immune responses against the whole pathogen from which they were originally purified. The isolation and characterization of immunodominant protein components of the CW of S. schenckii have become relevant because of their potential in the development of protective and therapeutic immune responses against sporotrichosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  13. Regulated shift from helical to polar localization of Listeria monocytogenes cell wall-anchored proteins.

    Science.gov (United States)

    Bruck, Serawit; Personnic, Nicolas; Prevost, Marie-Christine; Cossart, Pascale; Bierne, Hélène

    2011-09-01

    Many virulence factors of Gram-positive bacterial pathogens are covalently anchored to the peptidoglycan (PG) by sortase enzymes. However, for rod-shaped bacteria little is known about the spatiotemporal organization of these surface proteins in the cell wall. Here we report the three-dimensional (3D) localization of the PG-bound virulence factors InlA, InlH, InlJ, and SvpA in the envelope of Listeria monocytogenes under different growth conditions. We found that all PG-anchored proteins are positioned along the lateral cell wall in nonoverlapping helices. However, these surface proteins can also become localized at the pole and asymmetrically distributed when specific regulatory pathways are activated. InlA and InlJ are enriched at poles when expressed at high levels in exponential-phase bacteria. InlA and InlH, which are σ(B)dependent, specifically relocalize to the septal cell wall and subsequently to the new pole in cells entering stationary phase. The accumulation of InlA and InlH in the septal region also occurs when oxidative stress impairs bacterial growth. In contrast, the iron-dependent protein SvpA is present at the old pole and is excluded from the septum and new pole of bacteria grown under low-iron conditions. We conclude that L. monocytogenes rapidly reorganizes the spatial localization of its PG proteins in response to changes in environmental conditions such as nutrient deprivation or other stresses. This dynamic control would distribute virulence factors at specific sites during the infectious process.

  14. WD40-Repeat Proteins in Plant Cell Wall Formation: Current Evidence and Research Prospects

    National Research Council Canada - National Science Library

    Guerriero, Gea; Hausman, Jean-Francois; Ezcurra, Inés

    2015-01-01

    The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis...

  15. HYDROGEN BOND DYNAMICS IN MEMBRANE PROTEIN FUNCTION

    OpenAIRE

    Bondar, Ana-Nicoleta; White, Stephen H.

    2011-01-01

    Changes in inter-helical hydrogen bonding are associated with the conformational dynamics of membrane proteins. The function of the protein depends on the surrounding lipid membrane. Here we review through specific examples how dynamical hydrogen bonds can ensure an elegant and efficient mechanism of long-distance intra-protein and protein-lipid coupling, contributing to the stability of discrete protein conformational substates and to rapid propagation of structural perturbations.

  16. Electric-field-driven dynamics of magnetic domain walls in magnetic nanowires patterned on ferroelectric domains

    OpenAIRE

    Wiele, Ben Van de; Leliaert, Jonathan; Franke, Kévin J A; Dijken, Sebastiaan van

    2016-01-01

    Strong coupling of magnetic domain walls onto straight ferroelastic boundaries of a ferroelectric layer enables full and reversible electric-field control of magnetic domain wall motion. In this paper, the dynamics of this new driving mechanism is analyzed using micromagnetic simulations. We show that transverse domain walls with a near-180° spin structure are stabilized in magnetic nanowires and that electric fields can move these walls with high velocities. Above a critical velocity, which ...

  17. Universality and Specificity in Protein Fluctuation Dynamics

    Science.gov (United States)

    Copperman, J.; Dinpajooh, M.; Beyerle, E. R.; Guenza, M. G.

    2017-10-01

    We investigate the universal scaling of protein fluctuation dynamics with a site-specific diffusive model of protein motion, which predicts an initial subdiffusive regime in the configurational relaxation. The long-time dynamics of proteins is controlled by an activated regime. We argue that the hierarchical free energy barriers set the time scales of biological processes and establish an upper limit to the size of single protein domains. We find it compelling that the scaling behavior for the protein dynamics is in close agreement with the Kardar-Parisi-Zhang scaling exponents.

  18. Comprehensive Evaluation of Streptococcus sanguinis Cell Wall-Anchored Proteins in Early Infective Endocarditis▿ †

    Science.gov (United States)

    Turner, Lauren Senty; Kanamoto, Taisei; Unoki, Takeshi; Munro, Cindy L.; Wu, Hui; Kitten, Todd

    2009-01-01

    Streptococcus sanguinis is a member of the viridans group of streptococci and a leading cause of the life-threatening endovascular disease infective endocarditis. Initial contact with the cardiac infection site is likely mediated by S. sanguinis surface proteins. In an attempt to identify the proteins required for this crucial step in pathogenesis, we searched for surface-exposed, cell wall-anchored proteins encoded by S. sanguinis and then used a targeted signature-tagged mutagenesis (STM) approach to evaluate their contributions to virulence. Thirty-three predicted cell wall-anchored proteins were identified—a number much larger than those found in related species. The requirement of each cell wall-anchored protein for infective endocarditis was assessed in the rabbit model. It was found that no single cell wall-anchored protein was essential for the development of early infective endocarditis. STM screening was also employed for the evaluation of three predicted sortase transpeptidase enzymes, which mediate the cell surface presentation of cell wall-anchored proteins. The sortase A mutant exhibited a modest (∼2-fold) reduction in competitiveness, while the other two sortase mutants were indistinguishable from the parental strain. The combined results suggest that while cell wall-anchored proteins may play a role in S. sanguinis infective endocarditis, strategies designed to interfere with individual cell wall-anchored proteins or sortases would not be effective for disease prevention. PMID:19703977

  19. Expression and characterization of a novel spore wall protein from ...

    African Journals Online (AJOL)

    Microsporidia are obligate intracellular, eukaryotic, spore-forming parasites. The environmentally resistant spores, which harbor a rigid cell wall, are critical for their survival outside their host cells and host-to-host transmission. The spore wall comprises two major layers: the exospore and the endospore. In Nosema ...

  20. Loss of the Arabidopsis Protein Kinases ANPs Affects Root Cell Wall Composition, and Triggers the Cell Wall Damage Syndrome

    Directory of Open Access Journals (Sweden)

    Nora Gigli Bisceglia

    2018-01-01

    Full Text Available The Arabidopsis NPK1-related Protein kinases ANP1, ANP2 and ANP3 belong to the MAP kinase kinase kinase (MAPKKK superfamily and were previously described to be crucial for cytokinesis, elicitor-induced immunity and development. Here we investigate the basis of their role in development by using conditional β-estradiol-inducible triple mutants to overcome lethality. In seedlings, lack of ANPs causes root cell bulging, with the transition zone being the most sensitive region. We uncover a role of ANPs in the regulation of cell wall composition and suggest that developmental defects of the triple mutants, observed at the cellular level, might be a consequence of the alterations of the pectic and cellulosic cell wall components. Lack of ANPs also induced a typical cell wall damage syndrome (CWDS similar to that observed in plants treated with the cellulose biosynthesis inhibitor isoxaben (ISX. Moreover, anp double mutants and plants overexpressing single ANPs (ANP1 or ANP3 respectively showed increased and reduced accumulation of jasmonic acid and PDF1.2 transcripts upon ISX treatment, suggesting that ANPs are part of the pathway targeted by this inhibitor and play a role in cell wall integrity surveillance.Highlights: The loss of ANP function affects cell wall composition and leads to typical cell wall damage-induced phenotypes, such as ectopic lignification and jasmonic acid accumulation.

  1. The plant cell wall: A dynamic barrier against pathogen invasion.

    Directory of Open Access Journals (Sweden)

    William eUnderwood

    2012-05-01

    Full Text Available Prospective plant pathogens must overcome the physical barrier presented by the plant cell wall. In addition to being a preformed, passive barrier limiting access of pathogens to plant cells, the cell wall is actively remodeled and reinforced specifically at discrete sites of interaction with potentially pathogenic microbes. Active reinforcement of the cell wall through the deposition of call wall appositions, referred to as papillae, is an early response to perception of numerous categories of pathogens including fungi and bacteria. Rapid deposition of papillae is generally correlated with resistance to fungal pathogens that attempt to penetrate plant cell walls for the establishment of feeding structures. Despite the ubiquity and apparent importance of this early defense response, relatively little is known about the underlying molecular mechanisms and cellular processes involved in the targeting and assembly of papillae. This review summarizes recent advances in our understanding of call wall-associated defenses induced by pathogen perception as well as the impact of changes in cell wall polymers on interactions with pathogens and highlights significant unanswered questions driving future research in the area.

  2. The Direct Effect of Flexible Walls on Fontan Connection Fluid Dynamics

    Science.gov (United States)

    Tree, Mike; Fagan, Kiley; Yoganathan, Ajit

    2014-11-01

    The current standard treatment for sufferers of congenital heart defects is the palliative Fontan procedure. The Fontan procedure results in an anastomosis of major veins directly to the branched pulmonary arteries bypassing the dysfunctional ventricle. This total cavopulmonary connection (TCPC) extends life past birth, but Fontan patients still suffer long-term complications like decreased exercise capacity, protein-losing enteropathy, and pulmonary arteriovenous malformations (PAVM). These complications have direct ties to fluid dynamics within the connection. Previous experimental and computation studies of Fontan connection fluid dynamics employed rigid vessel models. More recent studies utilize flexible models, but a direct comparison of the fundamental fluid dynamics between rigid and flexible vessels only exists for a computational model, without a direct experimental validation. Thus, this study was a direct comparison of fluid dynamics within a rigid and two compliant idealized TCPCs. 2D particle image velocimetry measurements were collected at the connection center plane. Results include power loss, hepatic flow distribution, fluid shear stress, and flow structure recognition. The effect of flexible walls on these values and clinical impact will be discussed.

  3. Dynamic characteristics of multi-walled carbon nanotubes under a ...

    Indian Academy of Sciences (India)

    walled carbon nanotubes; transverse magnetic field; van der Waals force. 1. Introduction. Since the discovery of carbon nanotubes (CNTs) (Iijima. 1991), extensive research related to the carbon nanotubes in the fields of chemistry, physics, ...

  4. Dissecting the regulation of pollen tube growth by modelling the interplay of hydrodynamics, cell wall and ion dynamics

    Directory of Open Access Journals (Sweden)

    Junli eLiu

    2014-08-01

    Full Text Available Hydrodynamics, cell wall and ion dynamics are all important properties that regulate pollen tube growth. Currently, the two main pollen tube growth models, the cell wall model and the hydrodynamic model do not appear to be reconcilable. Here we develop an integrative model for pollen tube growth and show that our model reproduces key experimental observations: 1 that the hypertonic condition leads to a much longer oscillatory period and that the hypotonic condition halves the oscillatory period; 2 that oscillations in turgor are experimentally undetectable; 3 that increasing the extracellular calcium concentration or decreasing the pH decreases the growth oscillatory amplitude; 4 that knockout of Raba4d, a member of the Rab family of small GTPase proteins, decreases pollen tube length after germination for 24 hours. Using the model generated here, we reveal that 1 when cell wall extensibility is large, pollen tube may sustain growth at different volume changes and maintain relatively stable turgor; 2 turgor increases if cell wall extensibility decreases; 3 increasing turgor due to decrease in osmolarity in the media, although very small, increases volume change . However, increasing turgor due to decrease in cell wall extensibility decreases volume change. In this way regulation of pollen tube growth by turgor is context dependent. By changing the osmolarity in the media, the main regulatory points are extracellular osmolarity for water flow and turgor for the volume encompassed by the cell wall. However, if the viscosity of cell wall changes, the main regulatory points are turgor for water flow and wall extensibility for the volume encompassed by the cell wall. The novel methodology developed here reveals the underlying context-dependent regulatory principle of pollen tube growth.

  5. Coupling of protein dynamics with the solvent

    Science.gov (United States)

    Caliskan, Gokhan; Sauzan, Azzam; Mehtani, Disha; Sokolov, Alexei

    2003-03-01

    Glycerol and trehalose are among the many viscous solvents that are widely used for biostabilization and controlling the dynamics of proteins. It is believed that the suppression of the structural relaxations by high viscosity of solvent is responsible for improved stability in proteins. However, results of [1] and [2] demonstrate stronger suppression of biochemical activity and dynamics of proteins by liquid glycerol than by solid trehalose in a wide temperature range. The authors tried to explain the counterintuitive observations by a possible decoupling of the dynamics of the protein from trehalose. In order to test the validity of this assumption and to investigate the influence of the fast dynamics in proteins, the low frequency Raman scattering spectroscopy technique is used. Both relaxational and vibrational dynamics of glycerol, trehalose, and lysozyme in glycerol and in trehalose are studied in a wide temperature range. Dynamics of lysozyme in glycerol follows the strong temperature dependence of relaxational and vibrational dynamics of the bulk glycerol. On the other hand, the weak temperature dependence of dynamics of lysozyme in trehalose follows exactly the behavior of pure trehalose. This proves that there is a strong dynamic coupling between the protein and the solvents used. Interestingly, stronger relaxations in solid trehalose as compared to liquid glycerol are observed in the GHz region at low temperatures. This could be the reason for the enhanced protein activity observed in trehalose, compared to that in glycerol in this temperature range. Suppression of these fast relaxations should be the key for providing long-term stability to proteins. 1. Sastry, G.M. and N. Agmon, Trehalose prevents myoglobin collapse and preserves its internal mobility. BIOCHEMISTRY, 1997, 36(23): p. 7097-108. 2. Caliskan, G., et al., Influence of solvent on dynamics and stability of a protein. Journal of Non-Crystalline Solids, 2002, 307-310: p. 887-893.

  6. Water-Protein Interactions: The Secret of Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Silvia Martini

    2013-01-01

    Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

  7. The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence

    Energy Technology Data Exchange (ETDEWEB)

    Tomita, Tadakimi; Bzik, David J.; Ma, Yan Fen; Fox, Barbara A.; Markillie, Lye Meng; Taylor, Ronald C.; Kim, Kami; Weiss, Louis M.

    2013-12-26

    Toxoplasma gondii infects up to one third of the world’s population. A key to the success of T.gondii is its ability to persist for the life of its host as bradyzoites within tissue cysts. The glycosylated cyst wall is the key structural feature that facilitates persistence and oral transmission of this parasite. We have identified CST1 (TGME49_064660) as a 250 kDa SRS (SAG1 related sequence) domain protein with a large mucin-like domain. CST1 is responsible for the Dolichos biflorus Agglutinin (DBA) lectin binding characteristic of T. gondii cysts. Deletion of CST1 results in a fragile brain cyst phenotype revealed by a thinning and disruption of the underlying region of the cyst wall. These defects are reversed by complementation of CST1. Additional complementation experiments demonstrate that the CST1-mucin domain is necessary for the formation of a normal cyst wall structure, the ability of the cyst to resist mechanical stress and binding of DBA to the cyst wall. RNA-seq transcriptome analysis demonstrated dysregulation of bradyzoite genes within the various cst1 mutants. These results indicate that CST1 functions as a key structural component that reinforces the cyst wall structure and confers essential sturdiness to the T. gondii tissue cyst.

  8. Predicting Protein Interactions by Brownian Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Xuan-Yu Meng

    2012-01-01

    Full Text Available We present a newly adapted Brownian-Dynamics (BD-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.

  9. Molecular Dynamics and Protein Function

    National Research Council Canada - National Science Library

    M. Karplus; J. Kuriyan; Bruce J. Berne

    2005-01-01

    .... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...

  10. Evidence against the involvement of ionically bound cell wall proteins in pea epicotyl growth

    Science.gov (United States)

    Melan, M. A.; Cosgrove, D. J.

    1988-01-01

    Ionically bound cell wall proteins were extracted from 7 day old etiolated pea (Pisum sativum L. cv Alaska) epicotyls with 3 molar LiCl. Polyclonal antiserum was raised in rabbits against the cell wall proteins. Growth assays showed that treatment of growing region segments (5-7 millimeters) of peas with either dialyzed serum, serum globulin fraction, affinity purified immunoglobulin, or papain-cleaved antibody fragments had no effect on growth. Immunofluorescence microscopy confirmed antibody binding to cell walls and penetration of the antibodies into the tissues. Western blot analysis, immunoassay results, and affinity chromatography utilizing Sepharose-bound antibodies confirmed recognition of the protein preparation by the antibodies. Experiments employing in vitro extension as a screening measure indicated no effect upon extension by antibodies, by 50 millimolar LiCl perfusion of the apoplast or by 3 molar LiCl extraction. Addition of cell wall protein to protease pretreated segments did not restore extension nor did addition of cell wall protein to untreated segments increase extension. It is concluded that, although evidence suggests that protein is responsible for the process of extension, the class(es) of proteins which are extracted from pea cell walls with 3 molar LiCl are probably not involved in this process.

  11. Static and dynamic thermal characterisation of a hollow brick wall: Tests and numerical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sala, J.M.; Urresti, A. [Thermal Engineering Department, Universidad del Pais Vasco (UPV/EHU), Alda. Urquijo s/n, 48013 Bilbao (Spain); Martin, K.; Flores, I.; Apaolaza, A. [Construction Quality Control Laboratory of the Basque Government, C/Aguirrelanda n 10, 01013 Vitoria-Gasteiz (Spain)

    2008-07-01

    This article explains the adjustment procedure of a calibrated hot-box unit and the execution of the corresponding tests to measure the dynamic thermal properties of walls needed to calculate the thermal load of buildings. The results of a test for a heterogeneous wall are also presented, in a dynamic temperature rating. These results are compared with those obtained from a simulation carried out on the performance of the same wall through the application of a finite volume software. Subsequently, the error introduced by assuming one-dimensional heat flow through a nonhomogeneous wall is discussed. This is equivalent to considering the heterogeneous layer of the wall as an equivalent homogeneous layer, which is done in several whole building simulation programs. It is concluded that the error committed may be appreciable, even when the heterogeneities are not excessive. (author)

  12. Dynamic conductivity of ferroelectric domain walls in BiFeO₃.

    Science.gov (United States)

    Maksymovych, Peter; Seidel, Jan; Chu, Ying Hao; Wu, Pingping; Baddorf, Arthur P; Chen, Long-Qing; Kalinin, Sergei V; Ramesh, Ramamoorthy

    2011-05-11

    Topological walls separating domains of continuous polarization, magnetization, and strain in ferroic materials hold promise of novel electronic properties, that are intrinsically localized on the nanoscale and that can be patterned on demand without change of material volume or elemental composition. We have revealed that ferroelectric domain walls in multiferroic BiFeO(3) are inherently dynamic electronic conductors, closely mimicking memristive behavior and contrary to the usual assumption of rigid conductivity. Applied electric field can cause a localized transition between insulating and conducting domain walls, tune domain wall conductance by over an order of magnitude, and create a quasicontinuous spectrum of metastable conductance states. Our measurements identified that subtle and microscopically reversible distortion of the polarization structure at the domain wall is at the origin of the dynamic conductivity. The latter is therefore likely to be a universal property of topological defects in ferroelectric semiconductors.

  13. Prion protein dynamics before aggregation

    National Research Council Canada - National Science Library

    Srivastava, Kinshuk Raj; Lapidusa, Lisa J

    2017-01-01

      Prion diseases, like Alzheimer's disease and Parkinson disease, are rapidly progressive neurodegenerative disorders caused by misfolding followed by aggregation and accumulation of protein deposits in neuronal cells...

  14. Thermal dynamic simulation of wall for building energy efficiency under varied climate environment

    Science.gov (United States)

    Wang, Xuejin; Zhang, Yujin; Hong, Jing

    2017-08-01

    Aiming at different kind of walls in five cities of different zoning for thermal design, using thermal instantaneous response factors method, the author develops software to calculation air conditioning cooling load temperature, thermal response factors, and periodic response factors. On the basis of the data, the author gives the net work analysis about the influence of dynamic thermal of wall on air-conditioning load and thermal environment in building of different zoning for thermal design regional, and put forward the strategy how to design thermal insulation and heat preservation wall base on dynamic thermal characteristic of wall under different zoning for thermal design regional. And then provide the theory basis and the technical references for the further study on the heat preservation with the insulation are in the service of energy saving wall design. All-year thermal dynamic load simulating and energy consumption analysis for new energy-saving building is very important in building environment. This software will provide the referable scientific foundation for all-year new thermal dynamic load simulation, energy consumption analysis, building environment systems control, carrying through farther research on thermal particularity and general particularity evaluation for new energy -saving walls building. Based on which, we will not only expediently design system of building energy, but also analyze building energy consumption and carry through scientific energy management. The study will provide the referable scientific foundation for carrying through farther research on thermal particularity and general particularity evaluation for new energy saving walls building.

  15. Investigation of the functional role of CSLD proteins in plant cell wall deposition

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Erik Etlar [Univ. of Michigan, Ann Arbor, MI (United States)

    2017-11-21

    The overall goal of this research proposal was to characterize the molecular machinery responsible for polarized secretion of cell wall components in Arabidopsis thaliana. We have used the polarized expansion that occurs during root hair cell growth to identify membrane trafficking pathways involved in polarized secretion of cell wall components to the expanding tips of these cells, and we have recently shown that CSLD3 is preferentially targeted to the apical plasma membranes in root hair cells, where it plays essential roles during cell wall deposition in these cells. The specific aims of the project are designed to answer the following objective: Identification of the cell wall polysaccharide class that CSLD proteins synthesize.

  16. Lattice Boltzmann simulations for wall-flow dynamics in porous ceramic diesel particulate filters

    Science.gov (United States)

    Lee, Da Young; Lee, Gi Wook; Yoon, Kyu; Chun, Byoungjin; Jung, Hyun Wook

    2018-01-01

    Flows through porous filter walls of wall-flow diesel particulate filter are investigated using the lattice Boltzmann method (LBM). The microscopic model of the realistic filter wall is represented by randomly overlapped arrays of solid spheres. The LB simulation results are first validated by comparison to those from previous hydrodynamic theories and constitutive models for flows in porous media with simple regular and random solid-wall configurations. We demonstrate that the newly designed randomly overlapped array structures of porous walls allow reliable and accurate simulations for the porous wall-flow dynamics in a wide range of solid volume fractions from 0.01 to about 0.8, which is beyond the maximum random packing limit of 0.625. The permeable performance of porous media is scrutinized by changing the solid volume fraction and particle Reynolds number using Darcy's law and Forchheimer's extension in the laminar flow region.

  17. Quantum Dynamics of Spin Wave Propagation through Domain Walls

    NARCIS (Netherlands)

    Yuan, S.; Raedt, H. De; Miyashita, S.

    Through numerical solution of the time-dependent Schrödinger equation, we demonstrate that magnetic chains with uniaxial anisotropy support stable structures, separating ferromagnetic domains of opposite magnetization. These structures, domain walls in a quantum system, are shown to remain stable if

  18. Explosion induced dynamic responses of blast wall on FPSO topside: Blast loading application methods

    Directory of Open Access Journals (Sweden)

    Ki-Yeob Kang

    2017-03-01

    Full Text Available Topside areas on an offshore oil and gas platform are highly susceptible to explosion. A blast wall on these areas plays an important role in preventing explosion damage and must withstand the expected explosion loads. The uniformly distributed loading condition, predicted by Explosion Risk Analyses (ERAs, has been applied in most of the previous analysis methods. However, analysis methods related to load conditions are inaccurate because the blast overpressure around the wall tends to be of low-level in the open area and high-level in the enclosed area. The main objectives of this paper are to study the effects of applying different load applications and compare the dynamic responses of the blast wall. To do so, various kinds of blast pressures were measured by Computational Fluid Dynamics (CFD simulations on the target area. Nonlinear finite element analyses of the blast wall under two types of identified dynamic loadings were also conducted.

  19. Flow induced by ependymal cilia dominates near-wall cerebrospinal fluid dynamics in the lateral ventricles

    Science.gov (United States)

    Siyahhan, Bercan; Knobloch, Verena; de Zélicourt, Diane; Asgari, Mahdi; Schmid Daners, Marianne; Poulikakos, Dimos; Kurtcuoglu, Vartan

    2014-01-01

    While there is growing experimental evidence that cerebrospinal fluid (CSF) flow induced by the beating of ependymal cilia is an important factor for neuronal guidance, the respective contribution of vascular pulsation-driven macroscale oscillatory CSF flow remains unclear. This work uses computational fluid dynamics to elucidate the interplay between macroscale and cilia-induced CSF flows and their relative impact on near-wall dynamics. Physiological macroscale CSF dynamics are simulated in the ventricular space using subject-specific anatomy, wall motion and choroid plexus pulsations derived from magnetic resonance imaging. Near-wall flow is quantified in two subdomains selected from the right lateral ventricle, for which dynamic boundary conditions are extracted from the macroscale simulations. When cilia are neglected, CSF pulsation leads to periodic flow reversals along the ventricular surface, resulting in close to zero time-averaged force on the ventricle wall. The cilia promote more aligned wall shear stresses that are on average two orders of magnitude larger compared with those produced by macroscopic pulsatile flow. These findings indicate that CSF flow-mediated neuronal guidance is likely to be dominated by the action of the ependymal cilia in the lateral ventricles, whereas CSF dynamics in the centre regions of the ventricles is driven predominantly by wall motion and choroid plexus pulsation. PMID:24621815

  20. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  1. Inactivation of Tor proteins affects the dynamics of endocytic proteins ...

    Indian Academy of Sciences (India)

    Tor2 is an activator of the Rom2/Rho1 pathway that regulates -factor internalization. Since the recruitment of endocytic proteins such as actin-binding proteins and the amphiphysins precedes the internalization of -factor, we hypothesized that loss of Tor function leads to an alteration in the dynamics of the endocytic ...

  2. Is a malleable protein necessarily highly dynamic?

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Teilum, Kaare

    2012-01-01

    The nuclear coactivator binding domain of CREB binding protein folds into remarkably different structures in complex with different ligands. To understand the mechanism of the structural adaptability in the nuclear coactivator binding domain (NCBD), we have compared the dynamics of the hydrophobic...... in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures...... in a single cooperative process. The molten globule characteristics of NCBD are thus restricted to a slowly fluctuating tertiary structure. Consequently, the conformational plasticity of the protein is most likely related to its low overall stability rather than an intrinsically flexible protein structure...

  3. WD40-repeat proteins in plant cell wall formation: current evidence and research prospects

    Directory of Open Access Journals (Sweden)

    Gea eGuerriero

    2015-12-01

    Full Text Available The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis. In eukaryotes WD40-repeat (WDR proteins often function as molecular hubs mediating supramolecular interactions. WDR proteins may display a variety of interacting partners and participate in the assembly of complexes involved in distinct cellular functions. In plants, the formation of lignocellulosic biomass involves extensive synthesis of cell wall polysaccharides, a process that requires the assembly of large transmembrane enzyme complexes, intensive vesicle trafficking, interactions with the cytoskeleton, and coordinated gene expression. Because of their function as supramolecular hubs, WDR proteins could participate in each or any of these steps, although to date only few WDR proteins have been linked to the cell wall by experimental evidence. Nevertheless, several potential cell wall-related WDR proteins were recently identified using in silico aproaches, such as analyses of co-expression, interactome and conserved gene neighbourhood. Notably, some WDR genes are frequently genomic neighbours of genes coding for GT2-family polysaccharide synthases in eukaryotes, and this WDR-GT2 collinear microsynteny is detected in diverse taxa. In angiosperms, two WDR genes are collinear to cellulose synthase genes, CESAs, whereas in ascomycetous fungi several WDR genes are adjacent to chitin synthase genes, chs. In this Perspective we summarize and discuss experimental and in silico studies on the possible involvement of WDR proteins in plant cell wall formation. The prospects of biotechnological engineering for enhanced biomass production are discussed.

  4. wall

    Directory of Open Access Journals (Sweden)

    Irshad Kashif

    2016-01-01

    Full Text Available Maintaining indoor climatic conditions of buildings compatible with the occupant comfort by consuming minimum energy, especially in a tropical climate becomes a challenging problem for researchers. This paper aims to investigate this problem by evaluating the effect of different kind of Photovoltaic Trombe wall system (PV-TW on thermal comfort, energy consumption and CO2 emission. A detailed simulation model of a single room building integrated with PV-TW was modelled using TRNSYS software. Results show that 14-35% PMV index and 26-38% PPD index reduces as system shifted from SPV-TW to DGPV-TW as compared to normal buildings. Thermal comfort indexes (PMV and PPD lie in the recommended range of ASHARE for both DPV-TW and DGPV-TW except for the few months when RH%, solar radiation intensity and ambient temperature were high. Moreover PVTW system significantly reduces energy consumption and CO2 emission of the building and also 2-4.8 °C of temperature differences between indoor and outdoor climate of building was examined.

  5. Heat transfer enhancement by dynamic corrugated heat exchanger wall: Numerical study

    Science.gov (United States)

    Kumar, P.; Schmidmayer, K.; Topin, F.; Miscevic, M.

    2016-09-01

    A new concept of heat exchanger at sub-millimeter scale is proposed for applications in cooling on-board electronics devices, in which the quality of the exchanges between fluid and wall is very critical. In the proposed system, the upper wall of the channel is deformed dynamically to obtain a sinusoidal wave on this surface. The lower wall is exposed to constant heat flux simulating the imprint of an electronic component. A systematic 3-D numerical study in transient regime on the different deformation parameters allowed obtaining both the pumping characteristics and the heat transfer characteristics of the system. It was observed that the dynamic deformation of the wall induces a significant pumping effect. The intensification of the heat transfer is very important even for highly degraded waveforms, although the pumping efficiency is reduced in this case.

  6. Influence of surface anisotropy on domain wall dynamics in magnetic nanotube

    Science.gov (United States)

    Usov, N. A.; Serebryakova, O. N.

    2017-11-01

    It is shown that surface domain structure arises in magnetic nanotube with uniaxial anisotropy if surface anisotropy constant is negative and sufficiently high in absolute value. The surface magnetic anisotropy affects also the structure and dynamics of a head-to-head domain wall propagating along the nanotube axis in applied magnetic field. The hopping mode is observed for stationary movement of a head-to-head domain wall. The average speed of the domain wall in the hopping mode is found to be several times less than the stationary velocity of the wall in the absence of surface anisotropy. This effect is important for various applications where fast propagation of the domain wall along the sample is essential.

  7. Coupled Dzyaloshinskii walls and their current-induced dynamics by the spin Hall effect

    Energy Technology Data Exchange (ETDEWEB)

    Martínez, Eduardo, E-mail: edumartinez@usal.es [Dpto. de Fisica Aplicada, Universidad de Salamanca, Plaza de los Caídos s/n, E-37008 Salamanca (Spain); Alejos, Óscar [Dpto. de Electricidad y Electrónica, Universidad de Valladolid, Paseo de Belén, 7, E-47011 Valladolid (Spain)

    2014-07-14

    The nucleation of domain walls in ultrathin ferromagnetic/heavy-metal bilayers is studied by means of micromagnetic simulations. In the presence of interfacial Dzyaloshinskii-Moriya interaction, the nucleated walls naturally adopt a homochiral configuration with internal magnetization pointing antiparallely. The interaction between these walls was analyzed and described in terms of a classical dipolar force between the magnetic moments of the walls, which couples their dynamics. Additionally, the current-induced motion of two homochiral walls in the presence of longitudinal fields was also studied by means of a simple one-dimensional model and micromagnetic modeling, considering both one free-defect strip and another one with random edge roughness. It is evidenced that in the presence of pinning due to edge roughness, the in-plane longitudinal field introduces an asymmetry in the current-induced depinning, in agreement with recent experimental results.

  8. Structural constraints and dynamics of bacterial cell wall architecture

    Directory of Open Access Journals (Sweden)

    Miguel Angel De Pedro

    2015-05-01

    Full Text Available The peptidoglycan wall (PG is a unique structure which confers physical strength and defined shape to bacteria. It consists of a net-like macromolecule of peptide interlinked glycan chains overlying the cell membrane. The structure and layout of the PG dictates that the wall has to be continuously modified as bacteria go through division, morphological differentiation and adaptive responses. The PG is poorly known in structural terms. However, to understand morphogenesis a precise knowledge of glycan strand arrangement and of local effects of the different kinds of subunits is essential. The scarcity of data led to a conception of the PG as a regular, highly ordered structure which strongly influenced growth models. Here, we review the structure of the PG to define a more realistic conceptual framework. We discuss the consequences of the plasticity of murein architecture in morphogenesis and try to define a set of minimal structural constraints that must be fulfilled by any model to be compatible with present day information.

  9. Identification of a novel spore wall protein (SWP26) from microsporidia Nosema bombycis.

    Science.gov (United States)

    Li, Yanhong; Wu, Zhengli; Pan, Guoqing; He, Weiwei; Zhang, Ruizhi; Hu, Junhua; Zhou, Zeyang

    2009-03-01

    Microsporidia are obligate intracellular parasites related to fungi with resistant spores against various environmental stresses. The rigid spore walls of these organisms are composed of two major layers, which are the exospore and the endospore. Two spore wall proteins (the endosporal protein-SWP30 and the exosporal protein-SWP32) have been previously identified in Nosema bombycis. In this study, using the MALDI-TOF-MS technique, we have characterised a new 25.7-kDa spore wall protein (SWP26) recognised by monoclonal antibody 2G10. SWP26 is predicted to have a signal peptide, four potential N-glycosylation sites, and a C-terminal heparin-binding motif (HBM) which is known to interact with extracellular glycosaminoglycans. By using a host cell binding assay, recombinant SWP26 protein (rSWP26) can inhibit spore adherence by 10%, resulting in decreased host cell infection. In contrast, the mutant rSWP26 (rDeltaSWP26, without HBM) was not effective in inhibiting spore adherence. Immuno-electron microscopy revealed that this protein was expressed largely in endospore and plasma membrane during endospore development, but sparsely distributed in the exospore of mature spores. The present results suggest that SWP26 is a microsporidia cell wall protein that is involved in endospore formation, host cell adherence and infection in vitro. Moreover, SWP26 could be used as a good prospective target for diagnostic research and drug design in controlling the silkworm, Bombyx mori, pebrine disease in sericulture.

  10. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  11. Chest wall dynamics and muscle recruitment during professional flute playing.

    Science.gov (United States)

    Cossette, Isabelle; Monaco, Pierpaolo; Aliverti, Andrea; Macklem, Peter T

    2008-02-01

    Respiratory parameters and sound were recorded during professional flute playing in order to assess what physiological processes were associated with the control of sound production that results in 'breath support' which in turn is associated with high quality playing. Four standing young professional flautists played flute excerpts with and without breath support. Recordings included optoelectronic plethysmographic measurements of chest wall volume (V(cw)) and its compartments, surface electromyography of the scalene, lateral abdominal, rectus abdominus, parasternal and sternocleidomastoid muscles, mouth pressure, and sound. Flow was estimated from differentiating V(cw) during playing. Results showed that flute support entails antagonistic contraction of non-diaphragmatic inspiratory muscles that tends to hold the rib cage at higher lung volume. This relieves the expiratory muscles from the task of producing the right mouth pressure, especially at the end of the phrases, so they can contribute more to the finer control of mouth pressure modulations required for high quality playing.

  12. Electric-field-driven domain wall dynamics in perpendicularly magnetized multilayers

    Directory of Open Access Journals (Sweden)

    Diego López González

    2017-03-01

    Full Text Available We report on reversible electric-field-driven magnetic domain wall motion in a Cu/Ni multilayer on a ferroelectric BaTiO3 substrate. In our heterostructure, strain-coupling to ferroelastic domains with in-plane and perpendicular polarization in the BaTiO3 substrate causes the formation of domains with perpendicular and in-plane magnetic anisotropy, respectively, in the Cu/Ni multilayer. Walls that separate magnetic domains are elastically pinned onto ferroelectric domain walls. Using magneto-optical Kerr effect microscopy, we demonstrate that out-of-plane electric field pulses across the BaTiO3 substrate move the magnetic and ferroelectric domain walls in unison. Our experiments indicate an exponential increase of domain wall velocity with electric field strength and opposite domain wall motion for positive and negative field pulses. The application of a magnetic field does not affect the velocity of magnetic domain walls, but independently tailors their internal spin structure, causing a change in domain wall dynamics at high velocities.

  13. Extraction of proteins from yeast cell wall | Huang | African Journal of ...

    African Journals Online (AJOL)

    The proteins from yeast cell wall were extracted by autolysis and depositing in turn. The results show that the change of pH value greatly affects the yield of the final product. The content of obtained crude proteins is maximal (more than 66%) when the autolysis time is 3 h, and pH value is 6 - 7. The extracted proteins can be ...

  14. Polarizable protein model for Dissipative Particle Dynamics

    Science.gov (United States)

    Peter, Emanuel; Lykov, Kirill; Pivkin, Igor

    2015-11-01

    In this talk, we present a novel polarizable protein model for the Dissipative Particle Dynamics (DPD) simulation technique, a coarse-grained particle-based method widely used in modeling of fluid systems at the mesoscale. We employ long-range electrostatics and Drude oscillators in combination with a newly developed polarizable water model. The protein in our model is resembled by a polarizable backbone and a simplified representation of the sidechains. We define the model parameters using the experimental structures of 2 proteins: TrpZip2 and TrpCage. We validate the model on folding of five other proteins and demonstrate that it successfully predicts folding of these proteins into their native conformations. As a perspective of this model, we will give a short outlook on simulations of protein aggregation in the bulk and near a model membrane, a relevant process in several Amyloid diseases, e.g. Alzheimer's and Diabetes II.

  15. Dynamical corrections to the anomalous holographic soft-wall model: the pomeron and the odderon

    Energy Technology Data Exchange (ETDEWEB)

    Capossoli, Eduardo Folco [Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil); Colegio Pedro II, Departamento de Fisica, Rio de Janeiro, RJ (Brazil); Li, Danning [Institute of Theoretical Physics, Chinese Academy of Science (ITP, CAS), Beijing (China); Boschi-Filho, Henrique [Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil)

    2016-06-15

    In this work we use the holographic soft-wall AdS/QCD model with anomalous dimension contributions coming from two different QCD beta functions to calculate the masses of higher spin glueball states for both even and odd spins and their Regge trajectories, related to the pomeron and the odderon, respectively. We further investigate this model taking into account dynamical corrections due to a dilaton potential consistent with the Einstein equations in five dimensions. The results found in this work for the Regge trajectories within the anomalous soft-wall model with dynamical corrections are consistent with those present in the literature. (orig.)

  16. Asymmetric driven dynamics of Dzyaloshinskii domain walls in ultrathin ferromagnetic strips with perpendicular magnetic anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Tejerina, L. [Dpto. Electricidad y Electrónica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid (Spain); Alejos, Ó., E-mail: oscaral@ee.uva.es [Dpto. Electricidad y Electrónica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid (Spain); Martínez, E. [Dpto. Física Aplicada, Facultad de Ciencias, Universidad de Salamanca, 37011 Salamanca (Spain); Muñoz, J.M. [Dpto. Electricidad y Electrónica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid (Spain)

    2016-07-01

    The dynamics of domain walls in ultrathin ferromagnetic strips with perpendicular magnetic anisotropy is studied from both numerical and analytical micromagnetics. The influence of a moderate interfacial Dzyaloshinskii–Moriya interaction associated to a bi-layer strip arrangement has been considered, giving rise to the formation of Dzyaloshinskii domain walls. Such walls possess under equilibrium conditions an inner magnetization structure defined by a certain orientation angle that make them to be considered as intermediate configurations between Bloch and Néel walls. Two different dynamics are considered, a field-driven and a current-driven dynamics, in particular, the one promoted by the spin torque due to the spin-Hall effect. Results show an inherent asymmetry associated with the rotation of the domain wall magnetization orientation before reaching the stationary regime, characterized by a constant terminal speed. For a certain initial DW magnetization orientation at rest, the rotation determines whether the reorientation of the DW magnetization prior to reach stationary motion is smooth or abrupt. This asymmetry affects the DW motion, which can even reverse for a short period of time. Additionally, it is found that the terminal speed in the case of the current-driven dynamics may depend on either the initial DW magnetization orientation at rest or the sign of the longitudinally injected current. - Highlights: • The asymmetric response of domain walls in bilayer strips with PMA is studied. • Out-of-plane fields and SHE longitudinal currents are applied. • The response is associated to the rotation of the domain wall inner magnetization. • Clockwise and counter-clockwise magnetization rotations are not equivalent. • The asymmetry results in different travelled distances and/or terminal speeds.

  17. Dynamics and Friction in Double Walled Carbon Nanotubes

    OpenAIRE

    Servantie, James

    2006-01-01

    The objective of this PhD thesis was the study of friction in carbon nanotubes by analytical methods and molecular dynamics simulations. The goal of this research was to characterize the properties of friction in nanotubes and from a more general point of view the understanding of the microscopic origin of friction. Indeed, the relative simplicity of the system allows us to interpret more easily the physical phenomenon observed than in larger systems. In order to achieve this goal, non-equili...

  18. Characterizing the dynamic property of the vortex tail in a gas cyclone by wall pressure measurements

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Cuizhi; Sun, Guogang; Dong, Ruiqian; Fu, Shuangcheng [State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249 (China)

    2010-08-15

    To explore a determination method for cyclone vortex tail, the wall pressures at different axial and radial positions of a cylinder-on-cone cyclone were measured and analyzed by the Fast Fourier Transform (FFT) and probability density analyses in this paper. The cyclone vortex tail was also visualized by a red ink tracer. The results show that the cyclone wall pressure does not change in the cylindrical section and gradually decreases in the conical section. The magnitudes of wall pressure at different azimuths are almost identical, indicating an axisymmetrical wall pressure radial profile in these parts of the cyclone. Whereas in the lower part of the cone and/or the upper part of dipleg, there is a sudden fall of wall pressure and non-axisymmetrical pressure radial profile. The minimum wall pressure occurs at about 270 azimuth in this region. Underneath in the next part of the dipleg, the wall pressure rapidly rises and returns to axisymmetry. These characteristics indicate that the vortex tail is bended to wall, turns around in this region, and can be used as evidences of the vortex tail. The position determined by the pressure measurement is close to the position of the rotating ring observed in the tracing experiment. It is also found that the frequency of the inner vortex is different from that of the outer vortex. The inner vortex flow fluctuates stronger and faster than its outer partner. At the vortex tail zone, the vortex breaks and the inner vortex fluctuation is involved in the wall pressure signal. Therefore, the position and dynamic property of the vortex tail can be well identified from the wall pressure measurement. The pressure measurement could provide some solid experimental basis for assessing relations of natural vortex length. (author)

  19. Moisture dynamics in wall paintings monitored by single-sided NMR.

    Science.gov (United States)

    Oligschläger, D; Waldow, S; Haber, A; Zia, W; Blümich, B

    2015-01-01

    The durability of historic wall paintings is highly dependent on environmental influences such as moisture ingress, salt crystallization and temperature changes. A fundamental understanding of dynamic transport processes in wall paintings is necessary to apply suitable conservation and restoration methods to preserve such objects with high cultural value. Non-invasive, mobile-NMR techniques with single-sided sensors, such as the NMR-MOUSE(®), enable to monitor the moisture content, transport and apparent diffusion constants in wall paintings. We investigated this technique by experiment and modeling to correlate salt crystallization, moisture transport and local diffusion in wall-painting samples. Moreover, the influence of different painting techniques (fresco and secco) and conservation/consolidation methods on moisture transport and diffusion is discussed. The results are compared with results from field measurements on real fresco paintings in Casa del Salone Nero and the Villa of the Papyri, Herculaneum, Italy. Copyright © 2014 John Wiley & Sons, Ltd.

  20. Nonlinear dynamics of domain-wall propagation in epitaxial ferroelectric thin films.

    Science.gov (United States)

    Jo, J Y; Yang, S M; Kim, T H; Lee, H N; Yoon, J-G; Park, S; Jo, Y; Jung, M H; Noh, T W

    2009-01-30

    We investigated the ferroelectric domain-wall propagation in epitaxial Pb(Zr,Ti)O3 thin film over a wide temperature range (3-300 K). We measured the domain-wall velocity under various electric fields and found that the velocity data is strongly nonlinear with electric fields, especially at low temperature. We found that, as one of surface growth issues, our domain-wall velocity data from ferroelectric epitaxial film could be classified into the creep, depinning, and flow regimes due to competition between disorder and elasticity. The measured values of velocity and dynamical exponents indicate that the ferroelectric domain walls in the epitaxial films are fractal and pinned by a disorder-induced local field.

  1. Influence of Housing Wall Compliance on Shock Absorbers in the Context of Vehicle Dynamics

    Science.gov (United States)

    Pulvirenti, G.; Faria, C.

    2017-10-01

    Shock absorbers play a key role in vehicle dynamics. Researchers have spent significant effort in order to understand phenomena associated with this component, but there are still several issues to address, in part because new technology development and design trends continually lead to new challenges, among which weight reduction is crucial. For shock absorbers, weight reduction is related to the use of new materials (e.g. composite) or new design paradigms (e.g. more complex geometry, wall thickness, etc.). All of them are directly linked to wall compliance values higher than the actual ones. The present article proposes a first analysis of the phenomena introduced by a high wall compliance, through a modelling approach and various simulations in order to understand the vehicle behaviour changes. It is shown that high values of wall compliance lead to increased hysteresis in the force-velocity curve. However, comfort, handling and ride performances are not significantly affected by this designing parameter.

  2. Wood cell-wall structure requires local 2D-microtubule disassembly by a novel plasma membrane-anchored protein.

    Science.gov (United States)

    Oda, Yoshihisa; Iida, Yuki; Kondo, Yuki; Fukuda, Hiroo

    2010-07-13

    Plant cells have evolved cortical microtubules, in a two-dimensional space beneath the plasma membrane, that regulate patterning of cellulose deposition. Although recent studies have revealed that several microtubule-associated proteins facilitate self-organization of transverse cortical microtubules, it is still unknown how diverse patterns of cortical microtubules are organized in different xylem cells, which are the major components of wood. Using our newly established in vitro xylem cell differentiation system, we found that a novel microtubule end-tracking protein, microtubule depletion domain 1 (MIDD1), was anchored to distinct plasma membrane domains and promoted local microtubule disassembly, resulting in pits on xylem cell walls. The introduction of RNA interference for MIDD1 resulted in the failure of local microtubule depletion and the formation of secondary walls without pits. Conversely, the overexpression of MIDD1 reduced microtubule density. MIDD1 has two coiled-coil domains for the binding to microtubules and for the anchorage to plasma membrane domains, respectively. Combination of the two coils caused end tracking of microtubules during shrinkage and suppressed their rescue events. Our results indicate that MIDD1 integrates spatial information in the plasma membrane with cortical microtubule dynamics for determining xylem cell wall pattern. Copyright 2010 Elsevier Ltd. All rights reserved.

  3. On the Vibration of Single-Walled Carbon Nanocones: Molecular Mechanics Approach versus Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    R. Ansari

    2014-01-01

    Full Text Available The vibrational behavior of single-walled carbon nanocones is studied using molecular structural method and molecular dynamics simulations. In molecular structural approach, point mass and beam elements are employed to model the carbon atoms and the connecting covalent bonds, respectively. Single-walled carbon nanocones with different apex angles are considered. Besides, the vibrational behavior of nanocones under various types of boundary conditions is studied. Predicted natural frequencies are compared with the existing results in the literature and also with the ones obtained by molecular dynamics simulations. It is found that decreasing apex angle and the length of carbon nanocone results in an increase in the natural frequency. Comparing the vibrational behavior of single-walled carbon nanocones under different boundary conditions shows that the effect of end condition on the natural frequency is more prominent for nanocones with smaller apex angles.

  4. Evolutionary conservation of protein vibrational dynamics.

    Science.gov (United States)

    Maguid, Sandra; Fernandez-Alberti, Sebastian; Echave, Julian

    2008-10-01

    The aim of the present work is to study the evolutionary divergence of vibrational protein dynamics. To this end, we used the Gaussian Network Model to perform a systematic analysis of normal mode conservation on a large dataset of proteins classified into homologous sets of family pairs and superfamily pairs. We found that the lowest most collective normal modes are the most conserved ones. More precisely, there is, on average, a linear correlation between normal mode conservation and mode collectivity. These results imply that the previously observed conservation of backbone flexibility (B-factor) profiles is due to the conservation of the most collective modes, which contribute the most to such profiles. We discuss the possible roles of normal mode robustness and natural selection in the determination of the observed behavior. Finally, we draw some practical implications for dynamics-based protein alignment and classification and discuss possible caveats of the present approach.

  5. Microencapsulation of canola oil by lentil protein isolate-based wall materials.

    Science.gov (United States)

    Chang, C; Varankovich, N; Nickerson, M T

    2016-12-01

    The overall goal was to encapsulate canola oil using a mixture of lentil protein isolate and maltodextrin with/without lecithin and/or sodium alginate by spray drying. Initially, emulsion and microcapsule properties as a function of oil (20%-30%), protein (2%-8%) and maltodextrin concentration (9.5%-18%) were characterized by emulsion stability, droplet size, viscosity, surface oil and entrapment efficiency. Microcapsules with 20% oil, 2% protein and 18% maltodextrin were shown to have the highest entrapment efficiency, and selected for further re-design using different preparation conditions and wall ingredients (lentil protein isolate, maltodextrin, lecithin and/or sodium alginate). The combination of the lentil protein, maltodextrin and sodium alginate represented the best wall material to produce microcapsules with the highest entrapment efficiency (∼88%). The lentil protein-maltodextrin-alginate microcapsules showed better oxidative stability and had a stronger wall structure than the lentil protein-maltodextrin microcapsules. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. The phylogenetics of dynamics in DNA clamp proteins.

    Science.gov (United States)

    Balasubramaniam, Deepa; Komives, Elizabeth A

    2014-04-08

    Using HXMS to measure protein dynamics, Fang and colleagues (in this issue of Structure) probe the dynamics of processivity clamp proteins from all kingdoms of life. The proteins have similar structures but divergent sequences. Their results show conserved dynamics correlating with primary functions and divergent dynamics for divergent functions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Delivering Single-Walled Carbon Nanotubes to the Nucleus Using Engineered Nuclear Protein Domains.

    Science.gov (United States)

    Boyer, Patrick D; Ganesh, Sairaam; Qin, Zhao; Holt, Brian D; Buehler, Markus J; Islam, Mohammad F; Dahl, Kris Noel

    2016-02-10

    Single-walled carbon nanotubes (SWCNTs) have great potential for cell-based therapies due to their unique intrinsic optical and physical characteristics. Consequently, broad classes of dispersants have been identified that individually suspend SWCNTs in water and cell media in addition to reducing nanotube toxicity to cells. Unambiguous control and verification of the localization and distribution of SWCNTs within cells, particularly to the nucleus, is needed to advance subcellular technologies utilizing nanotubes. Here we report delivery of SWCNTs to the nucleus by noncovalently attaching the tail domain of the nuclear protein lamin B1 (LB1), which we engineer from the full-length LMNB1 cDNA. More than half of this low molecular weight globular protein is intrinsically disordered but has an immunoglobulin-fold composed of a central hydrophobic core, which is highly suitable for associating with SWCNTs, stably suspending SWCNTs in water and cell media. In addition, LB1 has an exposed nuclear localization sequence to promote active nuclear import of SWCNTs. These SWCNTs-LB1 dispersions in water and cell media display near-infrared (NIR) absorption spectra with sharp van Hove peaks and an NIR fluorescence spectra, suggesting that LB1 individually disperses nanotubes. The dispersing capability of SWCNTs by LB1 is similar to that by albumin proteins. The SWCNTs-LB1 dispersions with concentrations ≥150 μg/mL (≥30 μg/mL) in water (cell media) remain stable for ≥75 days (≥3 days) at 4 °C (37 °C). Further, molecular dynamics modeling of association of LB1 with SWCNTs reveal that the exposure of the nuclear localization sequence is independent of LB1 binding conformation. Measurements from confocal Raman spectroscopy and microscopy, NIR fluorescence imaging of SWCNTs, and fluorescence lifetime imaging microscopy show that millions of these SWCNTs-LB1 complexes enter HeLa cells, localize to the nucleus of cells, and interact with DNA. We postulate that the

  8. Protein electron transfer: Dynamics and statistics.

    Science.gov (United States)

    Matyushov, Dmitry V

    2013-07-14

    Electron transfer between redox proteins participating in energy chains of biology is required to proceed with high energetic efficiency, minimizing losses of redox energy to heat. Within the standard models of electron transfer, this requirement, combined with the need for unidirectional (preferably activationless) transitions, is translated into the need to minimize the reorganization energy of electron transfer. This design program is, however, unrealistic for proteins whose active sites are typically positioned close to the polar and flexible protein-water interface to allow inter-protein electron tunneling. The high flexibility of the interfacial region makes both the hydration water and the surface protein layer act as highly polar solvents. The reorganization energy, as measured by fluctuations, is not minimized, but rather maximized in this region. Natural systems in fact utilize the broad breadth of interfacial electrostatic fluctuations, but in the ways not anticipated by the standard models based on equilibrium thermodynamics. The combination of the broad spectrum of static fluctuations with their dispersive dynamics offers the mechanism of dynamical freezing (ergodicity breaking) of subsets of nuclear modes on the time of reaction/residence of the electron at a redox cofactor. The separation of time-scales of nuclear modes coupled to electron transfer allows dynamical freezing. In particular, the separation between the relaxation time of electro-elastic fluctuations of the interface and the time of conformational transitions of the protein caused by changing redox state results in dynamical freezing of the latter for sufficiently fast electron transfer. The observable consequence of this dynamical freezing is significantly different reorganization energies describing the curvature at the bottom of electron-transfer free energy surfaces (large) and the distance between their minima (Stokes shift, small). The ratio of the two reorganization energies

  9. Cytoskeletal proteins in the follicular wall of normal andcystic ovaries of sows

    OpenAIRE

    Sant'Ana, Fabiano J.F. de; Reis Junior, Janildo L.; Araújo, Rosélia L.S.; J.Gimeno, Eduardo; Ortega, Hugo H.

    2015-01-01

    The expression of cytoskeletal proteins was evaluated immunohistochemically in 36 normal ovaries sampled from 18 sows and 44 cystic ovaries sampled from of 22 sows, was evaluated. All sows had history of reproductive problems, such as infertility or subfertility. The immunohistochemically stained area (IHCSA) was quantified through image analysis to evaluate the expression of these proteins in the follicular wall of secondary, tertiary, and cystic follicles. Cytokeratins (CK) immunoreactivity...

  10. On-Chip Manipulation of Protein-Coated Magnetic Beads via Domain-Wall Conduits

    DEFF Research Database (Denmark)

    Donolato, Marco; Vavassori, Paolo; Gobbi, Marco

    2010-01-01

    Geometrically constrained magnetic domain walls (DWs) in magnetic nanowires can be manipulated at the nanometer scale. The inhomogeneous magnetic stray field generated by a DW can capture a magnetic nanoparticle in solution. On-chip nanomanipulation of individual magnetic beads coated with proteins...

  11. Cell Wall-anchored Proteins of Enterococcus faecium: Exploring a Novel Surface

    NARCIS (Netherlands)

    Hendrickx, A.P.A.|info:eu-repo/dai/nl/304820741

    2009-01-01

    The past 4 years my research focussed on the identification, expression and function of surface-exposed LPXTG proteins and filamentous structures (also called pili or fimbriae) at the Enterococcus faecium cell wall. E. faecium is a commensal organism of the mammalian gastrointestinal tract, but the

  12. Dynamic fluctuations of protein-carbohydrate interactions promote protein aggregation.

    Directory of Open Access Journals (Sweden)

    Vladimir Voynov

    2009-12-01

    Full Text Available Protein-carbohydrate interactions are important for glycoprotein structure and function. Antibodies of the IgG class, with increasing significance as therapeutics, are glycosylated at a conserved site in the constant Fc region. We hypothesized that disruption of protein-carbohydrate interactions in the glycosylated domain of antibodies leads to the exposure of aggregation-prone motifs. Aggregation is one of the main problems in protein-based therapeutics because of immunogenicity concerns and decreased efficacy. To explore the significance of intramolecular interactions between aromatic amino acids and carbohydrates in the IgG glycosylated domain, we utilized computer simulations, fluorescence analysis, and site-directed mutagenesis. We find that the surface exposure of one aromatic amino acid increases due to dynamic fluctuations. Moreover, protein-carbohydrate interactions decrease upon stress, while protein-protein and carbohydrate-carbohydrate interactions increase. Substitution of the carbohydrate-interacting aromatic amino acids with non-aromatic residues leads to a significantly lower stability than wild type, and to compromised binding to Fc receptors. Our results support a mechanism for antibody aggregation via decreased protein-carbohydrate interactions, leading to the exposure of aggregation-prone regions, and to aggregation.

  13. Geometric evolutionary dynamics of protein interaction networks.

    Science.gov (United States)

    Przulj, Natasa; Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne

    2010-01-01

    Understanding the evolution and structure of protein-protein interaction (PPI) networks is a central problem of systems biology. Since most processes in the cell are carried out by groups of proteins acting together, a theoretical model of how PPI networks develop based on duplications and mutations is an essential ingredient for understanding the complex wiring of the cell. Many different network models have been proposed, from those that follow power-law degree distributions and those that model complementarity of protein binding domains, to those that have geometric properties. Here, we introduce a new model for PPI network (and thus gene) evolution that produces well-fitting network models for currently available PPI networks. The model integrates geometric network properties with evolutionary dynamics of PPI network evolution.

  14. Experimental studies of tearing mode and resistive wall mode dynamics in the reversed field pinch configuration

    Energy Technology Data Exchange (ETDEWEB)

    Malmberg, Jenny-Ann

    2003-06-01

    It is relatively straightforward to establish equilibrium in magnetically confined plasmas, but the plasma is frequently susceptible to a variety of instabilities that are driven by the free energy in the magnetic field or in the pressure gradient. These unstable modes exhibit effects that affect the particle, momentum and heat confinement properties of the configuration. Studies of the dynamics of several of the most important modes are the subject of this thesis. The studies are carried out on plasmas in the reversed field pinch (RFP) configuration. One phenomenon commonly observed in RFPs is mode wall locking. The localized nature of these phase- and wall locked structures results in localized power loads on the wall which are detrimental for confinement. A detailed study of the wall locked mode phenomenon is performed based on magnetic measurements from three RFP devices. The two possible mechanisms for wall locking are investigated. Locking as a result of tearing modes interacting with a static field error and locking due to the presence of a non-ideal boundary. The characteristics of the wall locked mode are qualitatively similar in a device with a conducting shell system (TPE-RX) compared to a device with a resistive shell (Extrap T2). A theoretical model is used for evaluating the threshold values for wall locking due to eddy currents in the vacuum vessel in these devices. A good correlation with experiment is observed for the conducting shell device. The possibility of successfully sustaining discharges in a resistive shell RFP is introduced in the recently rebuilt device Extrap T2R. Fast spontaneous mode rotation is observed, resulting in low magnetic fluctuations, low loop voltage and improved confinement. Wall locking is rarely observed. The low tearing mode amplitudes allow for the theoretically predicted internal non-resonant on-axis resistive wall modes to be observed. These modes have not previously been distinguished due to the formation of wall

  15. A HYBRID SYSTEM FOR DYNAMIC ANALYSIS AND DESIGN OF COUPLED SHEAR WALLS

    Directory of Open Access Journals (Sweden)

    A BERRAIS

    2000-06-01

    Full Text Available Non-linear dynamic analysis techniques are rapidly being developed and have been recognized as indispensable tools. However, their use in the design office requires special experience. Consequently they are not generally accepted as analysis/design tools. Additionally, uncertainties are associated with the determination of the earthquake forces, the stiffness and strength of the structure; the selection of the mathematical models; and the form of the earthquake. In this paper a hybrid system for the non-linear dynamic analysis/design of coupled shear walls is briefly described. The system combines expert system technology with finite element method to carry out the dynamic analysis of coupled walls under earthquake forces. The system has been implemented using Quintec-Prolog, Quintec-Flex and FORTRAN 77, and runs on a SUN SPARC station under Unix system.

  16. Curvature Perturbation and Domain Wall Formation with Pseudo Scaling Scalar Dynamics

    CERN Document Server

    Ema, Yohei; Takimoto, Masahiro

    2015-01-01

    Cosmological dynamics of scalar field with a monomial potential $\\phi^{n}$ with a general background equation of state is revisited. It is known that if $n$ is smaller than a critical value, the scalar field exhibits a coherent oscillation and if $n$ is larger it obeys a scaling solution without oscillation. We study in detail the case where $n$ is equal to the critical value, and find a peculiar scalar dynamics which is neither oscillating nor scaling solution, and we call it a pseudo scaling solution. We also discuss cosmological implications of a pseudo scaling scalar dynamics, such as the curvature perturbation and the domain wall problem.

  17. Computational Fluid Dynamics Simulations of Gas-Phase Radial Dispersion in Fixed Beds with Wall Effects

    Directory of Open Access Journals (Sweden)

    Anthony G. Dixon

    2017-10-01

    Full Text Available The effective medium approach to radial fixed bed dispersion models, in which radial dispersion of mass is superimposed on axial plug flow, is based on a constant effective dispersion coefficient, DT. For packed beds of a small tube-to-particle diameter ratio (N, the experimentally-observed decrease in this parameter near the tube wall is accounted for by a lumped resistance located at the tube wall, the wall mass transfer coefficient km. This work presents validated computational fluid dynamics (CFD simulations to obtain detailed radial velocity and concentration profiles for eight different computer-generated packed tubes of spheres in the range 5.04 ≤ N ≤ 9.3 and over a range of flow rates 87 ≤ Re ≤ 870 where Re is based on superficial velocity and the particle diameter dp. Initial runs with pure air gave axial velocity profiles vz(r averaged over the length of the packing. Then, simulations with the tube wall coated with methane yielded radial concentration profiles. A model with only DT could not describe the radial concentration profiles. The two-parameter model with DT and km agreed better with the bed-center concentration profiles, but not with the sharp decreases in concentration close to the tube wall. A three-parameter model based on classical two-layer mixing length theory, with a wall-function for the decrease in transverse radial convective transport in the near-wall region, showed greatly improved ability to reproduce the near-wall concentration profiles.

  18. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis

    Science.gov (United States)

    Klopffleisch, Karsten; Phan, Nguyen; Augustin, Kelsey; Bayne, Robert S; Booker, Katherine S; Botella, Jose R; Carpita, Nicholas C; Carr, Tyrell; Chen, Jin-Gui; Cooke, Thomas Ryan; Frick-Cheng, Arwen; Friedman, Erin J; Fulk, Brandon; Hahn, Michael G; Jiang, Kun; Jorda, Lucia; Kruppe, Lydia; Liu, Chenggang; Lorek, Justine; McCann, Maureen C; Molina, Antonio; Moriyama, Etsuko N; Mukhtar, M Shahid; Mudgil, Yashwanti; Pattathil, Sivakumar; Schwarz, John; Seta, Steven; Tan, Matthew; Temp, Ulrike; Trusov, Yuri; Urano, Daisuke; Welter, Bastian; Yang, Jing; Panstruga, Ralph; Uhrig, Joachim F; Jones, Alan M

    2011-01-01

    The heterotrimeric G-protein complex is minimally composed of Gα, Gβ, and Gγ subunits. In the classic scenario, the G-protein complex is the nexus in signaling from the plasma membrane, where the heterotrimeric G-protein associates with heptahelical G-protein-coupled receptors (GPCRs), to cytoplasmic target proteins called effectors. Although a number of effectors are known in metazoans and fungi, none of these are predicted to exist in their canonical forms in plants. To identify ab initio plant G-protein effectors and scaffold proteins, we screened a set of proteins from the G-protein complex using two-hybrid complementation in yeast. After deep and exhaustive interrogation, we detected 544 interactions between 434 proteins, of which 68 highly interconnected proteins form the core G-protein interactome. Within this core, over half of the interactions comprising two-thirds of the nodes were retested and validated as genuine in planta. Co-expression analysis in combination with phenotyping of loss-of-function mutations in a set of core interactome genes revealed a novel role for G-proteins in regulating cell wall modification. PMID:21952135

  19. In situ atom scale visualization of domain wall dynamics in VO2 insulator-metal phase transition.

    Science.gov (United States)

    He, Xinfeng; Xu, Tao; Xu, Xiaofeng; Zeng, Yijie; Xu, Jing; Sun, Litao; Wang, Chunrui; Xing, Huaizhong; Wu, Binhe; Lu, Aijiang; Liu, Dingquan; Chen, Xiaoshuang; Chu, Junhao

    2014-10-08

    A domain wall, as a device, can bring about a revolution in developing manipulation of semiconductor heterostructures devices at the atom scale. However, it is a challenge for these new devices to control domain wall motion through insulator-metal transition of correlated-electron materials. To fully understand and harness this motion, it requires visualization of domain wall dynamics in real space. Here, domain wall dynamics in VO2 insulator-metal phase transition was observed directly by in situ TEM at atom scale. Experimental results depict atom scale evolution of domain morphologies and domain wall exact positions in (202) and (040) planes referring to rutile structure at 50°C. In addition, microscopic mechanism of domain wall dynamics and accurate lattice basis vector relationship of two domains were investigated with the assistance of X-ray diffraction, ab initio calculations and image simulations. This work offers a route to atom scale tunable heterostructure device application.

  20. Molecular Dynamics Simulations of the Thermal Conductivity of Single-Wall Carbon Nanotubes

    Science.gov (United States)

    Osman, M.; Srivastava, Deepak; Govindan,T. R. (Technical Monitor)

    2000-01-01

    Carbon nanotubes (CNT) have very attractive electronic, mechanical. and thermal properties. Recently, measurements of thermal conductivity in single wall CNT mats showed estimated thermal conductivity magnitudes ranging from 17.5 to 58 W/cm-K at room temperature. which are better than bulk graphite. The cylinderical symmetry of CNT leads to large thermal conductivity along the tube axis, additionally, unlike graphite. CNTs can be made into ropes that can be used as heat conducting pipes for nanoscale applications. The thermal conductivity of several single wall carbon nanotubes has been calculated over temperature range from l00 K to 600 K using non-equilibrium molecular dynamics using Tersoff-Brenner potential for C-C interactions. Thermal conductivity of single wall CNTs shows a peaking behavior as a function of temperature. Dependence of the peak position on the chirality and radius of the tube will be discussed and explained in this presentation.

  1. Stipe wall extension of Flammulina velutipes could be induced by an expansin-like protein from Helix aspersa.

    Science.gov (United States)

    Fang, Hejian; Zhang, Wenming; Niu, Xin; Liu, Zhonghua; Lu, Changmei; Wei, Hua; Yuan, Sheng

    2014-01-01

    Expansin proteins extend plant cell walls by a hydrolysis-free process that disrupts hydrogen bonding between cell wall polysaccharides. However, it is unknown if this mechanism is operative in mushrooms. Herein we report that the native wall extension activity was located exclusively in the 10 mm apical region of 30 mm Flammulina velutipes stipes. The elongation growth was restricted also to the 9 mm apical region of the stipes where the elongation growth of the 1st millimetre was 40-fold greater than that of the 5th millimetre. Therefore, the wall extension activity represents elongation growth of the stipe. The low concentration of expansin-like protein in F. velutipes stipes prevented its isolation. However, we purified an expansin-like protein from snail stomach juice which reconstituted heat-inactivated stipe wall extension without hydrolytic activity. So the previous hypotheses that stipe wall extension was resulted from hydrolysis of wall polymers by enzymes or disruption of hydrogen bonding of wall polymers exclusively by turgor pressure are challenged. We suggest that stipe wall extension may be mediated by endogenous expansin-like proteins that facilitate cell wall polymer slippage by disrupting noncovalent bonding between glucan chains or chitin chains. Copyright © 2013 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  2. A computational fluid dynamics modeling study of guide walls for downstream fish passage

    Science.gov (United States)

    Mulligan, Kevin; Towler, Brett; Haro, Alexander J.; Ahlfeld, David P.

    2017-01-01

    A partial-depth, impermeable guidance structure (or guide wall) for downstream fish passage is typically constructed as a series of panels attached to a floating boom and anchored across a water body (e.g. river channel, reservoir, or power canal). The downstream terminus of the wall is generally located nearby to a fish bypass structure. If guidance is successful, the fish will avoid entrainment in a dangerous intake structure (i.e. turbine intakes) while passing from the headpond to the tailwater of a hydroelectric facility through a safer passage route (i.e. the bypass). The goal of this study is to determine the combination of guide wall design parameters that will most likely increase the chance of surface-oriented fish being successfully guided to the bypass. To evaluate the flow field immediately upstream of a guide wall, a parameterized computational fluid dynamics model of an idealized power canal was constructed in © ANSYS Fluent v 14.5 (ANSYS Inc., 2012). The design parameters investigated were the angle and depth of the guide wall and the average approach velocity in the power canal. Results call attention to the importance of the downward to sweeping flow ratio and demonstrate how a change in guide wall depth and angle can affect this important hydraulic cue to out-migrating fish. The key findings indicate that a guide wall set at a small angle (15° is the minimum in this study) and deep enough such that sweeping flow dominant conditions prevail within the expected vertical distribution of fish approaching the structure will produce hydraulic conditions that are more likely to result in effective passage.

  3. Characterization of Cell Wall Proteins in Saccharomyces cerevisiae Clinical Isolates Elucidates Hsp150p in Virulence.

    Directory of Open Access Journals (Sweden)

    Pang-Hung Hsu

    Full Text Available The budding yeast Saccharomyces cerevisiae has recently been described as an emerging opportunistic fungal pathogen. Fungal cell wall mannoproteins have been demonstrated to be involved in adhesion to inert surfaces and might be engaged in virulence. In this study, we observed four clinical isolates of S. cerevisiae with relatively hydrophobic cell surfaces. Yeast cell wall subproteome was evaluated quantitatively by liquid chromatography/tandem mass spectrometry. We identified totally 25 cell wall proteins (CWPs from log-phase cells, within which 15 CWPs were quantified. The abundance of Scw10p, Pst1p, and Hsp150p/Pir2p were at least 2 folds higher in the clinical isolates than in S288c lab strain. Hsp150p is one of the members in Pir family conserved in pathogenic fungi Candida glabrata and Candida albicans. Overexpression of Hsp150p in lab strain increased cell wall integrity and potentially enhanced the virulence of yeast. Altogether, these results demonstrated that quantitative cell wall subproteome was analyzed in clinical isolates of S. cerevisiae, and several CWPs, especially Hsp150p, were found to be expressed at higher levels which presumably contribute to strain virulence and fungal pathogenicity.

  4. Relationships between hydroxyproline-containing proteins secreted into the cell wall and medium by suspension-cultured Acer psedoplatanus cells

    Energy Technology Data Exchange (ETDEWEB)

    Pope, D.G.

    1977-05-01

    The pathway of hydroxyproline-containing proteins to the cell wall and to the growth medium in suspension-cultured Acer pseudoplatanus cells is traced by following the kinetics of the transfer of protein-bound /sup 14/C-hydroxyproline into various fractions, and by comparing the hydroxyproline-arabinoside profiles of these fractions after alkaline hydrolysis. Hydroxyproline-rich protein passes directly from a membrane-bound compartment in the cytoplasm to the cell wall, not via an intermediate salt-soluble pool in the wall. There are at least three hydroxyproline-containing glycoproteins in the cell wall. One which possesses mono-, tri-, and tetraarabinoside side chains accounts for over 90% of the total hydroxyproline. This glycoprotein is ''extensin.'' The hydroxyproline-containing proteins secreted into the medium have a glycosylation pattern markedly different from that of the major cell wall glycoprotein. It appears that there is little or no wall-like extensin in the medium. Approximately half of the protein-bound hydroxyproline secreted into the medium is linked to an arabinogalactan. This linkage is also found in a particulate wall protein precursor fraction from the cytoplasm, but only trace amounts can be detected in the cell wall.

  5. Dynamic prestress in a globular protein.

    Directory of Open Access Journals (Sweden)

    Scott A Edwards

    Full Text Available A protein at equilibrium is commonly thought of as a fully relaxed structure, with the intra-molecular interactions showing fluctuations around their energy minimum. In contrast, here we find direct evidence for a protein as a molecular tensegrity structure, comprising a balance of tensed and compressed interactions, a concept that has been put forward for macroscopic structures. We quantified the distribution of inter-residue prestress in ubiquitin and immunoglobulin from all-atom molecular dynamics simulations. The network of highly fluctuating yet significant inter-residue forces in proteins is a consequence of the intrinsic frustration of a protein when sampling its rugged energy landscape. In beta sheets, this balance of forces is found to compress the intra-strand hydrogen bonds. We estimate that the observed magnitude of this pre-compression is enough to induce significant changes in the hydrogen bond lifetimes; thus, prestress, which can be as high as a few 100 pN, can be considered a key factor in determining the unfolding kinetics and pathway of proteins under force. Strong pre-tension in certain salt bridges on the other hand is connected to the thermodynamic stability of ubiquitin. Effective force profiles between some side-chains reveal the signature of multiple, distinct conformational states, and such static disorder could be one factor explaining the growing body of experiments revealing non-exponential unfolding kinetics of proteins. The design of prestress distributions in engineering proteins promises to be a new tool for tailoring the mechanical properties of made-to-order nanomaterials.

  6. Numerical Investigation on Dynamic Crushing Behavior of Auxetic Honeycombs with Various Cell-Wall Angles

    Directory of Open Access Journals (Sweden)

    Xin-chun Zhang

    2015-02-01

    Full Text Available Auxetic honeycombs have proven to be an attractive advantage in actual engineering applications owing to their unique mechanical characteristic and better energy absorption ability. The in-plane dynamic crushing behaviors of the honeycombs with various cell-wall angles are studied by means of explicit dynamic finite element simulation. The influences of the cell-wall angle, the impact velocity, and the edge thickness on the macro/microdeformation behaviors, the plateau stresses, and the specific energy absorption of auxetic honeycombs are discussed in detail. Numerical results show, that except for the impact velocity and the edge thickness, the in-plane dynamic performances of auxetic honeycombs also rely on the cell-wall angle. The “> <”-mode local deformation bands form under low- or moderate-velocity impacting, which results in lateral compression shrinkage and shows negative Poisson's ratio during the crushing. For the given impact velocity, the plateau stress at the proximal end and the energy-absorbed ability can be improved by increasing the negative cell angle, the relative density, the impact velocity, and the matrix material strength. When the microcell parameters are the constant, the plateau stresses are proportional to the square of impact velocity.

  7. Dynamic control of magnetic nanowires by light-induced domain-wall kickoffs

    Science.gov (United States)

    Heintze, Eric; El Hallak, Fadi; Clauß, Conrad; Rettori, Angelo; Pini, Maria Gloria; Totti, Federico; Dressel, Martin; Bogani, Lapo

    2013-03-01

    Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. In contrast to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiance is very low, a substantial improvement over present methods of magneto-optical switching. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to numerous fields, ranging from social evolution to neural networks and chemical reactivity.

  8. Bacillus anthracis Sortase A (SrtA) Anchors LPXTG Motif-Containing Surface Proteins to the Cell Wall Envelope

    OpenAIRE

    Gaspar, Andrew H.; Marraffini, Luciano A.; Glass, Elizabeth M.; DeBord, Kristin L.; Ton-That, Hung; Schneewind, Olaf

    2005-01-01

    Cell wall-anchored surface proteins of gram-positive pathogens play important roles during the establishment of many infectious diseases, but the contributions of surface proteins to the pathogenesis of anthrax have not yet been revealed. Cell wall anchoring in Staphylococcus aureus occurs by a transpeptidation mechanism requiring surface proteins with C-terminal sorting signals as well as sortase enzymes. The genome sequence of Bacillus anthracis encodes three sortase genes and eleven surfac...

  9. Determination of Cell Wall Protein from Selected Feedstuffs and its Relationship with Ruminal Protein Digestibility in Vitro

    Directory of Open Access Journals (Sweden)

    Anuraga Jayanegara

    2016-08-01

    Full Text Available This study was aimed to analyze neutral detergent insoluble crude protein (NDICP and acid detergent insoluble crude protein (ADICP contents of various commonly used forage and concentrate feedstuffs in Indonesia. A number of forages and concentrates, i.e. gliricidia, trichantera, indigofera, calliandra, papaya leaves, cassava leaves, leucaena, rapeseed meal, corn gluten feed, soybean meal, copra meal, palm kernel meal, fish and bone meal and wheat bran were subjected to proximate analysis, cell wall nitrogen determination and in vitro rumen fermentation evaluation. Chemical composition analysis was done in duplicate. The in vitro incubation was conducted in 14 treatments and 3 replicates by following a randomized complete block design. Variables measured after the incubation were total volatile fatty acid (VFA, ammonia, dry matter digestibility (DMD, organic matter digestibility (OMD and crude protein digestibility (CPD. Results revealed that among the forages, cassava leaf had the highest proportion of NDICP while corn gluten feed was the highest among the concentrates. Different from that of NDICP, the highest proportion of ADICP was obtained in papaya leaf and copra meal for the forages and concentrates, respectively. Higher proportion of NDICP tended to decrease CPD (P<0.1. Although higher ADICP apparently tended to decrease CPD as well, the relationship was insignificant due to the higher variation of the dependent variable. It was concluded that cell wall protein proportion in feed may be used as an indicator to determine the quality of protein and its utilization in the rumen.

  10. Accurate simulation of protein dynamics in solution

    Energy Technology Data Exchange (ETDEWEB)

    Levitt, M.; Sharon, R. (Weizmann Institute of Science, Rehovot (Israel))

    1988-10-01

    Simulation of the molecular dynamics of a small protein, bovine pancreatic trypsin inhibitor, was found to be more realistic when water molecules were included than when in vacuo: the time-averaged structure was much more like that observed in high-resolution x-ray studies, the amplitudes of atomic vibration in solution were smaller, and fewer incorrect hydrogen bonds were formed. The authors approach, which provides a sound basis for reliable simulation of diverse properties of biological macromolecules in solution, uses atom-centered forces and classical mechanics.

  11. Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

    Science.gov (United States)

    Weaver, D. L.

    1982-01-01

    Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

  12. Numerical Analysis of Dynamic Force Acting Perpendicularly on a Wall Made of Concrete Blocks with Rubber Inserts

    Directory of Open Access Journals (Sweden)

    Major Maciej

    2016-12-01

    Full Text Available In this paper numerical analysis considering the influence of dynamical force acting on wall made of concrete blocks with rubber inserts is presented. By examining the stress values on front and back surface of the analysed wall structure model, the effectiveness of proposed solution can be measured comparing to the wall made of concrete blocks without rubber inserts. Complete numerical analysis was performed in ADINA program.

  13. The cell wall of the human pathogen Candida glabrata: differential incorporation of novel adhesin-like wall proteins

    NARCIS (Netherlands)

    de Groot, P.W.J.; Kraneveld, E.A.; Yin, Q.Y.; Dekker, H.L.; Groß, U.; Crielaard, W.; de Koster, C.G.; Bader, O.; Klis, F.M.; Weig, M.

    2008-01-01

    The cell wall of the human pathogen Candida glabrata governs initial host-pathogen interactions that underlie the establishment of fungal infections. With the aim of identifying species-specific features that may directly relate to its virulence, we have investigated the cell wall of C. glabrata

  14. Capture of unstable protein complex on the streptavidin-coated single-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Liu Zunfeng, E-mail: liuz2@chem.leidenuniv.nl; Voskamp, Patrick [Cell Observatory, Biophysical Structural Chemistry, Leiden Institute of Chemistry (Netherlands); Zhang Yue; Chu Fuqiang [Changzhou University, School of Pharmaceutical Engineering and Life Science (China); Abrahams, Jan Pieter, E-mail: abrahams@chem.leidenuniv.nl [Cell Observatory, Biophysical Structural Chemistry, Leiden Institute of Chemistry (Netherlands)

    2013-04-15

    Purification of unstable protein complexes is a bottleneck for investigation of their 3D structure and in protein-protein interaction studies. In this paper, we demonstrate that streptavidin-coated single-walled carbon nanotubes (Strep Bullet SWNT) can be used to capture the biotinylated DNA-EcoRI complexes on a 2D surface and in solution using atomic force microscopy and electrophoresis analysis, respectively. The restriction enzyme EcoRI forms unstable complexes with DNA in the absence of Mg{sup 2+}. Capturing the EcoRI-DNA complexes on the Strep Bullet SWNT succeeded in the absence of Mg{sup 2+}, demonstrating that the Strep Bullet SWNT can be used for purifying unstable protein complexes.

  15. Glycosylation of Candida albicans cell wall proteins is critical for induction of innate immune responses and apoptosis of epithelial cells.

    Directory of Open Access Journals (Sweden)

    Jeanette Wagener

    Full Text Available C. albicans is one of the most common fungal pathogen of humans, causing local and superficial mucosal infections in immunocompromised individuals. Given that the key structure mediating host-C. albicans interactions is the fungal cell wall, we aimed to identify features of the cell wall inducing epithelial responses and be associated with fungal pathogenesis. We demonstrate here the importance of cell wall protein glycosylation in epithelial immune activation with a predominant role for the highly branched N-glycosylation residues. Moreover, these glycan moieties induce growth arrest and apoptosis of epithelial cells. Using an in vitro model of oral candidosis we demonstrate, that apoptosis induction by C. albicans wild-type occurs in early stage of infection and strongly depends on intact cell wall protein glycosylation. These novel findings demonstrate that glycosylation of the C. albicans cell wall proteins appears essential for modulation of epithelial immunity and apoptosis induction, both of which may promote fungal pathogenesis in vivo.

  16. Numerical study of acoustically driven bubble cloud dynamics near a rigid wall.

    Science.gov (United States)

    Ma, Jingsen; Hsiao, Chao-Tsung; Chahine, Georges L

    2018-01-01

    The dynamics of a bubble cloud excited by a sinusoidal pressure field near a rigid wall is studied using a novel Eulerian/Lagrangian two-phase flow model. The effects of key parameters such as the amplitude and frequency of the excitation pressure, the cloud and bubble sizes, the void fraction, and the initial standoff distance on the bubbles' collective behavior and the resulting pressure loads on the nearby wall are investigated. The study shows that nonlinear bubble cloud dynamics becomes more pronounced and results in higher pressure loading at the wall as the excitation pressure amplitude increases. The strongest collective bubble behavior occurs at a preferred resonance frequency. At this resonance frequency, pressure peaks orders of magnitudes higher than the excitation pressure result from the bubble interaction when the amplitude of the pressure excitation is high. The numerically obtained resonance frequency is significantly different from the reported natural frequency of a spherical cloud derived from linear theory, which assumes small amplitude oscillations in an unbounded medium. At high amplitudes of the excitation, the resonance frequency decreases almost linearly with the ratio of excitation pressure amplitude to ambient pressure until the ratio is larger than one. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Designable and dynamic single-walled stiff nanotubes assembled from sequence-defined peptoids

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Haibao; Ding, Yanhuai; Wang, Mingming; Song, Yang; Liao, Zhihao; Newcomb, Christina J.; Wu, Xuepeng; Tang, Xian-Qiong; Li, Zheng; Lin, Yuehe; Yan, Feng; Jian, Teng-Yue; Mu, Peng; Chen, Chunlong

    2018-01-18

    Despite recent advances in assembly of organic nanotubes, conferral of sequence-defined engineering and dynamic response characteristics to the tubules remains a challenge. Here we report a new family of highly-designable and dynamic single-walled nanotubes assembled from sequence-defined peptoids through a unique “rolling-up and closure of nanosheet” mechanism. During the assembly process, amorphous spherical particles of amphiphilic peptoid oligomers (APOs) crystallized to form well-defined nanosheets which were then folded to form single-walled peptoid nanotubes (SW-PNTs). These SW-PNTs undergo a pH-triggered, reversible contraction-expansion motion. By varying the number of hydrophobic residues of APOs, we demonstrate the tuning of PNT wall thickness and diameter, and mechanical properties. AFM-based mechanical measurements indicate that PNTs are highly stiff (Young’s Modulus ~13-17 GPa), comparable to the stiffest known biological materials. We further demonstrate that the precise incorporation of functional groups within PNTs and the application of functional PNTs in water decontamination. We believe these SW-PNTs can provide a robust platform for development of biomimetic materials tailored to specific applications.

  18. Dynamic vessel wall properties and their reproducibility in subjects with increased cardiovascular risk.

    Science.gov (United States)

    van den Berkmortel, F; Wollersheim, H; van Langen, H; Thien, T

    1998-06-01

    To determine reproducibility figures of dynamic arterial wall properties such as cross-sectional compliance (CC) and distensibility (DC) in subjects with increased cardiovascular risk, in comparison with healthy adults. A total of 34 persons were divided into three groups with varying cardiovascular risk factors. Diameters (D) and diameter changes (deltaD) during the heart cycle of both common carotid (CCA) and right common femoral (CFA) arteries were measured by a vessel wall movement detector system. Blood pressures (BP) were recorded non-invasively by a semi-automated oscillometric device. CC (=piD(deltaD/2deltaP) in unit mm2/kPa) and DC (=2deltaD/D)/deltaP in unit 10(-3)/kPa) were calculated from the above-mentioned parameters. Measurements were performed twice during one visit and twice again with a time interval of at least 3 days to determine intra-observer intra- and intersession variability. Reproducibility figures of CC and DC of the CCA varied between 8 and 12%, and between 13 and 22% for the CFA. Intra-observer intra- and intersession variability were similar in the three groups. In our studies the reproducibility of dynamic vascular wall properties determined by ultrasound was good. Despite differences in the absolute values for CC and DC in groups with increased cardiovascular risk, mean reproducibility figures remained at a similar level (8-12%) as in healthy volunteers.

  19. Pseudo-dynamic tests on masonry residential buildings seismically retrofitted by precast steel reinforced concrete walls

    Science.gov (United States)

    Li, Wenfeng; Wang, Tao; Chen, Xi; Zhong, Xiang; Pan, Peng

    2017-07-01

    A retrofitting technology using precast steel reinforced concrete (PSRC) panels is developed to improve the seismic performance of old masonry buildings. The PSRC panels are built up as an external PSRC wall system surrounding the existing masonry building. The PSRC walls are well connected to the existing masonry building, which provides enough confinement to effectively improve the ductility, strength, and stiffenss of old masonry structures. The PSRC panels are prefabricated in a factory, significantly reducing the situ work and associated construction time. To demonstrate the feasibility and mechanical effectivenss of the proposed retrofitting system, a full-scale five-story specimen was constructed. The retrofitting process was completed within five weeks with very limited indoor operation. The specimen was then tested in the lateral direction, which could potentially suffer sigifnicant damage in a large earthquake. The technical feasibility, construction workability, and seismic performance were thoroughly demonstrated by a full-scale specimen construction and pseudo-dynamic tests.

  20. Cell wall dynamics modulate acetic acid-induced apoptotic cell death of Saccharomyces cerevisiae

    Science.gov (United States)

    Rego, António; Duarte, Ana M.; Azevedo, Flávio; Sousa, Maria J.; Côrte-Real, Manuela; Chaves, Susana R.

    2014-01-01

    Acetic acid triggers apoptotic cell death in Saccharomyces cerevisiae, similar to mammalian apoptosis. To uncover novel regulators of this process, we analyzed whether impairing MAPK signaling affected acetic acid-induced apoptosis and found the mating-pheromone response and, especially, the cell wall integrity pathways were the major mediators, especially the latter, which we characterized further. Screening downstream effectors of this pathway, namely targets of the transcription factor Rlm1p, highlighted decreased cell wall remodeling as particularly important for acetic acid resistance. Modulation of cell surface dynamics therefore emerges as a powerful strategy to increase acetic acid resistance, with potential application in industrial fermentations using yeast, and in biomedicine to exploit the higher sensitivity of colorectal carcinoma cells to apoptosis induced by acetate produced by intestinal propionibacteria. PMID:28357256

  1. A model of cell-wall dynamics during sporulation in Bacillus subtilis

    Science.gov (United States)

    Yap, Li-Wei; Endres, Robert G.

    To survive starvation, Bacillus subtilis forms durable spores. After asymmetric cell division, the septum grows around the forespore in a process called engulfment, but the mechanism of force generation is unknown. Here, we derived a novel biophysical model for the dynamics of cell-wall remodeling during engulfment based on a balancing of dissipative, active, and mechanical forces. By plotting phase diagrams, we predict that sporulation is promoted by a line tension from the attachment of the septum to the outer cell wall, as well as by an imbalance in turgor pressures in the mother-cell and forespore compartments. We also predict that significant mother-cell growth hinders engulfment. Hence, relatively simple physical principles may guide this complex biological process.

  2. Dynamic expression patterns of differential proteins during early invasion of hepatocellular carcinoma.

    Science.gov (United States)

    Chen, Rong-Xin; Song, Hai-Yan; Dong, Yin-Ying; Hu, Chao; Zheng, Qiong-Dan; Xue, Tong-Chun; Liu, Xiao-Hui; Zhang, Yang; Chen, Jie; Ren, Zheng-Gang; Liu, Yin-Kun; Cui, Jie-Feng

    2014-01-01

    Tumor cell invasion into the surrounding matrix has been well documented as an early event of metastasis occurrence. However, the dynamic expression patterns of proteins during early invasion of hepatocellular carcinoma (HCC) are largely unknown. Using a three-dimensional HCC invasion culture model established previously, we investigated the dynamic expression patterns of identified proteins during early invasion of HCC. Highly metastatic MHCC97H cells and a liver tissue fragment were long-term co-cultured in a rotating wall vessel (RWV) bioreactor to simulate different pathological states of HCC invasion. The established spherical co-cultures were collected on days 0, 5, 10, and 15 for dynamic expression pattern analysis. Significantly different proteins among spheroids at different time points were screened and identified using quantitative proteomics of iTRAQ labeling coupled with LC-MS/MS. Dynamic expression patterns of differential proteins were further categorized by K-means clustering. The expression modes of several differentially expressed proteins were confirmed by Western blot and qRT-PCR. Time course analysis of invasion/metastasis gene expressions (MMP2, MMP7, MMP9, CD44, SPP1, CXCR4, CXCL12, and CDH1) showed remarkable, dynamic alterations during the invasion process of HCC. A total of 1,028 proteins were identified in spherical co-cultures collected at different time points by quantitative proteomics. Among these proteins, 529 common differential proteins related to HCC invasion were clustered into 25 types of expression patterns. Some proteins displayed significant dynamic alterations during the early invasion process of HCC, such as upregulation at the early invasion stage and downregulation at the late invasion stage (e.g., MAPRE1, PHB2, cathepsin D, etc.) or continuous upregulation during the entire invasion process (e.g., vitronectin, Met, clusterin, ICAM1, GSN, etc.). Dynamic expression patterns of candidate proteins during the early invasion

  3. The effects of Candida albicans cell wall protein fraction on dendritic cell maturation.

    Science.gov (United States)

    Roudbary, Maryam; Roudbar Mohammadi, Shahla; Bozorgmehr, Mahmood; Moazzeni, Seyed Mohammad

    2009-06-01

    Candida albicans is a member of the normal human microflora. C. albicans cell wall is composed of several protein and carbohydrate components which have been shown to play a crucial role in C. albicans interaction with the host immune system. Major components of C. albican cell wall are carbohydrates such as mannans, beta glucans and chitins, and proteins that partially modulate the host immune responses. Dendritic cells (DC), as the most important antigen-presenting cells of the immune system, play a critical role in inducing immune responses against different pathogens. We investigated the effect of the cell wall protein fraction (CPF) of C. albicans on DC maturation. The CPF of C. albicans cells was extracted by a lysis buffer containing sodium dodecyl sulphate, 2-mercaptoethanol and phosphate-buffered saline. The extract was dialyzed and its protein pattern was evaluated by electrophoresis. Dendritic cells were purified from Balb/c mice spleens through a three-step method including mononuclear cell separation, as well as 2-h and overnight cultures. The purified CPF was added at different concentrations to DC. The purity and maturation status of DC were determined by flow cytometry using monoclonal antibodies against CD11c, MHC-II, CD40 and CD86. Treatment of DC with 10 microg/ml of CPF increased the expression of maturation markers including MHC-II, CD86 and CD40 on DC compared to the control group. In this study we used C. albicans CPF with the molecular weight of 40-45 kDa for pulsing and maturation of dendritic cells. Since according to our results CPF significantly increased the expression of maturation markers on DC, we suggest that CPF may act as an efficient immunomodulator, or may be used as a potential adjuvant to boost the host immune system against infections.

  4. In silicio identification of glycosyl-phosphatidylinositol-anchored plasma-membrane and cell wall proteins of Saccharomyces cerevisiae.

    Science.gov (United States)

    Caro, L H; Tettelin, H; Vossen, J H; Ram, A F; van den Ende, H; Klis, F M

    1997-12-01

    Use of the Von Heijne algorithm allowed the identification of 686 open reading frames (ORFs) in the genome of Saccharomyces cerevisiae that encode proteins with a potential N-terminal signal sequence for entering the secretory pathway. On further analysis, 51 of these proteins contain a potential glycosyl-phosphatidylinositol (GPI)-attachment signal. Seven additional ORFs were found to belong to this group. Upon examination of the possible GPI-attachment sites, it was found that in yeast the most probable amino acids for GPI-attachment as asparagine and glycine. In yeast, GPI-proteins are found at the cell surface, either attached to the plasma-membrane or as an intrinsic part of the cell wall. It was noted that plasma-membrane GPI-proteins possess a dibasic residue motif just before their predicted GPI-attachment site. Based on this, and on homologies between proteins, families of plasma-membrane and cell wall proteins were assigned, revealing 20 potential plasma-membrane and 38 potential cell wall proteins. For members of three plasma-membrane protein families, a function has been described. On the other hand, most of the cell wall proteins seem to be structural components of the wall, responsive to different growth conditions. The GPI-attachment site of yeast slightly differs from mammalian cells. This might be of use in the development of anti-fungal drugs.

  5. Use of bacteriophage cell wall-binding proteins for rapid diagnostics of Listeria.

    Science.gov (United States)

    Schmelcher, Mathias; Loessner, Martin J

    2014-01-01

    Diagnostic protocols for food-borne bacterial pathogens such as Listeria need to be sensitive, specific, rapid, and inexpensive. Conventional culture methods are hampered by lengthy enrichment and incubation steps. Bacteriophage-derived high-affinity binding molecules (cell wall-binding domains, CBDs) specific for Listeria cells have recently been introduced as tools for detection and differentiation of this pathogen in foods. When coupled with magnetic separation, these proteins offer advantages in sensitivity and speed compared to the standard diagnostic methods. Furthermore, fusion of CBDs to differently colored fluorescent reporter proteins enables differentiation of Listeria strains in mixed cultures. This chapter provides protocols for detection of Listeria in food by CBD-based magnetic separation and subsequent multiplexed identification of strains of different serotypes with reporter-CBD fusion proteins.

  6. Topological susceptibility of QCD with dynamical M\\"obius domain wall fermions

    OpenAIRE

    Aoki, S.; Cossu, G.; Fukaya, H.; Hashimoto, S.; Kaneko, T.

    2017-01-01

    We compute the topological susceptibility $\\chi_t$ of lattice QCD with $2+1$ dynamical quark flavors described by the M\\"obius domain wall fermion. Violation of chiral symmetry as measured by the residual mass is kept at $\\sim$1 MeV or smaller. We measure the fluctuation of the topological charge density in a "slab" sub-volume of the simulated lattice using the method proposed by Bietenholz et al. The quark mass dependence of $\\chi_t$ agrees with the prediction of chiral perturbation theory, ...

  7. IFE thick liquid wall chamber dynamics: Governing mechanisms andmodeling and experimental capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Raffray, A.R.; Meier, W.; Abdel-Khalik, S.; Bonazza, R.; Calderoni, P.; Debonnel, C.S.; Dragojlovic, Z.; El-Guebaly, L.; Haynes,D.; Latkowski, J.; Olson, C.; Peterson, P.F.; Reyes, S.; Sharpe, P.; Tillack, M.S.; Zaghloul, M.

    2005-01-24

    For thick liquid wall concepts, it is important to understand the different mechanisms affecting the chamber dynamics and the state of the chamber prior to each shot a compared with requirements from the driver and target. These include ablation mechanisms, vapor transport and control, possible aerosol formation, as well as protective jet behavior. This paper was motivated by a town meeting on this subject which helped identify the major issues, assess the latest results, review the capabilities of existing modeling and experimental facilities with respect to addressing remaining issues, and helping guide future analysis and R&D efforts; the paper covers these exact points.

  8. A New Boundary Model for Simulating Complex and Flexible Wall Bounded Domain in Dissipative Particle Dynamics

    Directory of Open Access Journals (Sweden)

    Saeid Mokhtarian

    2014-01-01

    Full Text Available Despite extensive area of applications, simulation of complex wall bounded problems or any deformable boundary is still a challenge in a Dissipative Particle Dynamics simulation. This limitation is rooted in the soft force nature of DPD and the fact that we need to use an antipenetration model for escaped particles. In the present paper, we propose a new model of antipenetration which preserves the conservation of linear momentum on the boundaries and enables us to simulate complex and flexible boundaries. Finally by performing numerical simulations, we demonstrate the validity of our new model.

  9. Visualizing the growth dynamics of individual single-wall carbon nanotubes

    DEFF Research Database (Denmark)

    Wagner, Jakob Birkedal; Zhang, Lili; He, Maoshuai

    In order to meet the increasing demand of faster and more flexible electronics and optical devices and at the same time decrease the use of the critical metals, carbon based devices are in fast development. Single walled carbon nanotube (SWCNT) based electronics is a way of addressing...... around the studied sample at elevated temperature gives a unique way of monitoring gas-solid interactions such as CNT growth. Here we show the direct experimental evidence on the growth dynamics of SW-CNTs from Co/MgO catalysts using CO as carbon source inside the environmental TEM. The evolution...

  10. Nonlinear Dynamic Analysis of RC Shear Walls using Damage Mechanics Approach Considering Bond-Slip Effects

    Directory of Open Access Journals (Sweden)

    N. Davoodi

    2015-07-01

    Full Text Available In this research, nonlinear dynamic analysis of concrete shear wall using a new nonlinear model based on damage mechanics approach and considering bond slip effects is presented. Nonlinear behavior of concrete is modeled by a rotational smeared crack model using damage mechanics approach. The proposed model considers major characteristics of the concrete subjected to two and three dimensional loading conditions. These characteristics are pre-softening behavior, softening initiation criteria and fracture energy conservation. The model was used in current research analysis after verification by some available numerical tests. Reinforcements are modeled by a bilinear relationship using two models: Discrete truss steel element and Smeared model. In Discrete model the effects of bond-slide between concrete and rebar is mentioned using the bond-link element model concept. Based on the presented algorithms and methodology, an FEM code is developed in FORTRAN. The validity of the proposed models and numerical algorithms has been checked using the available experimental results. Finally, numerical simulation of CAMUS I and CAMUS III reinforced concrete shear walls is carried out. Comparisons of deduced results confirm the validity of proposed models. The obtained results, both in the expected displacements and crack profiles for the walls, show a good accuracy with respect to the experimental results. Also, using discrete truss element model with respect to the smeared steel model leads to increasing the accuracy of maximum displacement response to 7% in analysis.

  11. Dynamics of the collision of a vortex ring with a vertical heated wall

    Science.gov (United States)

    Gelderblom, G.; Palacios-Morales, C. A.; Zenit, R.; Solorio-Ordaz, F. J.

    2012-11-01

    We study the dynamics of the impact of a vortex ring with a vertical heated plate (at constant temperature). Laminar vortex rings were generated with a piston cylinder arrangement. The vertical wall is heated by a thermal bath which is held at constant temperature producing a laminar and stable thermal boundary layer. Measurements of the 2D velocity field were obtained with a PIV technique. The experimental results for the isothermal case are in agreement with previous investigations reported in the literature. To avoid azimuthal instabilities, we mainly conducted experiments for L /D0 = 1 (where L is the piston displacement and D0 is the cylinder inner diameter) with different wall temperatures and vortex translation velocities. For this case, secondary vortices were not observed. Using ink visualization we observed the evolution of the vortex shape. The initial circular shape evolves into a ``cat head'' shape after reaching the wall. The top and bottom regions of the vortex reduce and increase their vorticity, respectively. The sides are stretched and convected. An analysis of the different mechanisms leading to this shape evolution is presented and discussed.

  12. Analysis of Dynamic Coupling Characteristics of the Slope Reinforced by Sheet Pile Wall

    Directory of Open Access Journals (Sweden)

    H. L. Qu

    2017-01-01

    Full Text Available Large deformation of slope caused by earthquake can lead to the loss of stability of slope and its retaining structures. At present, there have been some research achievements about the slope reinforcement of stabilizing piles. However, due to the complexity of the structural system, the coupling relationship between soil and pile is still not well understood. Hence it is of great necessity to study its dynamic characteristics further. In view of this, a numerical model was established by FLAC3D in this paper, and the deformation and stress nephogram of sheet pile wall in peak ground motion acceleration (PGA at 0.1 g, 0.2 g, and 0.4 g were obtained. Through the analysis, some conclusions were obtained. Firstly, based on the nephogram of motion characteristics and the positions of the slip surface and the retaining wall, the reinforced slope can be divided into 6 sections approximatively, namely, the sliding body parts of A, B, C, D, and E and the bedrock part F. Secondly, the deformation and stress distributions of slope reinforced by sheet pile wall were carefully studied. Based on the results of deformation calculation from time history analysis, the interaction force between structure and soil can be estimated by the difference of peak horizontal displacements, and the structure-soil coupling law under earthquake can be studied by this approach.

  13. Influence of Transient Thermal Response of Solid Wall on Bubble Dynamics in Pool Boiling

    Directory of Open Access Journals (Sweden)

    Liang Zhang

    2014-09-01

    Full Text Available Numerical simulation of single bubble pool boiling process including transient thermal response of solid wall is performed using the ghost fluid method and the level set method for the sharp interface representation. The results show that non-physical initial condition in the numerical simulation deeply affects the process of bubble growth, and then multi-cycle simulation is necessary to eliminate its influence. It is shown by the present results that two nucleate criteria, i.e. constant waiting time and constant nucleate superheat, for determining the appearance time for the subsequent bubble lead to the same quasi-steady process of bubble growth if they are matched with each other. A periodically expanding and receding thermal “hollow” can be observed inside solid wall underneath the growing bubble. The recovery of the temperature on the nucleate site and the thermal boundary layer near the heating surface is influenced by transient heat conduction inside solid wall, which can affect evidently bubble thermal dynamics and heat transfer.

  14. Influence of Transient Thermal Response of Solid Wall on Bubble Dynamics in Pool Boiling

    Directory of Open Access Journals (Sweden)

    Liang Zhang

    2014-12-01

    Full Text Available Numerical simulation of single bubble pool boiling process including transient thermal response of solid wall is performed using the ghost fluid method and the level set method for the sharp interface representation. The results show that non-physical initial condition in the numerical simulation deeply affects the process of bubble growth, and then multicycle simulation is necessary to eliminate its influence. It is shown by the present results that two nucleate criteria, i.e. constant waiting time and constant nucleate superheat, for determining the appearance time for the subsequent bubble lead to the same quasi-steady process of bubble growth if they are matched with each other. A periodically expanding and receding thermal “hollow” can be observed inside solid wall underneath the growing bubble. The recovery of the temperature on the nucleate site and the thermal boundary layer near the heating surface is influenced by transient heat conduction inside solid wall, which can affect evidently bubble thermal dynamics and heat transfer.

  15. Reconstitution of membrane protein complexes involved in pneumococcal septal cell wall assembly.

    Directory of Open Access Journals (Sweden)

    Marjolaine Noirclerc-Savoye

    Full Text Available The synthesis of peptidoglycan, the major component of the bacterial cell wall, is essential to cell survival, yet its mechanism remains poorly understood. In the present work, we have isolated several membrane protein complexes consisting of the late division proteins of Streptococcus pneumoniae: DivIB, DivIC, FtsL, PBP2x and FtsW, or subsets thereof. We have co-expressed membrane proteins from S. pneumoniae in Escherichia coli. By combining two successive affinity chromatography steps, we obtained membrane protein complexes with a very good purity. These complexes are functional, as indicated by the retained activity of PBP2x to bind a fluorescent derivative of penicillin and to hydrolyze the substrate analogue S2d. Moreover, we have evidenced the stabilizing role of protein-protein interactions within each complex. This work paves the way for a complete reconstitution of peptidoglycan synthesis in vitro, which will be critical to the elucidation of its intricate regulation mechanisms.

  16. Maintenance of native-like protein dynamics may not be required for engineering functional proteins.

    Science.gov (United States)

    Gobeil, Sophie M C; Clouthier, Christopher M; Park, Jaeok; Gagné, Donald; Berghuis, Albert M; Doucet, Nicolas; Pelletier, Joelle N

    2014-10-23

    Proteins are dynamic systems, and understanding dynamics is critical for fully understanding protein function. Therefore, the question of whether laboratory engineering has an impact on protein dynamics is of general interest. Here, we demonstrate that two homologous, naturally evolved enzymes with high degrees of structural and functional conservation also exhibit conserved dynamics. Their similar set of slow timescale dynamics is highly restricted, consistent with evolutionary conservation of a functionally important feature. However, we also show that dynamics of a laboratory-engineered chimeric enzyme obtained by recombination of the two homologs exhibits striking difference on the millisecond timescale, despite function and high-resolution crystal structure (1.05 Å) being conserved. The laboratory-engineered chimera is thus functionally tolerant to modified dynamics on the timescale of catalytic turnover. Tolerance to dynamic variation implies that maintenance of native-like protein dynamics may not be required when engineering functional proteins.

  17. Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

    Science.gov (United States)

    Hensen, Ulf; Meyer, Tim; Haas, Jürgen; Rex, René; Vriend, Gert; Grubmüller, Helmut

    2012-01-01

    Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics. PMID:22606222

  18. Magnetic Domain Wall Dynamics and Pulsed Magnetization Reversal in Four Soft Ferromagnetic Alloys.

    Science.gov (United States)

    Williams, Peter

    Available from UMI in association with The British Library. Pulsed magnetization reversal has been studied experimentally and theoretically in four soft ferromagnetic materials. Two important industrial polycrystalline alloys HCR (50% Ni, 50% Fe) and Mumetal (77% Ni, 14% Fe, 5% Cu, 4% Mo) of thickness 6 to 25mum were investigated in toroidal format during rapid (0.1 to 7.0 Tmu s^{-1}) approximately constant voltage magnetization reversal. Drive field and magneto-optic measurements are interpreted in terms of domain wall motion. Particular attention is paid to the intermediate drive field termed step field region. Bar and surface domain models which assume a detailed balance between domain wall surface tension and magnetic field pressure are used for interpretation of the experimental data. Accord with HCR results is particularly encouraging. Comparison between HCR and Mumetal behaviour does allow some insight into the dynamic behaviour of the latter material. Metglas 2826 (rm Fe_{40 } Ni_{40} P_{14} B_6) and Metglas 2605 (rm Fe_{80} B_{20}) are amorphous alloys manufactured by Allied Chemical Company. These members of a relatively new class of soft ferromagnetic material are prepared by splat cooling from the melt at rates of over 10^{6} ^{0}Ks^ {-1}. Low coercivity and high resistivity are particularly attractive properties associated with these alloys offering considerable practical application. Long ribbons of Metglas 2826 and 2605 under tension were subjected to square magnetic field pulses. At low fields propagating head-on domain boundaries of the Sixtus Tonks type were observed of lengths 20 to 50 cms. A magneto-static model provides estimates of specific domain wall energy and exchange constant. Low field domain wall motion measurements on 2826 are consistent with eddy current damping. At high fields, however, eddy current damping is estimated to contribute about 50% of the total damping. At these fields, magnetization reversal is initiated at only one of

  19. Dynamics and scaling properties for a one-dimensional impact system with two periodically vibrating walls

    Science.gov (United States)

    Livorati, André L. P.

    2017-07-01

    We investigate the dynamics of a system composed of a particle suffering impacts between two heavy periodically vibrating walls. An original, nonlinear area preserving mapping is obtained. The control parameters of amplitude of perturbation and frequency of oscillation play an important role in the phase space, shaping the portion of chaotic seas, position of invariant curves and the amount of KAM islands. The study of the behavior of the root mean square velocity was made via analytical description and numerical simulations. We proposed scaling arguments to describe its dynamics and our results show remarkably good agreement between the theory and the simulations concerning a scaling invariance with respect to the control parameters. Also, an analysis of the diffusion coefficient confirms the validity of the scaling invariance, giving robustness to our modeling.

  20. Nonoperative Treatment of Posterior Wall Acetabular Fractures After Dynamic Stress Examination Under Anesthesia: Revisited.

    Science.gov (United States)

    McNamara, Andrew R; Boudreau, John A; Moed, Berton R

    2015-08-01

    Performing an examination under general anesthesia (EUA) using dynamic stress fluoroscopy of patients with posterior wall acetabular fractures has been used as a tool to determine hip stability and the need for surgical intervention. The purpose of this study was to further evaluate the effectiveness of this technique, from a source other than its primary advocates, in patients with posterior wall acetabular fractures less than or equal to 50% who were stable on EUA and treated nonoperatively. Retrospective case series. University Level 1 Trauma Center. Seventeen patients with a posterior wall acetabular fracture stable on EUA treated nonoperatively. The patients were treated nonoperatively as guided by an EUA negative for instability. Patient follow-up averaged 30 months (range, 6-64 months). Outcome evaluation included the modified Merle d'Aubigné clinical score and the Short Musculoskeletal Function Assessment Questionnaire. Radiographic evaluation for subluxation or arthritis consisted of the 3 standard pelvic radiographs. Radiographic evaluation showed all hips to be congruent with a normal joint space. Sixteen of the 17 patients had radiographic outcomes rated as "excellent"; 1 patient was rated "good." The modified Merle d'Aubigné score (obtained in 12 patients) averaged very good, with only 1 having less than a good (graded as fair) clinical outcome. The Short Musculoskeletal Function Assessment Questionnaire scores (from 11 patients) were not significantly different from normal and were within the normal reported values for all indices and categories. There was no correlation between fracture fragment size and outcome. This study further supports the contention that a stable hip joint, as determined by EUA, after posterior wall acetabular fracture treated nonoperatively is predictive of continued joint congruity, an excellent radiographic outcome, and good-to-excellent early clinical and functional outcomes. Therapeutic Level IV. See Instructions for

  1. Rac Regulates Giardia lamblia Encystation by Coordinating Cyst Wall Protein Trafficking and Secretion.

    Science.gov (United States)

    Krtková, Jana; Thomas, Elizabeth B; Alas, Germain C M; Schraner, Elisabeth M; Behjatnia, Habib R; Hehl, Adrian B; Paredez, Alexander R

    2016-08-23

    Encystation of the common intestinal parasite Giardia lamblia involves the production, trafficking, and secretion of cyst wall material (CWM). However, the molecular mechanism responsible for the regulation of these sequential processes remains elusive. Here, we examined the role of GlRac, Giardia's sole Rho family GTPase, in the regulation of endomembrane organization and cyst wall protein (CWP) trafficking. Localization studies indicated that GlRac is associated with the endoplasmic reticulum (ER) and the Golgi apparatus-like encystation-specific vesicles (ESVs). Constitutive GlRac signaling increased levels of the ER marker PDI2, induced ER swelling, reduced overall CWP1 production, and promoted the early maturation of ESVs. Quantitative analysis of cells expressing constitutively active hemagglutinin (HA)-tagged GlRac (HA-Rac(CA)) revealed fewer but larger ESVs than control cells. Consistent with the phenotype of premature maturation of ESVs in HA-Rac(CA)-expressing cells, constitutive GlRac signaling resulted in increased CWP1 secretion and, conversely, morpholino depletion of GlRac blocked CWP1 secretion. Wild-type cells unexpectedly secreted large quantities of CWP1 into the medium, and free CWP1 was used cooperatively during cyst formation. These results, in part, could account for the previously reported observation that G. lamblia encysts more efficiently at high cell densities. These studies of GlRac show that it regulates encystation at several levels, and our findings support its coordinating role as a regulator of CWP trafficking and secretion. The central role of GlRac in regulating membrane trafficking and the cytoskeleton, both of which are essential to Giardia parasitism, further suggests its potential as a novel target for drug development to treat giardiasis. The encystation process is crucial for the transmission of giardiasis and the life cycle of many protists. Encystation for Giardia lamblia involves the assembly of a protective cyst wall

  2. Protein dynamics and enzyme catalysis: insights from simulations.

    Science.gov (United States)

    McGeagh, John D; Ranaghan, Kara E; Mulholland, Adrian J

    2011-08-01

    The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. Copyright © 2010 Elsevier B.V. All rights reserved.

  3. Identification and differential gene expression of adhesin-like wall proteins in Candida glabrata biofilms.

    Science.gov (United States)

    Kraneveld, E A; de Soet, J J; Deng, D M; Dekker, H L; de Koster, C G; Klis, F M; Crielaard, W; de Groot, P W J

    2011-12-01

    An important initial step in biofilm development and subsequent establishment of fungal infections by the human pathogen Candida glabrata is adherence to a surface. Adherence is mediated through a large number of differentially regulated cell wall-bound adhesins. The fungus can modify the incorporation of adhesins in the cell wall allowing crucial adaptations to new environments. In this study, expression and cell wall incorporation of C. glabrata adhesins were evaluated in biofilms cultured in two different media: YPD and a semi-defined medium SdmYg. Tandem mass spectrometry of isolated C. glabrata cell walls identified 22 proteins including six adhesins: the novel adhesins Awp5 and Awp6, Epa3 and the previously identified adhesins Epa6, Awp2 and Awp4. Regulation of expression of these and other relevant adhesin genes was investigated using real-time qPCR analysis. For most adhesin genes, significant up-regulation was observed in biofilms in at least one of the culturing media. However, this was not the case for EPA6 and AWP2, which is consistent with their gene products already being abundantly present in planktonic cultures grown in YPD medium. Furthermore, most of the adhesin genes tested also show medium-dependent differential regulation. These results underline the idea that many adhesins in C. glabrata are involved in biofilm formation and that their expression is tightly regulated and dependent on environmental conditions and growth phase. This may contribute to its potential to form resilient biofilms and cause infection in various host tissues.

  4. Selective condensation drives partitioning and sequential secretion of cyst wall proteins in differentiating Giardia lamblia.

    Directory of Open Access Journals (Sweden)

    Christian Konrad

    2010-04-01

    Full Text Available Controlled secretion of a protective extracellular matrix is required for transmission of the infective stage of a large number of protozoan and metazoan parasites. Differentiating trophozoites of the highly minimized protozoan parasite Giardia lamblia secrete the proteinaceous portion of the cyst wall material (CWM consisting of three paralogous cyst wall proteins (CWP1-3 via organelles termed encystation-specific vesicles (ESVs. Phylogenetic and molecular data indicate that Diplomonads have lost a classical Golgi during reductive evolution. However, neogenesis of ESVs in encysting Giardia trophozoites transiently provides basic Golgi functions by accumulating presorted CWM exported from the ER for maturation. Based on this "minimal Golgi" hypothesis we predicted maturation of ESVs to a trans Golgi-like stage, which would manifest as a sorting event before regulated secretion of the CWM. Here we show that proteolytic processing of pro-CWP2 in maturing ESVs coincides with partitioning of CWM into two fractions, which are sorted and secreted sequentially with different kinetics. This novel sorting function leads to rapid assembly of a structurally defined outer cyst wall, followed by slow secretion of the remaining components. Using live cell microscopy we find direct evidence for condensed core formation in maturing ESVs. Core formation suggests that a mechanism controlled by phase transitions of the CWM from fluid to condensed and back likely drives CWM partitioning and makes sorting and sequential secretion possible. Blocking of CWP2 processing by a protease inhibitor leads to mis-sorting of a CWP2 reporter. Nevertheless, partitioning and sequential secretion of two portions of the CWM are unaffected in these cells. Although these cysts have a normal appearance they are not water resistant and therefore not infective. Our findings suggest that sequential assembly is a basic architectural principle of protective wall formation and requires

  5. Protein Adsorption on Hybrids of Thermoresponsive Polymers and Single-Walled Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Kazuo Umemura

    2016-01-01

    Full Text Available Poly(N-isopropylacrylamide (PNIPAAm is one of the most popular thermoresponsive polymers. Adsorption of RecA proteins onto hybrids of PNIPAAm and single-walled carbon nanotubes (SWNTs was observed in the presence and absence of DNA molecules. Although RecA molecules were adsorbed efficiently onto the hybrid surfaces at 37°C, even in the absence of DNA molecules, the adsorption of RecA was inhibited at 4°C. These results suggest that the thermoresponsive functions of PNIPAAm were effective, even on the SWNT surfaces, which supports the possibility of developing nanobiodevices using PNIPAAm-SWNT hybrids. However, although RecA is a DNA binding protein, there was no significant difference in the adsorption of RecA onto PNIPAAm-SWNT surfaces with and without DNA molecules. This study provides fundamental information for potential biological applications of PNIPAAm-SWNT hybrids.

  6. Reduced Wall Acetylation Proteins Play Vital and Distinct Roles in Cell Wall O-Acetylation in Arabidopsis

    DEFF Research Database (Denmark)

    Manabe, Yuzuki; Verhertbruggen, Yves; Gille, Sascha

    2013-01-01

    , triple, and quadruple loss-of-function mutants of all four members of the RWA family in Arabidopsis (Arabidopsis thaliana). In contrast to rwa2, the triple and quadruple rwa mutants display severe growth phenotypes revealing the importance of wall acetylation for plant growth and development...

  7. NMR Studies of Protein Structure and Dynamics

    Science.gov (United States)

    Li, Xiang

    Available from UMI in association with The British Library. Requires signed TDF. This thesis describes applications of 2D homonuclear NMR techniques to the study of protein structure and dynamics in solution. The sequential assignments for the 3G-residue bovine Pancreatic Polypeptide (bPP) are reported. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. bPP has a well defined C-terminal alpha-helix and a rather ordered conformation in the N-terminal region. The two segments are joined by a turn which is poorly defined. Both the N- and the C-terminus are highly disordered. The mean solution structure of bPP is remarkably similar to the crystal structure of avian Pancreatic Polypeptide (aPP). The average conformations of most side-chains from the alpha-helix of bPP in solution are closely similar to those of aPP in the crystalline state. A large number of side-chains of bPP, however, show significant conformational averaging in solution. The 89-residue kringle domain of urokinase from both human and recombinant sources has been investigated. Sequential assignments based primarily on the recombinant sample and the determination of secondary structure are presented. Two helices have been identified; one of these corresponds to that reported for t-PA kringle 2, but does not exist in other kringles with known structures. The second helix is thus far unique to the urokinase kringle. Three antiparallel beta-sheets and three tight turns have also been identified. The tertiary fold of the molecule conforms broadly to that found for other kringles. Three regions in the urokinase kringle exhibit high local mobility; one of these, the Pro56-Pro62 segment, forms part of the proposed binding site. The other two mobile regions are the N- and C-termini which are likely to form the interfaces between the kringle and the other two domains (EGF and protease) in urokinase. The differential dynamic behaviours of the kringle and

  8. A protocol for combining fluorescent proteins with histological stains for diverse cell wall components.

    Science.gov (United States)

    Ursache, Robertas; Andersen, Tonni Grube; Marhavý, Peter; Geldner, Niko

    2018-01-01

    Higher plant function is contingent upon the complex three-dimensional (3D) architecture of plant tissues, yet severe light scattering renders deep, 3D tissue imaging very problematic. Although efforts to 'clear' tissues have been ongoing for over a century, many innovations have been made in recent years. Among them, a protocol called ClearSee efficiently clears tissues and diminishes chlorophyll autofluorescence while maintaining fluorescent proteins - thereby allowing analysis of gene expression and protein localisation in cleared samples. To further increase the usefulness of this protocol, we have developed a ClearSee-based toolbox in which a number of classical histological stains for lignin, suberin and other cell wall components can be used in conjunction with fluorescent reporter lines. We found that a number of classical dyes are highly soluble in ClearSee solution, allowing the old staining protocols to be enormously simplified; these additionally have been unsuitable for co-visualisation with fluorescent markers due to harsh fixation and clearing. Consecutive staining with several dyes allows 3D co-visualisation of distinct cell wall modifications with fluorescent proteins - used as transcriptional reporters or protein localisation tools - deep within tissues. Moreover, the protocol is easily applied on hand sections of different organs. In combination with confocal microscopy, this improves image quality while decreasing the time and cost of embedding/sectioning. It thus provides a low-cost, efficient method for studying thick plant tissues which are usually cumbersome to visualise. Our ClearSee-adapted protocols significantly improve and speed up anatomical and developmental investigations in numerous plant species, and we hope they will contribute to new discoveries in many areas of plant research. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  9. Probing nuclear dynamics and architecture using single-walled carbon nanotubes

    Science.gov (United States)

    Jung, Yoon; Li, Junang; Fakhri, Nikta

    Chromatin is a multiscale dynamic architecture that acts as a template for many biochemical processes such as transcription and DNA replication. Recent developments such as Hi-C technology enable an identification of chromatin interactions across an entire genome. However, a single cell dynamic view of chromatin organization is far from understood. We discuss a new live cell imaging technique to probe the dynamics of the nucleus at a single cell level using single-walled carbon nanotubes (SWNTs). SWNTs are non-perturbing rigid rods (diameter of 1 nm and length of roughly 100 nm) that fluoresce in the near infrared region. Due to their high aspect ratio, they can diffuse in tight spaces and report on the architecture and dynamics of the nucleoplasm. We develop 3D imaging and tracking of SWNTs in the volume of the nucleus using double helix point spread function microscopy (DH-PSF) and discuss the capabilities of the DH-PSF for inferring the 3D orientation of nanotubes based on vectorial diffraction theory.

  10. Numerical Study of Current-Induced Domain-Wall Dynamics: Crossover from Spin Transfer to Momentum Transfer

    Science.gov (United States)

    Matsubayashi, Daisuke; Udagawa, Masafumi; Ogata, Masao

    2009-03-01

    We study current-induced dynamics of a magnetic domain wall by solving a time-dependent Schrödinger equation combined with Landau-Lifshitz-Gilbert equation in a one-dimensional electron system coupled to localized spins. Two types of domain-wall motions are observed depending on the hard-axis anisotropy, K\\bot, of the localized spin system. For small values of K\\bot, the magnetic domain wall shows a streaming motion driven by spin transfer. In contrast, for large values of K\\bot, a stick-slip motion driven by momentum transfer is obtained. We clarify the origin of these characters of domain-wall motions in terms of the dynamics of one-particle energy levels and distribution functions.

  11. Is dynamic heterogeneity of water in presence of a protein ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 12. Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study. SANDIPA INDRA RANJIT BISWAS BISWAS. Regular Article Volume 128 Issue 12 ...

  12. A natural-product switch for a dynamic protein interface

    NARCIS (Netherlands)

    Scheepstra, Marcel; Nieto, Lidia; Hirsch, Anna K H; Fuchs, Sascha; Leysen, Seppe; Lam, Chan Vinh; In Het Panhuis, Leslie; Van Boeckel, Constant A A; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech Gustav; Brunsveld, Luc

    2014-01-01

    Small ligands are a powerful way to control the function of protein complexes via dynamic binding interfaces. The classic example is found in gene transcription where small ligands regulate nuclear receptor binding to coactivator proteins via the dynamic activation function 2 (AF2) interface.

  13. A Natural-Product Switch for a Dynamic Protein Interface

    NARCIS (Netherlands)

    Scheepstra, Marcel; Nieto, Lidia; Hirsch, Anna K. H.; Fuchs, Sascha; Leysen, Seppe; Vinh Lam, Chan; Panhuis, Leslie In Het; van Boeckel, Constant A. A.; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech-Gustav; Brunsveld, Luc

    2014-01-01

    Small ligands are a powerful way to control the function of protein complexes via dynamic binding interfaces. The classic example is found in gene transcription where small ligands regulate nuclear receptor binding to coactivator proteins via the dynamic activation function 2 (AF2) interface.

  14. One repeat of the cell wall binding domain is sufficient for anchoring the Lactobacillus acidophilus surface layer protein

    NARCIS (Netherlands)

    Smit, E.; Pouwels, P.H.

    2002-01-01

    The N-terminal repeat (SAC1) of the S-protein of Lactobacillus acidophilus bound efficiently and specifically to cell wall fragments (CWFs) when fused to green fluorescent protein, whereas the C-terminal repeat (SAC2) did not. Treatment of CWFs with hydrofluoric acid, but not phenol, prevented

  15. The role of Listeria monocytogenes cell wall surface anchor protein LapB in virulence, adherence, and intracellular replication

    Science.gov (United States)

    Lmof2365_2117 is a Listeria monocytogenes putative cell wall surface anchor protein with a conserved domain found in collagen binding proteins. We constructed a deletion mutation in lmof2365_2117 in serotype 4b strain F2365, evaluated its virulence, and determined its ability to adhere and invade co...

  16. Expression of cytoskeletal proteins in the follicular wall of induced ovarian cysts.

    Science.gov (United States)

    Salvetti, Natalia R; Gimeno, Eduardo J; Lorente, Juan A; Ortega, Hugo H

    2004-01-01

    Several experimental models have been developed for the study of the polycystic ovarian syndrome in the rat. In the present study, the syndrome was induced by exposure to constant light, and the expression of cytoskeletal proteins in the follicular wall was evaluated by immunohistochemistry. We analyzed the immunohistochemically stained area (IHCSA) by image analysis to evaluate the expression of intermediate filaments (vimentin, desmin, cytokeratins, gliofibrillary acidic protein and neurofilaments) and alpha-smooth muscle actin (alpha-SMA) in cystic ovaries in relation to normal ovaries. The granulosa cell layer of cystic follicles had a significantly greater IHCSA for vimentin than the normal antral follicles. This difference was also significant between atretic and antral follicles. Cytokeratins showed a very low expression in the granulosa cells of antral follicles of control ovaries while in granulosa cells of atretic and cystic follicles they showed a significantly higher IHCSA. Immunohistochemical localization of desmin and alpha-SMA was restricted to the theca externa. Immunoreactivity for gliofibrillary acidic protein and neurofilament was negative. The highest intensity in the staining with vimentin and cytokeratins observed in the granulosa cells of the cystic follicles is probably due to structural and functional changes that occur during the process of cystogenesis and they could be associated with intense changes in the expression of cytoskeletal proteins that may be essential to the proper cellular functioning. 2004 S. Karger AG, Basel.

  17. Insights from molecular dynamics simulations for computational protein design.

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-02-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

  18. Insights from molecular dynamics simulations for computational protein design

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-01-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

  19. The dynamic multisite interactions between two intrinsically disordered proteins

    KAUST Repository

    Wu, Shaowen

    2017-05-11

    Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a structured protein, while the Interaction between two IDPs is poorly understood. In this study, we combined NMR, smFRET, and molecular dynamics (MD) simulation to characterize the interaction between two IDPs, the C-terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by MD and mutagenesis studies. Our study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.

  20. Interpreting Dynamically-Averaged Scalar Couplings in Proteins

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; Vendruscolo, Michele

    2005-01-01

    The experimental determination of scalar three-bond coupling constants represents a powerful method to probe both the structure and dynamics of proteins. The detailed structural interpretation of such coupling constants is usually based on Karplus relationships, which allow the measured couplings...... present a method to derive such parameters that uses ensembles of conformations determined through dynamic-ensemble refinement - a method that provides structural ensembles that simultaneously represent both the structure and the associated dynamics of a protein....

  1. A Multifaceted Study of Scedosporium boydii Cell Wall Changes during Germination and Identification of GPI-Anchored Proteins.

    Directory of Open Access Journals (Sweden)

    Sarah Ghamrawi

    Full Text Available Scedosporium boydii is a pathogenic filamentous fungus that causes a wide range of human infections, notably respiratory infections in patients with cystic fibrosis. The development of new therapeutic strategies targeting S. boydii necessitates a better understanding of the physiology of this fungus and the identification of new molecular targets. In this work, we studied the conidium-to-germ tube transition using a variety of techniques including scanning and transmission electron microscopy, atomic force microscopy, two-phase partitioning, microelectrophoresis and cationized ferritin labeling, chemical force spectroscopy, lectin labeling, and nanoLC-MS/MS for cell wall GPI-anchored protein analysis. We demonstrated that the cell wall undergoes structural changes with germination accompanied with a lower hydrophobicity, electrostatic charge and binding capacity to cationized ferritin. Changes during germination also included a higher accessibility of some cell wall polysaccharides to lectins and less CH3/CH3 interactions (hydrophobic adhesion forces mainly due to glycoproteins. We also extracted and identified 20 GPI-anchored proteins from the cell wall of S. boydii, among which one was detected only in the conidial wall extract and 12 only in the mycelial wall extract. The identified sequences belonged to protein families involved in virulence in other fungi like Gelp/Gasp, Crhp, Bglp/Bgtp families and a superoxide dismutase. These results highlighted the cell wall remodeling during germination in S. boydii with the identification of a substantial number of cell wall GPI-anchored conidial or hyphal specific proteins, which provides a basis to investigate the role of these molecules in the host-pathogen interaction and fungal virulence.

  2. Characterization of applied tensile stress using domain wall dynamic behavior of grain-oriented electrical steel

    Science.gov (United States)

    Qiu, Fasheng; Ren, Wenwei; Tian, Gui Yun; Gao, Bin

    2017-06-01

    Stress measurement that provides early indication of stress status has become increasingly demanding in the field of Non-destructive testing and evaluation (NDT&E). Bridging the correlation between micro magnetic properties and the applied tensile stress is the first conceptual step to come up with a new method of non-destructive testing. This study investigates the characterization of applied tensile stress with in-situ magnetic domain imaging and their dynamic behaviors by using magneto-optical Kerr effect (MOKE) microscopy assisted with magneto-optical indicator film (MOIF). Threshold magnetic field (TMF) feature to reflect 180 ° domain wall (DW) characteristics behaviors in different grains is proposed for stress detection. It is verified that TMF is a threshold feature with better sensitivity and brings linear correlation for stress characterization in comparison to classical coercive field, remanent magnetization, hysteresis loss and permeability parameters. The results indicate that 180 ° DWs dynamic in the inner grain is highly correlated with stress. The DW dynamics of turn over (TO) tests for different grains is studied to illustrate the repeatability of TMF. Experimental tests of high permeability grain oriented (HGO) electrical steels under stress loading have been conducted to verify this study.

  3. Large eddy simulation of flow over a wall-mounted cube: Comparison of different semi dynamic subgrid scale models

    Directory of Open Access Journals (Sweden)

    M Nooroullahi

    2016-09-01

    Full Text Available In this paper the ability of different semi dynamic subgrid scale models for large eddy simulation was studied in a challenging test case. The semi dynamic subgrid scale models were examined in this investigation is Selective Structure model, Coherent structure model, Wall Adaptive Large Eddy model. The test case is a simulation of flow over a wall-mounted cube in a channel. The results of these models were compared to structure function model, dynamic models and experimental data at Reynolds number 40000. Results show that these semi dynamic models could improve the ability of numerical simulation in comparison with other models which use a constant coefficient for simulation of subgrid scale viscosity. In addition, these models don't have the instability problems of dynamic models.

  4. Impact of flame-wall interaction on premixed flame dynamics and transfer function characteristics

    KAUST Repository

    Kedia, K.S.

    2011-01-01

    In this paper, we numerically investigate the response of a perforated-plate stabilized laminar methane-air premixed flame to imposed inlet velocity perturbations. A flame model using detailed chemical kinetics mechanism is applied and heat exchange between the burner plate and the gas mixture is incorporated. Linear transfer functions, for low mean inlet velocity oscillations, are analyzed for different equivalence ratio, mean inlet velocity, plate thermal conductivity and distance between adjacent holes. The oscillations of the heat exchange rate at the top of the burner surface plays a critical role in driving the growth of the perturbations over a wide range of conditions, including resonance. The flame response to the perturbations at its base takes the form of consumption speed oscillations in this region. Flame stand-off distance increases/decreases when the flame-wall interaction strengthens/weakens, impacting the overall dynamics of the heat release. The convective lag between the perturbations and the flame base response govern the phase of heat release rate oscillations. There is an additional convective lag between the perturbations at the flame base and the flame tip which has a weaker impact on the heat release rate oscillations. At higher frequencies, the flame-wall interaction is weaker and the heat release oscillations are driven by the flame area oscillations. The response of the flame to higher amplitude oscillations are used to gain further insight into the mechanisms. © 2010 Published by Elsevier Inc. on behalf of The Combustion Institute. All rights reserved.

  5. Dynamic Analysis of Horizontally Curved Thin-Walled Box-Girder Bridge due to Moving Vehicle

    Directory of Open Access Journals (Sweden)

    K. Nallasivam

    2007-01-01

    Full Text Available The impact on curved box-girder bridges due to vehicle moving across rough bridge deck have been analyzed using bridge-vehicle coupled dynamics. The bridge deck unevenness has been assumed to be a homogeneous random process in space specified by a PSD function. The analysis incorporates the effect of centrifugal forces due to vehicle moving on curved bridge. The curved box-girder bridge has been numerically modeled using computationally efficient thin-walled box-beam finite elements which take into account the torsional warping, distortion and distortional warping, that are important features of thin-walled box girders. Rigid vehicle with longitudinal and transverse input to the wheels giving rise to heave-pitch-roll degrees of freedom has been considered. The theoretical bridge model used in simulation study has been validated by a free vibration experiment using impact excitation. The impact factors for several response parameters such as bending moment, shear force, torsional moment, torsional bi-moment, distortional moment, distortional bi-moment and vertical deflections have been obtained for various bridge-vehicle parameters. Both constant velocity and forward acceleration of the vehicle have been considered to examine impact factor. The results highlighted that the impact factors of a curved box girder bridge corresponding to torsion, distortion and their corresponding bimoments have been observed to be generally very high, while those of the other responses are also relatively higher than that of corresponding straight box girder bridge.

  6. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics.

    Science.gov (United States)

    Zimmermann, Jörg; Oakman, Erin L; Thorpe, Ian F; Shi, Xinghua; Abbyad, Paul; Brooks, Charles L; Boxer, Steven G; Romesberg, Floyd E

    2006-09-12

    The evolution of proteins with novel function is thought to start from precursor proteins that are conformationally heterogeneous. The corresponding genes may be duplicated and then mutated to select and optimize a specific conformation. However, testing this idea has been difficult because of the challenge of quantifying protein flexibility and conformational heterogeneity as a function of evolution. Here, we report the characterization of protein heterogeneity and dynamics as a function of evolution for the antifluorescein antibody 4-4-20. Using nonlinear laser spectroscopy, surface plasmon resonance, and molecular dynamics simulations, we demonstrate that evolution localized the Ab-combining site from a heterogeneous ensemble of conformations to a single conformation by introducing mutations that act cooperatively and over significant distances to rigidify the protein. This study demonstrates how protein dynamics may be tailored by evolution and has important implications for our understanding of how novel protein functions are evolved.

  7. Changes in cell wall properties coincide with overexpression of extensin fusion proteins in suspension cultured tobacco cells.

    Directory of Open Access Journals (Sweden)

    Li Tan

    Full Text Available Extensins are one subfamily of the cell wall hydroxyproline-rich glycoproteins, containing characteristic SerHyp4 glycosylation motifs and intermolecular cross-linking motifs such as the TyrXaaTyr sequence. Extensins are believed to form a cross-linked network in the plant cell wall through the tyrosine-derivatives isodityrosine, pulcherosine, and di-isodityrosine. Overexpression of three synthetic genes encoding different elastin-arabinogalactan protein-extensin hybrids in tobacco suspension cultured cells yielded novel cross-linking glycoproteins that shared features of the extensins, arabinogalactan proteins and elastin. The cell wall properties of the three transgenic cell lines were all changed, but in different ways. One transgenic cell line showed decreased cellulose crystallinity and increased wall xyloglucan content; the second transgenic cell line contained dramatically increased hydration capacity and notably increased cell wall biomass, increased di-isodityrosine, and increased protein content; the third transgenic cell line displayed wall phenotypes similar to wild type cells, except changed xyloglucan epitope extractability. These data indicate that overexpression of modified extensins may be a route to engineer plants for bioenergy and biomaterial production.

  8. Dynamics of the spin-1/2 Heisenberg chain initialized in a domain-wall state

    Science.gov (United States)

    Misguich, Grégoire; Mallick, Kirone; Krapivsky, P. L.

    2017-11-01

    We study the dynamics of an isotropic spin-1/2 Heisenberg chain starting in a domain-wall initial condition where the spins are initially up on the left half-line and down on the right half-line. We focus on the long-time behavior of the magnetization profile. We perform extensive time-dependent density-matrix renormalization-group simulations (up to t =350 ) and find that the data are compatible with a diffusive behavior. Subleading corrections decay slowly blurring the emergence of the diffusive behavior. We also compare our results with two alternative scenarios: superdiffusive behavior and enhanced diffusion with a logarithmic correction. We finally discuss the evolution of the entanglement entropy.

  9. Computational fluid dynamics modeling of momentum transport in rotating wall perfused bioreactor for cartilage tissue engineering.

    Science.gov (United States)

    Cinbiz, Mahmut N; Tığli, R Seda; Beşkardeş, Işil Gerçek; Gümüşderelioğlu, Menemşe; Colak, Uner

    2010-11-01

    In this study, computational fluid dynamics (CFD) analysis of a rotating-wall perfused-vessel (RWPV) bioreactor is performed to characterize the complex hydrodynamic environment for the simulation of cartilage development in RWPV bioreactor in the presence of tissue-engineered cartilage constructs, i.e., cell-chitosan scaffolds. Shear stress exerted on chitosan scaffolds in bioreactor was calculated for different rotational velocities in the range of 33-38 rpm. According to the calculations, the lateral and lower surfaces were exposed to 0.07926-0.11069 dyne/cm(2) and 0.05974-0.08345 dyne/cm(2), respectively, while upper surfaces of constructs were exposed to 0.09196-0.12847 dyne/cm(2). Results validate adequate hydrodynamic environment for scaffolds in RWPV bioreactor for cartilage tissue development which concludes the suitability of operational conditions of RWPV bioreactor. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wong, C.H., E-mail: chwong@ntu.edu.sg; Vijayaraghavan, V.

    2014-01-24

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  11. Open and closed shear-walls in high-rise structural systems: Static and dynamic analysis

    Science.gov (United States)

    Carpinteri, Alberto; Lacidogna, Giuseppe; Nitti, Giuseppe

    2016-06-01

    In the present paper, a General Algorithm is applied to the analysis of high-rise structures. This algorithm is to be used as a calculation tool in preliminary design; it allows to define the interaction between closed and open, straight or curved shear-walls, and the forces exchanged in structures subject to mainly horizontal loads. The analysis can be performed in both static and dynamic regimes, the mode shapes and the natural frequencies being assessed. This general formulation allows analyses of high-rise structures by taking into account the torsional rigidity and the warping deformations of the elements composing the building without gross simplifications. In thisway it is possible to model the structure as a single equivalent cantilever, thus minimising the degrees of freedom of the system, and consequently the calculation time. Finally, potentials of the method proposed are demonstrated by a numerical example which emphasizes the link between global displacements and stresses in the elements composing the structure.

  12. Effects of dynamic shear and transmural pressure on wall shear stress sensitivity in collecting lymphatic vessels.

    Science.gov (United States)

    Kornuta, Jeffrey A; Nepiyushchikh, Zhanna; Gasheva, Olga Y; Mukherjee, Anish; Zawieja, David C; Dixon, J Brandon

    2015-11-01

    Given the known mechanosensitivity of the lymphatic vasculature, we sought to investigate the effects of dynamic wall shear stress (WSS) on collecting lymphatic vessels while controlling for transmural pressure. Using a previously developed ex vivo lymphatic perfusion system (ELPS) capable of independently controlling both transaxial pressure gradient and average transmural pressure on an isolated lymphatic vessel, we imposed a multitude of flow conditions on rat thoracic ducts, while controlling for transmural pressure and measuring diameter changes. By gradually increasing the imposed flow through a vessel, we determined the WSS at which the vessel first shows sign of contraction inhibition, defining this point as the shear stress sensitivity of the vessel. The shear stress threshold that triggered a contractile response was significantly greater at a transmural pressure of 5 cmH2O (0.97 dyne/cm(2)) than at 3 cmH2O (0.64 dyne/cm(2)). While contraction frequency was reduced when a steady WSS was applied, this inhibition was reversed when the applied WSS oscillated, even though the mean wall shear stresses between the conditions were not significantly different. When the applied oscillatory WSS was large enough, flow itself synchronized the lymphatic contractions to the exact frequency of the applied waveform. Both transmural pressure and the rate of change of WSS have significant impacts on the contractile response of lymphatic vessels to flow. Specifically, time-varying shear stress can alter the inhibition of phasic contraction frequency and even coordinate contractions, providing evidence that dynamic shear could play an important role in the contractile function of collecting lymphatic vessels. Copyright © 2015 the American Physiological Society.

  13. Cytoskeletal proteins in the follicular wall of normal andcystic ovaries of sows

    Directory of Open Access Journals (Sweden)

    Fabiano J.F. de Sant'Ana

    2015-02-01

    Full Text Available The expression of cytoskeletal proteins was evaluated immunohistochemically in 36 normal ovaries sampled from 18 sows and 44 cystic ovaries sampled from of 22 sows, was evaluated. All sows had history of reproductive problems, such as infertility or subfertility. The immunohistochemically stained area (IHCSA was quantified through image analysis to evaluate the expression of these proteins in the follicular wall of secondary, tertiary, and cystic follicles. Cytokeratins (CK immunoreactivity was strong in the granulosa cell layer (GC and mild in the theca interna (TI and externa (TE of the normal follicles. There was severe reduction of the reaction to CK in the GC in the cystic follicles, mainly in the luteinized cysts. The immunoreactivity for vimentin was higher in the GC from normal and cystic follicles in contrast with the other follicular structures. In the luteinized cysts, the IHCSA for vimentin was significantly higher in TI and in both observed cysts, the labeling was more accentuated in TE. Immunohistochemical detection of desmin and α-SMA was restricted to the TE, without differences between the normal and cystic follicles. The results of the current study show that the development of ovarian cysts in sows is associated to changes in the expression of the cytoskeletal proteins CK and vimentin.

  14. A cell wall protein-based vaccine candidate induce protective immune response against Sporothrix schenckii infection.

    Science.gov (United States)

    Portuondo, Deivys Leandro; Batista-Duharte, Alexander; Ferreira, Lucas Souza; Martínez, Damiana Téllez; Polesi, Marisa Campos; Duarte, Roberta Aparecida; de Paula E Silva, Ana Carolina Alves; Marcos, Caroline Maria; Almeida, Ana Marisa Fusco de; Carlos, Iracilda Zeppone

    2016-02-01

    Sporotrichosis is a subcutaneous mycosis caused by several closely related thermo-dimorphic fungi of the Sporothrix schenckii species complex, affecting humans and other mammals. In the last few years, new strategies have been proposed for controlling sporotrichosis owning to concerns about its growing incidence in humans, cats, and dogs in Brazil, as well as the toxicity and limited efficacy of conventional antifungal drugs. In this study, we assessed the immunogenicity and protective properties of two aluminum hydroxide (AH)-adsorbed S. schenckii cell wall protein (ssCWP)-based vaccine formulations in a mouse model of systemic S. schenckii infection. Fractioning by SDS-PAGE revealed nine protein bands, two of which were functionally characterized: a 44kDa peptide hydrolase and a 47kDa enolase, which was predicted to be an adhesin. Sera from immunized mice recognized the 47kDa enolase and another unidentified 71kDa protein, whereas serum from S. schenckii-infected mice recognized both these proteins plus another unidentified 9.4kDa protein. Furthermore, opsonization with the anti-ssCWP sera led to markedly increased phagocytosis and was able to strongly inhibit the fungus' adhesion to fibroblasts. Immunization with the higher-dose AH-adjuvanted formulation led to increased ex vivo release of IL-12, IFN-γ, IL-4, and IL-17, whereas only IL-12 and IFN-γ were induced by the higher-dose non-adjuvanted formulation. Lastly, passive transference of the higher-dose AH-adjuvanted formulation's anti-ssCWP serum was able to afford in vivo protection in a subsequent challenge with S. schenckii, becoming a viable vaccine candidate for further testing. Copyright © 2015 Elsevier GmbH. All rights reserved.

  15. Polymer dynamics from synthetic polymers to proteins

    Indian Academy of Sciences (India)

    tures of polymer melt rheology. Large-scale protein motions on the other hand are critical for proteins to coordi- nate precise biological functions. Structural studies have documented the confor- mational flexibility in proteins accompanying their activity. Results from macro- scopic studies such as biochemical kinetics and ...

  16. Interaction of amidated single-walled carbon nanotubes with protein by multiple spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lili [China Pharmaceutical University, Nanjing 210009 (China); The Nursing College of Pingdingshan University, Pingdingshan 467000 (China); Lin, Rui [Yancheng Health Vocational and Technical College, Yancheng 224005 (China); He, Hua, E-mail: dochehua@163.com [China Pharmaceutical University, Nanjing 210009 (China); Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009 (China); Sun, Meiling, E-mail: sml-nir@sohu.com [China Pharmaceutical University, Nanjing 210009 (China); Jiang, Li; Gao, Mengmeng [China Pharmaceutical University, Nanjing 210009 (China)

    2014-01-15

    The aim of this work was to investigate the detailed interaction between BSA and amidated single walled carbon nanotubes (e-SWNTs) in vitro. Ethylenediamine (EDA) was successfully linked on the surface of single-walled carbon nanotubes (SWNTs) via acylation to improve their dispersion and to introduce active groups. Bovine serum albumin (BSA) was selected as the template protein to inspect the interaction of e-SWNTs with protein. Decreases in fluorescence intensity of BSA induced by e-SWNTs demonstrated the occurrence of interaction between BSA and e-SWNTs. Quenching parameters and different absorption spectra for e-SWNTs–BSA show that the quenching effect of e-SWNTs was static quenching. Hydrophobic force had a leading contribution to the binding roles of BSA on e-SWNTs, which was confirmed by positive enthalpy change and entropy change. The interference of Na{sup +} with the quenching effect of e-SWNTs authenticated that electrostatic force existed in the interactive process simultaneously. The hydrophobicity of amino acid residues markedly increased with the addition of e-SWNTs viewed from UV spectra of BSA. The content of α-helix structure in BSA decreased by 6.8% due to the addition of e-SWNTs, indicating that e-SWNTs have an effect on the secondary conformation of BSA. -- Highlights: • The interaction between e-SWNTs and BSA was investigated by multiple spectroscopic methods. • Quenching mechanism was static quenching. • Changes in structure of BSA were inspected by synchronous fluorescence, UV–vis and CD spectrum.

  17. Computational models of protein kinematics and dynamics: beyond simulation.

    Science.gov (United States)

    Gipson, Bryant; Hsu, David; Kavraki, Lydia E; Latombe, Jean-Claude

    2012-01-01

    Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein.

  18. Influence of confinement by smooth and rough walls on particle dynamics in dense hard-sphere suspensions.

    Science.gov (United States)

    Eral, H B; van den Ende, D; Mugele, F; Duits, M H G

    2009-12-01

    We used video microscopy and particle tracking to study the dynamics of confined hard-sphere suspensions. Our fluids consisted of 1.1-microm-diameter silica spheres suspended at volume fractions of 0.33-0.42 in water-dimethyl sulfoxide. Suspensions were confined in a quasiparallel geometry between two glass surfaces: a millimeter-sized rough sphere and a smooth flat wall. First, as the separation distance (H) is decreased from 18 to 1 particle diameter, a transition takes place from a subdiffusive behavior (as in bulk) at large H, to completely caged particle dynamics at small H. These changes are accompanied by a strong decrease in the amplitude of the mean-square displacement (MSD) in the horizontal plane parallel to the confining surfaces. In contrast, the global volume fraction essentially remains constant when H is decreased. Second, measuring the MSD as a function of distance from the confining walls, we found that the MSD is not spatially uniform but smaller close to the walls. This effect is the strongest near the smooth wall where layering takes place. Although confinement also induces local variations in volume fraction, the spatial variations in MSD can be attributed only partially to this effect. The changes in MSD are predominantly a direct effect of the confining surfaces. Hence, both the wall roughness and the separation distance (H) influence the dynamics in confined geometries.

  19. Dynamics of DNA conformations and DNA-protein interaction

    DEFF Research Database (Denmark)

    Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

    2005-01-01

    Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturat......Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...

  20. Discriminating lysosomal membrane protein types using dynamic neural network.

    Science.gov (United States)

    Tripathi, Vijay; Gupta, Dwijendra Kumar

    2014-01-01

    This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.

  1. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    Science.gov (United States)

    Xia, Kelin; Wei, Guo-Wei

    2014-01-01

    This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365

  2. Water Determines the Structure and Dynamics of Proteins.

    Science.gov (United States)

    Bellissent-Funel, Marie-Claire; Hassanali, Ali; Havenith, Martina; Henchman, Richard; Pohl, Peter; Sterpone, Fabio; van der Spoel, David; Xu, Yao; Garcia, Angel E

    2016-07-13

    Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

  3. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    Science.gov (United States)

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  4. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

    Science.gov (United States)

    Fogarty, Aoife C; Laage, Damien

    2014-07-17

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

  5. The importance of connections between the cell wall integrity pathway and the unfolded protein response in filamentous fungi.

    Science.gov (United States)

    Malavazi, Iran; Goldman, Gustavo Henrique; Brown, Neil Andrew

    2014-11-01

    In the external environment, or within a host organism, filamentous fungi experience sudden changes in nutrient availability, osmolality, pH, temperature and the exposure to toxic compounds. The fungal cell wall represents the first line of defense, while also performing essential roles in morphology, development and virulence. A polarized secretion system is paramount for cell wall biosynthesis, filamentous growth, nutrient acquisition and interactions with the environment. The unique ability of filamentous fungi to secrete has resulted in their industrial adoption as fungal cell factories. Protein maturation and secretion commences in the endoplasmic reticulum (ER). The unfolded protein response (UPR) maintains ER functionality during exposure to secretion and cell wall stress. UPR, therefore, influences secretion and cell wall homeostasis, which in turn impacts upon numerous fungal traits important to pathogenesis and biotechnology. Subsequently, this review describes the relevance of the cell wall and UPR systems to filamentous fungal pathogens or industrial microbes and then highlights interconnections between the two systems. Ultimately, the possible biotechnological applications of an enhanced understanding of such regulatory systems in combating fungal disease, or the removal of natural bottlenecks in protein secretion in an industrial setting, are discussed. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Coupled Static and Dynamic Buckling Modelling of Thin-Walled Structures in Elastic Range Review of Selected Problems

    Directory of Open Access Journals (Sweden)

    Kołakowski Zbigniew

    2016-06-01

    Full Text Available A review of papers that investigate the static and dynamic coupled buckling and post-buckling behaviour of thin-walled structures is carried out. The problem of static coupled buckling is sufficiently well-recognized. The analysis of dynamic interactive buckling is limited in practice to columns, single plates and shells. The applications of finite element method (FEM or/and analytical-numerical method (ANM to solve interaction buckling problems are on-going. In Poland, the team of scientists from the Department of Strength of Materials, Lodz University of Technology and co-workers developed the analytical-numerical method. This method allows to determine static buckling stresses, natural frequencies, coefficients of the equation describing the post-buckling equilibrium path and dynamic response of the plate structure subjected to compression load and/or bending moment. Using the dynamic buckling criteria, it is possible to determine the dynamic critical load. They presented a lot of interesting results for problems of the static and dynamic coupled buckling of thin-walled plate structures with complex shapes of cross-sections, including an interaction of component plates. The most important advantage of presented analytical-numerical method is that it enables to describe all buckling modes and the post-buckling behaviours of thin-walled columns made of different materials. Thin isotropic, orthotropic or laminate structures were considered.

  7. Plasmonic welded single walled carbon nanotubes on monolayer graphene for sensing target protein

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jangheon; Kim, Soohyun [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 373-1 Guseong, Yuseong, Daejeon 305-806 (Korea, Republic of); Kim, Gi Gyu; Jung, Wonsuk, E-mail: wonsuk81@wku.ac.kr [Department of Mechanical and Automotive Engineering, Wonkwang University, Iksan, Jeonbuk 570-749 (Korea, Republic of)

    2016-05-16

    We developed plasmonic welded single walled carbon nanotubes (SWCNTs) on monolayer graphene as a biosensor to detect target antigen molecules, fc fusion protein without any treatment to generate binder groups for linker and antibody. This plasmonic welding induces atomic networks between SWCNTs as junctions containing carboxylic groups and improves the electrical sensitivity of a SWCNTs and the graphene membrane to detect target protein. We investigated generation of the atomic networks between SWCNTs by field-emission scanning electron microscopy and atomic force microscopy after plasmonic welding process. We compared the intensity ratios of D to G peaks from the Raman spectra and electrical sheet resistance of welded SWCNTs with the results of normal SWCNTs, which decreased from 0.115 to 0.086 and from 10.5 to 4.12, respectively. Additionally, we measured the drain current via source/drain voltage after binding of the antigen to the antibody molecules. This electrical sensitivity of the welded SWCNTs was 1.55 times larger than normal SWCNTs.

  8. High performance dendrimer functionalized single-walled carbon nanotubes field effect transistor biosensor for protein detection

    Science.gov (United States)

    Rajesh, Sharma, Vikash; Puri, Nitin K.; Mulchandani, Ashok; Kotnala, Ravinder K.

    2016-12-01

    We report a single-walled carbon nanotube (SWNT) field-effect transistor (FET) functionalized with Polyamidoamine (PAMAM) dendrimer with 128 carboxyl groups as anchors for site specific biomolecular immobilization of protein antibody for C-reactive protein (CRP) detection. The FET device was characterized by scanning electron microscopy and current-gate voltage (I-Vg) characteristic studies. A concentration-dependent decrease in the source-drain current was observed in the regime of clinical significance, with a detection limit of ˜85 pM and a high sensitivity of 20% change in current (ΔI/I) per decade CRP concentration, showing SWNT being locally gated by the binding of CRP to antibody (anti-CRP) on the FET device. The low value of the dissociation constant (Kd = 0.31 ± 0.13 μg ml-1) indicated a high affinity of the device towards CRP analyte arising due to high anti-CRP loading with a better probe orientation on the 3-dimensional PAMAM structure.

  9. Dynamically searching for a domain for protein function prediction.

    Science.gov (United States)

    Hou, Jingyu; Jiang, Yongqing

    2013-08-01

    The availability of large amounts of protein-protein interaction (PPI) data makes it feasible to use computational approaches to predict protein functions. The base of existing computational approaches is to exploit the known function information of annotated proteins in the PPI data to predict functions of un-annotated proteins. However, these approaches consider the prediction domain (i.e. the set of proteins from which the functions are predicted) as unchangeable during the prediction procedure. This may lead to valuable information being overwhelmed by the unavoidable noise information in the PPI data when predicting protein functions, and in turn, the prediction results will be distorted. In this paper, we propose a novel method to dynamically predict protein functions from the PPI data. Our method regards the function prediction as a dynamic process of finding a suitable prediction domain, from which representative functions of the domain are selected to predict functions of un-annotated proteins. Our method exploits the topological structural information of a PPI network and the semantic relationship between protein functions to measure the relationship between proteins, dynamically select a suitable prediction domain and predict functions. The evaluation on real PPI datasets demonstrated the effectiveness of our proposed method, and generated better prediction results.

  10. Mild and Selective Protein Release of Cell Wall Deficient Microalgae with Pulsed Electric Field

    NARCIS (Netherlands)

    Lam, 't Gerard; Kolk, van der Jelmer A.; Chordia, Akshita; Vermuë, Marian H.; Olivieri, Giuseppe; Eppink, Michel H.M.; Wijffels, René H.

    2017-01-01

    Pulsed electric field (PEF) is considered to be a very promising technology for mild cell disruption. The application of PEF for microalgae that have a rigid cell wall, however, is hampered by the presence of that rigid outer cell wall. A cell wall free mutant of C. reinhardtii was used to mimic

  11. Protein dynamics in individual human cells: experiment and theory.

    Directory of Open Access Journals (Sweden)

    Ariel Aharon Cohen

    Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

  12. Molecular Dynamics Simulation of a Multi-Walled Carbon Nanotube Based Gear

    Science.gov (United States)

    Han, Jie; Globus, Al; Srivastava, Deepak; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    We used molecular dynamics to investigate the properties of a multi-walled carbon nanotube based gear. Previous work computationally suggested that molecular gears fashioned from (14,0) single-walled carbon nanotubes operate well at 50-100 gigahertz. The gears were formed from nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. The gear in this study was based on the smallest multi-walled nanotube supported by some experimental evidence. Each gear was a (52,0) nanotube surrounding a (37,10) nanotube with approximate 20.4 and 16,8 A radii respectively. These sizes were chosen to be consistent with inter-tube spacing observed by and were slightly larger than graphite inter-layer spacings. The benzyne teeth were attached via 2+4 cycloaddition to exterior of the (52,0) tube. 2+4 bonds were used rather than the 2+2 bonds observed by Hoke since 2+4 bonds are preferred by naphthalene and quantum calculations by Jaffe suggest that 2+4 bonds are preferred on carbon nanotubes of sufficient diameter. One gear was 'powered' by forcing the atoms near the end of the outside buckytube to rotate to simulate a motor. A second gear was allowed to rotate by keeping the atoms near the end of its outside buckytube on a cylinder. The ends of both gears were constrained to stay in an approximately constant position relative to each other, simulating a casing, to insure that the gear teeth meshed. The stiff meshing aromatic gear teeth transferred angular momentum from the powered gear to the driven gear. The simulation was performed in a vacuum and with a software thermostat. Preliminary results suggest that the powered gear had trouble turning the driven gear without slip. The larger radius and greater mass of these gears relative to the (14,0) gears previously studied requires a

  13. Dynamic expression patterns of differential proteins during early invasion of hepatocellular carcinoma.

    Directory of Open Access Journals (Sweden)

    Rong-Xin Chen

    Full Text Available Tumor cell invasion into the surrounding matrix has been well documented as an early event of metastasis occurrence. However, the dynamic expression patterns of proteins during early invasion of hepatocellular carcinoma (HCC are largely unknown. Using a three-dimensional HCC invasion culture model established previously, we investigated the dynamic expression patterns of identified proteins during early invasion of HCC.Highly metastatic MHCC97H cells and a liver tissue fragment were long-term co-cultured in a rotating wall vessel (RWV bioreactor to simulate different pathological states of HCC invasion. The established spherical co-cultures were collected on days 0, 5, 10, and 15 for dynamic expression pattern analysis. Significantly different proteins among spheroids at different time points were screened and identified using quantitative proteomics of iTRAQ labeling coupled with LC-MS/MS. Dynamic expression patterns of differential proteins were further categorized by K-means clustering. The expression modes of several differentially expressed proteins were confirmed by Western blot and qRT-PCR.Time course analysis of invasion/metastasis gene expressions (MMP2, MMP7, MMP9, CD44, SPP1, CXCR4, CXCL12, and CDH1 showed remarkable, dynamic alterations during the invasion process of HCC. A total of 1,028 proteins were identified in spherical co-cultures collected at different time points by quantitative proteomics. Among these proteins, 529 common differential proteins related to HCC invasion were clustered into 25 types of expression patterns. Some proteins displayed significant dynamic alterations during the early invasion process of HCC, such as upregulation at the early invasion stage and downregulation at the late invasion stage (e.g., MAPRE1, PHB2, cathepsin D, etc. or continuous upregulation during the entire invasion process (e.g., vitronectin, Met, clusterin, ICAM1, GSN, etc..Dynamic expression patterns of candidate proteins during the

  14. Niche-Specific Requirement for Hyphal Wall protein 1 in Virulence of Candida albicans

    Science.gov (United States)

    Staab, Janet F.; Datta, Kausik; Rhee, Peter

    2013-01-01

    Specialized Candida albicans cell surface proteins called adhesins mediate binding of the fungus to host cells. The mammalian transglutaminase (TG) substrate and adhesin, Hyphal wall protein 1 (Hwp1), is expressed on the hyphal form of C. albicans where it mediates fungal adhesion to epithelial cells. Hwp1 is also required for biofilm formation and mating thus the protein functions in both fungal-host and self-interactions. Hwp1 is required for full virulence of C. albicans in murine models of disseminated candidiasis and of esophageal candidiasis. Previous studies correlated TG activity on the surface of oral epithelial cells, produced by epithelial TG (TG1), with tight binding of C. albicans via Hwp1 to the host cell surfaces. However, the contribution of other Tgs, specifically tissue TG (TG2), to disseminated candidiasis mediated by Hwp1 was not known. A newly created hwp1 null strain in the wild type SC5314 background was as virulent as the parental strain in C57BL/6 mice, and virulence was retained in C57BL/6 mice deleted for Tgm2 (TG2). Further, the hwp1 null strains displayed modestly reduced virulence in BALB/c mice as did strain DD27-U1, an independently created hwp1Δ/Δ in CAI4 corrected for its ura3Δ defect at the URA3 locus. Hwp1 was still needed to produce wild type biofilms, and persist on murine tongues in an oral model of oropharyngeal candidiasis consistent with previous studies by us and others. Finally, lack of Hwp1 affected the translocation of C. albicans from the mouse intestine into the bloodstream of mice. Together, Hwp1 appears to have a minor role in disseminated candidiasis, independent of tissue TG, but a key function in host- and self-association to the surface of oral mucosa. PMID:24260489

  15. Niche-specific requirement for hyphal wall protein 1 in virulence of Candida albicans.

    Directory of Open Access Journals (Sweden)

    Janet F Staab

    Full Text Available Specialized Candida albicans cell surface proteins called adhesins mediate binding of the fungus to host cells. The mammalian transglutaminase (TG substrate and adhesin, Hyphal wall protein 1 (Hwp1, is expressed on the hyphal form of C. albicans where it mediates fungal adhesion to epithelial cells. Hwp1 is also required for biofilm formation and mating thus the protein functions in both fungal-host and self-interactions. Hwp1 is required for full virulence of C. albicans in murine models of disseminated candidiasis and of esophageal candidiasis. Previous studies correlated TG activity on the surface of oral epithelial cells, produced by epithelial TG (TG1, with tight binding of C. albicans via Hwp1 to the host cell surfaces. However, the contribution of other Tgs, specifically tissue TG (TG2, to disseminated candidiasis mediated by Hwp1 was not known. A newly created hwp1 null strain in the wild type SC5314 background was as virulent as the parental strain in C57BL/6 mice, and virulence was retained in C57BL/6 mice deleted for Tgm2 (TG2. Further, the hwp1 null strains displayed modestly reduced virulence in BALB/c mice as did strain DD27-U1, an independently created hwp1Δ/Δ in CAI4 corrected for its ura3Δ defect at the URA3 locus. Hwp1 was still needed to produce wild type biofilms, and persist on murine tongues in an oral model of oropharyngeal candidiasis consistent with previous studies by us and others. Finally, lack of Hwp1 affected the translocation of C. albicans from the mouse intestine into the bloodstream of mice. Together, Hwp1 appears to have a minor role in disseminated candidiasis, independent of tissue TG, but a key function in host- and self-association to the surface of oral mucosa.

  16. [Study of the adsorption behaviors of plasma proteins on the single-walled carbon nanotubes nonwoven].

    Science.gov (United States)

    Meng, Jie; Song, Li; Meng, Jie; Kong, Hua; Wang, Chaoying; Guo, Xiaotian; Xu, Haiyan; Xie, Sishen

    2007-02-01

    Single walled carbon nanotubes (SWNT) have attracted increasing research interests for the purpose of biomedical application because they provide not only nanostructured topography, but also chemical composition of pure carbon atoms, as well as ultra high strength and excellent flexibility. Regarding the interactions of nanomaterials to biological systems, non-specific adsorption of plasma proteins is one of the most important issues to be concerned, which plays a crucial role that would determine how biological systems response to the biomaterials. Motivated by application of SWNT materials in biomedical fields, in this study, the adsorption behaviors of plasma proteins on the surface of SWNT nonwoven, prepared directly by floating chemical vapor observation and energy deposition method were investigated by means of scanning electron microscope (SEM), dispersive X-ray (EDX) analysis and ELISA. Results indicated the SWNT non-woven showed a clear adsorption preference of fibrinogen over albumin. There was no human serum albumin detected using above analysis methods on the SWNT nonwoven even incubated in the albumin solution of 4 mg/ml. While more than 0.15 microg of human fibrinogen was detected by ELISA on the SWNT nonwoven with area of 40 mm x 40 mm incubated in the fibrinogen solution of 5 microg/ml. In addition, IgG of sheep-anti-human serum fibrinogen exhibited strong nonspecific adsorption on the surface of SWNT nonwoven. The adsorption behaviors are different significantly from those of other carbon materials and conventional biomaterials. The unique interaction of SWNT nonwoven to plasma proteins is of significance to further studies of blood cells responses.

  17. A comparison of techniques for calculating protein essential dynamics

    NARCIS (Netherlands)

    van Aalten, D.M.F.; de Groot, B.L.; Findlay, J.B.C.; Berendsen, H.J.C.; Amadei, A

    1997-01-01

    Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to

  18. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

    Science.gov (United States)

    Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

    2015-12-08

    Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

  19. Proteomics of plasma membranes from poplar trees reveals tissue distribution of transporters, receptors, and proteins in cell wall formation.

    Science.gov (United States)

    Nilsson, Robert; Bernfur, Katja; Gustavsson, Niklas; Bygdell, Joakim; Wingsle, Gunnar; Larsson, Christer

    2010-02-01

    By exploiting the abundant tissues available from Populus trees, 3-4 m high, we have been able to isolate plasma membranes of high purity from leaves, xylem, and cambium/phloem at a time (4 weeks after bud break) when photosynthesis in the leaves and wood formation in the xylem should have reached a steady state. More than 40% of the 956 proteins identified were found in the plasma membranes of all three tissues and may be classified as "housekeeping" proteins, a typical example being P-type H(+)-ATPases. Among the 213 proteins predicted to be integral membrane proteins, transporters constitute the largest class (41%) followed by receptors (14%) and proteins involved in cell wall and carbohydrate metabolism (8%) and membrane trafficking (8%). ATP-binding cassette transporters (all members of subfamilies B, C, and G) and receptor-like kinases (four subfamilies) were two of the largest protein families found, and the members of these two families showed pronounced tissue distribution. Leaf plasma membranes were characterized by a very high proportion of transporters, constituting almost half of the integral proteins. Proteins involved in cell wall synthesis (such as cellulose and sucrose synthases) and membrane trafficking were most abundant in xylem plasma membranes in agreement with the role of the xylem in wood formation. Twenty-five integral proteins and 83 soluble proteins were exclusively found in xylem plasma membranes, which identifies new candidates associated with cell wall synthesis and wood formation. Among the proteins uniquely found in xylem plasma membranes were most of the enzymes involved in lignin biosynthesis, which suggests that they may exist as a complex linked to the plasma membrane.

  20. Molecular dynamics of surfactant protein C

    DEFF Research Database (Denmark)

    Ramírez, Eunice; Santana, Alberto; Cruz, Anthony

    2006-01-01

    Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... occurs at the amino terminal, and despite this unfolding, no transition from alpha-helix to beta-strand was observed....

  1. Michaelis-Menten dynamics in protein subnetworks

    Science.gov (United States)

    Rubin, Katy J.; Sollich, Peter

    2016-05-01

    To understand the behaviour of complex systems, it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe, e.g., enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension, we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary, and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly and is also more efficient computationally.

  2. Static Properties and Current-Driven Dynamics of Domain Walls in Perpendicular Magnetocrystalline Anisotropy Nanostrips with Rectangular Cross-Section

    Directory of Open Access Journals (Sweden)

    Eduardo Martinez

    2012-01-01

    Full Text Available The current-induced domain wall motion along thin ferromagnetic strips with high perpendicular magnetocrystalline anisotropy is studied by means of full micromagnetic simulations and the extended one-dimensional model, taking into account thermal effects and edge roughness. A slow creep regime, where the motion is controlled by wall pinning and thermal activation, and a flow regime with linear variation of the DW velocity, are observed. In asymmetric stacks, where the Rashba spin-orbit field stabilizes the domain wall against turbulent transformations, the steady linear regime is extended to higher currents, leading to higher velocities than in single-layer or symmetric stacks. The pinning and depinning at and from a local constriction were also studied. The results indicate that engineering pinning sites in these strips provide an efficient pathway to achieve both high stability against thermal fluctuations and low-current depinning avoiding Joule heating. Finally, the current-driven dynamics of a pinned domain wall is examined, and both the direct and the alternating contributions to the induced voltage signal induced are characterized. It was confirmed that the direct contribution to the voltage signal can be linearly enhanced with the number of pinned walls, an observation which could be useful to develop domain-wall-based nano-oscillators.

  3. Michaelis-Menten dynamics in protein subnetworks

    CERN Document Server

    Rubin, Katy J

    2016-01-01

    To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain ...

  4. Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans.

    Science.gov (United States)

    Li, Y; Liu, Z; Zhang, Y; Su, Q P; Xue, B; Shao, S; Zhu, Y; Xu, X; Wei, S; Sun, Y

    2015-10-01

    Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Use of the Plant Defense Protein Osmotin To Identify Fusarium oxysporum Genes That Control Cell Wall Properties

    KAUST Repository

    Lee, H.

    2010-02-26

    Fusarium oxysporum is the causative agent of fungal wilt disease in a variety of crops. The capacity of a fungal pathogen such as F. oxysporum f. sp. nicotianae to establish infection on its tobacco (Nicotiana tabacum) host depends in part on its capacity to evade the toxicity of tobacco defense proteins, such as osmotin. Fusarium genes that control resistance to osmotin would therefore reflect coevolutionary pressures and include genes that control mutual recognition, avoidance, and detoxification. We identified FOR (Fusarium Osmotin Resistance) genes on the basis of their ability to confer osmotin resistance to an osmotin-sensitive strain of Saccharomyces cerevisiae. FOR1 encodes a putative cell wall glycoprotein. FOR2 encodes the structural gene for glutamine:fructose-6-phosphate amidotransferase, the first and rate-limiting step in the biosynthesis of hexosamine and cell wall chitin. FOR3 encodes a homolog of SSD1, which controls cell wall composition, longevity, and virulence in S. cerevisiae. A for3 null mutation increased osmotin sensitivity of conidia and hyphae of F. oxysporum f. sp. nicotianae and also reduced cell wall β-1,3-glucan content. Together our findings show that conserved fungal genes that determine cell wall properties play a crucial role in regulating fungal susceptibility to the plant defense protein osmotin.

  6. Simplified Dynamic Structural Time History Response Analysis of Flexible Approach Walls Founded on Clustered Pile Groups Using Impact_Deck

    Science.gov (United States)

    2016-07-01

    Approach Walls Founded on Clustered Pile Groups Using Impact_Deck In fo rm at io n an d Te ch no lo gy L ab or at or y Barry C. White, José...Time-History Response Analysis of Flexible Approach Walls Founded on Clustered Pile Groups Using Impact_Deck Barry C. White and Robert M. Ebeling...clustered pile groups and subjected to barge train impact events. This software tool, Impact_Deck, is used to perform a dynamic, time- domain

  7. Calculation of the neutron electric dipole moment with two dynamical flavors of domain wall fermions

    Energy Technology Data Exchange (ETDEWEB)

    F. Berruto; T. Blum; K. Orginos; A. Soni

    2005-12-08

    We present a study of the neutron electric dipole moment ({rvec d}{sub N}) within the framework of lattice QCD with two flavors of dynamical light quarks. The dipole moment is sensitive to the topological structure of the gauge fields, and accuracy can only be achieved by using dynamical, or sea quark, calculations. However, the topological charge evolves slowly in these calculations, leading to a relatively large uncertainty in {rvec d}{sub N}. It is shown, using quenched configurations, that a better sampling of the charge distribution reduces this problem, but because the CP even part of the fermion determinant is absent, both the topological charge distribution and {rvec d}{sub N} are pathological in the chiral limit. We discuss the statistical and systematic uncertainties arising from the topological charge distribution and unphysical size of the quark mass in our calculations and prospects for eliminating them. Our calculations employ the RBC collaboration two flavor domain wall fermion and DBW2 gauge action lattices with inverse lattice spacing a{sup -1} {approx} 1.7 GeV, physical volume V {approx} (2 fm){sup 3}, and light quark mass roughly equal to the strange quark mass (m{sub sea} = 0.03 and 0.04). We determine a value of the electric dipole moment that is zero within (statistical) errors, |{rvec d}{sub N}| = -0.04(20) e-{theta}-fm at the smaller sea quark mass. Satisfactory results for the magnetic and electric form factors of the proton and neutron are also obtained and presented.

  8. Spin wave dynamics in Heisenberg ferromagnetic/antiferromagnetic single-walled nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Mi, Bin-Zhou, E-mail: mbzfjerry2008@126.com [Department of Basic Curriculum, North China Institute of Science and Technology, Beijing 101601 (China); Department of Physics, School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083 (China)

    2016-09-15

    The spin wave dynamics, including the magnetization, spin wave dispersion relation, and energy level splitting, of Heisenberg ferromagnetic/antiferromagnetic single-walled nanotubes are systematically calculated by use of the double-time Green’s function method within the random phase approximation. The role of temperature, diameter of the tube, and wave vector on spin wave energy spectrum and energy level splitting are carefully analyzed. There are two categories of spin wave modes, which are quantized and degenerate, and the total number of independent magnon branches is dependent on diameter of the tube, caused by the physical symmetry of nanotubes. Moreover, the number of flat spin wave modes increases with diameter of the tube rising. The spin wave energy and the energy level splitting decrease with temperature rising, and become zero as temperature reaches the critical point. At any temperature, the energy level splitting varies with wave vector, and for a larger wave vector it is smaller. When pb=π, the boundary of first Brillouin zone, spin wave energies are degenerate, and the energy level splittings are zero.

  9. Phase-space dynamics of opposition control in wall-bounded turbulent flows

    Science.gov (United States)

    Hwang, Yongyun; Ibrahim, Joseph; Yang, Qiang; Doohan, Patrick

    2017-11-01

    The phase-space dynamics of wall-bounded shear flow in the presence of opposition control is explored by examining the behaviours of a pair of nonlinear equilibrium solutions (exact coherent structures), edge state and life time of turbulence at low Reynolds numbers. While the control modifies statistics and phase-space location of the edge state and the lower-branch equilibrium solution very little, it is also found to regularise the periodic orbit on the edge state by reverting a period-doubling bifurcation. Only the upper-branch equilibrium solution and mean turbulent state are significantly modified by the control, and, in phase space, they gradually approach the edge state on increasing the control gain. It is found that this behaviour results in a significant reduction of the life time of turbulence, indicating that the opposition control significantly increases the probability that the turbulent solution trajectory passes through the edge state. Finally, it is shown that the opposition control increases the critical Reynolds number of the onset of the equilibrium solutions, indicating its capability of transition delay. This work is sponsored by the Engineering and Physical Sciences Research Council (EPSRC) in the UK (EP/N019342/1).

  10. The Effect of Wettability on the Dynamical Behaviors of Single-Walled Carbon Nanotube

    Directory of Open Access Journals (Sweden)

    Yan Yan

    2015-01-01

    Full Text Available The dynamical behaviors of single-walled carbon nanotube (SWCNT with the internal and external wettability are studied based on a multiple flexible shell model in the paper. The SWCNT-water system comprises five constituent parts, that is, the SWCNT, the absorbed inner and outer layers of water molecules, the water in the center of the SWCNT, and the water surrounding the absorbed outer water layer. Here we consider the absorbed water layers as infinitesimally thin shells, which interact with the nanotube via a continuum Lennard-Jones potential, and the water in the center of the SWCNT and the counterpart surrounding the absorbed outer water layer as the potential flow. It is found that the interactions of SWCNT and the water layer are responsible for an upshift in the frequency of the SWCNT and the total upshift is approximately the sum of the two corresponding upshifts. The vdW interactions also cause the increase of the frequency of internal and external water shells. We hope that the paper can offer a new modeling approach to determine whether carbon nanotubes have adsorbed fluids inside their pores and could be used for detecting changes in their filling state.

  11. Polymer dynamics from synthetic polymers to proteins

    Indian Academy of Sciences (India)

    Starting from the standard model of polymer motion - the Rouse model - we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement.

  12. Hindered protein dynamics in the presence of a cryoprotecting agent

    Energy Technology Data Exchange (ETDEWEB)

    Koeper, I. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Physikdepartment E13, TU Muenchen, 85747 Garching (Germany); Bellissent-Funel, M.C. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France)

    2002-07-01

    We present a study of the influence of trehalose, a well-known cryoprotecting disaccharide, on the dynamics of a protein, the C-phycocyanin. The dynamics is investigated in a time range from some picoseconds to several nanoseconds using different neutron-scattering techniques. Data obtained on samples containing hydrated powders of the protein in the presence of trehalose are compared to that of the protein alone, studied by neutron-scattering techniques as well as by molecular dynamics simulations. The analysis of time-of-flight data gives access to the geometry of the observed motions. These motions can be described via a model of a particle diffusing inside a sphere. We observe a slowing down of the movements of the protein due to the presence of trehalose of one to two orders of magnitude, while the geometry of the motions is conserved. (orig.)

  13. Coherent Protein Dynamics Explored at FELIX

    CERN Document Server

    Austin, Robert

    2004-01-01

    We have discovered that there exists a very narrow (less than 0.02 microns) wide resonance in the amide I band of myoglobin and photoactive yellow protein that can be driven to greater than 30% saturation using very narrow linewidth pump-probe spectroscopy at FELIX. The extraordinary narrowness of this transition and the extraordinary ease of saturation inplies that this band is highly anharmonic and decoupled from the other oscillators in the amide I band. We will present detailed measurments on this discovery and implications for energy flow in proteins.

  14. Species-Specific Immunodetection of an Entamoeba histolytica Cyst Wall Protein.

    Science.gov (United States)

    Spadafora, Lauren J; Kearney, Moira R; Siddique, Abdullah; Ali, Ibne K; Gilchrist, Carol A; Arju, Tuhinur; Hoffstrom, Benjamin; Nguyen, Felicia K; Petri, William A; Haque, Rashidul; Cangelosi, Gerard A

    2016-05-01

    Entamoeba histolytica causes intestinal disease in endemic settings throughout the world. Diagnosis of E. histolytica infection would be improved by the identification of biomarkers that are expressed by cysts of E. histolytica, but not by cysts of closely related commensal species of Entamoeba. Herein, we describe two novel monoclonal antibodies (1A4 and 1D3) produced against a spacer region of the E. histolytica Jacob2 lectin, an outer cyst wall protein. These reagents demonstrated no cross-reaction to E. dispar recombinant antigen and low picomolar molecular detection limits when paired in ELISA sandwich assays. In an immunofluorescence microscopy assay, the α-Jacob2 murine antibodies labeled cysts of three xenically cultured E. histolytica isolates but did not label cysts of three E. bangladeshi isolates. Monoclonal antibody 1A4 did not cross-react with xenic cultures of three E. dispar isolates, demonstrating specificity to E. histolytica, while monoclonal antibody 1D3 cross-reacted with two out of three E. dispar isolates. Both antibodies labeled cysts in formalin-fixed slides, a potential logistical advantage in some settings. The monoclonal antibody 1A4 was also used in an immunofluorescence microscopy assay with formalin-fixed stool specimens. Seven out of ten ELISA-positive stool specimens exhibited 1A4-labeled cyst-like objects, compared to one out of seven ELISA-negative specimens. These results demonstrate that antibodies generated against the flexible spacer of E. histolytica Jacob2 lectin recognize and bind to Jacob2 protein in whole cysts and are capable of differentiating Entamoeba species in fixed specimens. Thus, Jacob2 is a promising biomarker for use in diagnosing E. histolytica infection.

  15. Plasma protein corona modulates the vascular wall interaction of drug carriers in a material and donor specific manner.

    Directory of Open Access Journals (Sweden)

    Daniel J Sobczynski

    Full Text Available The nanoscale plasma protein interaction with intravenously injected particulate carrier systems is known to modulate their organ distribution and clearance from the bloodstream. However, the role of this plasma protein interaction in prescribing the adhesion of carriers to the vascular wall remains relatively unknown. Here, we show that the adhesion of vascular-targeted poly(lactide-co-glycolic-acid (PLGA spheres to endothelial cells is significantly inhibited in human blood flow, with up to 90% reduction in adhesion observed relative to adhesion in simple buffer flow, depending on the particle size and the magnitude and pattern of blood flow. This reduced PLGA adhesion in blood flow is linked to the adsorption of certain high molecular weight plasma proteins on PLGA and is donor specific, where large reductions in particle adhesion in blood flow (>80% relative to buffer is seen with ∼60% of unique donor bloods while others exhibit moderate to no reductions. The depletion of high molecular weight immunoglobulins from plasma is shown to successfully restore PLGA vascular wall adhesion. The observed plasma protein effect on PLGA is likely due to material characteristics since the effect is not replicated with polystyrene or silica spheres. These particles effectively adhere to the endothelium at a higher level in blood over buffer flow. Overall, understanding how distinct plasma proteins modulate the vascular wall interaction of vascular-targeted carriers of different material characteristics would allow for the design of highly functional delivery vehicles for the treatment of many serious human diseases.

  16. Post-translational modifications of plant cell wall proteins and peptides: A survey from a proteomics point of view.

    Science.gov (United States)

    Canut, Hervé; Albenne, Cécile; Jamet, Elisabeth

    2016-08-01

    Plant cell wall proteins (CWPs) and peptides are important players in cell walls contributing to their assembly and their remodeling during development and in response to environmental constraints. Since the rise of proteomics technologies at the beginning of the 2000's, the knowledge of CWPs has greatly increased leading to the discovery of new CWP families and to the description of the cell wall proteomes of different organs of many plants. Conversely, cell wall peptidomics data are still lacking. In addition to the identification of CWPs and peptides by mass spectrometry (MS) and bioinformatics, proteomics has allowed to describe their post-translational modifications (PTMs). At present, the best known PTMs consist in proteolytic cleavage, N-glycosylation, hydroxylation of P residues into hydroxyproline residues (O), O-glycosylation and glypiation. In this review, the methods allowing the capture of the modified proteins based on the specific properties of their PTMs as well as the MS technologies used for their characterization are briefly described. A focus is done on proteolytic cleavage leading to protein maturation or release of signaling peptides and on O-glycosylation. Some new technologies, like top-down proteomics and terminomics, are described. They aim at a finer description of proteoforms resulting from PTMs or degradation mechanisms. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Dynamics of force impulses and bubble oscillations during gas burning on a thrust wall in water

    Science.gov (United States)

    Teslenko, V. S.; Drozhzhin, A. P.; Medvedev, R. N.

    2017-09-01

    Comparative experiments are formed for measuring the force impulses during combustion of a stoichiometric propane-oxygen mixture on a thrust wall in cylindrical combustors and on an open wall shaped as a flat disk. For identical gas charges, the mean specific impulse generated by pulsed burning of the gas on an open thrust wall is found to be higher than that in the case of gas charge burning in cylindrical barrels.

  18. Outcomes of posterior wall fractures of the acetabulum treated nonoperatively after diagnostic screening with dynamic stress examination under anesthesia.

    Science.gov (United States)

    Grimshaw, Charles S; Moed, Berton R

    2010-12-01

    Dynamic stress fluoroscopy with the patient under general anesthesia has been advocated as a clinical measure of hip stability and congruity in patients with a posterior wall acetabular fracture. The purpose of this study was to establish the predictive value of the dynamic stress fluoroscopic examination for these fractures by evaluating clinical and radiographic outcomes after nonoperative treatment of fractures found to be stable with this examination. Twenty-one consecutive patients with an acute posterior wall fracture of the acetabulum who were shown to have a stable hip joint by dynamic stress fluoroscopy while they were under general anesthesia were treated nonoperatively. At the time of follow-up, the patients underwent clinical and/or radiographic evaluation. Clinical follow-up was performed for eighteen patients at a minimum of two years after injury, at which time the average modified Merle d'Aubigné score was very good, with no one having less than a good clinical outcome. Fifteen of these eighteen patients had radiographic evaluation at a minimum of two years, and all were found to have a congruent joint with a normal joint space and no evidence of posttraumatic arthritis. Hip joint stability determined with dynamic stress fluoroscopy with the patient under general anesthesia after a posterior wall acetabular fracture is predictive of hip joint congruity, an excellent radiographic outcome, and a good-to-excellent early clinical outcome after nonoperative treatment.

  19. Domain wall dynamics in Fe-rich glass covered amorphous microwires

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Jesus Daniel [Departamento de Fisica, Facultad de Ciencias, Universidad de Oviedo (Spain); Institute of Physics, Faculty of Science, UPJS, Kosice (Slovakia); Ruiz, Alvaro; Cobos, Raul F.; Ribot, Ivan; Vega, Victor; Alvarez, Pablo; Sanchez, Maria Luisa; Sanchez Ll., Jose Luis; Prida, Victor M. de la; Hernando, Blanca [Departamento de Fisica, Facultad de Ciencias, Universidad de Oviedo (Spain)

    2009-04-15

    The influence of glass covering on domain wall propagation in Fe{sub 65}B{sub 15}Si{sub 15}C{sub 5} amorphous microwires is studied, before and after glass removal. High values of domain wall velocity and mobility have been obtained. The domain wall velocity depends linearly on the driving magnetic field. However, the mobility of the domain wall is very different in both situations studied. The results are explained due to the modification of internal stress distribution after glass removing, that change the domain structure of the sample. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  20. Lectin receptor kinases participate in protein-protein interactions to mediate plasma membrane-cell wall adhesions in Arabidopsis

    NARCIS (Netherlands)

    Gouget, A.; Senchou, V.; Govers, F.; Sanson, A.; Barre, A.; Rougé, P.; Pont-Lezica, R.; Canut, H.

    2006-01-01

    Interactions between plant cell walls and plasma membranes are essential for cells to function properly, but the molecules that mediate the structural continuity between wall and membrane are unknown. Some of these interactions, which are visualized upon tissue plasmolysis in Arabidopsis

  1. Protein dynamics and the diversity of an antibody response.

    Science.gov (United States)

    Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Zimmermann, Jörg; Romesberg, Floyd E

    2012-08-03

    The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.

  2. Protein Dynamics and the Diversity of an Antibody Response*

    Science.gov (United States)

    Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Zimmermann, Jörg; Romesberg, Floyd E.

    2012-01-01

    The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved. PMID:22685303

  3. Multiscale molecular dynamics simulations of rotary motor proteins.

    Science.gov (United States)

    Ekimoto, Toru; Ikeguchi, Mitsunori

    2017-12-04

    Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

  4. Tandem fluorescent protein timers for in vivo analysis of protein dynamics.

    Science.gov (United States)

    Khmelinskii, Anton; Keller, Philipp J; Bartosik, Anna; Meurer, Matthias; Barry, Joseph D; Mardin, Balca R; Kaufmann, Andreas; Trautmann, Susanne; Wachsmuth, Malte; Pereira, Gislene; Huber, Wolfgang; Schiebel, Elmar; Knop, Michael

    2012-06-24

    The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here we describe tandem fluorescent protein timers (tFTs), fusions of two single-color fluorescent proteins that mature with different kinetics, which we use to analyze protein turnover and mobility in living cells. We fuse tFTs to proteins in yeast to study the longevity, segregation and inheritance of cellular components and the mobility of proteins between subcellular compartments; to measure protein degradation kinetics without the need for time-course measurements; and to conduct high-throughput screens for regulators of protein turnover. Our experiments reveal the stable nature and asymmetric inheritance of nuclear pore complexes and identify regulators of N-end rule–mediated protein degradation.

  5. Communication: Protein dynamical transition vs. liquid-liquid phase transition in protein hydration water

    Science.gov (United States)

    Schirò, Giorgio; Fomina, Margarita; Cupane, Antonio

    2013-09-01

    In this work, we compare experimental data on myoglobin hydrated powders from elastic neutron scattering, broadband dielectric spectroscopy, and differential scanning calorimetry. Our aim is to obtain new insights on the connection between the protein dynamical transition, a fundamental phenomenon observed in proteins whose physical origin is highly debated, and the liquid-liquid phase transition (LLPT) possibly occurring in protein hydration water and related to the existence of a low temperature critical point in supercooled water. Our results provide a consistent thermodynamic/dynamic description which gives experimental support to the LLPT hypothesis and further reveals how fundamental properties of water and proteins are tightly related.

  6. Pea border cell maturation and release involve complex cell wall structural dynamics

    DEFF Research Database (Denmark)

    Mravec, Jozef; Guo, Xiaoyuan; Hansen, Aleksander Riise

    2017-01-01

    of hydrolytic activities, transmission electron microscopy (TEM) and immunolocalization of cell wall components. Using this integrated glycobiology approach, we identified multiple novel modes of cell wall structural and compositional rearrangement during root cap growth and the release of border cells. Our...

  7. Order parameter prediction from molecular dynamics simulations in proteins

    CERN Document Server

    Perilla, Juan R

    2011-01-01

    A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that ma...

  8. Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

    Science.gov (United States)

    Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

    2013-01-01

    We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

  9. Cyst-Wall-Protein-1 is fundamental for Golgi-like organelle neogenesis and cyst-wall biosynthesis in Giardia lamblia.

    Science.gov (United States)

    Ebneter, Jacqueline A; Heusser, Sally D; Schraner, Elisabeth M; Hehl, Adrian B; Faso, Carmen

    2016-12-15

    The genome of the protozoan parasite Giardia lamblia is organized in two diploid nuclei, which has so far precluded complete analysis of gene function. Here we use a previously developed Cre/loxP-based knock-out and selection marker salvage strategy in the human-derived isolate WB-C6 to eliminate all four copies of the Cyst-Wall-Protein-1 locus (CWP1). Because these loci are silenced in proliferating trophozoites and highly expressed only in encysting cells, CWP1 ablation allows functional characterization of a conditional phenotype in parasites induced to encyst. We show that encysting Δcwp1 cells are unable to establish the stage-regulated trafficking machinery with Golgi-like encystation-specific vesicles required for cyst-wall formation but show morphological hallmarks of cyst development and karyokinesis. This 'pseudocyst' phenotype is rescued by transfection of Δcwp1 cells with an episomally maintained CWP1 expression vector. Genome editing in genera Giardia and Trypanosoma are the only reported examples addressing questions on pathogen transmission within the Excavata supergroup.

  10. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

    Energy Technology Data Exchange (ETDEWEB)

    Economou, Nicoleta J.; Zentner, Isaac J. [Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 (United States); Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian [Brookhaven National Laboratory, Upton, NY 11973 (United States); Weeks, Stephen D.; Grasty, Kimberly C.; Cocklin, Simon; Loll, Patrick J. [Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 (United States)

    2013-04-01

    Using a carrier-protein strategy, the structure of teicoplanin bound to its bacterial cell-wall target has been determined. The structure reveals the molecular determinants of target recognition, flexibility in the antibiotic backbone and intrinsic radiation sensitivity of teicoplanin. Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a d-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein–peptide–antibiotic complex. The 2.05 Å resolution MBP–peptide–teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.

  11. The Aspergillus giganteus antifungal protein AFPNN5353 activates the cell wall integrity pathway and perturbs calcium homeostasis

    Directory of Open Access Journals (Sweden)

    Eigentler Andrea

    2011-09-01

    Full Text Available Abstract Background The antifungal protein AFPNN5353 is a defensin-like protein of Aspergillus giganteus. It belongs to a group of secretory proteins with low molecular mass, cationic character and a high content of cysteine residues. The protein inhibits the germination and growth of filamentous ascomycetes, including important human and plant pathogens and the model organsims Aspergillus nidulans and Aspergillus niger. Results We determined an AFPNN5353 hypersensitive phenotype of non-functional A. nidulans mutants in the protein kinase C (Pkc/mitogen-activated protein kinase (Mpk signalling pathway and the induction of the α-glucan synthase A (agsA promoter in a transgenic A. niger strain which point at the activation of the cell wall integrity pathway (CWIP and the remodelling of the cell wall in response to AFPNN5353. The activation of the CWIP by AFPNN5353, however, operates independently from RhoA which is the central regulator of CWIP signal transduction in fungi. Furthermore, we provide evidence that calcium (Ca2+ signalling plays an important role in the mechanistic function of this antifungal protein. AFPNN5353 increased about 2-fold the cytosolic free Ca2+ ([Ca2+]c of a transgenic A. niger strain expressing codon optimized aequorin. Supplementation of the growth medium with CaCl2 counteracted AFPNN5353 toxicity, ameliorated the perturbation of the [Ca2+]c resting level and prevented protein uptake into Aspergillus sp. cells. Conclusions The present study contributes new insights into the molecular mechanisms of action of the A. giganteus antifungal protein AFPNN5353. We identified its antifungal activity, initiated the investigation of pathways that determine protein toxicity, namely the CWIP and the Ca2+ signalling cascade, and studied in detail the cellular uptake mechanism in sensitive target fungi. This knowledge contributes to define new potential targets for the development of novel antifungal strategies to prevent and combat

  12. Pilot-scale cultivation of wall-deficient transgenic Chlamydomonas reinhardtii strains expressing recombinant proteins in the chloroplast

    DEFF Research Database (Denmark)

    Zedler, Julie A.Z.; Gangl, Doris; Guerra, Tiago

    2016-01-01

    Microalgae have emerged as potentially powerful platforms for the production of recombinant proteins and high-value products. Chlamydomonas reinhardtii is a potentially important host species due to the range of genetic tools that have been developed for this unicellular green alga. Transformation...... growth data for C. reinhardtii grown at pilot scale, and the growth of cell wall-deficient strains has not been reported at all. Here, we report the first pilot-scale growth study for transgenic, cell wall-deficient C. reinhardtii strains. Strains expressing a cytochrome P450 (CYP79A1) or bifunctional...... diterpene synthase (cis-abienol synthase, TPS4) were grown for 7 days under mixotrophic conditions in a Tris-acetate-phosphate medium. The strains reached dry cell weights of 0.3 g/L within 3–4 days with stable expression levels of the recombinant proteins during the whole upscaling process. The strains...

  13. Radiation damage limits to XPCS studies of protein dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Vodnala, Preeti, E-mail: preeti.vodnala@gmail.com; Karunaratne, Nuwan; Lurio, Laurence [Department of Physics, Northern Illinois University, DeKalb IL, 60115 (United States); Bera, Sambhunath [Amity Center for Spintronic Materials, Amity University UP, Sector 125, NOIDA 201313 (India); Thurston, George M. [School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623-5603 (United States); Karonis, Nick [Department of Computer Science, Northern Illinois University, DeKalb, IL 60115 (United States); Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL 60495 (United States); Winans, John [Department of Computer Science, Northern Illinois University, DeKalb, IL 60115 (United States); Sandy, Alec; Narayanan, Suresh [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60495 (United States); Yasui, Linda [Department of Biology, Northern Illinois University, DeKalb, IL 60115 (United States); Gaillard, Elizabeth; Karumanchi, Kalyan [Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb IL, 60115 (United States)

    2016-07-27

    The limitations to x-ray photon correlation spectroscopy (XPCS) imposed by radiation damage have been evaluated for suspensions of alpha crystallin. We find that the threshold for radiation damage to the measured protein diffusion rate is significantly lower than the threshold for damage to the protein structure. We provide damage thresholds beyond which the measured diffusion coeffcients have been modified using both XPCS and dynamic light scattering (DLS).

  14. Plasma levels of the arterial wall protein fibulin-1 are associated with carotid-femoral pulse wave velocity

    DEFF Research Database (Denmark)

    Laugesen, Esben; Høyem, Pernille; Christiansen, Jens Sandahl

    2013-01-01

    -associated extracellular matrix protein, fibulin-1, was recently found in higher concentrations in the arterial wall and in plasma in patients with long duration type 2 diabetes. Furthermore, plasma fibulin-1 independently predicted total mortality and was associated with pulse pressure, an indirect measure of arterial...... stiffness. Whether plasma fibulin-1 is associated with arterial stiffness at earlier phases of type 2 diabetes has not been determined....

  15. Molecular determinants of the interaction between human high molecular weight kininogen and Candida albicans cell wall: Identification of kininogen-binding proteins on fungal cell wall and mapping the cell wall-binding regions on kininogen molecule.

    Science.gov (United States)

    Karkowska-Kuleta, Justyna; Kedracka-Krok, Sylwia; Rapala-Kozik, Maria; Kamysz, Wojciech; Bielinska, Sylwia; Karafova, Anna; Kozik, Andrzej

    2011-12-01

    An excessive production of vasoactive and proinflammatory bradykinin-related peptides, the kinins, is often involved in the human host defense against microbial infections. Recent studies have shown that a major fungal pathogen to humans, Candida albicans, can bind the proteinaceous kinin precursor, the high molecular weight kininogen (HK) and trigger the kinin-forming cascade on the cell surface. In this work, we preliminarily characterized a molecular mechanism underlying the HK adhesion to the fungal surface by (i) identification of major kininogen-binding constituents on the candidial cell wall and (ii) mapping the cell wall-binding regions on HK molecule. A major fraction of total fungal kininogen-binding capacity was assigned to β-1,3-glucanase-extractable cell wall proteins (CWP). By adsorption of CWP on HK-coupled agarose gel and mass spectrometric analysis of the eluted material, major putative HK receptors were identified, including Als3 adhesin and three glycolytic enzymes, i.e., enolase 1, phosphoglycerate mutase 1 and triosephosphate isomerase 1. Using monoclonal antibodies directed against selected parts of HK molecule and synthetic peptides with sequences matching selected HK fragments, we assigned the major fungal cell wall-binding ability to a short stretch of amino acids in the C-terminal part of domain 3 and a large continuous region involving the C-terminal part of domain 5 and N-terminal part of domain 6 (residues 479-564). The latter characteristics of HK binding to C. albicans surface differ from those reported for bacteria and host cells. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. Comparative Analysis of the Proteins with Tandem Repeats from 8 Microsporidia and Characterization of a Novel Endospore Wall Protein Colocalizing with Polar Tube from Nosema bombycis.

    Science.gov (United States)

    Wang, Ying; Geng, Huixia; Dang, Xiaoqun; Xiang, Heng; Li, Tian; Pan, Guoqing; Zhou, Zeyang

    2017-09-01

    As a common feature of eukaryotic proteins, tandem amino acid repeat has been studied extensively in both animal and plant proteins. Here, a comparative analysis focusing on the proteins having tandem repeats was conducted in eight microsporidia, including four mammal-infecting microsporidia (Encephalitozoon cuniculi, Encephalitozoon intestinalis, Encephalitozoon hellem and Encephalitozoon bieneusi) and four insect-infecting microsporidia (Nosema apis, Nosema ceranae, Vavraia culicis and Nosema bombycis). We found that the proteins with tandem repeats were abundant in these species. The quantity of these proteins in insect-infecting microsporidia was larger than that of mammal-infecting microsporidia. Additionally, the hydrophilic residues were overrepresented in the tandem repeats of these eight microsporidian proteins and the amino acids residues in these tandem repeat sequences tend to be encoded by GC-rich codons. The tandem repeat position within proteins of insect-infecting microsporidia was randomly distributed, whereas the tandem repeats within proteins of mammal-infecting microsporidia rarely tend to be present in the N terminal regions, when compared with those present in the C terminal and middle regions. Finally, a hypothetical protein EOB14572 possessing four tandem repeats was successfully characterized as a novel endospore wall protein, which colocalized with polar tube of N. bombycis. Our study provided useful insight for the study of the proteins with tandem repeats in N. bombycis, but also further enriched the spore wall components of this obligate unicellular eukaryotic parasite. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

  17. Detailed Dynamic Heat Transfer in Thick Brick Walls Typical of Lille Metropolis

    Directory of Open Access Journals (Sweden)

    Antczak E.

    2012-10-01

    Full Text Available The study of thermal transfer in old houses massive walls offers a big interest permitting the understanding of their specificities and the choice of a suitable material for their eventual insulation. We propose to study the thermal transfer in massive brick walls that characterize the Northern Europe old houses. To do so, we will begin by defining the thermal transfer mode: we proved that the transfer mode can be reduced to a unidirectional transfer. Then, an experimental wall is built and submitted to two different solicitation types (constant temperature in steady state mode and sinusoidal temperature through a wooden insulated box containing a radiator. The interest of these solicitations is to determine the thermal properties of the wall: the steady-state regime permits to determine the thermal resistances of the system when the harmonic regime permits to determine the thermal capacities of the system.

  18. Dynamics of cell wall elasticity pattern shapes the cell during yeast mating morphogenesis.

    Science.gov (United States)

    Goldenbogen, Björn; Giese, Wolfgang; Hemmen, Marie; Uhlendorf, Jannis; Herrmann, Andreas; Klipp, Edda

    2016-09-01

    The cell wall defines cell shape and maintains integrity of fungi and plants. When exposed to mating pheromone, Saccharomyces cerevisiae grows a mating projection and alters in morphology from spherical to shmoo form. Although structural and compositional alterations of the cell wall accompany shape transitions, their impact on cell wall elasticity is unknown. In a combined theoretical and experimental approach using finite-element modelling and atomic force microscopy (AFM), we investigated the influence of spatially and temporally varying material properties on mating morphogenesis. Time-resolved elasticity maps of shmooing yeast acquired with AFM in vivo revealed distinct patterns, with soft material at the emerging mating projection and stiff material at the tip. The observed cell wall softening in the protrusion region is necessary for the formation of the characteristic shmoo shape, and results in wider and longer mating projections. The approach is generally applicable to tip-growing fungi and plants cells. © 2016 The Authors.

  19. Electric-field-driven domain wall dynamics in perpendicularly magnetized multilayers

    OpenAIRE

    González, Diego López; Shirahata, Yasuhiro; Van de Wiele, Ben; Franke, Kévin J. A.; Casiraghi, Arianna; Taniyama, Tomoyasu; van Dijken, Sebastiaan

    2017-01-01

    We report on reversible electric-field-driven magnetic domain wall motion in a Cu/Ni multilayer on a ferroelectric BaTiO3 substrate. In our heterostructure, strain-coupling to ferroelastic domains with in-plane and perpendicular polarization in the BaTiO3 substrate causes the formation of domains with perpendicular and in-plane magnetic anisotropy, respectively, in the Cu/Ni multilayer. Walls that separate magnetic domains are...

  20. Explosion induced dynamic responses of blast wall on FPSO topside: Blast loading application methods

    OpenAIRE

    Kang, Ki-Yeob; Choi, Kwang-Ho; Choi, Jae Woong; Ryu, Yong Hee; Lee, Jae-Myung

    2017-01-01

    Topside areas on an offshore oil and gas platform are highly susceptible to explosion. A blast wall on these areas plays an important role in preventing explosion damage and must withstand the expected explosion loads. The uniformly distributed loading condition, predicted by Explosion Risk Analyses (ERAs), has been applied in most of the previous analysis methods. However, analysis methods related to load conditions are inaccurate because the blast overpressure around the wall tends to be of...

  1. Efficient mapping of ligand migration channel networks in dynamic proteins.

    Science.gov (United States)

    Lin, Tu-Liang; Song, Guang

    2011-08-01

    For many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. Ligand migration in a dynamic protein resembles closely a well-studied problem in robotics, namely, the navigation of a mobile robot in a dynamic environment. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their inter-connectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory-based approaches, are in agreement with previous simulation results. Additionally, the method clearly illustrates how and what conformational changes open or close a channel. Copyright © 2011 Wiley-Liss, Inc.

  2. Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays

    Science.gov (United States)

    Landry, Markita Patricia; Ando, Hiroki; Chen, Allen Y.; Cao, Jicong; Kottadiel, Vishal Isaac; Chio, Linda; Yang, Darwin; Dong, Juyao; Lu, Timothy K.; Strano, Michael S.

    2017-05-01

    A distinct advantage of nanosensor arrays is their ability to achieve ultralow detection limits in solution by proximity placement to an analyte. Here, we demonstrate label-free detection of individual proteins from Escherichia coli (bacteria) and Pichia pastoris (yeast) immobilized in a microfluidic chamber, measuring protein efflux from single organisms in real time. The array is fabricated using non-covalent conjugation of an aptamer-anchor polynucleotide sequence to near-infrared emissive single-walled carbon nanotubes, using a variable chemical spacer shown to optimize sensor response. Unlabelled RAP1 GTPase and HIV integrase proteins were selectively detected from various cell lines, via large near-infrared fluorescent turn-on responses. We show that the process of E. coli induction, protein synthesis and protein export is highly stochastic, yielding variability in protein secretion, with E. coli cells undergoing division under starved conditions producing 66% fewer secreted protein products than their non-dividing counterparts. We further demonstrate the detection of a unique protein product resulting from T7 bacteriophage infection of E. coli, illustrating that nanosensor arrays can enable real-time, single-cell analysis of a broad range of protein products from various cell types.

  3. Hydration dynamics of protein molecules in aqueous solution: Unity ...

    Indian Academy of Sciences (India)

    Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account ...

  4. The dynamics of fat, protein and sugar metabolism during walnut ...

    African Journals Online (AJOL)

    Walnut (Juglans regia L.) is named the “super food” in the 21st century. In this study, the 9-year-old precocious walnut cultivar 'Xiangling' were used to exam the developmental process, and the dynamics of fat, protein and sugar content in the fruit, and the activities of enzymes related with sugar metabolism were further ...

  5. Protein dynamics derived from clusters of crystal structures

    NARCIS (Netherlands)

    van Aalten, D.M.F.; Conn, D.A.; de Groot, B.L.; Berendsen, H.J.C.; Findlay, J.B.C.; Amadei, A

    1997-01-01

    A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The ''essential dynamics'' procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes

  6. Simulation of evacuation processes in a square with a partition wall using a cellular automaton model for pedestrian dynamics

    Science.gov (United States)

    Zheng, Xiaoping; Li, Wei; Guan, Chao

    2010-06-01

    The level of service in public walking spaces is mainly determined by the differences in pedestrian traffic demand and infrastructure supply. A problem worth studying is the evacuation process in a closed square with partition wall. In this paper, a cellular automaton model is presented to simulate the evacuation process in the square. This model defines a floor field and considers the selection of an exit and effect of social forces. Some simulation results show the model’s correct description of the pedestrian dynamics. Both the total evacuation time and the degree of pedestrians jamming in a certain area are regarded as the indicators of the evacuation progress and the measure of evacuation efficiency. Concerning the two indicators, some viewpoints on the evacuation design of the partition wall are put forward: (1) changing the length of the partition wall could reduce the evacuation time, however, it could also bring the serious pedestrians jamming in a certain area, which may cause potential injury; (2) with the prior consideration for evacuation time, the length of the partition wall should be better chosen to make the pedestrians jamming less severe.

  7. Universal domain wall dynamics under electric field in Ta/CoFeB/MgO devices with perpendicular anisotropy.

    Science.gov (United States)

    Lin, Weiwei; Vernier, Nicolas; Agnus, Guillaume; Garcia, Karin; Ocker, Berthold; Zhao, Weisheng; Fullerton, Eric E; Ravelosona, Dafiné

    2016-11-16

    Electric field effects in ferromagnetic metal/dielectric structures provide a new route to control domain wall dynamics with low-power dissipation. However, electric field effects on domain wall velocities have only been observed so far in the creep regime where domain wall velocities are low due to strong interactions with pinning sites. Here we show gate voltage modulation of domain wall velocities ranging from the creep to the flow regime in Ta/Co 40 Fe 40 B 20 /MgO/TiO 2 structures with perpendicular magnetic anisotropy. We demonstrate a universal description of the role of applied electric fields in the various pinning-dependent regimes by taking into account an effective magnetic field being linear with the electric field. In addition, the electric field effect is found to change sign in the Walker regime. Our results are consistent with voltage-induced modification of magnetic anisotropy. Our work opens new opportunities for the study and optimization of electric field effect at ferromagnetic metal/insulator interfaces.

  8. Universal domain wall dynamics under electric field in Ta/CoFeB/MgO devices with perpendicular anisotropy

    Science.gov (United States)

    Lin, Weiwei; Vernier, Nicolas; Agnus, Guillaume; Garcia, Karin; Ocker, Berthold; Zhao, Weisheng; Fullerton, Eric E.; Ravelosona, Dafiné

    2016-01-01

    Electric field effects in ferromagnetic metal/dielectric structures provide a new route to control domain wall dynamics with low-power dissipation. However, electric field effects on domain wall velocities have only been observed so far in the creep regime where domain wall velocities are low due to strong interactions with pinning sites. Here we show gate voltage modulation of domain wall velocities ranging from the creep to the flow regime in Ta/Co40Fe40B20/MgO/TiO2 structures with perpendicular magnetic anisotropy. We demonstrate a universal description of the role of applied electric fields in the various pinning-dependent regimes by taking into account an effective magnetic field being linear with the electric field. In addition, the electric field effect is found to change sign in the Walker regime. Our results are consistent with voltage-induced modification of magnetic anisotropy. Our work opens new opportunities for the study and optimization of electric field effect at ferromagnetic metal/insulator interfaces. PMID:27848936

  9. Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

    Science.gov (United States)

    Rydzewski, J; Nowak, W

    2017-12-01

    Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Molecular dynamics study of naturally existing cavity couplings in proteins.

    Science.gov (United States)

    Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

    2015-01-01

    Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

  11. SRPP, a Cell Wall Protein is Involved in Development and Protection of Seeds and Root Hairs in Arabidopsis thaliana.

    Science.gov (United States)

    Tanaka, Natsuki; Uno, Hiroshi; Okuda, Shohei; Gunji, Shizuka; Ferjani, Ali; Aoyama, Takashi; Maeshima, Masayoshi

    2017-04-01

    Enhancement of root hair development in response to phosphate (Pi) deficit has been reported extensively. Root hairs are involved in major root functions such as the absorption of water, acquisition of nutrients and secretion of organic acids and enzymes. Individual root hair cells maintain these functions and appropriate structure under various physiological conditions. We carried out a study to identify protein(s) which maintain the structure and function of root hairs, and identified a protein (SEED AND ROOT HAIR PROTECTIVE PROTEIN, SRPP) that was induced in root hairs under Pi-deficient conditions. Promoter assay and mRNA quantification revealed that SRPP was expressed in root hairs and seeds. A knockout mutant, srpp-1, consistently displayed defects in root hairs and seeds. Root hairs in srpp-1 were short and the phenotypes observed under Pi-deficient conditions were also detected in ethylene-treated srpp-1 plants. Propidium iodide stained most root hairs of srpp-1 grown under Pi-deficient conditions, suggesting cell death. In addition to root hairs, most srpp-1 seeds were withered and their embryos were dead. SRPP tagged with green fluorescent protein was detected in the cell wall. Electron microscopy showed abnormal morphology of the cell wall. Wild-type phenotypes were restored when the SRPP gene was expressed in srpp-1. These data strongly suggest that SRPP contributes to the construction of robust cell walls, whereby it plays a key role in the development of root hairs and seeds. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. Dynamical scaling, domain-growth kinetics, and domain-wall shapes of quenched two-dimensional anisotropic XY models

    DEFF Research Database (Denmark)

    Mouritsen, Ole G.; Praestgaard, Eigil

    1988-01-01

    obeys dynamical scaling and the shape of the dynamical scaling function pertaining to the structure factor is found to depend on P. Specifically, this function is described by a Porod-law behavior, q-ω, where ω increases with the wall softness. The kinetic exponent, which describes how the linear domain...... infinite to zero temperature as well as to nonzero temperatures below the ordering transition. The continuous nature of the spin variables causes the domain walls to be ‘‘soft’’ and characterized by a finite thickness. The steady-state thickness of the walls can be varied by a model parameter, P. At zero...... size varies with time, R(t)∼tn, is for both models at zero temperature determined to be n≃0.25, independent of P. At finite temperatures, the growth kinetics is found to cross over to the Lifshitz-Allen-Cahn law characterized by n≃0.50. The results support the idea of two separate zero...

  13. On the indirect relationship between protein dynamics and enzyme activity.

    Science.gov (United States)

    Zhao, Qinyi

    2017-05-01

    The behaviors of simple thermal systems have been well studied in physical chemistry and the principles obtained from such studies have been applied to complex thermal systems, such as proteins and enzymes. But the simple application of such principles is questionable and may lead to mistakes under some circumstances. In enzymology, the transition state theory of chemical reactions has been accepted as a fundamental theory, but the role of protein dynamics in enzyme catalysis is controversial in the context of transition state theory. By studying behaviors of complex thermal systems, we have revised the Arrhenius equation and transition state theory and our model is validated in enzymology. Formally speaking, the revised Arrhenius equation is apparently similar to a conventional Arrhenius equation, but the physical meanings of its parameters differ from that of traditional forms in principle. Within this model, the role of protein dynamics in enzyme catalysis is well defined and quantified. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Unveiling protein functions through the dynamics of the interaction network.

    Directory of Open Access Journals (Sweden)

    Irene Sendiña-Nadal

    Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

  15. Neutron scattering studies on protein dynamics using the human myelin peripheral membrane protein P2

    Science.gov (United States)

    Laulumaa, Saara; Kursula, Petri; Natali, Francesca

    2015-01-01

    Myelin is a multilayered proteolipid membrane structure surrounding selected axons in the vertebrate nervous system, which allows the rapid saltatory conduction of nerve impulses. Deficits in myelin formation and maintenance may lead to chronic neurological disease. P2 is an abundant myelin protein from peripheral nerves, binding between two apposing lipid bilayers. We studied the dynamics of the human myelin protein P2 and its mutated P38G variant in hydrated powders using elastic incoherent neutron scattering. The local harmonic vibrations at low temperatures were very similar for both samples, but the mutant protein had increased flexibility and softness close to physiological temperatures. The results indicate that a drastic mutation of proline to glycine at a functional site can affect protein dynamics, and in the case of P2, they may explain functional differences between the two proteins.

  16. Neutron scattering studies on protein dynamics using the human myelin peripheral membrane protein P2

    Directory of Open Access Journals (Sweden)

    Laulumaa Saara

    2015-01-01

    Full Text Available Myelin is a multilayered proteolipid membrane structure surrounding selected axons in the vertebrate nervous system, which allows the rapid saltatory conduction of nerve impulses. Deficits in myelin formation and maintenance may lead to chronic neurological disease. P2 is an abundant myelin protein from peripheral nerves, binding between two apposing lipid bilayers. We studied the dynamics of the human myelin protein P2 and its mutated P38G variant in hydrated powders using elastic incoherent neutron scattering. The local harmonic vibrations at low temperatures were very similar for both samples, but the mutant protein had increased flexibility and softness close to physiological temperatures. The results indicate that a drastic mutation of proline to glycine at a functional site can affect protein dynamics, and in the case of P2, they may explain functional differences between the two proteins.

  17. Coupled dynamics of vortex-induced vibration and stationary wall at low Reynolds number

    Science.gov (United States)

    Li, Zhong; Jaiman, Rajeev K.; Khoo, Boo Cheong

    2017-09-01

    The flow past an elastically mounted circular cylinder placed in proximity to a plane wall is numerically studied in both two dimensions (2D) and three dimensions (3D). This paper aims to explain the mechanism of the cylinder bottom shear layer roll-up suppression in the context of laminar vortex-induced vibration (VIV) of a cylinder placed in the vicinity of a plane stationary wall. In 2D simulations, VIV of a near-wall cylinder with structure-to-displaced fluid mass ratios of m* = 2 and 10 is investigated at the Reynolds number of Re = 100 at a representative gap ratio of e/D = 0.90, where e denotes the gap distance between the cylinder surface and the plane wall. First, the cylinder is placed at five different upstream distances, LU, to study the effects of the normalized wall boundary layer thickness, δ /D , on the hydrodynamic quantities involved in the VIV of a near-wall cylinder. It is found that the lock-in range shifts towards the direction of the higher reduced velocity Ur as δ /D increases and that the lock-in range widens as m* reduces. Second, via visualization of the vortex shedding patterns, four different modes are classified and the regime maps are provided for both m* = 2 and 10. Third, the proper orthogonal decomposition analysis is employed to assess the cylinder bottom shear layer roll-up suppression mechanism. For 3D simulations at Re = 200, the circular cylinder of a mass ratio of m* = 10 with a spanwise length of 4D is placed at a gap ratio of e/D = 0.90 and an upstream distance of LU = 10D. The 3D vortex patterns are investigated to re-affirm the vortex shedding suppression mechanism. The pressure distributions around the cylinder are identified within one oscillation cycle of VIV. The pressure and the shear stress distributions on the bottom wall are examined to demonstrate the effects of near-wall VIV on the force distributions along the plane wall. It is found that both the suction pressure and the shear stress right below the cylinder

  18. Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.

    Directory of Open Access Journals (Sweden)

    Thomas Wallach

    2013-03-01

    Full Text Available Essentially all biological processes depend on protein-protein interactions (PPIs. Timing of such interactions is crucial for regulatory function. Although circadian (~24-hour clocks constitute fundamental cellular timing mechanisms regulating important physiological processes, PPI dynamics on this timescale are largely unknown. Here, we identified 109 novel PPIs among circadian clock proteins via a yeast-two-hybrid approach. Among them, the interaction of protein phosphatase 1 and CLOCK/BMAL1 was found to result in BMAL1 destabilization. We constructed a dynamic circadian PPI network predicting the PPI timing using circadian expression data. Systematic circadian phenotyping (RNAi and overexpression suggests a crucial role for components involved in dynamic interactions. Systems analysis of a global dynamic network in liver revealed that interacting proteins are expressed at similar times likely to restrict regulatory interactions to specific phases. Moreover, we predict that circadian PPIs dynamically connect many important cellular processes (signal transduction, cell cycle, etc. contributing to temporal organization of cellular physiology in an unprecedented manner.

  19. Protein Methionine Sulfoxide Dynamics in Arabidopsis thaliana under Oxidative Stress

    Science.gov (United States)

    Jacques, Silke; Ghesquière, Bart; De Bock, Pieter-Jan; Demol, Hans; Wahni, Khadija; Willems, Patrick; Messens, Joris; Van Breusegem, Frank; Gevaert, Kris

    2015-01-01

    Reactive oxygen species such as hydrogen peroxide can modify proteins via direct oxidation of their sulfur-containing amino acids, cysteine and methionine. Methionine oxidation, studied here, is a reversible posttranslational modification that is emerging as a mechanism by which proteins perceive oxidative stress and function in redox signaling. Identification of proteins with oxidized methionines is the first prerequisite toward understanding the functional effect of methionine oxidation on proteins and the biological processes in which they are involved. Here, we describe a proteome-wide study of in vivo protein-bound methionine oxidation in plants upon oxidative stress using Arabidopsis thaliana catalase 2 knock-out plants as a model system. We identified over 500 sites of oxidation in about 400 proteins and quantified the differences in oxidation between wild-type and catalase 2 knock-out plants. We show that the activity of two plant-specific glutathione S-transferases, GSTF9 and GSTT23, is significantly reduced upon oxidation. And, by sampling over time, we mapped the dynamics of methionine oxidation and gained new insights into this complex and dynamic landscape of a part of the plant proteome that is sculpted by oxidative stress. PMID:25693801

  20. Single-molecule imaging studies of protein dynamics

    Science.gov (United States)

    Zareh, Shannon Kian G.

    2011-12-01

    Single-molecule fluorescence imaging is a powerful method for studying biological events. The work of this thesis primarily focuses on single molecule studies of the dynamics of Green Fluorescent Protein (GFP) and other fluorescent-labeled proteins by utilizing Total Internal Reflection Fluorescence (TIRF) microscopy and imaging. The single molecule experiments of this thesis covered three broad topics. First, the adsorption mechanisms of proteins onto hydrophobic and hydrophilic fused silica surfaces were imaged and reversible and irreversible adsorption mechanisms were observed. The second topic covered a new technique for measuring the diffusion coefficient of Brownian diffusing proteins, in particular GFP, in solution via a single image. The corresponding experiments showed a relationship between the intensity profile width and the diffusion coefficient of the diffusing molecules. The third topic covered an in vivo experiment involving imaging and quantifying prokaryotic cell metabolism protein dynamics inside the Bacillus subtilis bacteria, in which a helical diffusion pattern for the protein was observed. These topics are presented in the chronological order of the experiments conducted.

  1. Dynamic behavior of radiant cooling system based on capillary tubes in walls made of high performance concrete

    DEFF Research Database (Denmark)

    Mikeska, Tomás; Svendsen, Svend

    2015-01-01

    using cooling water for the radiant cooling system with a temperature only about 4K lower than the temperature of the room air. The relatively high speed reaction of the designed system is a result of the slim construction of the sandwich wall elements made of high performance concrete. (C) 2015...... the small amount of fresh air required by standards to provide a healthy indoor environment.This paper reports on experimental analyses evaluating the dynamic behavior of a test room equipped with a radiant cooling system composed of plastic capillary tubes integrated into the inner layer of sandwich wall...... elements made of high performance concrete. The influence of the radiant cooling system on the indoor climate of the test room in terms of the air, surface and operative temperatures and velocities was investigated.The results show that the temperature of the room air can be kept in a comfortable range...

  2. Contact forces between a particle and a wet wall at both quasi-static and dynamic state

    Directory of Open Access Journals (Sweden)

    Zhang Huang

    2017-01-01

    Full Text Available The contact regime of particle-wall is investigated by the atomic force microscope (AFM and theoretical models. First, AFM is used to measure the cohesive force between a micron-sized grain and a glass plate at quasi-static state under various humidity. It is found out that the cohesive force starts to grow slowly and suddenly increase rapidly beyond a critical Relative Humidity (RH. Second, mathematical models of contacting forces are presented to depict the dynamic process that a particle impacts on a wet wall. Then the energy loss of a falling grain is calculated in comparison with the models and the experimental data from the previous references. The simulation results show that the force models presented here are adaptive for both low and high viscosity fluid films with different thickness.

  3. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach.

    Science.gov (United States)

    Economou, Nicoleta J; Zentner, Isaac J; Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian; Weeks, Stephen D; Grasty, Kimberly C; Cocklin, Simon; Loll, Patrick J

    2013-04-01

    Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a D-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein-peptide-antibiotic complex. The 2.05 Å resolution MBP-peptide-teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.

  4. Nanosecond domain wall dynamics in ferroelectric Pb(Zr, Ti)O(3) thin films.

    Science.gov (United States)

    Grigoriev, Alexei; Do, Dal-Hyun; Kim, Dong Min; Eom, Chang-Beom; Adams, Bernhard; Dufresne, Eric M; Evans, Paul G

    2006-05-12

    Domain wall motion during polarization switching in ferroelectric thin films is fundamentally important and poses challenges for both experiments and modeling. We have visualized the switching of a Pb(Zr, Ti)O(3) capacitor using time-resolved x-ray microdiffraction. The structural signatures of switching include a reversal in the sign of the piezoelectric coefficient and a change in the intensity of x-ray reflections. The propagation of polarization domain walls is highly reproducible from cycle to cycle of the electric field. Domain wall velocities of 40 m s(-1) are consistent with the results of other methods, but are far less than saturation values expected at high electric fields.

  5. Re-analysis of protein data reveals the germination pathway and up accumulation mechanism of cell wall hydrolases during the radicle protrusion step of seed germination in Podophyllum hexandrum- a high altitude plant

    Directory of Open Access Journals (Sweden)

    Vivek eDogra

    2015-10-01

    Full Text Available Podophyllum hexandrum Royle is an important high-altitude plant of Himalayas with immense medicinal value. Earlier, it was reported that the cell wall hydrolases were up accumulated during radicle protrusion step of Podophyllum seed germination. In the present study, Podophyllum Germination protein interactome Network (PGN was constructed by using the differentially accumulated protein data set of Podophyllum during the radicle protrusion step of seed germination, with reference to Arabidopsis protein–protein interactome network (AtPIN. The developed PGN is comprised of a giant cluster with 1028 proteins having 10519 interactions and a few small clusters with relevant gene ontological signatures. In this analysis, a germination pathway related cluster which is also central to the topology and information dynamics of PGN was obtained with a set of 60 key proteins. Among these, 8 proteins which are known to be involved in signalling, metabolism, protein modification, cell wall modification and cell cycle regulation processes were found commonly highlighted in both the proteomic and interactome analysis. The systems-level analysis of PGN identified the key proteins involved in radicle protrusion step of seed germination in Podophyllum.

  6. C lostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII

    Science.gov (United States)

    Willing, Stephanie E.; Candela, Thomas; Shaw, Helen Alexandra; Seager, Zoe; Mesnage, Stéphane; Fagan, Robert P.

    2015-01-01

    Summary Gram‐positive surface proteins can be covalently or non‐covalently anchored to the cell wall and can impart important properties on the bacterium in respect of cell envelope organisation and interaction with the environment. We describe here a mechanism of protein anchoring involving tandem CWB2 motifs found in a large number of cell wall proteins in the Firmicutes. In the Clostridium difficile cell wall protein family, we show the three tandem repeats of the CWB2 motif are essential for correct anchoring to the cell wall. CWB2 repeats are non‐identical and cannot substitute for each other, as shown by the secretion into the culture supernatant of proteins containing variations in the patterns of repeats. A conserved Ile Leu Leu sequence within the CWB2 repeats is essential for correct anchoring, although a preceding proline residue is dispensable. We propose a likely genetic locus encoding synthesis of the anionic polymer PSII and, using RNA knock‐down of key genes, reveal subtle effects on cell wall composition. We show that the anionic polymer PSII binds two cell wall proteins, SlpA and Cwp2, and these interactions require the CWB2 repeats, defining a new mechanism of protein anchoring in Gram‐positive bacteria. PMID:25649385

  7. Disruption of Protein Mannosylation Affects Candida guilliermondii Cell Wall, Immune Sensing, and Virulence

    Directory of Open Access Journals (Sweden)

    María J. Navarro-Arias

    2016-12-01

    Full Text Available The fungal cell wall contains glycoproteins that interact with the host immune system. In the prominent pathogenic yeast Candida albicans, Pmr1 acts as a Golgi-resident ion pump that provides cofactors to mannosyltransferases, regulating the synthesis of mannans attached to glycoproteins. To gain insight into a putative conservation of such a crucial process within opportunistic yeasts, we were particularly interested in studying the role of the PMR1 homolog in a low-virulent species that rarely causes candidiasis, Candida guilliermondii. We disrupted C. guilliermondii PMR1 and found that loss of Pmr1 affected cell growth and morphology, biofilm formation, susceptibility to cell wall perturbing agents, mannan levels, and the wall composition and organization. Despite there was a significant increment in the amount of β1,3-glucan exposed at the wall surface, this positively influenced only the ability of the mutant to stimulate IL-10 production by human monocytes, suggesting that recognition of both mannan and β1,3-glucan, is required to stimulate strong levels of pro-inflammatory cytokines. Accordingly, our results indicate C. guilliermondii sensing by monocytes was critically dependent on the recognition of N-linked mannans and β1,3-glucan, as reported in other Candida species. In addition, chemical remotion of cell wall O-linked mannans was found to positively influence the recognition of C. guilliermondii by human monocytes, suggesting that O-linked mannans mask other cell wall components from immune cells. This observation contrasts with that reported in C. albicans. Finally, mice infected with C. guilliermondii pmr1 null mutant cells had significantly lower fungal burdens compared to animals challenged with the parental strain. Accordingly, the null mutant showed inability to kill larvae in the Galleria mellonella infection model. This study thus demonstrates that mannans are relevant for the C. guilliermondii-host interaction, with

  8. Dynamic Contact Angle Analysis of Protein Adsorption on Polysaccharide Multilayer’s Films for Biomaterial Reendothelialization

    Directory of Open Access Journals (Sweden)

    Safiya Benni

    2014-01-01

    Full Text Available Atherosclerosis is a major cardiovascular disease. One of the side effects is restenosis. The aim of this work was to study the coating of stents by dextran derivates based polyelectrolyte’s multilayer (PEM films in order to increase endothelialization of injured arterial wall after stent implantation. Films were composed with diethylaminoethyl dextran (DEAE as polycation and dextran sulphate (DS as polyanion. One film was composed with 4 bilayers of (DEAE-DS4 and was labeled D−. The other film was the same as D− but with an added terminal layer of DEAE polycation: (DEAE-DS4-DEAE (labeled D+. The dynamic adsorption/desorption of proteins on the films were characterized by dynamic contact angle (DCA and atomic force microscopy (AFM. Human endothelial cell (HUVEC adhesion and proliferation were quantified and correlated to protein adsorption analyzed by DCA for fibronectin, vitronectin, and bovine serum albumin (BSA. Our results showed that the endothelial cell response was optimal for films composed of DS as external layer. Fibronectin was found to be the only protein to exhibit a reversible change in conformation after desorption test. This behavior was only observed for (DEAE-DS4 films. (DEAE-DS4 films could enhance HUVEC proliferation in agreement with fibronectin ability to easily change from conformation.

  9. Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

    Science.gov (United States)

    Luk, Louis Y. P.; Javier Ruiz-Pernía, J.; Dawson, William M.; Roca, Maite; Loveridge, E. Joel; Glowacki, David R.; Harvey, Jeremy N.; Mulholland, Adrian J.; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K.

    2013-01-01

    Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (15N, 13C, 2H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate. PMID:24065822

  10. Complement proteins bind to nanoparticle protein corona and undergo dynamic exchange in vivo

    Science.gov (United States)

    Chen, Fangfang; Wang, Guankui; Griffin, James I.; Brenneman, Barbara; Banda, Nirmal K.; Holers, V. Michael; Backos, Donald S.; Wu, Linping; Moghimi, Seyed Moein; Simberg, Dmitri

    2017-05-01

    When nanoparticles are intravenously injected into the body, complement proteins deposit on the surface of nanoparticles in a process called opsonization. These proteins prime the particle for removal by immune cells and may contribute toward infusion-related adverse effects such as allergic responses. The ways complement proteins assemble on nanoparticles have remained unclear. Here, we show that dextran-coated superparamagnetic iron oxide core-shell nanoworms incubated in human serum and plasma are rapidly opsonized with the third complement component (C3) via the alternative pathway. Serum and plasma proteins bound to the nanoworms are mostly intercalated into the nanoworm shell. We show that C3 covalently binds to these absorbed proteins rather than the dextran shell and the protein-bound C3 undergoes dynamic exchange in vitro. Surface-bound proteins accelerate the assembly of the complement components of the alternative pathway on the nanoworm surface. When nanoworms pre-coated with human plasma were injected into mice, C3 and other adsorbed proteins undergo rapid loss. Our results provide important insight into dynamics of protein adsorption and complement opsonization of nanomedicines.

  11. Cell wall trapping of autocrine peptides for human G-protein-coupled receptors on the yeast cell surface.

    Directory of Open Access Journals (Sweden)

    Jun Ishii

    Full Text Available G-protein-coupled receptors (GPCRs regulate a wide variety of physiological processes and are important pharmaceutical targets for drug discovery. Here, we describe a unique concept based on yeast cell-surface display technology to selectively track eligible peptides with agonistic activity for human GPCRs (Cell Wall Trapping of Autocrine Peptides (CWTrAP strategy. In our strategy, individual recombinant yeast cells are able to report autocrine-positive activity for human GPCRs by expressing a candidate peptide fused to an anchoring motif. Following expression and activation, yeast cells trap autocrine peptides onto their cell walls. Because captured peptides are incapable of diffusion, they have no impact on surrounding yeast cells that express the target human GPCR and non-signaling peptides. Therefore, individual yeast cells can assemble the autonomous signaling complex and allow single-cell screening of a yeast population. Our strategy may be applied to identify eligible peptides with agonistic activity for target human GPCRs.

  12. Dynamics of chiral domain wall under the spin-orbit torques in heavy metal/ferromagnet bilayers with in-plane anisotropy

    Science.gov (United States)

    Yan, Han; He, Peng-Bin; Cai, Meng-Qiu; Li, Zai-Dong

    2017-11-01

    The dynamics of domain wall driven by the spin-orbit torques is theoretically studied in the heavy metal/ferromagnet bilayer with Dzyaloshinskii-Moriya interaction (DMI) and in-plane magnetic anisotropy. Based on the Walker profile, we infer that DMI has a selectivity for the chirality of head-to-head (tail-to-tail) static wall. By analyzing the dynamic equations obtained from the collective coordinates methods, we find that there exists a switching or a hysteresis of the polarity of wall in the low-current regime. In the presence of DMI, the wall can keep sustained propagation which velocity saturates for high current and is proportional to the strength of DMI. Furthermore, the DMI makes the adjacent walls possess the same chirality and move in the same direction.

  13. Protein turnover methods in single-celled organisms: dynamic SILAC.

    Science.gov (United States)

    Claydon, Amy J; Beynon, Robert J

    2011-01-01

    Early achievements in proteomics were qualitative, typified by the identification of very small quantities of proteins. However, as the subject has developed, there has been a pressure to develop approaches to define the amounts of each protein--whether in a relative or an absolute sense. A further dimension to quantitative proteomics embeds the behavior of each protein in terms of its turnover. Virtually every protein in the cell is in a dynamic state, subject to continuous synthesis and degradation, the relative rates of which control the expansion or the contraction of the protein pool, and the absolute values of which dictate the temporal responsiveness of the protein pool. Strategies must therefore be developed to assess the turnover of individual proteins in the proteome. Because a protein can be turning over rapidly even when the protein pool is in steady state, the only acceptable approach to measure turnover is to use metabolic labels that are incorporated or lost from the protein pool as it is replaced. Using metabolic labeling on a proteome-wide scale in turn requires metabolic labels that contain stable isotopes, the incorporation or loss of which can be assessed by mass spectrometry. A typical turnover experiment is complex. The choice of metabolic label is dictated by several factors, including abundance in the proteome, metabolic redistribution of the label in the precursor pool, and the downstream mass spectrometric analytical protocols. Key issues include the need to control and understand the relative isotope abundance of the precursor, the optimization of label flux into and out of the protein pool, and a sampling strategy that ensures the coverage of the greatest range of turnover rates. Finally, the informatics approaches to data analysis will not be as straightforward as in other areas of proteomics. In this chapter, we will discuss the principles and practice of workflow development for turnover analysis, exemplified by the development of

  14. Cell wall glycosidase activities and protein content variations during fruit development and ripening in three texture contrasted tomato cultivars

    Science.gov (United States)

    Konozy, Emadeldin H.E.; Causse, Mathilde; Faurobert, Mireille

    2012-01-01

    Excessive softening is the main factor limiting fruit shelf life and storage. It is generally acceptable now that softening of fruit which occurs during the ripening is due to synergistic actions of several enzymes on cell wall polysaccharides. As a subject for this study, we have assayed some glycosidase activities using three tomato species (Lycopersicon esculentum) contrasted for their texture phenotypes; the cherry tomato line Cervil (Solanum lycopersicum var. cerasiforme), a common taste tomato line Levovil (S. lycopersicum Mill.) and VilB a modern line, large, firmer and with good storage capability. Four glycosidase activities namely α-galactosidase, β-galactosidase, β-mannosidase and β-glucosidase were extracted from tomato’s cell wall of the three species. Cell wall protein from fruits pericarp was extracted and compared among the three cultivars at the following stages; 14 days post anthesis (14DPA) fruit; 21 days post anthesis (21DPA), turning (breaker), red and over ripe. When glycolytic activities were also compared among these cultivars at the precited development stages, gross variations were noticed from stage to stage and also from species to species in accordance with the fruit firmness status. Interestingly, VilB cultivar, the firmer among the other two, though possessed the highest total protein content, exhibited the lowest enzymatic activities. Taken together, these results may therefore allow us to conclude that studies of glycolytic activities in a single tomato cultivar cannot be generalized to all species. On the other hand, relating fruit development to glycosidase activities should logically be coupled to these enzymes from cell wall compartment. PMID:23961187

  15. Dynamic Glycosylation Governs the Vertebrate COPII Protein Trafficking Pathway.

    Science.gov (United States)

    Cox, Nathan J; Unlu, Gokhan; Bisnett, Brittany J; Meister, Thomas R; Condon, Brett M; Luo, Peter M; Smith, Timothy J; Hanna, Michael; Chhetri, Abhishek; Soderblom, Erik J; Audhya, Anjon; Knapik, Ela W; Boyce, Michael

    2018-01-09

    The COPII coat complex, which mediates secretory cargo trafficking from the endoplasmic reticulum, is a key control point for subcellular protein targeting. Because misdirected proteins cannot function, protein sorting by COPII is critical for establishing and maintaining normal cell and tissue homeostasis. Indeed, mutations in COPII genes cause a range of human pathologies, including cranio-lenticulo-sutural dysplasia (CLSD), which is characterized by collagen trafficking defects, craniofacial abnormalities, and skeletal dysmorphology. Detailed knowledge of the COPII pathway is required to understand its role in normal cell physiology and to devise new treatments for disorders in which it is disrupted. However, little is known about how vertebrates dynamically regulate COPII activity in response to developmental, metabolic, or pathological cues. Several COPII proteins are modified by O-linked β-N-acetylglucosamine (O-GlcNAc), a dynamic form of intracellular protein glycosylation, but the biochemical and functional effects of these modifications remain unclear. Here, we use a combination of chemical, biochemical, cellular, and genetic approaches to demonstrate that site-specific O-GlcNAcylation of COPII proteins mediates their protein-protein interactions and modulates cargo secretion. In particular, we show that individual O-GlcNAcylation sites of SEC23A, an essential COPII component, are required for its function in human cells and vertebrate development, because mutation of these sites impairs SEC23A-dependent in vivo collagen trafficking and skeletogenesis in a zebrafish model of CLSD. Our results indicate that O-GlcNAc is a conserved and critical regulatory modification in the vertebrate COPII-dependent trafficking pathway.

  16. A small cellulose binding domain protein in Phytophtora is cell wall localized

    Science.gov (United States)

    Cellulose binding domains (CBD) are structurally conserved regions linked to catalytic regions of cellulolytic enzymes. While widespread amongst saprophytic fungi that subsist on plant cell wall polysaccharides, they are not generally present in plant pathogenic fungi. A genome wide survey of CBDs w...

  17. Clinical Application of a Silk Fibroin Protein Biologic Scaffold for Abdominal Wall Fascial Reinforcement

    Directory of Open Access Journals (Sweden)

    Mark W. Clemens, MD

    2014-11-01

    Conclusions: Postoperative complication rates after 18 months were low, and most surgical complications were managed nonoperatively on an outpatient basis without mesh removal. To our knowledge, this is the only series to report on a long-lasting, transitory SBS for abdominal wall repair and reinforcement. Procedure-specific outcome studies are warranted to delineate optimal patient selection and define potential device characteristic advantages.

  18. Identification and differential gene expression of adhesin-like wall proteins in Candida glabrata biofilms

    NARCIS (Netherlands)

    Kraneveld, E.A.; de Soet, J.J.; Deng, D.M.; Dekker, H.L.; de Koster, C.G.; Klis, F.M.; Crielaard, W.; de Groot, P.W.J.

    2011-01-01

    An important initial step in biofilm development and subsequent establishment of fungal infections by the human pathogen Candida glabrata is adherence to a surface. Adherence is mediated through a large number of differentially regulated cell wall-bound adhesins. The fungus can modify the

  19. Nonadiabatic Spin Torque Investigated Using Thermally Activated Magnetic Domain Wall Dynamics

    DEFF Research Database (Denmark)

    Eltschka, M.; Woetzel, Mathias; Rhensius, J.

    2010-01-01

    Using transmission electron microscopy, we investigate the thermally activated motion of domain walls (DWs) between two positions in Permalloy (Ni80Fe20) nanowires at room temperature. We show that this purely thermal motion is well described by an Arrhenius law, allowing for a description...

  20. Analysis of domain wall dynamics based on skewness of magnetic Barkhausen noise for applied stress determination

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Song [College of Electrical Engineering and Control Science, Nanjing Tech University, Nanjing, Jiangsu 211816 (China); School of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu 210016 (China); Tian, GuiYun, E-mail: tian280@hotmail.com [School of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu 210016 (China); School of Electrical and Electronic Engineering, Merz Court, University of Newcastle upon Tyne, Newcastle NE1 7RU (United Kingdom); Dobmann, Gerd; Wang, Ping [School of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu 210016 (China)

    2017-01-01

    Skewness of Magnetic Barkhausen Noise (MBN) signal is used as a new feature for applied stress determination. After experimental studies, skewness presents its ability for measuring applied tensile stress compared with conventional feature, meanwhile, a non-linear behavior of this new feature and an independence of the excitation conditions under compressive stress are found and discussed. Effective damping during domain wall motion influencing the asymmetric shape of the MBN statistical distribution function is discussed under compressive and tensile stress variation. Domain wall (DW) energy and distance between pinning edges of the DW are considered altering the characteristic relaxation time, which is the reason for the non-linear phenomenon of skewness. - Highlights: • The skewness of magnetic Barkhausen noise profile is proposed as a new feature for applied stress determination. • The skewness is sensitive to applied stress and independent to excitation frequency. • Domain wall energy and pinning distance influence the relaxation time of domain wall, which leads to a non-linear behavior of skewness under compressive stress.

  1. Coupling between Current and Dynamic Magnetization : from Domain Walls to Spin Waves

    NARCIS (Netherlands)

    Lucassen, M.E.

    2012-01-01

    So far, we have derived some general expressions for domain-wall motion and the spin motive force. We have seen that the β parameter plays a large role in both subjects. In all chapters of this thesis, there is an emphasis on the determination of this parameter. We also know how to incorporate

  2. A multiscale SPH particle model of the near-wall dynamics of leukocytes in flow.

    Science.gov (United States)

    Gholami, Babak; Comerford, Andrew; Ellero, Marco

    2014-01-01

    A novel multiscale Lagrangian particle solver based on SPH is developed with the intended application of leukocyte transport in large arteries. In such arteries, the transport of leukocytes and red blood cells can be divided into two distinct regions: the bulk flow and the near-wall region. In the bulk flow, the transport can be modeled on a continuum basis as the transport of passive scalar concentrations. Whereas in the near-wall region, specific particle tracking of the leukocytes is required and lubrication forces need to be separately taken into account. Because of large separation of spatio-temporal scales involved in the problem, simulations of red blood cells and leukocytes are handled separately. In order to take the exchange of leukocytes between the bulk fluid and the near-wall region into account, solutions are communicated through coupling of conserved quantities at the interface between these regions. Because the particle tracking is limited to those leukocytes lying in the near-wall region only, our approach brings considerable speedup to the simulation of leukocyte circulation in a test geometry of a backward-facing step, which encompasses many flow features observed in vivo. Copyright © 2013 John Wiley & Sons, Ltd.

  3. Dynamics and control of a heat pump assisted extractive dividing-wall column for bioethanol dehydration

    NARCIS (Netherlands)

    Patraşcu, Iulian; Bildea, Costin Sorin; Kiss, Anton A.

    Recently, a novel heat-pump-assisted extractive distillation process taking place in a dividing-wall column was proposed for bioethanol dehydration. This integrated design combines three distillation columns into a single unit that allows over 40% energy savings and low specific energy requirements

  4. Arabinogalactan protein-rich cell walls, paramural deposits and ergastic globules define the hyaline bodies of rhinanthoid Orobanchaceae haustoria.

    Science.gov (United States)

    Pielach, Anna; Leroux, Olivier; Domozych, David S; Knox, J Paul; Popper, Zoë A

    2014-10-01

    Parasitic plants obtain nutrients from their hosts through organs called haustoria. The hyaline body is a specialized parenchymatous tissue occupying the central parts of haustoria in many Orobanchaceae species. The structure and functions of hyaline bodies are poorly understood despite their apparent necessity for the proper functioning of haustoria. Reported here is a cell wall-focused immunohistochemical study of the hyaline bodies of three species from the ecologically important clade of rhinanthoid Orobanchaceae. Haustoria collected from laboratory-grown and field-collected plants of Rhinanthus minor, Odontites vernus and Melampyrum pratense attached to various hosts were immunolabelled for cell wall matrix glycans and glycoproteins using specific monoclonal antibodies (mAbs). Hyaline body cell wall architecture differed from that of the surrounding parenchyma in all species investigated. Enrichment in arabinogalactan protein (AGP) epitopes labelled with mAbs LM2, JIM8, JIM13, JIM14 and CCRC-M7 was prominent and coincided with reduced labelling of de-esterified homogalacturonan with mAbs JIM5, LM18 and LM19. Furthermore, paramural bodies, intercellular deposits and globular ergastic bodies composed of pectins, xyloglucans, extensins and AGPs were common. In Rhinanthus they were particularly abundant in pairings with legume hosts. Hyaline body cells were not in direct contact with haustorial xylem, which was surrounded by a single layer of paratracheal parenchyma with thickened cell walls abutting the xylem. The distinctive anatomy and cell wall architecture indicate hyaline body specialization. Altered proportions of AGPs and pectins may affect the mechanical properties of hyaline body cell walls. This and the association with a transfer-like type of paratracheal parenchyma suggest a role in nutrient translocation. Organelle-rich protoplasts and the presence of exceptionally profuse intra- and intercellular wall materials when attached to a nitrogen

  5. Markov dynamic models for long-timescale protein motion.

    KAUST Repository

    Chiang, Tsung-Han

    2010-06-01

    Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.

  6. Analysis of protein dynamics in the pericellular matrix

    Science.gov (United States)

    Scrimgeour, Jan; Young, Dylan

    2015-03-01

    The pericellular matrix (PCM) is a low density, hydrated polymer coating that extends into the extracellular space from the surface of many living cells. The PCM controls access to cell and tissue surfaces, regulating a diverse set of processes from cell adhesion to protein transport and storage. The cell coat consists of a malleable backbone - the large polysaccharide hyaluronan (HA) - with its structure, its material properties, and its bio-functionality tuned by a diverse set of HA binding proteins. These proteins add charge, cross-links and growth factor-like ligands into the brush. Dynamic interactions between the HA and its binding proteins can be observed using single particle tracking in a fluorescence microscope. The resulting single molecule trajectories can contain evidence of site hoping, with the proteins dynamically moving between different states of motion as they bind and unbind from the HA. Here, we present an evaluation of hidden Markov models for the analysis of such multi-mobility trajectories. Simulated trajectories are used to probe the limits of this approach for molecular trajectories of limited length and the results are used to inform the design of particle tracking experiments.

  7. Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein

    Directory of Open Access Journals (Sweden)

    Michael T. Zimmermann

    2012-04-01

    Full Text Available We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular Dynamics confirm the differences in loop dynamics between the free and structured contexts; there is strong agreement between the behaviors observed from molecular dynamics and the elastic network models. There is no apparent simple relationship between loop mobility and its size, exposure, or position within a loop. Free peptides do not behave the same as the loops in the proteins. Surface loops do not behave as if they were random coils, and the tertiary structure has a critical influence upon the apparent motions. This strongly implies that entropy evaluation of protein loops requires knowledge of the motions of the entire protein structure.

  8. Giardia cyst wall protein 1 is a lectin that binds to curled fibrils of the GalNAc homopolymer.

    Directory of Open Access Journals (Sweden)

    Aparajita Chatterjee

    2010-08-01

    Full Text Available The infectious and diagnostic stage of Giardia lamblia (also known as G. intestinalis or G. duodenalis is the cyst. The Giardia cyst wall contains fibrils of a unique beta-1,3-linked N-acetylgalactosamine (GalNAc homopolymer and at least three cyst wall proteins (CWPs composed of Leu-rich repeats (CWP(LRR and a C-terminal conserved Cys-rich region (CWP(CRR. Our goals were to dissect the structure of the cyst wall and determine how it is disrupted during excystation. The intact Giardia cyst wall is thin (approximately 400 nm, easily fractured by sonication, and impermeable to small molecules. Curled fibrils of the GalNAc homopolymer are restricted to a narrow plane and are coated with linear arrays of oval-shaped protein complex. In contrast, cyst walls of Giardia treated with hot alkali to deproteinate fibrils of the GalNAc homopolymer are thick (approximately 1.2 microm, resistant to sonication, and permeable. The deproteinated GalNAc homopolymer, which forms a loose lattice of curled fibrils, is bound by native CWP1 and CWP2, as well as by maltose-binding protein (MBP-fusions containing the full-length CWP1 or CWP1(LRR. In contrast, neither MBP alone nor MBP fused to CWP1(CRR bind to the GalNAc homopolymer. Recombinant CWP1 binds to the GalNAc homopolymer within secretory vesicles of Giardia encysting in vitro. Fibrils of the GalNAc homopolymer are exposed during excystation or by treatment of heat-killed cysts with chymotrypsin, while deproteinated fibrils of the GalNAc homopolymer are degraded by extracts of Giardia cysts but not trophozoites. These results show the Leu-rich repeat domain of CWP1 is a lectin that binds to curled fibrils of the GalNAc homopolymer. During excystation, host and Giardia proteases appear to degrade bound CWPs, exposing fibrils of the GalNAc homopolymer that are digested by a stage-specific glycohydrolase.

  9. Structure and function of the first full-length murein peptide ligase (Mpl cell wall recycling protein.

    Directory of Open Access Journals (Sweden)

    Debanu Das

    2011-03-01

    Full Text Available Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc. MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl, which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl. Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters. Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

  10. Protein phosphatase CaPpz1 is involved in cation homeostasis, cell wall integrity and virulence of Candida albicans.

    Science.gov (United States)

    Adám, Csaba; Erdei, Eva; Casado, Carlos; Kovács, László; González, Asier; Majoros, László; Petrényi, Katalin; Bagossi, Péter; Farkas, Ilona; Molnar, Monika; Pócsi, István; Ariño, Joaquín; Dombrádi, Viktor

    2012-05-01

    The opportunistic pathogen Candida albicans has a single protein phosphatase Z (PPZ) candidate gene termed CaPPZ1, which shows significant allele variability. We demonstrate here that bacterially expressed CaPpz1 protein exhibits phosphatase activity which can be inhibited by recombinant Hal3, a known inhibitor of Saccharomyces cerevisiae Ppz1. Site-directed mutagenesis experiments based on natural polymorphisms allowed the identification of three amino acid residues that affect enzyme activity or stability. The expression of CaPPZ1 in ppz1 S. cerevisiae and pzh1 Schizosaccharomyces pombe cells partially rescued the salt and caffeine phenotypes of the deletion mutants. CaPpz1 also complemented the slt2 S. cerevisiae mutant, which is crippled in the mitogen-activated protein (MAP) kinase that mediates the cell wall integrity signalling pathway. Collectively, our results suggest that the orthologous PPZ enzymes have similar but not identical functions in different fungi. The deletion of the CaPPZ1 gene in C. albicans resulted in a mutant that was sensitive to salts such as LiCl and KCl, to caffeine, and to agents that affect cell wall biogenesis such as Calcofluor White and Congo red, but was tolerant to spermine and hygromycin B. Reintegration of the CaPPZ1 gene into the deletion mutant alleviated all of the mutant phenotypes tested. Thus CaPpz1 is involved in cation homeostasis, cell wall integrity and the regulation of the membrane potential of C. albicans. In addition, the germ tube growth rate, and virulence in the BALB/c mouse model, were reduced in the null mutant, suggesting a novel function for CaPpz1 in the yeast to hypha transition that may have medical relevance.

  11. Folding of small proteins using constrained molecular dynamics.

    Science.gov (United States)

    Balaraman, Gouthaman S; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

    2011-06-16

    The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward "native-like" structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement. It is computationally expensive to perform all-atom simulations of protein folding because the processes occur on a time scale of microseconds. Compared to the all-atom MD simulation, constrained MD methods have the advantage that stable dynamics can be achieved for larger time steps and the number of degrees of freedom is an order of magnitude smaller, leading to a decrease in computational cost. We have developed a generalized constrained MD method that allows the user to "freeze and thaw" torsional degrees of freedom as fit for the problem studied. We have used this method to perform all-torsion constrained MD in implicit solvent coupled with the replica exchange method to study folding of small proteins with various secondary structural motifs such as, α-helix (polyalanine, WALP16), β-turn (1E0Q), and a mixed motif protein (Trp-cage). We demonstrate that constrained MD replica exchange method exhibits a wider conformational search than all-atom MD with increased enrichment of near-native structures. "Hierarchical" constrained MD simulations, where the partially formed helical regions in the initial stretch of the all-torsion folding simulation trajectory of Trp-cage were frozen, showed a better sampling of near-native structures than all-torsion constrained MD simulations. This is in agreement with the zipping-and-assembly folding model put forth by Dill and co-workers for folding proteins. The use of hierarchical "freeze and thaw" clustering schemes in constrained MD simulation can be used to sample conformations that contribute significantly to folding of proteins. © 2011 American Chemical Society

  12. Dynamic expression pattern of kinesin accessory protein in Drosophila

    Indian Academy of Sciences (India)

    Unknown

    We have identified the Drosophila homologue of the non-motor accessory subunit of kinesin-II motor complex. It is homologous to the SpKAP115 of the sea urchin, KAP3A and KAP3B of the mouse, and SMAP protein in humans. In situ hybridization using a DmKAP specific cRNA probe has revealed a dynamic pattern of ...

  13. NMR investigation of domain wall dynamics and hyperfine field anisotropy in magnets by the magnetic video-pulse excitation method

    Science.gov (United States)

    Gavasheli, Ts A.; Mamniashvili, GI; Gegechkori, T. O.

    2017-04-01

    Two-pulse nuclear spin echoes were studied experimentally depending on the time of application and pulse amplitudes of the DC magnetic field-magnetic video-pulses (MVP) as well as on the value of the external magnetic field. The measurements were performed with nanopowders and polycrystals of metallic cobalt, in lithium ferrite and half metal Co2MnSi. Two types of dependences of these signals on time of application of MVP with respect to moments of application of exciting radio-frequency pulses were established, which were determined by the degree of anisotropy of local hyperfine fields. The mechanisms of influence of the pinning and mobility of domain walls on the revealed specific features of the signals under study are also discussed. It is shown that temporal spectra of the MVP effect on two-pulse echoes in multidomain magnets are determined by the parameters of domain walls and can be used for qualitative and quantitative characterization of the domain wall dynamics of magnets.

  14. Investigation of the Relationship between Lactococcal Host Cell Wall Polysaccharide Genotype and 936 Phage Receptor Binding Protein Phylogeny

    DEFF Research Database (Denmark)

    Mahony, Jennifer; Kot, Witold Piotr; Murphy, James

    2013-01-01

    Comparative genomics of 11 lactococcal 936-type phages combined with host range analysis allowed subgrouping of these phage genomes, particularly with respect to their encoded receptor binding proteins. The so-called pellicle or cell wall polysaccharide of Lactococcus lactis, which has been...... of tested 936-type phages. Such a correlation would allow prediction of the intrinsic 936-type phage sensitivity of a particular lactococcal strain and substantiates the notion that the lactococcal pellicle polysaccharide represents the receptor for (certain) 936-type phages while also partially explaining...

  15. A fractional calculus approach to self-similar protein dynamics.

    Science.gov (United States)

    Glöckle, W G; Nonnenmacher, T F

    1995-01-01

    Relaxation processes and reaction kinetics of proteins deviate from exponential behavior because of their large amount of conformational substrates. The dynamics are governed by many time scales and, therefore, the decay of the relaxation function or reactant concentration is slower than exponential. Applying the idea of self-similar dynamics, we derive a fractal scaling model that results in an equation in which the time derivative is replaced by a differentiation (d/dt)beta of non-integer order beta. The fractional order differential equation is solved by a Mittag-Leffler function. It depends on two parameters, a fundamental time scale tau 0 and a fractional order beta that can be interpreted as a self-similarity dimension of the dynamics. Application of the fractal model to ligand rebinding and pressure release measurements of myoglobin is demonstrated, and the connection of the model to considerations of energy barrier height distributions is shown.

  16. Non-linear dynamic instability analysis of thin-walled stiffener beam subjected to uniform harmonic in-plane loading

    Science.gov (United States)

    Yadav, Amit; Panda, Sarat Kumar; Dey, Tanish

    2017-11-01

    Present analysis deals with nonlinear flexural-torsional vibration and dynamic instability of thin-walled stiffener beam with open section subjected to harmonic in-plane loading. The static and dynamic components of the applied harmonic in-plane loading are assumed to vary uniformly. A set of nonlinear partial differential equations (PDEs) describing the vibration of system is derived. Using Galerkin's method, these partial differential equations are reduced into coupled Mathieu equations. The steady state response of the system is determined by solving the condition for a non-trivial solution. The principal regions of parametric resonance are determined using the method suggested by Bolotin. The numerical results are presented to investigate the effect of aspect ratios, boundary conditions and static load factor on the frequency-amplitude responses and instability regions.

  17. Numerical investigation of flow dynamics and scalar transport in a wall-bounded turbulent jet

    Science.gov (United States)

    Hrebtov, M.; Bazhenov, A.; Borynyak, K.

    2017-11-01

    We present the results of Large Eddy Simulation of a turbulent jet discharging into a confined slot with the wall spacing to jet inlet width ratio = 0.1 and Re = 104. The jet exhibits a meandering motion accompanied by formation of checkerboard pattern of large vortices in the mixing layer. A passive scalar transport was simulated with uniform inlet distribution of the scalar. It was found that the fluctuations of spanwise velocity component grow downstream and their maximum location is migrating from the lateral boundaries of the jet (free-shear layers) to the wall-boundary layers. Some evidence of counter-gradient turbulent scalar transport was found in the mixing layers of the jet, which may be attributed to the influence of observed large-scale checkerboard-type vortices.

  18. A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis.

    Science.gov (United States)

    Lewis, Daniel R; Olex, Amy L; Lundy, Stacey R; Turkett, William H; Fetrow, Jacquelyn S; Muday, Gloria K

    2013-09-01

    To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in cellulase3/glycosylhydrolase9b3 and leucine rich extensin2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.

  19. AUXIN BINDING PROTEIN1 Links Cell Wall Remodeling, Auxin Signaling, and Cell Expansion in Arabidopsis[W

    Science.gov (United States)

    Paque, Sébastien; Mouille, Grégory; Grandont, Laurie; Alabadí, David; Gaertner, Cyril; Goyallon, Arnaud; Muller, Philippe; Primard-Brisset, Catherine; Sormani, Rodnay; Blázquez, Miguel A.; Perrot-Rechenmann, Catherine

    2014-01-01

    Cell expansion is an increase in cell size and thus plays an essential role in plant growth and development. Phytohormones and the primary plant cell wall play major roles in the complex process of cell expansion. In shoot tissues, cell expansion requires the auxin receptor AUXIN BINDING PROTEIN1 (ABP1), but the mechanism by which ABP1 affects expansion remains unknown. We analyzed the effect of functional inactivation of ABP1 on transcriptomic changes in dark-grown hypocotyls and investigated the consequences of gene expression on cell wall composition and cell expansion. Molecular and genetic evidence indicates that ABP1 affects the expression of a broad range of cell wall–related genes, especially cell wall remodeling genes, mainly via an SCFTIR/AFB-dependent pathway. ABP1 also functions in the modulation of hemicellulose xyloglucan structure. Furthermore, fucosidase-mediated defucosylation of xyloglucan, but not biosynthesis of nonfucosylated xyloglucan, rescued dark-grown hypocotyl lengthening of ABP1 knockdown seedlings. In muro remodeling of xyloglucan side chains via an ABP1-dependent pathway appears to be of critical importance for temporal and spatial control of cell expansion. PMID:24424095

  20. Dynamic Raman Spectroelectrochemistry of Single Walled Carbon Nanotubes modified electrodes using a Langmuir-Schaefer method

    OpenAIRE

    Ibáñez, David; Romero, Edna Cecilia; Colina, Álvaro; Heras, Aránzazu

    2014-01-01

    Raman spectroelectrochemistry is a fundamental technique to characterize single walled carbon nanotube (SWCNT) films. In this work, we have performed the study of SWCNT films transferred to a glassy carbon electrode using a Langmuir-Schaefer method. Langmuir balance has allowed us to control the characteristics of the film that can be easily transferred to the electrode support. Time-resolved Raman spectroelectrochemistry experiments at scan rates between 20 and 400 mV s−1 were done in two di...

  1. The dynamics of a capsule in a wall-bounded oscillating shear flow

    CERN Document Server

    Zhu, LaiLai; Brandt, Luca

    2015-01-01

    The motion of an initially spherical capsule in a wall-bounded oscillating shear flow is investigated via an accelerated boundary integral implementation. The neo-Hookean model is used as the constitutive law of the capsule membrane. The maximum wall-normal migration is observed when the oscillation period of the imposed shear is of the order of the relaxation time of the elastic membrane; hence, the optimal capillary number scales with the inverse of the oscillation frequency and the ratio agrees well with the theoretical prediction in the limit of high-frequency oscillation. The migration velocity decreases monotonically with the frequency of the applied shear and the capsule-wall distance. We report a significant correlation between the capsule lateral migration and the normal stress difference induced in the flow. The periodic variation of the capsule deformation is roughly in phase with that of the migration velocity and normal stress difference, with twice the frequency of the imposed shear. The maximum...

  2. Suitability of pharmacokinetic models for dynamic contrast-enhanced MRI of abdominal aortic aneurysm vessel wall: a comparison.

    Directory of Open Access Journals (Sweden)

    V Lai Nguyen

    Full Text Available PURPOSE: Increased microvascularization of the abdominal aortic aneurysm (AAA vessel wall has been related to AAA progression and rupture. The aim of this study was to compare the suitability of three pharmacokinetic models to describe AAA vessel wall enhancement using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI. MATERIALS AND METHODS: Patients with AAA underwent DCE-MRI at 1.5 Tesla. The volume transfer constant (K(trans , which reflects microvascular flow, permeability and surface area, was calculated by fitting the blood and aneurysm vessel wall gadolinium concentration curves. The relative fit errors, parameter uncertainties and parameter reproducibilities for the Patlak, Tofts and Extended Tofts model were compared to find the most suitable model. Scan-rescan reproducibility was assessed using the interclass correlation coefficient and coefficient of variation (CV. Further, the relationship between K(trans and AAA size was investigated. RESULTS: DCE-MRI examinations from thirty-nine patients (mean age±SD: 72±6 years; M/F: 35/4 with an mean AAA maximal diameter of 49±6 mm could be included for pharmacokinetic analysis. Relative fit uncertainties for K(trans based on the Patlak model (17% were significantly lower compared to the Tofts (37% and Extended Tofts model (42% (p<0.001. K(trans scan-rescan reproducibility for the Patlak model (ICC = 0.61 and CV = 22% was comparable with the Tofts (ICC = 0.61, CV = 23% and Extended Tofts model (ICC = 0.76, CV = 22%. K(trans was positively correlated with maximal AAA diameter (Spearman's ρ = 0.38, p = 0.02 using the Patlak model. CONCLUSION: Using the presented imaging protocol, the Patlak model is most suited to describe DCE-MRI data of the AAA vessel wall with good K(trans scan-rescan reproducibility.

  3. Modeling, Characterization and Analysis of the dynamic behavior of heat transfers through polyethylene and glass walls of Greenhouses

    Science.gov (United States)

    Bibi-Triki, N.; Bendimerad, S.; Chermiti, A.; Mahdjoub, T.; Draoui, B.; Abène, A.

    The conventional agricultural tunnel greenhouse is highly widespread in Mediterranean countries, despite the shortcomings it presents, specifically the overheating during the day and the intense cooling at night. This can sometimes lead to an internal thermal inversion. The chapel-shaped glass greenhouse is relatively more efficient, but its evolution remains slow because of its investment cost and amortization. The objectives of the agricultural greenhouse are to create a microclimate that is favorable to the requirements and growth of plants from the surrounding climatic conditions and produce cheap off-season fruits, vegetables and flowers which must be highly available all along the year. The agricultural greenhouse is defined by its structural and functional architecture as well as by the optical, thermal and mechanical qualities of its wall and the accompanying technical support. The greenhouse is supposed to be a confined environment where there is an exchange of several components. The main intervening factors are: light, temperature and relative humidity. When protected, the culture heats up more than when in free air because of the wall that acts as a barrier to harmful influences of the wind and the surrounding climatic variations as well as to the reduction in internal air convection. This thermal evolution state depends on the air-tightness degree of the cover and its physical characteristics. It has to be transparent to solar rays, and must as well absorb and reflect infrared rays emitted by the soil. This leads to trapped solar rays, called the "greenhouse effect". In this article, we propose the dynamic modeling of the greenhouse system, the characterization and analysis of the thermal behavior of the wall for both experimental greenhouses, where the first one is made of polyethylene (tunnel greenhouse) and the second of glass (chapel-shaped greenhouse), throughout experimentation and simulation which finally lead to identifying the evolution in the

  4. Dynamics of chest wall volume regulation during constant work rate exercise in patients with chronic obstructive pulmonary disease

    Energy Technology Data Exchange (ETDEWEB)

    Takara, L.S.; Cunha, T.M.; Barbosa, P.; Rodrigues, M.K.; Oliveira, M.F.; Nery, L.E. [Setor de Função Pulmonar e Fisiologia Clínica do Exercício, Disciplina de Pneumologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Neder, J.A. [Setor de Função Pulmonar e Fisiologia Clínica do Exercício, Disciplina de Pneumologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Division of Respiratory and Critical Care Medicine, Department of Medicine, Queen' s University, Kingston, ON (Canada)

    2012-10-15

    This study evaluated the dynamic behavior of total and compartmental chest wall volumes [(V{sub CW}) = rib cage (V{sub RC}) + abdomen (V{sub AB})] as measured breath-by-breath by optoelectronic plethysmography during constant-load exercise in patients with stable chronic obstructive pulmonary disease. Thirty males (GOLD stages II-III) underwent a cardiopulmonary exercise test to the limit of tolerance (Tlim) at 75% of peak work rate on an electronically braked cycle ergometer. Exercise-induced dynamic hyperinflation was considered to be present when end-expiratory (EE) V{sub CW} increased in relation to resting values. There was a noticeable heterogeneity in the patterns of V{sub CW} regulation as EEV{sub CW} increased non-linearly in 17/30 “hyperinflators” and decreased in 13/30 “non-hyperinflators” (P < 0.05). EEV{sub AB} decreased slightly in 8 of the “hyperinflators”, thereby reducing and slowing the rate of increase in end-inspiratory (EI) V{sub CW} (P < 0.05). In contrast, decreases in EEV{sub CW} in the “non-hyperinflators” were due to the combination of stable EEV{sub RC} with marked reductions in EEV{sub AB}. These patients showed lower EIV{sub CW} and end-exercise dyspnea scores but longer Tlim than their counterparts (P < 0.05). Dyspnea increased and Tlim decreased non-linearly with a faster rate of increase in EIV{sub CW} regardless of the presence or absence of dynamic hyperinflation (P < 0.001). However, no significant between-group differences were observed in metabolic, pulmonary gas exchange and cardiovascular responses to exercise. Chest wall volumes are continuously regulated during exercise in order to postpone (or even avoid) their migration to higher operating volumes in patients with COPD, a dynamic process that is strongly dependent on the behavior of the abdominal compartment.

  5. Dynamics of chest wall volume regulation during constant work rate exercise in patients with chronic obstructive pulmonary disease

    Directory of Open Access Journals (Sweden)

    L.S. Takara

    2012-12-01

    Full Text Available This study evaluated the dynamic behavior of total and compartmental chest wall volumes [(V CW = rib cage (V RC + abdomen (V AB] as measured breath-by-breath by optoelectronic plethysmography during constant-load exercise in patients with stable chronic obstructive pulmonary disease. Thirty males (GOLD stages II-III underwent a cardiopulmonary exercise test to the limit of tolerance (Tlim at 75% of peak work rate on an electronically braked cycle ergometer. Exercise-induced dynamic hyperinflation was considered to be present when end-expiratory (EE V CW increased in relation to resting values. There was a noticeable heterogeneity in the patterns of V CW regulation as EEV CW increased non-linearly in 17/30 "hyperinflators" and decreased in 13/30 "non-hyperinflators" (P < 0.05. EEV AB decreased slightly in 8 of the "hyperinflators", thereby reducing and slowing the rate of increase in end-inspiratory (EI V CW (P < 0.05. In contrast, decreases in EEV CW in the "non-hyperinflators" were due to the combination of stable EEV RC with marked reductions in EEV AB. These patients showed lower EIV CW and end-exercise dyspnea scores but longer Tlim than their counterparts (P < 0.05. Dyspnea increased and Tlim decreased non-linearly with a faster rate of increase in EIV CW regardless of the presence or absence of dynamic hyperinflation (P < 0.001. However, no significant between-group differences were observed in metabolic, pulmonary gas exchange and cardiovascular responses to exercise. Chest wall volumes are continuously regulated during exercise in order to postpone (or even avoid their migration to higher operating volumes in patients with COPD, a dynamic process that is strongly dependent on the behavior of the abdominal compartment.

  6. Dynamic protein interaction networks and new structural paradigms in signaling

    Science.gov (United States)

    Csizmok, Veronika; Follis, Ariele Viacava; Kriwacki, Richard W.; Forman-Kay, Julie D.

    2017-01-01

    Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins and regions (IDPs/IDRs), which represent ~30% of the proteome and enable unique regulatory mechanisms. In this review we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as “ultrasensitivity” and “regulated folding and unfolding”. We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information. PMID:26922996

  7. TRIM22: A Diverse and Dynamic Antiviral Protein

    Directory of Open Access Journals (Sweden)

    Clayton J. Hattlmann

    2012-01-01

    Full Text Available The tripartite motif (TRIM family of proteins is an evolutionarily ancient group of proteins with homologues identified in both invertebrate and vertebrate species. Human TRIM22 is one such protein that has a dynamic evolutionary history that includes gene expansion, gene loss, and strong signatures of positive selection. To date, TRIM22 has been shown to restrict the replication of a number of viruses, including encephalomyocarditis virus (EMCV, hepatitis B virus (HBV, and human immunodeficiency virus type 1 (HIV-1. In addition, TRIM22 has also been implicated in cellular differentiation and proliferation and may play a role in certain cancers and autoimmune diseases. This comprehensive paper summarizes our current understanding of TRIM22 structure and function.

  8. Glycosylation of a Fasciclin-Like Arabinogalactan-Protein (SOS5) Mediates Root Growth and Seed Mucilage Adherence via a Cell Wall Receptor-Like Kinase (FEI1/FEI2) Pathway in Arabidopsis.

    Science.gov (United States)

    Basu, Debarati; Tian, Lu; Debrosse, Tayler; Poirier, Emily; Emch, Kirk; Herock, Hayley; Travers, Andrew; Showalter, Allan M

    2016-01-01

    Fundamental processes that underpin plant growth and development depend crucially on the action and assembly of the cell wall, a dynamic structure that changes in response to both developmental and environmental cues. While much is known about cell wall structure and biosynthesis, much less is known about the functions of the individual wall components, particularly with respect to their potential roles in cellular signaling. Loss-of-function mutants of two arabinogalactan-protein (AGP)-specific galactosyltransferases namely, GALT2 and GALT5, confer pleiotropic growth and development phenotypes indicating the important contributions of carbohydrate moieties towards AGP function. Notably, galt2galt5 double mutants displayed impaired root growth and root tip swelling in response to salt, likely as a result of decreased cellulose synthesis. These mutants phenocopy a salt-overly sensitive mutant called sos5, which lacks a fasciclin-like AGP (SOS5/FLA4) as well as a fei1fei2 double mutant, which lacks two cell wall-associated leucine-rich repeat receptor-like kinases. Additionally, galt2gal5 as well as sos5 and fei2 showed reduced seed mucilage adherence. Quintuple galt2galt5sos5fei1fei2 mutants were produced and provided evidence that these genes act in a single, linear genetic pathway. Further genetic and biochemical analysis of the quintuple mutant demonstrated involvement of these genes with the interplay between cellulose biosynthesis and two plant growth regulators, ethylene and ABA, in modulating root cell wall integrity.

  9. Energy consumption and water-soluble protein release by cell wall disruption of Nannochloropsis gaditana.

    Science.gov (United States)

    Safi, C; Cabas Rodriguez, L; Mulder, W J; Engelen-Smit, N; Spekking, W; van den Broek, L A M; Olivieri, G; Sijtsma, L

    2017-09-01

    Several cell disruption methods were tested on Nannochloropsis gaditana, to evaluate their efficiency in terms of cell disintegration, energy input and release of soluble proteins. High-pressure homogenization (HPH) and bead milling were the most efficient with >95% cell disintegration, ±50% (w/w) release of total proteins and low energy input (<0.5kWh.kg-1biomass). Enzymatic treatment required low energy input (<0.34kWh.kg-1biomass), but it only released ±35% protein (w/w). Pulsed Electric Field (PEF) was neither energy-efficient (10.44kWh.kg-1biomass) nor successful for protein release (only 10% proteins w/w) and cell disintegration. The release of proteins after applying HPH and bead milling always required less intensive operating conditions for cell disruption. The energy cost per unit of released protein ranged from 0.15-0.25 €.kgProtein-1 in case of HPH, and up to 2-20 €.kgProtein-1 in case of PEF. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Antimicrobial action and cell agglutination by the eosinophil cationic protein are modulated by the cell wall lipopolysaccharide structure.

    Science.gov (United States)

    Pulido, David; Moussaoui, Mohammed; Andreu, David; Nogués, M Victòria; Torrent, Marc; Boix, Ester

    2012-05-01

    Antimicrobial proteins and peptides (AMPs) are essential effectors of innate immunity, acting as a first line of defense against bacterial infections. Many AMPs exhibit high affinity for cell wall structures such as lipopolysaccharide (LPS), a potent endotoxin able to induce sepsis. Hence, understanding how AMPs can interact with and neutralize LPS endotoxin is of special relevance for human health. Eosinophil cationic protein (ECP) is an eosinophil secreted protein with high activity against both Gram-negative and Gram-positive bacteria. ECP has a remarkable affinity for LPS and a distinctive agglutinating activity. By using a battery of LPS-truncated E. coli mutant strains, we demonstrate that the polysaccharide moiety of LPS is essential for ECP-mediated bacterial agglutination, thereby modulating its antimicrobial action. The mechanism of action of ECP at the bacterial surface is drastically affected by the LPS structure and in particular by its polysaccharide moiety. We have also analyzed an N-terminal fragment that retains the whole protein activity and displays similar cell agglutination behavior. Conversely, a fragment with further minimization of the antimicrobial domain, though retaining the antimicrobial capacity, significantly loses its agglutinating activity, exhibiting a different mechanism of action which is not dependent on the LPS composition. The results highlight the correlation between the protein's antimicrobial activity and its ability to interact with the LPS outer layer and promote bacterial agglutination.

  11. Optimal conditions for decorating outer surface of single-walled carbon nanotubes with RecA proteins

    Science.gov (United States)

    Oura, Shusuke; Umemura, Kazuo

    2016-03-01

    In this study, we estimated the optimal reaction conditions for decorating the outer surface of single-walled carbon nanotubes (SWNTs) with RecA proteins by comparison with hybrids of RecA and single-stranded DNA (ssDNA). To react SWNTs with RecA proteins, we first prepared ssDNA-SWNT hybrids. The heights of the ssDNA-SWNT hybrids increased as the amount of RecA used in the reaction increased, as determined from atomic force microscopy images. We further confirmed the increasing adsorption of RecA proteins onto ssDNA on SWNT surfaces by agarose gel electrophoresis. These results suggest that the combination of RecA proteins and ssDNA-SWNT hybrids forms RecA-ssDNA-SWNT hybrids. We also successfully controlled the amount of RecA adsorbed on the ssDNA-SWNT hybrids. Our results thus indicate the optimized reaction conditions for decorating the outer surface of SWNTs with RecA proteins, which is the key to the development of novel biosensors and nanomaterial-based bioelectronics.

  12. NaCl effect on the distribution of wall ingrowth polymers and arabinogalactan proteins in type A transfer cells of Medicago sativa Gabès leaves.

    Science.gov (United States)

    Boughanmi, Néziha; Thibault, Florence; Decou, Raphael; Fleurat-Lessard, Pierrette; Béré, Emile; Costa, Guy; Lhernould, Sabine

    2010-06-01

    We studied the distribution of wall ingrowth (WI) polymers by probing thin sections of companion cells specialized as transfer cells in minor veins of Medicago sativa cv Gabès blade with affinity probes and antibodies specific to polysaccharides and glycoproteins. The wall polymers in the controls were similar in WIs and in the primary wall but differently distributed. The extent of labeling in these papillate WIs differed for JIM5 and JIM7 homogalacturonans but was in the same range for LM5 and LM6 rhamnogalacturonans and xyloglucans. These data show that WI enhancement probably requires arabinogalactan proteins (JIM8) mainly localized on the outer part of the primary wall and WIs. By comparison, NaCl-treated plants exhibited cell wall polysaccharide modifications indicating (1) an increase in unesterified homogalacturonans (JIM5), probably implicated in Na(+) binding and/or polysaccharide network interaction for limiting turgor variations in mesophyll cells; (2) enhancement of the xyloglucan network with an accumulation of fucosylated xyloglucans (CCRC-M1) known to increase the capacity of cellulose binding; and (3) specific recognition of JIM8 arabinogalactan proteins that could participate in both wall enlargement and cohesion by increasing the number of molecular interactions with the other polymers. In conclusion, the cell wall polysaccharide distribution in enlarged WIs might (1) participate in wall resistance to sequestration of Na(+), allowing a better control of hydric homeostasis in mesophyll cells to maintain metabolic activity in source leaves, and (2) maintain tolerance of M. sativa to NaCl.

  13. Which AO/OTA 31-A2 pertrochanteric fractures can be treated with a dynamic hip screw without developing a lateral wall fracture? A CT-based study.

    Science.gov (United States)

    Sharma, Gaurav; Singh, Ravijot; Gn, Kiran Kumar; Jain, Vaibhav; Gupta, Ankit; Gamanagatti, Shivanand; Farooque, Kamran; Sharma, Vijay

    2016-05-01

    To determine whether radiographic measurements derived from standard computed tomography (CT) evaluation can be used to predict likelihood of a peri-operative lateral femoral wall fracture in AO/OTA 31-A2 pertrochanteric fractures treated with a dynamic hip screw (DHS). Fifty-one patients with AO/OTA 31-A2 classified pertrochanteric fractures were evaluated using a pre-operative CT scan of the pelvis with both hips. Dimensions of the lateral wall were calculated for each patient using four parameters: (1) height of the lateral wall above the vastus ridge; (2) circumference of the lateral wall 2 cm below the vastus ridge at an angle of 135°; this circumference was further divided into an anterior, lateral and posterior component; (3) cortical thickness at the centre of the lateral component of the lateral wall; and (4) cortical index. All patients were treated with a 135° DHS. Postoperative radiographs were assessed for lateral femoral wall fracture. Patients with a lateral wall fracture (17/51) had a smaller circumference (4.47 cm vs 5.44 cm p value fractures with a lateral wall height of > 1.68 cm and an anterior component of > 2.10 cm in circumference are not likely to sustain a lateral wall fracture when treated with a DHS.

  14. The Human "Cochlear Battery" - Claudin-11 Barrier and Ion Transport Proteins in the Lateral Wall of the Cochlea.

    Science.gov (United States)

    Liu, Wei; Schrott-Fischer, Annelies; Glueckert, Rudolf; Benav, Heval; Rask-Andersen, Helge

    2017-01-01

    Background: The cochlea produces an electric field potential essential for hair cell transduction and hearing. This biological "battery" is situated in the lateral wall of the cochlea and contains molecular machinery that secretes and recycles K(+) ions. Its functioning depends on junctional proteins that restrict the para-cellular escape of ions. The tight junction protein Claudin-11 has been found to be one of the major constituents of this barrier that maintains ion gradients (Gow et al., 2004; Kitajiri et al., 2004a). We are the first to elucidate the human Claudin-11 framework and the associated ion transport machinery using super-resolution fluorescence illumination microscopy (SR-SIM). Methods: Archival cochleae obtained during meningioma surgery were used for SR-SIM together with transmission electron microscopy after ethical consent. Results: Claudin-11-expressing cells formed parallel tight junction lamellae that insulated the epithelial syncytium of the stria vascularis and extended to the suprastrial region. Intercellular gap junctions were found between the barrier cells and fibrocytes. Conclusion: Transmission electron microscopy, confocal microscopy and SR-SIM revealed exclusive cell specialization in the various subdomains of the lateral wall of the human cochlea. The Claudin-11-expressing cells exhibited both conductor and isolator characteristics, and these micro-porous separators may selectively mediate the movement of charged units to the intrastrial space in a manner that is analogous to a conventional electrochemical "battery." The function and relevance of this battery for the development of inner ear disease are discussed.

  15. Gold nanoparticle inclusion into protein nanotube as a layered wall component.

    Science.gov (United States)

    Goto, Shun; Amano, Yusuke; Akiyama, Motofusa; Böttcher, Christoph; Komatsu, Teruyuki

    2013-11-19

    We describe the synthesis, structure, and catalytic activity of human serum albumin (HSA) nanotubes (NTs) including gold nanoparticles (AuNPs) as a layered wall component. The NTs were fabricated as an alternating layer-by-layer assembly of AuNP and HSA admixture (a negatively charged part) and poly-l-arginine (PLA, a positively charged part) into a track-etched polycarbonate membrane (400 nm pore diameter) with subsequent dissolution of the template. SEM images showed the formation of uniform hollow cylinders of (PLA/AuNP-HSA)3 with a 426 ± 12 nm outer diameter and 65 ± 7 nm wall thickness. Transmission electron microscopy and energy dispersive X-ray measurements revealed high loading of AuNPs in the tubular wall. HSAs bind strongly onto the individual AuNP (K = 1.25 × 10(9) M(-1)), generating a core-shell AuNP-HSA corona, which is the requirement of the robust NT formation. Calcination of the (PLA/AuNP-HSA)3 NTs at 500 °C under air yielded red solid NTs composed of thermally fused AuNPs. From the mass decrease by heat treatment, we calculated the weight of the organic components (PLA and HSA) and thereby constructed a six-layer model of the tube. The (PLA/AuNP-HSA)3 NTs serve as a heterogeneous catalyst for reduction of 4-nitrophenol with sodium borohydrate. Furthermore, implantation of the stiff (PLA/AuNP-HSA)3 NTs vertically onto glass plate produced uniformly cylindrical tube arrays.

  16. Extended analysis of AL-amyloid protein from abdominal wall subcutaneous fat biopsy

    DEFF Research Database (Denmark)

    Olsen, K E; Sletten, K; Westermark, Per

    1998-01-01

    a subcutaneous fat tissue biopsy and submitted to extended protein separation, typing and amino acid sequence analyses. The AL-protein belonged to the rare immunoglobulin light chain kappa, subtype kappa IV and contained unique amino acid substitutions, mostly in the highly preserved framework regions. The study...... shows that subcutaneous fat biopsies are useful sources of amyloid material for biochemical studies....

  17. Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks.

    Science.gov (United States)

    Shen, Xianjun; Yi, Li; Yi, Yang; Yang, Jincai; He, Tingting; Hu, Xiaohua

    2015-01-01

    The identification of protein functional modules would be a great aid in furthering our knowledge of the principles of cellular organization. Most existing algorithms for identifying protein functional modules have a common defect -- once a protein node is assigned to a functional module, there is no chance to move the protein to the other functional modules during the follow-up processes, which lead the erroneous partitioning occurred at previous step to accumulate till to the end. In this paper, we design a new algorithm ADM (Adaptive Density Modularity) to detect protein functional modules based on adaptive density modularity. In ADM algorithm, according to the comparison between external closely associated degree and internal closely associated degree, the partitioning of a protein-protein interaction network into functional modules always evolves quickly to increase the density modularity of the network. The integration of density modularity into the new algorithm not only overcomes the drawback mentioned above, but also contributes to identifying protein functional modules more effectively. The experimental result reveals that the performance of ADM algorithm is superior to many state-of-the-art protein functional modules detection techniques in aspect of the accuracy of prediction. Moreover, the identified protein functional modules are statistically significant in terms of "Biological Process" annotated in Gene Ontology, which provides substantial support for revealing the principles of cellular organization.

  18. PRO40 is a scaffold protein of the cell wall integrity pathway, linking the MAP kinase module to the upstream activator protein kinase C.

    Directory of Open Access Journals (Sweden)

    Ines Teichert

    2014-09-01

    Full Text Available Mitogen-activated protein kinase (MAPK pathways are crucial signaling instruments in eukaryotes. Most ascomycetes possess three MAPK modules that are involved in key developmental processes like sexual propagation or pathogenesis. However, the regulation of these modules by adapters or scaffolds is largely unknown. Here, we studied the function of the cell wall integrity (CWI MAPK module in the model fungus Sordaria macrospora. Using a forward genetic approach, we found that sterile mutant pro30 has a mutated mik1 gene that encodes the MAPK kinase kinase (MAPKKK of the proposed CWI pathway. We generated single deletion mutants lacking MAPKKK MIK1, MAPK kinase (MAPKK MEK1, or MAPK MAK1 and found them all to be sterile, cell fusion-deficient and highly impaired in vegetative growth and cell wall stress response. By searching for MEK1 interaction partners via tandem affinity purification and mass spectrometry, we identified previously characterized developmental protein PRO40 as a MEK1 interaction partner. Although fungal PRO40 homologs have been implicated in diverse developmental processes, their molecular function is currently unknown. Extensive affinity purification, mass spectrometry, and yeast two-hybrid experiments showed that PRO40 is able to bind MIK1, MEK1, and the upstream activator protein kinase C (PKC1. We further found that the PRO40 N-terminal disordered region and the central region encompassing a WW interaction domain are sufficient to govern interaction with MEK1. Most importantly, time- and stress-dependent phosphorylation studies showed that PRO40 is required for MAK1 activity. The sum of our results implies that PRO40 is a scaffold protein for the CWI pathway, linking the MAPK module to the upstream activator PKC1. Our data provide important insights into the mechanistic role of a protein that has been implicated in sexual and asexual development, cell fusion, symbiosis, and pathogenicity in different fungal systems.

  19. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis

    Directory of Open Access Journals (Sweden)

    Kalyan S. Chakrabarti

    2016-01-01

    Full Text Available Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection or are caused in response to ligand binding (induced fit. Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here, we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using nuclear magnetic resonance (NMR spectroscopy, stopped-flow kinetics, and isothermal titration calorimetry, we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Protein dynamics in free recoverin limits the overall rate of binding.

  20. Dynamic testing of thin-walled composite box beams in a vacuum chamber

    Science.gov (United States)

    Chandra, Ramesh; Chopra, Inderjit

    1989-01-01

    Vibration characteristics of thin-walled composite box beams are measured in a rotating environment in a 10-ft diameter vacuum chamber. Symmetric and antisymmetric layup beams are fabricated out of graphite/epoxy prepreg material using an autoclave molding technique. These are excited using piezoelectric ceramic elements and responses are measured using strain gages and accelerometers. First three natural modes are identified using spectrum analyzer over a range of rotational speeds up to 1000 rpm. Measured frequencies and mode shapes (displacement as well as strain) are correlated satisfactorily with calculated finite element results.

  1. Dynamic behavior of adsorber membranes for protein recovery.

    Science.gov (United States)

    Avramescu, Maria-Elena; Borneman, Zandrie; Wessling, Matthias

    2003-12-05

    In recent years there has been a considerable interest in developing membrane chromatography systems that function as a short, wide chromatographic column in which the adsorptive packing consists of one or more microporous membranes. This study reports the use of new adsorber membranes prepared by the incorporation of various types of ion exchange resins into an EVAL porous membrane for protein recovery. The obtained heterogeneous matrixes composed of solid particles surrounded by the polymeric film possess a good accessibility for the protein to the adsorptive sites. Furthermore, small particles can be embedded into porous polymeric structures without the disadvantages of classical chromatographic columns (high pressure drop, fouling and plugging sensitivity, low flow rate), but with the advantages of membrane technology (easy scale-up, low-pressure drop, high flow rate). The adsorptive membranes feature high static as well as dynamic protein adsorption capacities for operating flow rates ranging from 200 to 400 L h bar per m(2) and ionic strength of 20-200 mM. In a sequential desorption step by changing the pH and/or the ionic strength of the eluent, up to 90% protein recovery was obtained. Next to the separation, the mixed matrix adsorber membrane functions as a concentration medium since the protein can be concentrated up to 20-fold in the eluent. The adsorber membranes can be reused in multiple adsorption/desorption cycles with good adsorption performances. Copyright 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 564-572, 2003.

  2. Noncovalent Protein and Peptide Functionalization of Single-Walled Carbon Nanotubes for Biodelivery and Optical Sensing Applications.

    Science.gov (United States)

    Antonucci, Alessandra; Kupis-Rozmysłowicz, Justyna; Boghossian, Ardemis A

    2017-04-05

    The exquisite structural and optical characteristics of single-walled carbon nanotubes (SWCNTs), combined with the tunable specificities of proteins and peptides, can be exploited to strongly benefit technologies with applications in fields ranging from biomedicine to industrial biocatalysis. The key to exploiting the synergism of these materials is designing protein/peptide-SWCNT conjugation schemes that preserve biomolecule activity while keeping the near-infrared optical and electronic properties of SWCNTs intact. Since sp(2) bond-breaking disrupts the optoelectronic properties of SWCNTs, noncovalent conjugation strategies are needed to interface biomolecules to the nanotube surface for optical biosensing and delivery applications. An underlying understanding of the forces contributing to protein and peptide interaction with the nanotube is thus necessary to identify the appropriate conjugation design rules for specific applications. This article explores the molecular interactions that govern the adsorption of peptides and proteins on SWCNT surfaces, elucidating contributions from individual amino acids as well as secondary and tertiary protein structure and conformation. Various noncovalent conjugation strategies for immobilizing peptides, homopolypeptides, and soluble and membrane proteins on SWCNT surfaces are presented, highlighting studies focused on developing near-infrared optical sensors and molecular scaffolds for self-assembly and biochemical analysis. The analysis presented herein suggests that though direct adsorption of proteins and peptides onto SWCNTs can be principally applied to drug and gene delivery, in vivo imaging and targeting, or cancer therapy, nondirect conjugation strategies using artificial or natural membranes, polymers, or linker molecules are often better suited for biosensing applications that require conservation of biomolecular functionality or precise control of the biomolecule's orientation. These design rules are intended to

  3. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  4. Role of vitamin K-dependent proteins in the arterial vessel wall.

    Science.gov (United States)

    Chatrou, M L L; Reutelingsperger, C P; Schurgers, L J

    2011-11-01

    Vitamin K was discovered early last century at the same time as the vitamin K-antagonists. For many years the role of vitamin K was solely ascribed to coagulation and coagulation was thought to be involved only at the venous blood side. This view has dramatically changed with the discovery of vitamin K-dependent proteins outside the coagulation cascade and the role of coagulation factors at the arterial side. Vitamin K-dependent proteins are involved in the regulation of vascular smooth muscle cell migration, apoptosis, and calcification. Vascular calcification has become an important independent predictor of cardiovascular disease. Vitamin K-antagonists induce inactivity of inhibitors of vascular calcification, leading to accelerated calcification. The involvement of vitamin K-dependent proteins such as MGP in vascular calcification make that calcification is amendable for intervention with high intake of vitamin K. This review focuses on the effect of vitamin K-dependent proteins in vascular disease.

  5. Combining optimal control theory and molecular dynamics for protein folding.

    Directory of Open Access Journals (Sweden)

    Yaman Arkun

    Full Text Available A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD. In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  6. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  7. AtPGL3 is an Arabidopsis BURP domain protein that is localized to the cell wall and promotes cell enlargement

    Directory of Open Access Journals (Sweden)

    Jiyoung ePark

    2015-06-01

    Full Text Available The BURP domain is a plant-specific protein domain that has been identified in secretory proteins, and some of these are involved in cell wall remodeling. Among Arabidopsis BURP domain proteins, three proteins exhibit strong amino acid similarities with the tomato polygalacturonase 1 beta (PG1β protein that interacts with a pectin-digesting enzyme. To investigate biological roles of the Arabidopsis PG1β-like proteins (AtPGLs, we generated Arabidopsis lines in which expression of AtPGLs is altered. Among the three AtPGLs, AtPGL3 exhibited highest transcriptional activity throughout all developmental stages. When tissue-specific expression pattern of AtPGL3 was examined, the gene was observed to be active in epidermal cell layers of rosette leaves and in the trichomes. AtPGL triple mutant plants were smaller than wild type plants because cells were smaller in the mutant plants. Interestingly, when we overexpressed AtPGL3 using a 35S promoter, cells in transgenic plants grew larger than those of the wild type, suggesting that AtPGL3 plays a role in cell expansion. A C-terminal GFP fusion protein of AtPGL3 complemented phenotypes of the triple mutant plants and localized to the cell wall. A truncated AtPGL3-GFP fusion protein that lacks the BURP domain failed to rescue the mutant phenotypes even though the GFP protein was targeted to the cell wall, indicating that the BURP domain is required for its effect on cell expansion. Quantitative RT-PCR and immunoblot analyses indicated that 2 α-expansin genes are down-regulated and up-regulated in the triple mutant and overexpressor lines, respectively. Taken together, AtPGL3 is a cell wall protein required for normal cell expansion and the coexpression results suggest that AtPGLs regulate cell wall loosening, in conjunction with α-expansins, to promote cell growth.

  8. Protein dynamics and enzyme catalysis: the ghost in the machine?

    Science.gov (United States)

    Glowacki, David R; Harvey, Jeremy N; Mulholland, Adrian J

    2012-06-01

    One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169-176] that is capable of reproducing intriguing temperature-dependences of enzyme reactions involving significant quantum tunnelling. This model relies on treating multiple conformations of the enzyme-substrate complex. The results show that direct 'driving' motions of proteins are not necessary to explain experimental observations, and show that enzyme reactivity can be understood and accounted for in the framework of transition state theory.

  9. Molecular Dynamics Studies on the Buffalo Prion Protein

    CERN Document Server

    Zhang, Jiapu

    2015-01-01

    It was reported that buffalo is a low susceptibility species resisting to TSEs (Transmissible Spongiform Encephalopathies) (same as rabbits, horses and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (in humans prion diseases are (v)CJDs, GSS, FFI, and kulu etc). It was reported that buffalo is a low susceptibility species resisting to prion diseases (as rabbits, dogs, horses). In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to find out the reason why buffaloes are resistant to prion diseases. We first did molecular modeling a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonanc...

  10. Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties.

    Science.gov (United States)

    Biggin, Philip C; Aldeghi, Matteo; Bodkin, Michael J; Heifetz, Alexander

    2016-01-01

    Most of the previous content of this book has focused on obtaining the structures of membrane proteins. In this chapter we explore how those structures can be further used in two key ways. The first is their use in structure based drug design (SBDD) and the second is how they can be used to extend our understanding of their functional activity via the use of molecular dynamics. Both aspects now heavily rely on computations. This area is vast, and alas, too large to consider in depth in a single book chapter. Thus where appropriate we have referred the reader to recent reviews for deeper assessment of the field. We discuss progress via the use of examples from two main drug target areas; G-protein coupled receptors (GPCRs) and ion channels. We end with a discussion of some of the main challenges in the area.

  11. Investigation of Thermal Expansion Properties of Single Walled Carbon Nanotubes by Raman Spectroscopy and Molecular Dynamics Simulation

    Science.gov (United States)

    Casimir, Daniel

    The mechanical properties of nano-sized materials seem to differ significantly from the predicted behavior of their bulk macroscopic counterparts (Smart, 2014, 16). The former tend to be stronger, more malleable and exhibit greater flexibility. The thermal properties of materials have also been shown to be altered significantly after having been shrunken to nanometer dimensions. The nano material that exhibits this peculiar behavior that is studied in this dissertation are single walled carbon nanotubes. Single walled carbon nanotubes are hollow cylindrical tubes that are one atomic layer in thickness and made up of sp2 hybridized carbon atoms. The majority of samples have diameters on the order 1 nm, with lengths ranging from 1 micron to sometimes a centimeter (Tomanek, 2008, v). The thermo-mechanical quantity that I specifically examine in this research is the linear and volume thermal expansion coefficients of SWCNTs. The mean linear thermal expansion coefficient is the ratio of the change in unit length in response to a 1 degree Celsius rise in temperature. The "true" value of this quantity is obtained in the theoretical limit of a vanishing temperature range DeltaT in the ratio stated above. However, this simply stated thermo-mechanical quantity for Carbon Nanotubes still remains a controversial topic, with widespread discrepancies among results of certain magnitudes - such as the temperature at the occurrence of maximum contraction, and at the transition from contraction to expansion. In conclusion, there is much incentive in examining the somewhat controversial variation in the behavior and quoted values of the thermal expansion of these quasi one-dimensional objects. In this study, I examine this important property of single walled carbon nanotubes using Resonant Raman Spectroscopy and Molecular Dynamics Simulation based on the Adaptive Intermolecular Reactive Empirical Bond Order potential. The latter is a well established potential that is well-suited to

  12. Altered protein dynamics of disease-associated lamin A mutants

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    Worman Howard J

    2004-12-01

    Full Text Available Abstract Background Recent interest in the function of the nuclear lamina has been provoked by the discovery of lamin A/C mutations in the laminopathy diseases. However, it is not understood why mutations in lamin A give such a range of tissue-specific phenotypes. Part of the problem in rationalising genotype-phenotype correlations in the laminopathies is our lack of understanding of the function of normal and mutant lamin A. To investigate this we have used photobleaching in human cells to analyse the dynamics of wild-type and mutant lamin A protein at the nuclear periphery. Results We have found that a large proportion of wild-type lamin A at the nuclear periphery is immobile, but that there is some slow movement of lamin A within the nuclear lamina. The mobility of an R482W mutant lamin A was indistinguishable from wild-type, but increased mobility of L85R and L530P mutant proteins within the nuclear lamina was found. However, the N195K mutant shows the most enhanced protein mobility, both within the nucleoplasm and within the lamina. Conclusion The slow kinetics of lamin A movement is compatible with its incorporation into a stable polymer that only exchanges subunits very slowly. All of the myopathy-associated lamin A mutants that we have studied show increased protein movement compared with wild-type. In contrast, the dynamic behaviour of the lipodystrophy-associated lamin A mutant was indistinguishable from wild-type. This supports the hypothesis that the underlying defect in lamin A function is quite distinct in the laminopathies that affect striated muscle, compared to the diseases that affect adipose tissue. Our data are consistent with an alteration in the stability of the lamin A molecules within the higher-order polymer at the nuclear lamina in myopathies.

  13. Protein stability and dynamics modulation: the case of human frataxin.

    Directory of Open Access Journals (Sweden)

    Ernesto A Roman

    Full Text Available Frataxin (FXN is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function.

  14. Dynamics of Peregrine combs and Peregrine walls in an inhomogeneous Hirota and Maxwell-Bloch system

    Science.gov (United States)

    Wang, Lei; Wang, Zi-Qi; Sun, Wen-Rong; Shi, Yu-Ying; Li, Min; Xu, Min

    2017-06-01

    Under investigation in this paper is an inhomogeneous Hirota-Maxwell-Bloch (IHMB) system which can describe the propagation of optical solitons in an erbium-doped optical fiber. The breather multiple births (BMBs) are derived with periodically varying group velocity dispersion (GVD) coefficients. Under large periodic modulations in the GVD coefficient of IHMB system, the Peregrine comb (PC) solution is produced, which can be viewed as the limiting case of the BMBs. When the amplitude of the modulation satisfies a special condition, the Peregrine wall (PW) that can be regarded as an intermediate state between rogue wave and PC is obtained. The effects of the third-order dispersion on the spatiotemporal characteristics of PCs and PWs are studied. Our results may be useful for the experimental control and manipulation of the formation of generalized Peregrine rogue waves in inhomogeneous erbium-doped optical fiber.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-14

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

  16. The flexibility and dynamics of protein disulfide isomerase.

    Science.gov (United States)

    Römer, Rudolf A; Wells, Stephen A; Emilio Jimenez-Roldan, J; Bhattacharyya, Moitrayee; Vishweshwara, Saraswathi; Freedman, Robert B

    2016-12-01

    We have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse-graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures-and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776-1785. © 2016 Wiley Periodicals, Inc. © 2016 The Authors. The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

  17. Allostery without conformation change: modelling protein dynamics at multiple scales

    Science.gov (United States)

    McLeish, T. C. B.; Rodgers, T. L.; Wilson, M. R.

    2013-10-01

    The original ideas of Cooper and Dryden, that allosteric signalling can be induced between distant binding sites on proteins without any change in mean structural conformation, has proved to be a remarkably prescient insight into the rich structure of protein dynamics. It represents an alternative to the celebrated Monod-Wyman-Changeux mechanism and proposes that modulation of the amplitude of thermal fluctuations around a mean structure, rather than shifts in the structure itself, give rise to allostery in ligand binding. In a complementary approach to experiments on real proteins, here we take a theoretical route to identify the necessary structural components of this mechanism. By reviewing and extending an approach that moves from very coarse-grained to more detailed models, we show that, a fundamental requirement for a body supporting fluctuation-induced allostery is a strongly inhomogeneous elastic modulus. This requirement is reflected in many real proteins, where a good approximation of the elastic structure maps strongly coherent domains onto rigid blocks connected by more flexible interface regions.

  18. Slug-flow dynamics with phase change heat transfer in compact heat exchangers with oblique wavy walls

    Science.gov (United States)

    Morimoto, Kenichi; Kinoshita, Hidenori; Matsushita, Ryo; Suzuki, Yuji

    2017-11-01

    With abundance of low-temperature geothermal energy source, small-scale binary-cycle power generation system has gained renewed attention. Although heat exchangers play a dominant role in thermal efficiency and the system size, the optimum design strategy has not been established due to complex flow phenomena and the lack of versatile heat transfer models. In the present study, the concept of oblique wavy walls, with which high j/f factor is achieved by strong secondary flows in single-phase system, is extended to two-phase exchangers. The present analyses are based on evaporation model coupled to a VOF technique, and a train of isolated bubbles is generated under the controlled inlet quality. R245fa is adopted as a low boiling-point working media, and two types of channels are considered with a hydraulic diameter of 4 mm: (i) a straight circular pipe and (ii) a duct with oblique wavy walls. The focus is on slug-flow dynamics with evaporation under small capillary but moderate Weber numbers, where the inertial effect as well as the surface tension is of significance. A possible direction of the change in thermo-physical properties is explored by assuming varied thermal conductivity. Effects of the vortical motions on evaporative heat transfer are highlighted. This work has been supported by the New Energy and Industrial Technology Development Organization (NEDO), Japan.

  19. Resistive wall instabilities and tearing mode dynamics in the EXTRAP T2R thin shell reversed-field pinch

    Science.gov (United States)

    Malmberg, J.-A.; Brunsell, P. R.

    2002-01-01

    Observations of resistive wall instabilities and tearing mode dynamics in the EXTRAP T2R thin shell (τw=6 ms) reversed field pinch are described. A nonresonant mode (m=1,n=-10) with the same handedness as the internal field grows nearly exponentially with an average growth time of about 2.6 ms (less than 1/2 of the shell time) consistent with linear stability theory. The externally nonresonant unstable modes (m=1,n>0), predicted by linear stability theory, are observed to have only low amplitudes (in the normal low-Θ operation mode of the device). The radial field of the dominant internally resonant tearing modes (m=1,n=-15 to n=-12) remain low due to spontaneous fast mode rotation, corresponding to angular phase velocities up to 280 krad/s. Phase aligned mode structures are observed to rotate toroidally with an average angular velocity of 40 krad/s, in the opposite direction of the plasma current. Toward the end of the discharge, the radial field of the internally resonant modes grows as the modes slow down and become wall-locked, in agreement with nonlinear computations. Fast rotation of the internally resonant modes has been observed only recently and is attributed to a change of the front-end system (vacuum vessel, shell, and TF coil) of the device.

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

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

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

  1. Three mitogen-activated protein kinases required for cell wall integrity contribute greatly to biocontrol potential of a fungal entomopathogen.

    Directory of Open Access Journals (Sweden)

    Ying Chen

    Full Text Available Bck1, Mkk1 and Slt2 are three mitogen-activated protein (MAP kinases constituting cell wall integrity (CWI pathway that may control multi-stress responses via crosstalk with high-osmolarity glycerol (HOG pathway in budding yeast. In this study, Bck1, Mkk1 and Slt2 orthologues in Beauveria bassiana were confirmed as the three-module cascade essential for CWI because cell wall impairment occurred in the hyphae and conidia of Δbck1, Δmkk1 and Δslt2 examined in multiple experiments. Strikingly, all the deletion mutants became more sensitive to hyperosmotic NaCl and sorbitol with the Western blot of Hog1 phosphorylation being weakened in Δbck1 and absent in Δmkk1 and Δslt2. Apart from crossing responses to cell wall perturbation and high osmolarity, three deletion mutants exhibited faster growth and conidiation on nutrition-rich medium, much less virulence to Galleria mellonella larvae, and higher sensitivity to nutritional, fungicidal, thermal and UV-B irradiative stresses, accompanied with less accumulation of intracellular mannitol and trehalose. Moreover, Δmkk1 and Δslt2 were equally more sensitive to all the stresses of different types except wet-heat stress than wild type and more or less different from Δbck1 in sensitivity to most of the stresses despite their null responses to two oxidants. All the changes in three deletion mutants were restored by each targeted gene complementation. Taken together, the CWI-required Bck1, Mkk1 and Slt2 are all positive, but differential, regulators of multi-stress tolerance and virulence perhaps due to interplay with the HOG pathway essential for osmoregulation, thereby contributing greatly to the biocontrol potential of the fungal entomopathogen.

  2. Addition of Phenylboronic Acid to Malus domestica Pollen Tubes Alters Calcium Dynamics, Disrupts Actin Filaments and Affects Cell Wall Architecture.

    Directory of Open Access Journals (Sweden)

    Kefeng Fang

    Full Text Available A key role of boron in plants is to cross-link the cell wall pectic polysaccharide rhamnogalacturonan-II (RG-II through borate diester linkages. Phenylboronic acid (PBA can form the same reversible ester bonds but cannot cross-link two molecules, so can be used as an antagonist to study the function of boron. This study aimed to evaluate the effect of PBA on apple (Malus domestica pollen tube growth and the underlying regulatory mechanism. We observed that PBA caused an inhibition of pollen germination, tube growth and led to pollen tube morphological abnormalities. Fluorescent labeling, coupled with a scanning ion-selective electrode technique, revealed that PBA induced an increase in extracellular Ca2+ influx, thereby elevating the cytosolic Ca2+ concentration [Ca2+]c and disrupting the [Ca2+]c gradient, which is critical for pollen tube growth. Moreover the organization of actin filaments was severely perturbed by the PBA treatment. Immunolocalization studies and fluorescent labeling, together with Fourier-transform infrared analysis (FTIR suggested that PBA caused an increase in the abundance of callose, de-esterified pectins and arabinogalactan proteins (AGPs at the tip. However, it had no effect on the deposition of the wall polymers cellulose. These effects are similar to those of boron deficiency in roots and other organs, indicating that PBA can induce boron deficiency symptoms. The results provide new insights into the roles of boron in pollen tube development, which likely include regulating [Ca2+]c and the formation of the actin cytoskeleton, in addition to the synthesis and assembly of cell wall components.

  3. Molecular dynamics study of effects of nickel coating on torsional behavior of single-walled carbon nanotube

    Energy Technology Data Exchange (ETDEWEB)

    Song Haiyang, E-mail: gsfshy@sohu.co [School of Science, Xi' an University of Posts and Telecommunications, Xi' an 710121 (China); Zha Xinwei [School of Science, Xi' an University of Posts and Telecommunications, Xi' an 710121 (China)

    2011-02-15

    The effects of nickel coating on the torsional behaviors of single-walled carbon nanotubes (SWCNTs) subject to torsion motion are investigated using the molecular dynamics (MD) simulation method. The simulation results show that regardless of chirality, defect or radius, nickel coating can considerably enhance the critical torque of SWCNTs. However, by comparing the critical torsion angle between nickel-coated SWCNTs and corresponding pristine SWCNTs, it is found that nickel coating in small-radius nanotubes does induce a reduction in the critical torsion angle. The results also show that the structural failure of nickel coated imperfect (9,0) SWCNT occurs at an obviously higher critical torque in comparison with uncoated (9,0) SWCNT with a vacancy defect. Furthermore, we also find that the critical torque of a short nickel coated SWCNT is bigger than that of a long one, while the critical torsion angle for a short tube is smaller than that for a long one.

  4. STUDY OF STATIC AND DYNAMIC STABILITY OF THIN-WALLED BARS EXCITED BY PERIODICAL AXIAL EXTERNAL FORCES.

    Directory of Open Access Journals (Sweden)

    Minodora Maria PASĂRE

    2010-10-01

    Full Text Available In these paper, starting from the relations for the displacements and spinning the transversal section of a bar with thin walls of sections opened expressed by the corresponding influence functions and introducing the components of the exterior forces distributed and the moments of the exterior forces distributed due to the inertia forces, the exciting axial forces together with the following effect of these and of the reaction forces of the elastic environment for leaning it may reach to the system of the equations of parametric vibrations under the form of three integral equation These equations may serve for the study of vibrations of the bars, to study the static stability and to study the dynamic stability

  5. Equilibration of experimentally determined protein structures for molecular dynamics simulation.

    Science.gov (United States)

    Walton, Emily B; Vanvliet, Krystyn J

    2006-12-01

    Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often equilibrated with respect to an initial configuration. This so-called equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to artifactual trajectories of protein dynamics. The time at which nonequilibrium effects from the initial configuration are minimized-what we will call the equilibration time-marks the beginning of equilibrium phase-space exploration. Note that the identification of this time does not imply exploration of the entire equilibrium phase space. We have found that current equilibration methodologies contain ambiguities that lead to uncertainty in determining the end of the equilibration stage of the trajectory. This results in equilibration times that are either too long, resulting in wasted computational resources, or too short, resulting in the simulation of molecular trajectories that do not accurately represent the physical system. We outline and demonstrate a protocol for identifying the equilibration time that is based on the physical model of Normal Mode Analysis. We attain the computational efficiency required of large-protein simulations via a stretched exponential approximation that enables an analytically tractable and physically meaningful form of the root-mean-square deviation of atoms comprising the protein. We find that the fitting parameters (which correspond to physical properties of the protein) fluctuate initially but then stabilize for increased simulation time, independently of the simulation duration or sampling frequency. We define the end of the equilibration stage--and thus the equilibration time--as the point in the simulation when these parameters attain constant values. Compared to existing methods, our approach provides the objective identification of the time at

  6. Structural insights into the pH-controlled targeting of plant cell-wall invertase by a specific inhibitor protein

    Science.gov (United States)

    Hothorn, Michael; Van den Ende, Wim; Lammens, Willem; Rybin, Vladimir; Scheffzek, Klaus

    2010-01-01

    Invertases are highly regulated enzymes with essential functions in carbohydrate partitioning, sugar signaling, and plant development. Here we present the 2.6 Å crystal structure of Arabidopsis cell-wall invertase 1 (INV1) in complex with a protein inhibitor (CIF, or cell-wall inhibitor of β-fructosidase) from tobacco. The structure identifies a small amino acid motif in CIF that directly targets the invertase active site. The activity of INV1 and its interaction with CIF are strictly pH-dependent with a maximum at about pH 4.5. At this pH, isothermal titration calorimetry reveals that CIF tightly binds its target with nanomolar affinity. CIF competes with sucrose (Suc) for the same binding site, suggesting that both the extracellular Suc concentration and the pH changes regulate association of the complex. A conserved glutamate residue in the complex interface was previously identified as an important quantitative trait locus affecting fruit quality, which implicates the invertase–inhibitor complex as a main regulator of carbon partitioning in plants. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. However, CIF and PMEI use distinct surface areas to selectively inhibit very different enzymatic scaffolds. PMID:20858733

  7. Protein kinase C activation of a blebbistatin sensitive contractile component in the wall of hypertrophying mouse urinary bladder.

    Science.gov (United States)

    Boberg, Lena; Rahman, Awahan; Poljakovic, Mirjana; Arner, Anders

    2015-02-01

    To examine the role of protein kinase C (PKC) and non-muscle myosin in regulation of wall tension in the hypertrophied urinary bladder. A partial urinary outflow obstruction was induced in the mouse. Tissue strips from sham operated controls and obstructed bladders were examined in vitro with quantitative gel electrophoresis, immunohistochemistry, and in vitro force recordings. Outlet obstruction (14-18 days) induced a significant growth of the bladder, 73 ± 6.13 mg compared to 19 ± 1 13 mg in sham operated controls. The hypertrophying bladder tissue had increased expression of non-muscle myosin B (SMemb) mainly localized to serosa and suburothelium. Direct activation of PKC with PDBu did not alter force in the control urinary bladder. In contrast, PDBu initiated a prominent and sustained contraction which had an increased sensitivity to the myosin type II inhibitor blebbistatin. PKC activates a significant contractile response in the wall of the hypertrophying urinary bladder, possibly supported by non-muscle myosin. This contractile component is not contributing to the physiological response to muscarinic stimulation, but might be separately regulated by other, yet unknown, mechanisms. © 2013 Wiley Periodicals, Inc.

  8. SpyB, a Small Heme-Binding Protein, Affects the Composition of the Cell Wall in Streptococcus pyogenes.

    Science.gov (United States)

    Edgar, Rebecca J; Chen, Jing; Kant, Sashi; Rechkina, Elena; Rush, Jeffrey S; Forsberg, Lennart S; Jaehrig, Bernhard; Azadi, Parastoo; Tchesnokova, Veronika; Sokurenko, Evgeni V; Zhu, Haining; Korotkov, Konstantin V; Pancholi, Vijay; Korotkova, Natalia

    2016-01-01

    Streptococcus pyogenes (Group A Streptococcus or GAS) is a hemolytic human pathogen associated with a wide variety of infections ranging from minor skin and throat infections to life-threatening invasive diseases. The cell wall of GAS consists of peptidoglycan sacculus decorated with a carbohydrate comprising a polyrhamnose backbone with immunodominant N-acetylglucosamine side-chains. All GAS genomes contain the spyBA operon, which encodes a 35-amino-acid membrane protein SpyB, and a membrane-bound C3-like ADP-ribosyltransferase SpyA. In this study, we addressed the function of SpyB in GAS. Phenotypic analysis of a spyB deletion mutant revealed increased bacterial aggregation, and reduced sensitivity to β-lactams of the cephalosporin class and peptidoglycan hydrolase PlyC. Glycosyl composition analysis of cell wall isolated from the spyB mutant suggested an altered carbohydrate structure compared with the wild-type strain. Furthermore, we found that SpyB associates with heme and protoporphyrin IX. Heme binding induces SpyB dimerization, which involves disulfide bond formation between the subunits. Thus, our data suggest the possibility that SpyB activity is regulated by heme.

  9. Structural insights into the pH-controlled targeting of plant cell-wall invertase by a specific inhibitor protein.

    Science.gov (United States)

    Hothorn, Michael; Van den Ende, Wim; Lammens, Willem; Rybin, Vladimir; Scheffzek, Klaus

    2010-10-05

    Invertases are highly regulated enzymes with essential functions in carbohydrate partitioning, sugar signaling, and plant development. Here we present the 2.6 Å crystal structure of Arabidopsis cell-wall invertase 1 (INV1) in complex with a protein inhibitor (CIF, or cell-wall inhibitor of β-fructosidase) from tobacco. The structure identifies a small amino acid motif in CIF that directly targets the invertase active site. The activity of INV1 and its interaction with CIF are strictly pH-dependent with a maximum at about pH 4.5. At this pH, isothermal titration calorimetry reveals that CIF tightly binds its target with nanomolar affinity. CIF competes with sucrose (Suc) for the same binding site, suggesting that both the extracellular Suc concentration and the pH changes regulate association of the complex. A conserved glutamate residue in the complex interface was previously identified as an important quantitative trait locus affecting fruit quality, which implicates the invertase-inhibitor complex as a main regulator of carbon partitioning in plants. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. However, CIF and PMEI use distinct surface areas to selectively inhibit very different enzymatic scaffolds.

  10. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Aboul-Magd Mohammed O

    2009-07-01

    Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input

  11. Mining the secretome of root-knot nematodes for cell wall modifying proteins

    NARCIS (Netherlands)

    Roze, E.H.A.

    2008-01-01

    The products of parasitism genes in nematodes must be secreted to reach their targets at the nematode-plant interface. These nematode secretory proteins are therefore recognised to play an important role in the nematode-plant interaction and as a result have been subject of intense study for years.

  12. Cell wall polysaccharides of Chinese Wolfberry (Lycium barbarum) : Part 2. Characterisation of arabinogalactan-proteins

    NARCIS (Netherlands)

    Redgwell, Robert J.; Curti, Delphine; Wang, Juankuan; Dobruchowska, Justyna M.; Gerwig, Gerrit J.; Kamerling, Johannis P.; Bucheli, Peter

    2011-01-01

    Arabinogalactan-proteins (AGPs) were isolated from Wolfberry fruit (Lycium barbarum) and purified by anion-exchange chromatography and precipitation with Yariv reagent. Linkage and NMR analysis established the structure of Wolfberry AGP as typical of AGP reported from other sources. The data were

  13. Energy consumption and water-soluble protein release by cell wall disruption of Nannochloropsis gaditana

    NARCIS (Netherlands)

    Safi, C.; Cabas Rodriguez, L.; Mulder, W.J.; Engelen-Smit, N.; Spekking, W.; Broek, van den L.A.M.; Olivieri, G.; Sijtsma, L.

    2017-01-01

    Several cell disruption methods were tested on Nannochloropsis gaditana, to evaluate their efficiency in terms of cell disintegration, energy input and release of soluble proteins. High-pressure homogenization (HPH) and bead milling were the most efficient with >95% cell disintegration, ±50%

  14. [Expression, purification and protective antigen analysis of cell wall protein MRP of Streptococcus suis type 2].

    Science.gov (United States)

    Wang, Ping-ping; Pian, Ya-ya; Yuan, Yuan; Zheng, Yu-ling; Jiang, Yong-qiang; Xiong, Zheng-ying

    2012-02-01

    To amplify the mrp gene of Streptococcus suis type 2 05ZYH33, express it in E.coli BL21 in order to acquire high purity recombinant protein MRP, then evaluate the protective antigen of recombinant protein MRP. Using PCR technology to obtain the product of mrp gene of 05ZYH33, and then cloned it into the expression vector pET28a(+). The recombinant protein was purified by affinity chromatography, later immunized New Zealand rabbit to gain anti-serum, then test the anti-serum titer by ELISA. The opsonophagocytic killing test demonstrated the abilities of protective antigen of MRP. The truncated of MRP recombinant protein in E.coli BL21 expressed by inclusion bodies, and purified it in high purity. After immunoprotection, the survival condition of CD-1 was significantly elevated. The survival rate of wild-type strain 05ZYH33 in blood was apparently decreased after anti-serum opsonophagocyticed, but the mutant delta; MRP showed no differences. MRP represent an important protective antigen activity.

  15. Local C-Reactive Protein Expression in Obliterative Lesions and the Bronchial Wall in Posttransplant Obliterative Bronchiolitis

    Directory of Open Access Journals (Sweden)

    Outi E. Päiväniemi

    2009-01-01

    Full Text Available The local immunoreactivity of C-reactive protein (CRP was studied in a heterotopic porcine model of posttranplant obliterative bronchiolitis (OB. Bronchial allografts and control autografts were examined serially 2–28 days after subcutaneous transplantation. The autografts stayed patent. In the allografts, proliferation of inflammatory cells (P<.0001 and fibroblasts (P=.02 resulted in occlusion of the bronchial lumens (P<.01. Influx of CD4+ (P<.001 and CD8+ (P<.0001 cells demonstrated allograft immune response. CRP positivity simultaneously increased in the bronchial walls (P<.01, in macrophages, myofibroblasts, and endothelial cells. Local CRP was predictive of features characteristic of OB (R=0.456–0.879, P< .05−P<.0001. Early obliterative lesions also showed CRP positivity, but not mature, collagen-rich obliterative plugs (P<.05. During OB development, CRP is localized in inflammatory cells, myofibroblasts and endothelial cells probably as a part of the local inflammatory response.

  16. UPF1, a conserved nonsense-mediated mRNA decay factor, regulates cyst wall protein transcripts in Giardia lamblia.

    Directory of Open Access Journals (Sweden)

    Yi-Hsiu Chen

    Full Text Available The Giardia lamblia cyst wall is required for survival outside the host and infection. Three cyst wall protein (cwp genes identified to date are highly up-regulated during encystation. However, little is known of the molecular mechanisms governing their gene regulation. Messenger RNAs containing premature stop codons are rapidly degraded by a nonsense-mediated mRNA decay (NMD system to avoid production of non-functional proteins. In addition to RNA surveillance, NMD also regulates thousands of naturally occurring transcripts through a variety of mechanisms. It is interesting to know the NMD pathway in the primitive eukaryotes. Previously, we have found that the giardial homologue of a conserved NMD factor, UPF1, may be functionally conserved and involved in NMD and in preventing nonsense suppression. In this study, we tested the hypothesis that NMD factors can regulate some naturally occurring transcripts in G. lamblia. We found that overexpression of UPF1 resulted in a significant decrease of the levels of CWP1 and cyst formation and of the endogenous cwp1-3, and myb2 mRNA levels and stability. This indicates that NMD could contribute to the regulation of the cwp1-3 and myb2 transcripts, which are key to G. lamblia differentiation into cyst. Interestingly, we also found that UPF1 may be involved in regulation of eight other endogenous genes, including up-regulation of the translation elongation factor gene, whose product increases translation which is required for NMD. Our results indicate that NMD factor could contribute to the regulation of not only nonsense containing mRNAs, but also mRNAs of the key encystation-induced genes and other endogenous genes in the early-diverging eukaryote, G. lamblia.

  17. Experimental studies of tearing mode and resistive wall mode dynamics in the reversed field pinch configuration

    OpenAIRE

    Malmberg, Jenny-Ann

    2003-01-01

    It is relatively straightforward to establish equilibrium inmagnetically confined plasmas, but the plasma is frequentlysucceptible to a variety of instabilities that are driven bythe free energy in the magnetic field or in the pressuregradient. These unstable modes exhibit effects that affect theparticle, momentum and heat confinement properties of theconfiguration. Studies of the dynamics of several of the mostimportant modes are the subject of this thesis. The studies arecarried out on plas...

  18. The dynamics of plant cell-wall polysaccharide decomposition in leaf-cutting ant fungus gardens.

    Directory of Open Access Journals (Sweden)

    Isabel E Moller

    Full Text Available The degradation of live plant biomass in fungus gardens of leaf-cutting ants is poorly characterised but fundamental for understanding the mutual advantages and efficiency of this obligate nutritional symbiosis. Controversies about the extent to which the garden-symbiont Leucocoprinus gongylophorus degrades cellulose have hampered our understanding of the selection forces that induced large scale herbivory and of the ensuing ecological footprint of these ants. Here we use a recently established technique, based on polysaccharide microarrays probed with antibodies and carbohydrate binding modules, to map the occurrence of cell wall polymers in consecutive sections of the fungus garden of the leaf-cutting ant Acromyrmex echinatior. We show that pectin, xyloglucan and some xylan epitopes are degraded, whereas more highly substituted xylan and cellulose epitopes remain as residuals in the waste material that the ants remove from their fungus garden. These results demonstrate that biomass entering leaf-cutting ant fungus gardens is only partially utilized and explain why disproportionally large amounts of plant material are needed to sustain colony growth. They also explain why substantial communities of microbial and invertebrate symbionts have evolved associations with the dump material from leaf-cutting ant nests, to exploit decomposition niches that the ant garden-fungus does not utilize. Our approach thus provides detailed insight into the nutritional benefits and shortcomings associated with fungus-farming in ants.

  19. Pulsed laser CVD investigations of single-wall carbon nanotube growth dynamics

    Science.gov (United States)

    Liu, Z.; Styers-Barnett, D. J.; Puretzky, A. A.; Rouleau, C. M.; Yuan, D.; Ivanov, I. N.; Xiao, K.; Liu, J.; Geohegan, D. B.

    2008-12-01

    The nucleation and rapid growth of single-wall carbon nanotubes (SWNTs) were explored by pulsed-laser assisted chemical vapor deposition (PLA-CVD). A special high-power, Nd:YAG laser system with tunable pulse width (>0.5 ms) was implemented to rapidly heat (>3×104°C/s) metal catalyst-covered substrates to different growth temperatures for very brief (sub-second) and controlled time periods as measured by in situ optical pyrometry. Utilizing growth directly on transmission electron microscopy grids, exclusively SWNTs were found to grow under rapid heating conditions, with a minimum nucleation time of >0.1 s. By measuring the length of nanotubes grown by single laser pulses, extremely fast growth rates (up to 100 microns/s) were found to result from the rapid heating and cooling induced by the laser treatment. Subsequent laser pulses were found not to incrementally continue the growth of these nanotubes, but instead activate previously inactive catalyst nanoparticles to grow new nanotubes. Localized growth of nanotubes with variable density was demonstrated through this process and was applied for the reliable direct-write synthesis of SWNTs onto pre-patterned, catalyst-covered metal electrodes for the synthesis of SWNT field-effect transistors.

  20. Pulsed Laser CVD Investigations of Single-Wall Carbon Nanotube Growth Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Geohegan, David B [ORNL; Liu, Zuqin [ORNL; Styers-Barnett, David J [ORNL; Puretzky, Alexander A [ORNL; Rouleau, Christopher M [ORNL; Yuan, Dongning [Duke University; Ivanov, Ilia N [ORNL; Xiao, Kai [ORNL; Liu, Jie [Duke University

    2008-01-01

    The nucleation and rapid growth of single-wall carbon nanotubes (SWNTs) were explored by pulsed-laser assisted chemical vapor deposition (PLA-CVD). A special high-power, Nd:YAG laser system with tunable pulse width (> 0.5 ms) was implemented to rapidly heat (>30,000 C/s) metal catalyst-covered substrates to different growth temperatures for very brief (sub-second) and controlled time periods as measured by in situ optical pyrometry. Utilizing growth directly on transmission electron microscopy grids, exclusively SWNTs were found to grow under rapid heating conditions, with a minimum nucleation time of >0.10 s. By measuring the length of nanotubes grown by single laser pulses, extremely fast growth rates (up to 100 microns/s) were found to result from the rapid heating and cooling induced by the laser treatment. Subsequent laser pulses were found not to incrementally continue the growth of these nanotubes, but instead activate previously inactive catalyst nanoparticles to grow new nanotubes. Localized growth of nanotubes with variable density was demonstrated through this process, and was applied for the reliable direct-write synthesis of SWNTs onto pre-patterned, catalyst-covered metal electrodes for the synthesis of SWNT field-effect transistors.

  1. Wall Layers

    Science.gov (United States)

    1992-01-14

    Sydney, Australia. December 6, 1990. Lumley, J. L. A dynamical-systems-theory approach to the wall region. Environmental Engineering Laboratory, CSIRO...Nonlinear Science. Holmes, P. Editor in Chief, Nonlinear Scinece Today. Holmes, P. Reviewer for Physica D, J. Sound Vib., J. Phys., Q. Appl. Math, Phys...Spring, 1994; Organizing committee member. Holmes, P. Editorial Board Member: Archive for Rational Mechanics and Analysis; Journal of Nonlinear Scinece

  2. Dynamics in protein powders on the nanosecond-picosecond time scale are dominated by localized motions.

    Science.gov (United States)

    Nickels, Jonathan D; García Sakai, Victoria; Sokolov, Alexei P

    2013-10-03

    We present analysis of nanosecond-picosecond dynamics of Green Fluorescence Protein (GFP) using neutron scattering data obtained on three spectrometers. GFP has a β-barrel structure that differs significantly from the structure of other globular proteins and is thought to result in a more rigid local environment. Despite this difference, our analysis reveals that the dynamics of GFP are similar to dynamics of other globular proteins such as lysozyme and myoglobin. We suggest that the same general concept of protein dynamics may be applicable to all these proteins. The dynamics of dry protein are dominated by methyl group rotations, while hydration facilitates localized diffusion-like motions in the protein. The latter has an extremely broad relaxation spectrum. The nanosecond-picosecond dynamics of both dry and hydrated GFP are localized to distances of ∼1-3.5 Å, in contrast to the longer range diffusion of hydration water.

  3. Involvement of Sortase Anchoring of Cell Wall Proteins in Biofilm Formation by Streptococcus mutans

    OpenAIRE

    Lévesque, Céline M.; Voronejskaia, Elena; Huang, Yi-Chen Cathy; Mair, Richard W.; Ellen, Richard P.; Cvitkovitch, Dennis G.

    2005-01-01

    Streptococcus mutans is one of the best-known biofilm-forming organisms associated with humans. We investigated the role of the sortase gene (srtA) in monospecies biofilm formation and observed that inactivation of srtA caused a decrease in biofilm formation. Genes encoding three putative sortase-dependent proteins were also found to be up-regulated in biofilms versus planktonic cells and mutations in these genes resulted in reduced biofilm biomass.

  4. Impact of inner-wall reflection on UV reactor performance as evaluated by using computational fluid dynamics: The role of diffuse reflection.

    Science.gov (United States)

    Li, Wentao; Li, Mengkai; Bolton, James R; Qu, Jiuhui; Qiang, Zhimin

    2017-02-01

    Making use of the reflected ultraviolet (UV) radiation with a reflective inner wall is a promising way to improve UV reactor performance. In this study, the impact of inner-wall reflection on UV reactor performance was evaluated in annular single-lamp UV reactors by using computational fluid dynamics, with an emphasis on the role of diffuse reflection. The UV radiation inside the reactor chamber was simulated using a calibrated discrete ordinates radiation model, which has been proven to be a reliable tool for modeling fluence rate (FR) distributions in UV reactors with a reflective inner wall. The results show that UV reactors with a highly reflective inner wall (Reflectivity = 0.80) had obviously higher FRs and reduction equivalent fluences (REFs) than those with an ordinary inner wall (Reflectivity = 0.26). The inner-wall diffuse reflection further increased the reactor REF, as a result of the elevated volume-averaged FR. The FR distribution uniformity had conditioned contributions to UV reactor performance. Specifically, in UV reactors with a plug-like flow the FR distribution uniformity contributed to the REF to some extent, while in UV reactors with a mixed flow it had little influence on the REF. This study has evaluated, for the first time, the impact of inner-wall diffuse reflection on UV reactor performance and has renewed the understanding about the contribution of FR distribution uniformity to UV reactor performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Multicomponent ballistic transport in narrow single wall carbon nanotubes: Analytic model and molecular dynamics simulations

    Science.gov (United States)

    Mutat, T.; Adler, J.; Sheintuch, M.

    2011-01-01

    The transport of gas mixtures through molecular-sieve membranes such as narrow nanotubes has many potential applications, but there remain open questions and a paucity of quantitative predictions. Our model, based on extensive molecular dynamics simulations, proposes that ballistic motion, hindered by counter diffusion, is the dominant mechanism. Our simulations of transport of mixtures of molecules between control volumes at both ends of nanotubes give quantitative support to the model's predictions. The combination of simulation and model enable extrapolation to longer tubes and pore networks.

  6. Molecular dynamics for lateral surface adhesion and peeling behavior of single-walled carbon nanotubes on gold surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Pei-Hsing, E-mail: phh@mail.npust.edu.tw [Department of Mechanical Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan (China)

    2011-12-15

    Highlights: Black-Right-Pointing-Pointer Adhesion and peeling behaviors of SWCNTs are investigated by detailed, fully atomistic MD simulations. Black-Right-Pointing-Pointer Adhesion energy of SWCNTs are discussed. Black-Right-Pointing-Pointer Dynamical behaviors of SWCNTs in low temperature adhesion are analyzed. Black-Right-Pointing-Pointer Adhesion strengths of SWCNTs obtained from MD simulations are compared with the predictions of Hamaker theory and JKR model. - Abstract: Functional gecko-inspired adhesives have attracted a lot of research attention in the last decade. In this work, the lateral surface adhesion and normal peeling-off behavior of single-walled carbon nanotubes (SWCNTs) on gold substrates are investigated by performing detailed, fully atomistic molecular dynamics (MD) simulations. The effects of the diameter and adhered length of CNTs on the adhesive properties were systematically examined. The simulation results indicate that adhesion energies between the SWCNTs and the Au surface varied from 220 to 320 mJ m{sup -2} over the reported chirality range. The adhesion forces on the lateral surface and the tip of the nanotubes obtained from MD simulations agree very well with the predictions of Hamaker theory and Johnson-Kendall-Roberts (JKR) model. The analyses of covalent bonds indicate that the SWCNTs exhibited excellent flexibility and extensibility when adhering at low temperatures ({approx}100 K). This mechanism substantially increases adhesion time compared to that obtained at higher temperatures (300-700 K), which makes SWCNTs promising for biomimetic adhesives in ultra-low temperature surroundings.

  7. Understanding the Effect of Gas Dynamics in Plasma Gun Performance for Simulating Fusion Wall Response to Disruption Events

    Science.gov (United States)

    Riedel, Will; Underwood, Thomas; Righetti, Fabio; Cappelli, Mark

    2017-10-01

    In this work, the suitability of a pulsed coaxial plasma accelerator to simulate the interaction of edge-localized modes with plasma first wall materials is investigated. Experimental measurements derived from a suite of diagnostics are presented that focus on both the properties of the plasma flow and the manner in which such jets couple with material interfaces. Specific emphasis is placed on quantifying the variation in these properties using tungsten tokens exposed to the plasma plume as the gun volume is progressively filled with more neutral gas. These results are mapped to the operational dynamics of the gun via a time-resolved Schlieren cinematic visualization of the density gradient within the flow. Resulting videos indicate the existence of two distinct modes with vastly different characteristic timescales, spatial evolution, and plasma properties. Time resolved quantification of the associated plasma heat flux for both modes, including a range spanning 150 MW m-2 - 10 GW m-2, is presented using both a fast thermocouple gauge and an IR camera. Both diagnostics in conjunction with a heat transfer model provide an accurate description of the energy transfer dynamics and operational characteristics of plasma guns. This work is supported by the U.S. Department of Energy Stewardship Science Academic Program.

  8. Protein-precipitable tannin in wines from Vitis vinifera and interspecific hybrid grapes (Vitis ssp.): differences in concentration, extractability, and cell wall binding.

    Science.gov (United States)

    Springer, Lindsay F; Sacks, Gavin L

    2014-07-30

    Although they possess significant viticultural advantages, interspecific hybrid grapes (Vitis spp.) are reported to produce wine with lower tannin concentrations than European wine varieties (Vitis vinifera). However, extensive quantitative data on this phenomenon as well as mechanistic explanations for these differences are lacking. A survey of primarily commercial wines from the Finger Lakes American Viticultural Area (New York) using a protein precipitation method determined that hybrid-based wines had >4-fold lower tannin concentrations than vinifera wines. To elucidate factors responsible for differences in wine tannin, 24 wines were produced from both red hybrid and vinifera cultivars under identical conditions. Lower wine tannin in French-American hybrid- than vinifera-based wines could be partially explained by lower grape tannin. However, experiments in which cell wall material was incubated with tannin indicated that cell wall binding may be of equal or greater importance in explaining lower wine tannin concentrations in hybrid-based wines. Subsequent characterization of cell wall material revealed that protein in flesh cell walls and, to a lesser extent, pectin in skin cell walls were correlated with cell wall binding.

  9. Proton Wire Dynamics in the Green Fluorescent Protein.

    Science.gov (United States)

    Shinobu, Ai; Agmon, Noam

    2017-01-10

    Inside proteins, protons move on proton wires (PWs). Starting from the highest resolution X-ray structure available, we conduct a 306 ns molecular dynamics simulation of the (A-state) wild-type (wt) green fluorescent protein (GFP) to study how its PWs change with time. We find that the PW from the chromophore via Ser205 to Glu222, observed in all X-ray structures, undergoes rapid water molecule insertion between Ser205 and Glu222. Sometimes, an alternate Ser205-bypassing PW exists. Side chain rotations of Thr203 and Ser205 play an important role in shaping the PW network in the chromophore region. Thr203, with its bulkier side chain, exhibits slower transitions between its three rotameric states. Ser205 experiences more frequent rotations, slowing down when the Thr203 methyl group is close by. The combined states of both residues affect the PW probabilities. A random walk search for PWs from the chromophore reveals several exit points to the bulk, one being a direct water wire (WW) from the chromophore to the bulk. A longer WW connects the "bottom" of the GFP barrel with a "water pool" (WP1) situated below Glu222. These two WWs were not observed in X-ray structures of wt-GFP, but their analogues have been reported in related fluorescent proteins. Surprisingly, the high-resolution X-ray structure utilized herein shows that Glu222 is protonated at low temperatures. At higher temperatures, we suggest ion pairing between anionic Glu222 and a proton hosted in WP1. Upon photoexcitation, these two recombine, while a second proton dissociates from the chromophore and either exits the protein using the short WW or migrates along the GFP-barrel axis on the long WW. This mechanism reconciles the conflicting experimental and theoretical data on proton motion within GFP.

  10. The dynamics of drops coating the underside of a flexible wall

    Science.gov (United States)

    Richard, Craster; Wray, Alex; Papageorgiou, Demetrios; Matar, Omar

    2012-11-01

    Lister et al., 2009, showed that a thin fluid coating the underside of a ceiling (a model which extends in particular the works of Hammond, 1983, and Lister et al., 2005) can give rise to pendent drops. If these are fixed in place by boundary conditions, they drain to give drops of constant pressure surrounded by annular trenches. These authors also showed that, on larger domains starting from an initial perturbation, these drops will undergo a self-induced quasi-steady translation. This is driven by the release of gravitational potential energy as the fluid in the film falls into the drop. The speed and growth of these drops is accessible to analytical computation by the self-similar study of the thin trenches surrounding them, and matching to far external conditions. The subsequent dynamics are intricate, allowing for coalescence (not seen in 1 dimension) as well as complex drop-drop interactions. We extend this model to allow for the ceiling to be a flexible substrate, and also to account for inertial effects in the drops. We then investigate the effect this has on the dynamics of the drops. EPSRC DTA.

  11. Evidence of active transport (filtration?) of plasma proteins across the capillary walls in muscle and subcutis

    DEFF Research Database (Denmark)

    Noer, Ivan; Lassen, N A

    1979-01-01

    Under slight lymphatic stasis (tilting the body 15 degrees) we measured the arrival of locally injected 131I-albumin in the plasma pool. From 30 min to 90 min after the injection the return rate was zero, i.e. local back transport in the two tissues studied, muscle and subcutaneous fat, is very...... passive flux is proportional to the concentration, and since the interstitial albumin concentration is about half the plasma concentration, then also diffusion and/or pinocytosis of albumin from the plasma is negligible in the resting normal human. We suggest that filtration through large leaks...... is the main mechanism for transendothelial protein transport....

  12. Evidence of active transport (filtration?) of plasma proteins across the capillary walls in muscle and subcutis

    DEFF Research Database (Denmark)

    Noer, Ivan; Lassen, N A

    1978-01-01

    Under slight lymphatic stasis (tilting the body 15 degrees) we measured the arrival of locally injected I-albumin to the plasma pool. From 30 min. to 90 min. after the injection the return rate was zero i.e. local back transport in the two tissues studied viz.muscle and subcutaneous fat is very....... As passive flux is proportional to the concentration and the interstitial albumin comcentration is about half the plasma concentration then also diffusion and or pinocytosis from the plasma of albumin is negligble in the resting normal man. We suggest filtration through big leaks as the main mechanism...... for transendothelial protein transport....

  13. Mining the secretome of root-knot nematodes for cell wall modifying proteins

    OpenAIRE

    Roze, E.H.A.

    2008-01-01

    The products of parasitism genes in nematodes must be secreted to reach their targets at the nematode-plant interface. These nematode secretory proteins are therefore recognised to play an important role in the nematode-plant interaction and as a result have been subject of intense study for years. In this thesis, the results on the identification of members of the parasitome in plant-parasitic nematodes, with a focus on the root-knot nematode species Meloidogyne chitwoodi and M. incognita, a...

  14. Structure and Dynamics of Membrane Proteins and Membrane Associated Proteins with Native Bicelles from Eukaryotic Tissues.

    Science.gov (United States)

    Smrt, Sean T; Draney, Adrian W; Singaram, Indira; Lorieau, Justin L

    2017-10-10

    In vitro studies of protein structure, function, and dynamics typically preclude the complex range of molecular interactions found in living tissues. In vivo studies elucidate these complex relationships, yet they are typically incompatible with the extensive and controlled biophysical experiments available in vitro. We present an alternative approach by extracting membranes from eukaryotic tissues to produce native bicelles to capture the rich and complex molecular environment of in vivo studies while retaining the advantages of in vitro experiments. Native bicelles derived from chicken egg or mouse cerebrum tissues contain a rich composition of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA), lysolipids, cholesterol, ceramides (CM), and sphingomyelin (SM). The bicelles also contain source-specific lipids such as triacylglycerides (TAGs) and sulfatides from egg and brain tissues, respectively. With the influenza hemagglutinin fusion peptide (HAfp) and the C-terminal Src homology domain of lymphocyte-specific protein-tyrosine kinase (lck-cSH2), we show that membrane proteins and membrane associated proteins reconstituted in native bicelles produce high-resolution NMR data and probe native protein-lipid interactions.

  15. Dynamic protein interaction modules in human hepatocellular carcinoma progression.

    Science.gov (United States)

    Yu, Hui; Lin, Chen-Ching; Li, Yuan-Yuan; Zhao, Zhongming

    2013-01-01

    Gene expression profiles have been frequently integrated with the human protein interactome to uncover functional modules under specific conditions like disease state. Beyond traditional differential expression analysis, differential co-expression analysis has emerged as a robust approach to reveal condition-specific network modules, with successful applications in a few human disease studies. Hepatocellular carcinoma (HCC), which is often interrelated with the Hepatitis C virus, typically develops through multiple stages. A comprehensive investigation of HCC progression-specific differential co-expression modules may advance our understanding of HCC's pathophysiological mechanisms. Compared with differentially expressed genes, differentially co-expressed genes were found more likely enriched with Hepatitis C virus binding proteins and cancer-mutated genes, and they were clustered more densely in the human reference protein interaction network. These observations indicated that a differential co-expression approach could outperform the standard differential expression network analysis in searching for disease-related modules. We then proposed a differential co-expression network approach to uncover network modules involved in HCC development. Specifically, we discovered subnetworks that enriched differentially co-expressed gene pairs in each HCC transition stage, and further resolved modules with coherent co-expression change patterns over all HCC developmental stages. Our identified network modules were enriched with HCC-related genes and implicated in cancer-related biological functions. In particular, APC and YWHAZ were highlighted as two most remarkable genes in the network modules, and their dynamic interaction partnership was resolved in HCC development. We demonstrated that integration of differential co-expression with the protein interactome could outperform the traditional differential expression approach in discovering network modules of human diseases

  16. Actin Cytoskeleton and Golgi Involvement in Barley stripe mosaic virus Movement and Cell Wall Localization of Triple Gene Block Proteins

    Directory of Open Access Journals (Sweden)

    Hyoun-Sub Lim

    2013-03-01

    Full Text Available Barley stripe mosaic virus (BSMV induces massive actin filament thickening at the infection front of infected Nicotiana benthamiana leaves. To determine the mechanisms leading to actin remodeling, fluorescent protein fusions of the BSMV triple gene block (TGB proteins were coexpressed in cells with the actin marker DsRed: Talin. TGB ectopic expression experiments revealed that TGB3 is a major elicitor of filament thickening, that TGB2 resulted in formation of intermediate DsRed:Talin filaments, and that TGB1 alone had no obvious effects on actin filament structure. Latrunculin B (LatB treatments retarded BSMV cell-to-cell movement, disrupted actin filament organization, and dramatically decreased the proportion of paired TGB3 foci appearing at the cell wall (CW. BSMV infection of transgenic plants tagged with GFP-KDEL exhibited membrane proliferation and vesicle formation that were especially evident around the nucleus. Similar membrane proliferation occurred in plants expressing TGB2 and/or TGB3, and DsRed: Talin fluorescence in these plants colocalized with the ER vesicles. TGB3 also associated with the Golgi apparatus and overlapped with cortical vesicles appearing at the cell periphery. Brefeldin A treatments disrupted Golgi and also altered vesicles at the CW, but failed to interfere with TGB CW localization. Our results indicate that actin cytoskeleton interactions are important in BSMV cell-to-cell movement and for CW localization of TGB3.

  17. Use of adjuvant containing mycobacterial cell-wall skeleton, monophosphoryl lipid A, and squalane in malaria circumsporozoite protein vaccine.

    Science.gov (United States)

    Rickman, L S; Gordon, D M; Wistar, R; Krzych, U; Gross, M; Hollingdale, M R; Egan, J E; Chulay, J D; Hoffman, S L

    1991-04-27

    Human immune responses to modern synthetic and recombinant peptide vaccines administered with the standard adjuvant, aluminum hydroxide, tend to be poor, hence the search for better adjuvants. Antibody responses to a Plasmodium falciparum circumsporozoite (CS) protein vaccine, R32NS1(81), administered with an adjuvant containing cell-wall skeleton of mycobacteria and monophosphoryl lipid A in squalane (MPL/CWS) have been compared to responses to the same immunogen administered with aluminum hydroxide. 2 weeks after the third dose the following indices were greater in the 5 patients who received MPL/CWS than in controls (p less than 0.05): the geometric mean concentration (2.0 vs 25.4 microgram/ml) and avidity index of antibodies to the P falciparum CS protein by ELISA, the geometric mean titre to P falciparum sporozoites by IFAT (1/115 vs 1/1600), and the geometric mean inhibition of sporozoite invasion of hepatoma cells in vitro (37.6 vs 90.3%). For R32NS1(81) MPL/CWS is superior to aluminum hydroxide as an adjuvant, and the data support the evaluation of this complex as an adjuvant for other vaccines.

  18. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with roles in Plant Cell Wall Degradation and Virulence

    KAUST Repository

    Lakshman, Dilip

    2016-03-28

    Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. Here we used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions; the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups; and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.

  19. Kinematics and dynamics of a solitary wave interacting with varying bathymetry and/or a vertical wall

    Science.gov (United States)

    Papoutsellis, Christos; Athanassoulis, Gerassimos; Charalampopoulos, Alexis-Tzianni

    2017-04-01

    In this work, we investigate the transformations that solitary surface waves undergo during their interaction with uneven seabed and/or fully reflective vertical boundaries. This is accomplished by performing simulations using a non-local Hamiltonian formulation, taking into account full nonlinearity and dispersion, in the presence of variable seabed [1]. This formulation is based on an exact coupled-mode representation of the velocity potential, leading to efficient and accurate computations of the Dirichlet to Neumann operator, required in Zakharov/Craig-Sulem formulation [2], [3]. In addition, it allows for the efficient computation of wave kinematics (velocity, acceleration) and the pressure field, in the time-dependent fluid domain, up to its physical boundaries. Such computations are performed for the case of high-amplitude solitary waves interacting with varying bathymetry and/or a vertical wall, shedding light to their kinematics and dynamics. More specifically, we first consider two benchmark cases, namely the transformation of solitary waves over a plane beach [4], and the reflection of solitary waves on a vertical wall [5]. As a further step, results on the scattering/reflection of a solitary wave due to an undulating seabed, and on the disintegration of a solitary wave travelling form shallow to deep water are also presented. References:[1] G.A. Athanassoulis. & Ch.E. Papoutsellis, in Volume 7: Ocean Engineering, ASME, OMAE2015-41452, p. V007T06A029 (2015)[2] W. Craig, C. Sulem, J. Comp. Phys. 108, 73-83 (1993) [3] V. Zakharov, J. Appl. Mech. Tech. Phys 9, 86-94 (1968)[4] S. Grilli, R. Subramanya, T. Svendsen. & J. Veeramony, J. Waterway, Port, Coastal, Ocean Eng. 120(6), 609-628. (1994)[5] Y.Y. Chen, C. Kharif , J.H. Yang, H.C. Hsu, J. Touboul & J. Chambarel, Eur. J. Mech B-Fluid 49, 20-28 (2015)

  20. On defining the dynamics of hydrophobic patches on protein surfaces.

    Science.gov (United States)

    Lijnzaad, Philip; Feenstra, K Anton; Heringa, Jaap; Holstege, Frank C P

    2008-07-01

    We present a simple and efficient method called PATCHTRACK, for studying the dynamics of hydrophobic surface patches. It tracks the patches on snapshot structures taken from a Molecular Dynamics simulation. They are connected into so-called patch runs, which are subsequently clustered into so-called recurrent patches. The method is applied to simulations of three different proteins. Protein motion causes addition and removal of one or more atoms to a patch, resulting in size fluctuations of around 25%. The fluctuations eventually lead to the break-up of a patch, and their average life span is therefore remarkably short at around 4 ps. However, some patch runs are much more stable, lasting hundreds of picoseconds. One such case is the largest patch in amicyanin that is known to be biologically relevant. Another case, previously not reported, is found in phospholipase A(2), where the functional significance of a large recurrent patch formed by Leu58 and Phe94 seems likely. This patch appears to have been overlooked as it is relatively small in the X-ray structure, demonstrating the utility of the current method. The most frequently occurring patch size is 40-60 A(2), but sizes of up to 500 A(2) are also observed. There is no clear relation between patch run durations and their average size. However, long-lasting patch runs tend not to have large fluctuations. The recurrent patches have alternating periods of "liveness" and "dormancy"; around 25% of them is predominantly in the live state. 2008 Wiley-Liss, Inc.

  1. Kinetic and thermodynamic characterization of the interactions between the components of human plasma kinin-forming system and isolated and purified cell wall proteins of Candida albicans.

    Science.gov (United States)

    Seweryn, Karolina; Karkowska-Kuleta, Justyna; Wolak, Natalia; Bochenska, Oliwia; Kedracka-Krok, Sylwia; Kozik, Andrzej; Rapala-Kozik, Maria

    2015-01-01

    Cell wall proteins of Candida albicans, besides their best known role in the adhesion of this fungal pathogen to host's tissues, also bind some soluble proteins, present in body fluids and involved in maintaining the biochemical homeostasis of the human organism. In particular, three plasma factors - high-molecular-mass kininogen (HK), factor XII (FXII) and prekallikrein (PPK) - have been shown to adhere to candidal cells. These proteins are involved in the surface-contact-catalyzed production of bradykinin-related peptides (kinins) that contribute to inflammatory states associated with microbial infections. We recently identified several proteins, associated with the candidal cell walls, and probably involved in the binding of HK. In our present study, a list of potential FXII- and PPK-binding proteins was proposed, using an affinity selection (on agarose-coupled FXII or PPK) from a whole mixture of β-1,3-glucanase-extrated cell wall-associated proteins and the mass-spectrometry protein identification. Five of these fungal proteins, including agglutinin-like sequence protein 3 (Als3), triosephosphate isomerase 1 (Tpi1), enolase 1 (Eno1), phosphoglycerate mutase 1 (Gpm1) and glucose-6-phosphate isomerase 1 (Gpi1), were purified and characterized in terms of affinities to the human contact factors, using the surface plasmon resonance measurements. Except Gpm1 that bound only PPK, and Als3 that exhibited an affinity to HK and FXII, the other isolated proteins interacted with all three contact factors. The determined dissociation constants for the identified protein complexes were of 10(-7) M order, and the association rate constants were in a range of 10(4)-10(5) M(-1)s(-1). The identified fungal pathogen-host protein interactions are potential targets for novel anticandidal therapeutic approaches.

  2. Improved methods for binding acma-type protein anchor fusions yo cell-wall material of micro-organisms

    NARCIS (Netherlands)

    Leenhouts, Cornelis; Ramasamy, R.; Steen, Anton; Kok, Jan; Buist, Girbe; Kuipers, Oscar

    2002-01-01

    The invention provides a method for improving binding of a proteinaceous substance to cell-wall material of a Gram-positive bacterium, said substance comprising an AcmA cell wall binding domain or homolog or functional derivative thereof, said method comprising treating said cell-wall material with

  3. Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells.

    Science.gov (United States)

    Frenkel-Morgenstern, Milana; Cohen, Ariel A; Geva-Zatorsky, Naama; Eden, Eran; Prilusky, Jaime; Issaeva, Irina; Sigal, Alex; Cohen-Saidon, Cellina; Liron, Yuvalal; Cohen, Lydia; Danon, Tamar; Perzov, Natalie; Alon, Uri

    2010-01-01

    Recent advances allow tracking the levels and locations of a thousand proteins in individual living human cells over time using a library of annotated reporter cell clones (LARC). This library was created by Cohen et al. to study the proteome dynamics of a human lung carcinoma cell-line treated with an anti-cancer drug. Here, we report the Dynamic Proteomics database for the proteins studied by Cohen et al. Each cell-line clone in LARC has a protein tagged with yellow fluorescent protein, expressed from its endogenous chromosomal location, under its natural regulation. The Dynamic Proteomics interface facilitates searches for genes of interest, downloads of protein fluorescent movies and alignments of dynamics following drug addition. Each protein in the database is displayed with its annotation, cDNA sequence, fluorescent images and movies obtained by the time-lapse microscopy. The protein dynamics in the database represents a quantitative trace of the protein fluorescence levels in nucleus and cytoplasm produced by image analysis of movies over time. Furthermore, a sequence analysis provides a search and comparison of up to 50 input DNA sequences with all cDNAs in the library. The raw movies may be useful as a benchmark for developing image analysis tools for individual-cell dynamic-proteomics. The database is available at http://www.dynamicproteomics.net/.

  4. Do homologous thermophilic-mesophilic proteins exhibit similar structures and dynamics at optimal growth temperatures? A molecular dynamics simulation study.

    Science.gov (United States)

    Basu, Sohini; Sen, Srikanta

    2013-02-25

    Structure and dynamics both are known to be important for the activity of a protein. A fundamental question is whether a thermophilic protein and its mesophilic homologue exhibit similar dynamics at their respective optimal growth temperatures. We have addressed this question by performing molecular dynamics (MD) simulations of a natural mesophilic-thermophilic homologue pair at their respective optimal growth temperatures to compare their structural, dynamical, and solvent properties. The MD simulations were done in explicit aqueous solvent under periodic boundary and constant pressure and temperature (CPT) conditions and continued for 10.0 ns using the same protocol for the two proteins, excepting the temperatures. The trajectories were analyzed to compare the properties of the two proteins. Results indicated that the dynamical behaviors of the two proteins at the respective optimal growth temperatures were remarkably similar. For the common residues in the thermophilic protein, the rms fluctuations have a general trend to be slightly higher compared to that in the mesophilic counterpart. Lindemann parameter values indicated that only a few residues exhibited solid-like dynamics while the protein as a whole appeared as a molten globule in each case. Interestingly, the water-water interaction was found to be strikingly similar in spite of the difference in temperatures while, the protein-water interaction was significantly different in the two simulations.

  5. Epitope tagging of legume root nodule extensin modifies protein structure and crosslinking in cell walls of transformed tobacco leaves.

    Science.gov (United States)

    Gucciardo, Sébastien; Rathbun, Elizabeth A; Shanks, Michael; Jenkyns, Susan; Mak, Lora; Durrant, Marcus C; Brewin, Nicholas J

    2005-01-01

    Root nodule extensins (RNEs) are highly glycosylated plant glycoproteins localized in the extracellular matrix of legume tissues and in the lumen of Rhizobium-induced infection threads. In pea and other legumes, a family of genes encode glycoproteins of different overall length but with the same basic composition. The predicted polypeptide sequence reveals repeating and alternating motifs characteristic of extensins and arabinogalactan proteins. In order to monitor the behavior of individual RNE gene products in the plant extracellular matrix, the coding sequence of PsRNE1 from Pisum sativum was expressed in insect cells and in tobacco leaves. RNE products extracted from tobacco tissues were of high molecular weight (in excess of 80 kDa), indicating extensive glycosylation similar to that in pea tissues. Epitope-tagged derivatives of PsRNE1 could be localized in cell walls. However, the introduction of epitope tags at the C-terminus of RNE altered the behavior of RNE in the extracellular matrix, apparently preventing intermolecular crosslinking of RNE molecules and their covalent association with other cell wall components. These observations are discussed in the light of a computational model for the RNE glycoprotein that is consistent with an extended rod-like structure. It is proposed that RNE can undergo three classes of tyrosine-based crosslinking. Intramolecular crosslinking of vicinal Tyr residues is rod stiffening, end-to-end linkage is rod lengthening, and side-to-side intermolecular crosslinking is rod bundling. The control of these interconversions could have important implications for the biomechanics of infection thread growth.

  6. Dynamic evolution of mitochondrial ribosomal proteins in Holozoa.

    Science.gov (United States)

    Scheel, Bettina M; Hausdorf, Bernhard

    2014-07-01

    We studied the highly dynamic evolution of mitochondrial ribosomal proteins (MRPs) in Holozoa. Most major clades within Holozoa are characterized by gains and/or losses of MRPs. The usefulness of gains of MRPs as rare genomic changes in phylogenetics is undermined by the high frequency of secondary losses. However, phylogenetic analyses of the MRP sequences provide evidence for the Acrosomata hypothesis, a sister group relationship between Ctenophora and Bilateria. An extensive restructuring of the mitochondrial genome and, as a consequence, of the mitochondrial ribosomes occurred in the ancestor of metazoans. The last MRP genes encoded in the mitochondrial genome were either moved to the nuclear genome or were lost. The strong decrease in size of the mitochondrial genome was probably caused by selection for rapid replication of mitochondrial DNA during oogenesis in the metazoan ancestor. A phylogenetic analysis of MRPL56 sequences provided evidence for a horizontal gene transfer of the corresponding MRP gene between metazoans and Dictyostelidae (Amoebozoa). The hypothesis that the requisition of additional MRPs compensated for a loss of rRNA segments in the mitochondrial ribosomes is corroborated by a significant negative correlation between the number of MRPs and length of the rRNA. Newly acquired MRPs evolved faster than bacterial MRPs and positions in eukaryote-specific MRPs were more strongly affected by coevolution than positions in prokaryotic MRPs in accordance with the necessity to fit these proteins into the pre-existing structure of the mitoribosome. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Ultrafast dynamics of epicocconone, a second generation fluorescent protein stain.

    Science.gov (United States)

    Chatterjee, Soumit; Burai, Tarak Nath; Karuso, Peter; Datta, Anindya

    2011-09-15

    Femtosecond upconversion experiment has been carried out for epicocconone and its butylamine adduct in acetonitrile and tert-butanol. An ultrafast component is found to dominate the decay of fluorescence of epicocconone in acetonitrile solution. Upon reacting with butylamine, a model for the epicocconone-protein adduct, this ultrafast component remains almost unaffected but an additional rise time occurs, indicating the formation of a highly emissive species from the locally excited state. This phenomenon is central to the extraordinary applications of epicocconone in biotechnology. The magnitude of the rise time of the butylamine adduct is similar to that of the longer component of the decay of epicocconone in acetonitrile, suggesting that the dynamics of epicocconone and its butylamine adduct are similar. The ultrafast component is slowed upon increasing the viscosity of the solvent. This results in a marked increase in quantum yield and suggests that it corresponds to rapid bond isomerization, leading to a nonradiative decay. Surprisingly, in water/sucrose mixtures, the ultrafast component remains unaffected but there is still an increase in quantum yield, suggesting that there are at least two nonradiative pathways, one involving bond isomerization and another involving proton transfer. The correct interpretation of these data will allow the design of second generation protein stains based on the epicocconone scaffold with increased quantum yields and photostability. © 2011 American Chemical Society

  8. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications

    Science.gov (United States)

    Polo, Sophie E.; Jackson, Stephen P.

    2011-01-01

    Genome integrity is constantly monitored by sophisticated cellular networks, collectively termed the DNA damage response (DDR). A common feature of DDR proteins is their mobilization in response to genotoxic stress. Here, we outline how the development of various complementary methodologies has provided valuable insights into the spatiotemporal dynamics of DDR protein assembly/disassembly at sites of DNA strand breaks in eukaryotic cells. Considerable advances have also been made in understanding the underlying molecular mechanisms for these events, with post-translational modifications of DDR factors being shown to play prominent roles in controlling the formation of foci in response to DNA-damaging agents. We review these regulatory mechanisms and discuss their biological significance to the DDR. PMID:21363960

  9. Local Structure and Dynamics of Hydration Water in Intrinsically Disordered Proteins.

    Science.gov (United States)

    Rani, Pooja; Biswas, Parbati

    2015-08-27

    Hydration water around protein surface plays a key role in structure, folding and dynamics of proteins. Intrinsically disordered proteins lack secondary and/or tertiary structure in their native state. Thus, characterizing the local structure and dynamics of hydration water around disordered proteins is challenging for both experimentalists and theoreticians. The local structure, orientation and dynamics of hydration water in the vicinity of intrinsically disordered proteins is investigated through molecular dynamics simulations. The analysis of the hydration capacity reveals that the disordered proteins have much larger binding capacity for hydration water than globular proteins. The surface and radial distribution of water molecules around the disordered proteins depict a similar trend. The local structure of the hydration water evaluated in terms of the tetrahedral order parameter, shows a higher order among the water molecules surrounding disordered proteins/regions. The residence time of water molecules clearly exhibits slow dynamics of hydration water around the surface of disordered proteins/regions as compared to globular proteins. The orientation of water molecules is found to be distinctly different for ordered and disordered proteins/regions. This analysis provides a better insight into the structure and dynamics of hydration water around disordered proteins.

  10. The role of cell wall-modifying proteins in plant penetration and feeding site proliferation by the potato cyst nematode Globodera rostochiensis

    NARCIS (Netherlands)

    Kudla, U.

    2006-01-01

    The main objective of this thesis was to investigate two distinct groups of proteins involved in plant cell walls modifications in the parasitism of the potato cyst nematode, Globodera rostochiensis , namely pectate lyases and expansins. Plant parasitism of potato cyst nematode proceeds through two

  11. Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5

    Directory of Open Access Journals (Sweden)

    Inger Lindin

    2014-03-01

    Full Text Available The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD simulations of: (1 MK5 alone; (2 MK5 in complex with an inhibitor; and (3 MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.

  12. Protein-Bound Uremic Toxins Stimulate Crosstalk between Leukocytes and Vessel Wall

    Science.gov (United States)

    Glorieux, Griet; Schepers, Eva; Cohen, Gerald; Gondouin, Bertrand; Van Landschoot, Maria; Eloot, Sunny; Rops, Angelique; Van de Voorde, Johan; De Vriese, An; van der Vlag, Johan; Brunet, Philippe; Van Biesen, Wim; Vanholder, Raymond

    2013-01-01

    Leukocyte activation and endothelial damage both contribute to cardiovascular disease, a major cause of morbidity and mortality in CKD. Experimental in vitro data link several protein-bound uremic retention solutes to the modulation of inflammatory stimuli, including endothelium and leukocyte responses and cardiovascular damage, corroborating observational in vivo data. However, the impact of these uremic toxins on the crosstalk between endothelium and leukocytes has not been assessed. This study evaluated the effects of acute and continuous exposure to uremic levels of indoxylsulfate (IS), p-cresylsulfate (pCS), and p-cresylglucuronide (pCG) on the recruitment of circulating leukocytes in the rat peritoneal vascular bed using intravital microscopy. Superfusion with IS induced strong leukocyte adhesion, enhanced extravasation, and interrupted blood flow, whereas pCS caused a rapid increase in leukocyte rolling. Superfusion with pCS and pCG combined caused impaired blood flow and vascular leakage but did not further enhance leukocyte rolling over pCS alone. Intravenous infusion with IS confirmed the superfusion results and caused shedding of heparan sulfate, pointing to disruption of the glycocalyx as the mechanism likely mediating IS-induced flow stagnation. These results provide the first clear in vivo evidence that IS, pCS, and pCG exert proinflammatory effects that contribute to vascular damage by stimulating crosstalk between leukocytes and vessels. PMID:24009240

  13. The impact of an underground cut-off wall on nutrient dynamics in groundwater in the lower Wang River watershed, China.

    Science.gov (United States)

    Kang, Pingping; Xu, Shiguo

    2017-03-01

    Underground cut-off walls in coastal regions are mainly used to prevent saltwater intrusion, but their impact on nutrient dynamics in groundwater is not clear. In this study, a combined analysis of multiple isotopes ([Formula: see text]) and nitrogen and phosphorus concentrations is used in order to assess the impact of the underground cut-off walls on the nutrient dynamics in groundwater in the lower Wang River watershed, China. Compared with the nitrogen and phosphorus concentrations in groundwater downstream of the underground cut-off walls, high [Formula: see text] and total dissolved nitrogen concentrations and similar concentration levels of [Formula: see text] and total dissolved phosphorus are found in groundwater upstream of the underground cut-off walls. The isotopic data indicated the probable occurrence of denitrification and nitrification processes in groundwater upstream, whereas the fingerprint of these processes was not shown in groundwater downstream. The management of fertilizer application is critical to control nitrogen concentrations in groundwater restricted by the underground cut-off walls.

  14. Plant cell wall proteomics: the leadership of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Cécile eALBENNE

    2013-05-01

    Full Text Available Plant cell wall proteins (CWPs progressively emerged as crucial components of cell walls although present in minor amounts. Cell wall polysaccharides such as pectins, hemicelluloses and cellulose represent more than 90% of primary cell wall mass, whereas hemicelluloses, cellulose and lignins are the main components of lignified secondary walls. All these polymers provide mechanical properties to cell walls, participate in cell shape and prevent water loss in aerial organs. However, cells walls need to be modified and customized during plant development and in response to environmental cues, thus contributing to plant adaptation. CWPs play essential roles in all these physiological processes and particularly in the dynamics of cell walls, which requires organization and rearrangements of polysaccharides as well as cell-to-cell communication. In the last ten years, plant cell wall proteomics has greatly contributed to a wider knowledge of CWPs. This update will deal with (i a survey of plant cell wall proteomics studies with a focus on Arabidopsis thaliana; (ii the main protein families identified and the still missing peptides; (iii the persistent issue of the non-canonical CWPs; (iv the present challenges to overcome technological bottlenecks; and (v the perspectives beyond cell wall proteomics to understand CWP functions.

  15. Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau.

    Science.gov (United States)

    Fichou, Yann; Heyden, Matthias; Zaccai, Giuseppe; Weik, Martin; Tobias, Douglas J

    2015-10-01

    The tau protein, whose aggregates are involved in Alzheimer's disease, is an intrinsically disordered protein (IDP) that regulates microtubule activity in neurons. An IDP lacks a single, well-defined structure and, rather, constantly exchanges among multiple conformations. In order to study IDP dynamics, the combination of experimental techniques, such as neutron scattering, and computational techniques, such as molecular dynamics (MD) simulations, is a powerful approach. Amorphous hydrated powder samples have been very useful for studying protein internal dynamics experimentally, e.g., using neutron scattering. Thus, there is demand for realistic in silico models of hydrated protein powders. Here we present an MD simulation analysis of a powder hydrated at 0.4 g water/g protein of the IDP tau in the temperature range 20-300 K. By comparing with neutron scattering data, we identify the protein-water interface as the predominant feature determining IDP dynamics. The so-called protein dynamical transition is shown to be attenuated, but not suppressed, in the parts of the protein that are not exposed to the solvent. In addition, we find similarities in the mean-squared displacements of the core of a globular protein and "dry" clusters formed by the IDP in hydrated powders. Thus, the ps to ns dynamics of proteins in hydrated powders originate mainly from those residues in contact with solvent. We propose that by measuring the dynamics of protein assemblies, such as aggregates, one might assess qualitatively their state of hydration.

  16. Glycosylation of a Fasciclin-Like Arabinogalactan-Protein (SOS5 Mediates Root Growth and Seed Mucilage Adherence via a Cell Wall Receptor-Like Kinase (FEI1/FEI2 Pathway in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Debarati Basu

    Full Text Available Fundamental processes that underpin plant growth and development depend crucially on the action and assembly of the cell wall, a dynamic structure that changes in response to both developmental and environmental cues. While much is known about cell wall structure and biosynthesis, much less is known about the functions of the individual wall components, particularly with respect to their potential roles in cellular signaling. Loss-of-function mutants of two arabinogalactan-protein (AGP-specific galactosyltransferases namely, GALT2 and GALT5, confer pleiotropic growth and development phenotypes indicating the important contributions of carbohydrate moieties towards AGP function. Notably, galt2galt5 double mutants displayed impaired root growth and root tip swelling in response to salt, likely as a result of decreased cellulose synthesis. These mutants phenocopy a salt-overly sensitive mutant called sos5, which lacks a fasciclin-like AGP (SOS5/FLA4 as well as a fei1fei2 double mutant, which lacks two cell wall-associated leucine-rich repeat receptor-like kinases. Additionally, galt2gal5 as well as sos5 and fei2 showed reduced seed mucilage adherence. Quintuple galt2galt5sos5fei1fei2 mutants were produced and provided evidence that these genes act in a single, linear genetic pathway. Further genetic and biochemical analysis of the quintuple mutant demonstrated involvement of these genes with the interplay between cellulose biosynthesis and two plant growth regulators, ethylene and ABA, in modulating root cell wall integrity.

  17. Temporal and spatial dynamics of optical emission from laser ablation of the first wall materials of fusion device

    Science.gov (United States)

    Dongye, ZHAO; Cong, LI; Yong, WANG; Zhiwei, WANG; Liang, GAO; Zhenhua, HU; Jing, WU; Guang-Nan, LUO; Hongbin, DING

    2018-01-01

    Laser-induced breakdown spectroscopy (LIBS) has been developed to in situ diagnose the chemical compositions of the first wall in the EAST tokamak. However, the dynamics of optical emission of the key plasma-facing materials, such as tungsten, molybdenum and graphite have not been investigated in a laser produced plasma (LPP) under vacuum. In this work, the temporal and spatial dynamics of optical emission were investigated using the spectrometer with ICCD. Plasma was produced by an Nd:YAG laser (1064 nm) with pulse duration of 6 ns. The results showed that the typical lifetime of LPP is less than 1.4 μs, and the lifetime of ions is shorter than atoms at ∼10‑6 mbar. Temporal features of optical emission showed that the optimized delay times for collecting spectra are from 100 to 400 ns which depended on the corresponding species. For spatial distribution, the maximum LIBS spectral intensity in plasma plume is obtained in the region from 1.5 to 3.0 mm above the sample surface. Moreover, the plasma expansion velocity involving the different species in a multicomponent system was measured for obtaining the proper timing (gate delay time and gate width) of the maximum emission intensity and for understanding the plasma expansion mechanism. The order of expansion velocities for various species is {V}{{{C}}+}> {V}{{H}}> {V}{{{Si}}+}> {V}{{Li}}> {V}{{Mo}}> {V}{{W}}. These results could be attributed to the plasma sheath acceleration and mass effect. In addition, an optimum signal-to-background ratio was investigated by varying both delay time and detecting position.

  18. Highly sensitive monitoring of chest wall dynamics and acoustics provides diverse valuable information for evaluating ventilation and diagnosing pneumothorax.

    Science.gov (United States)

    Pesin, Jimy; Faingersh, Anna; Waisman, Dan; Landesberg, Amir

    2014-06-15

    Current practice of monitoring lung ventilation in neonatal intensive care units, utilizing endotracheal tube pressure and flow, end-tidal CO2, arterial O2 saturation from pulse oximetry, and hemodynamic indexes, fails to account for asymmetric pathologies and to allow for early detection of deteriorating ventilation. This study investigated the utility of bilateral measurements of chest wall dynamics and sounds, in providing early detection of changes in the mechanics and distribution of lung ventilation. Nine healthy New Zealand rabbits were ventilated at a constant pressure, while miniature accelerometers were attached to each side of the chest. Slowly progressing pneumothorax was induced by injecting 1 ml/min air into the pleural space on either side of the chest. The end of the experiment (tPTX) was defined when arterial O2 saturation from pulse oximetry dropped acoustics provide novel information that is sensitive to asymmetric changes in ventilation, enabling early detection and localization of pneumothorax. Copyright © 2014 the American Physiological Society.

  19. Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

    Energy Technology Data Exchange (ETDEWEB)

    Li, Huan [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Tang, Xiaobin, E-mail: tangxiaobin@nuaa.edu.cn [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Jiangsu Key Laboratory of Nuclear Energy Equipment Materials Engineering, Nanjing (China); Chen, Feida; Huang, Hai; Liu, Jian [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Chen, Da [Department of Nuclear Science & Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing (China); Jiangsu Key Laboratory of Nuclear Energy Equipment Materials Engineering, Nanjing (China)

    2016-07-01

    Highlights: • Various incident sites of CNTs are classified into three types for the first time. • Different ion energies and fluences are considered to study the radiation damage. • CNTs have ability to heal the radiation-induced damage at higher temperature. • Stability of a large-diameter tube excels in a slim one under the same conditions. - Abstract: The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

  20. Glottis effects on the cough clearance process simulated with a CFD dynamic mesh and Eulerian wall film model.

    Science.gov (United States)

    Paz, Concepción; Suárez, Eduardo; Parga, Oscar; Vence, Jesús

    2017-09-01

    In this study, we have reproduced the cough clearance process with an Eulerian wall film model. The simulated domain is based on realistic geometry from the literature, which has been improved by adding the glottis and epiglottis. The vocal fold movement has been included due to the dynamic mesh method, considering different abduction and adduction angles and velocities. The proposed methodology captures the deformation of the flexible tissue, considers non-Newtonian properties for the mucus, and enables us to reproduce a single cough or a cough epoch. The cough efficiency (CE) has been used to quantify the overall performance of the cough, considering many different boundary conditions, for the analysis of the glottis effect. It was observed that a viscous shear force is the main mechanism in the cough clearance process, while the glottis closure time and the epiglottis position do not have a significant effect on the CE. The cough assistance devices improve the CE, and the enhancement rate grows logarithmically with the operating pressure. The cough can achieve an effective mucus clearance process, even with a fixed glottis. Nevertheless, the glottis closure substantially improves the CE results.

  1. The influence of covering a germanium nanowire with a single wall carbon nanotube on mechanical properties: A molecular dynamics study

    Science.gov (United States)

    Abdollahi, M.; Davoodi, J.

    2017-07-01

    Semiconductor nanowires are potential candidates for applications in quantum information processing, Josephson junctions, and field-effect transistors. Therefore, this study focused on the effects of covering a germanium nanowire (GeNW) with a single wall carbon nanotube (CNT) on the stress-strain diagram, failure points, and Young's modulus using molecular dynamics simulations. To describe the interactions between atoms in the system, we used Tersoff potential. Also, a Nose-Hoover thermostat was employed to control temperature of the system. The stress-strain curves of GeNW and GeNW inside CNT (CNT-GeNW) were obtained at various temperatures, radii, and strain velocities. It was found that coverage of GeNW with CNT led to 2-6 fold improved Young's modulus. It was also determined that a significant part of the Young's modulus in CNT-GeNW is due to the presence of CNT. Moreover, we defined the behavior of Young's modulus of GeNW as well as CNT-GeNW in the [100], [110], and [111] crystallography direction and found that Young's modulus decreased with increasing temperature. In addition, by increasing strain velocity, Young's modulus decreased for GeNW but increased for CNT-GeNW. Finally, we observed that when a GeNW is covered by a CNT, its failure point increased as compared with GeNW.

  2. A dynamic response regulator protein modulates G-protein-dependent polarity in the bacterium Myxococcus xanthus.

    Directory of Open Access Journals (Sweden)

    Yong Zhang

    Full Text Available Migrating cells employ sophisticated signal transduction systems to respond to their environment and polarize towards attractant sources. Bacterial cells also regulate their polarity dynamically to reverse their direction of movement. In Myxococcus xanthus, a GTP-bound Ras-like G-protein, MglA, activates the motility machineries at the leading cell pole. Reversals are provoked by pole-to-pole switching of MglA, which is under the control of a chemosensory-like signal transduction cascade (Frz. It was previously known that the asymmetric localization of MglA at one cell pole is regulated by MglB, a GTPase Activating Protein (GAP. In this process, MglB specifically localizes at the opposite lagging cell pole and blocks MglA localization at that pole. However, how MglA is targeted to the leading pole and how Frz activity switches the localizations of MglA and MglB synchronously remained unknown. Here, we show that MglA requires RomR, a previously known response regulator protein, to localize to the leading cell pole efficiently. Specifically, RomR-MglA and RomR-MglB complexes are formed and act complementarily to establish the polarity axis, segregating MglA and MglB to opposite cell poles. Finally, we present evidence that Frz signaling may regulate MglA localization through RomR, suggesting that RomR constitutes a link between the Frz-signaling and MglAB polarity modules. Thus, in Myxococcus xanthus, a response regulator protein governs the localization of a small G-protein, adding further insight to the polarization mechanism and suggesting that motility regulation evolved by recruiting and combining existing signaling modules of diverse origins.

  3. A novel peptidoglycan binding protein crucial for PBP1A-mediated cell wall biogenesis in Vibrio cholerae.

    Directory of Open Access Journals (Sweden)

    Tobias Dörr

    2014-06-01

    Full Text Available The bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG, is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA, which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A-encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.

  4. DNA topoisomerase II is involved in regulation of cyst wall protein genes and differentiation in Giardia lamblia.

    Science.gov (United States)

    Lin, Bo-Chi; Su, Li-Hsin; Weng, Shih-Che; Pan, Yu-Jiao; Chan, Nei-Li; Li, Tsai-Kun; Wang, Hsin-Chih; Sun, Chin-Hung

    2013-01-01

    The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission. Expression of the cyst wall protein (cwp) genes increases with similar kinetics during encystation. However, little is known how their gene regulation shares common mechanisms. DNA topoisomerases maintain normal topology of genomic DNA. They are necessary for cell proliferation and tissue development as they are involved in transcription, DNA replication, and chromosome condensation. A putative topoisomerase II (topo II) gene has been identified in the G. lamblia genome. We asked whether Topo II could regulate Giardia encystation. We found that Topo II was present in cell nuclei and its gene was up-regulated during encystation. Topo II has typical ATPase and DNA cleavage activity of type II topoisomerases. Mutation analysis revealed that the catalytic important Tyr residue and cleavage domain are important for Topo II function. We used etoposide-mediated topoisomerase immunoprecipitation assays to confirm the binding of Topo II to the cwp promoters in vivo. Interestingly, Topo II overexpression increased the levels of cwp gene expression and cyst formation. Microarray analysis identified up-regulation of cwp and specific vsp genes by Topo II. We also found that the type II topoisomerase inhibitor etoposide has growth inhibition effect on Giardia. Addition of etoposide significantly decreased the levels of cwp gene expression and cyst formation. Our results suggest that Topo II has been functionally conserved during evolution and that Topo II plays important roles in induction of the cwp genes, which is key to Giardia differentiation into cysts.

  5. Defective Pollen Wall is Required for Anther and Microspore Development in Rice and Encodes a Fatty Acyl Carrier Protein Reductase

    Energy Technology Data Exchange (ETDEWEB)

    Shi, J.; Shanklin, J.; Tan, H.; Yu, X.-H.; Liu, Y.; Liang, W.; Ranathunge, K.; Franke, R. B.; Schreiber, L.; Wang, Y.; Kai, G.; Ma, H.; Zhang, D.

    2011-06-01

    Aliphatic alcohols naturally exist in many organisms as important cellular components; however, their roles in extracellular polymer biosynthesis are poorly defined. We report here the isolation and characterization of a rice (Oryza sativa) male-sterile mutant, defective pollen wall (dpw), which displays defective anther development and degenerated pollen grains with an irregular exine. Chemical analysis revealed that dpw anthers had a dramatic reduction in cutin monomers and an altered composition of cuticular wax, as well as soluble fatty acids and alcohols. Using map-based cloning, we identified the DPW gene, which is expressed in both tapetal cells and microspores during anther development. Biochemical analysis of the recombinant DPW enzyme shows that it is a novel fatty acid reductase that produces 1-hexadecanol and exhibits >270-fold higher specificity for palmiltoyl-acyl carrier protein than for C16:0 CoA substrates. DPW was predominantly targeted to plastids mediated by its N-terminal transit peptide. Moreover, we demonstrate that the monocot DPW from rice complements the dicot Arabidopsis thaliana male sterile2 (ms2) mutant and is the probable ortholog of MS2. These data suggest that DPWs participate in a conserved step in primary fatty alcohol synthesis for anther cuticle and pollen sporopollenin biosynthesis in monocots and dicots.

  6. The Staphylococcus aureus Cell Wall-Anchored Protein Clumping Factor A Is an Important T Cell Antigen.

    Science.gov (United States)

    Lacey, Keenan A; Leech, John M; Lalor, Stephen J; McCormack, Niamh; Geoghegan, Joan A; McLoughlin, Rachel M

    2017-12-01

    Staphylococcus aureus has become increasingly resistant to antibiotics, and vaccines offer a potential solution to this epidemic of antimicrobial resistance. Targeting of specific T cell subsets is now considered crucial for next-generation anti- S. aureus vaccines; however, there is a paucity of information regarding T cell antigens of S. aureus This study highlights the importance of cell wall-anchored proteins as human CD4 + T cell activators capable of driving antigen-specific Th1 and Th17 cell activation. Clumping factor A (ClfA), which contains N1, N2, and N3 binding domains, was found to be a potent human T cell activator. We further investigated which subdomains of ClfA were involved in T cell activation and found that the full-length ClfA N123 and N23 were potent Th1 and Th17 activators. Interestingly, the N1 subdomain was capable of exclusively activating Th1 cells. Furthermore, when these subdomains were used in a model vaccine, N23 and N1 offered Th1- and Th17-mediated systemic protection in mice upon intraperitoneal challenge. Overall, however, full-length ClfA N123 is required for maximal protection both locally and systemically. Copyright © 2017 Lacey et al.

  7. Large-scale proteomic analysis of the grapevine leaf apoplastic fluid reveals mainly stress-related proteins and cell wall modifying enzymes.

    Science.gov (United States)

    Delaunois, Bertrand; Colby, Thomas; Belloy, Nicolas; Conreux, Alexandra; Harzen, Anne; Baillieul, Fabienne; Clément, Christophe; Schmidt, Jürgen; Jeandet, Philippe; Cordelier, Sylvain

    2013-02-08

    The extracellular space or apoplast forms a path through the whole plant and acts as an interface with the environment. The apoplast is composed of plant cell wall and space within which apoplastic fluid provides a means of delivering molecules and facilitates intercellular communications. However, the apoplastic fluid extraction from in planta systems remains challenging and this is particularly true for grapevine (Vitis vinifera L.), a worldwide-cultivated fruit plant. Large-scale proteomic analysis reveals the protein content of the grapevine leaf apoplastic fluid and the free interactive proteome map considerably facilitates the study of the grapevine proteome. To obtain a snapshot of the grapevine apoplastic fluid proteome, a vacuum-infiltration-centrifugation method was optimized to collect the apoplastic fluid from non-challenged grapevine leaves. Soluble apoplastic protein patterns were then compared to whole leaf soluble protein profiles by 2D-PAGE analyses. Subsequent MALDI-TOF/TOF mass spectrometry of tryptically digested protein spots was used to identify proteins. This large-scale proteomic analysis established a well-defined proteomic map of whole leaf and leaf apoplastic soluble proteins, with 223 and 177 analyzed spots, respectively. All data arising from proteomic, MS and MS/MS analyses were deposited in the public database world-2DPAGE. Prediction tools revealed a high proportion of (i) classical secreted proteins but also of non-classical secreted proteins namely Leaderless Secreted Proteins (LSPs) in the apoplastic protein content and (ii) proteins potentially involved in stress reactions and/or in cell wall metabolism. This approach provides free online interactive reference maps annotating a large number of soluble proteins of the whole leaf and the apoplastic fluid of grapevine leaf. To our knowledge, this is the first detailed proteome study of grapevine apoplastic fluid providing a comprehensive overview of the most abundant proteins

  8. An oligogalacturonide-derived molecular probe demonstrates the dynamics of calcium-mediated pectin complexation in cell walls of tip-growing structures

    DEFF Research Database (Denmark)

    Mravec, Jozef; Kracun, Stjepan Kresimir; Rydahl, Maja Gro

    2017-01-01

    Pectic homogalacturonan (HG) is one of the main constituents of plant cell walls. When processed to low degrees of esterification, HG can form complexes with divalent calcium ions. These macromolecular structures (also called egg boxes) play an important role in determining the biomechanics of cell...... walls and in mediating cell-to-cell adhesion. Current immunological methods enable only steady-state detection of egg box formation in situ. Here we present a tool for efficient real-time visualisation of available sites for HG crosslinking within cell wall microdomains. Our approach is based on calcium...... thermodynamic model. Using defined carbohydrate microarrays, we show that the long OG probe binds exclusively to HG that has a very low degree of esterification and in the presence of divalent ions. We used this probe to study real-time dynamics of HG during elongation of Arabidopsis pollen tubes and root hairs...

  9. On the vibrational behavior of single- and double-walled carbon nanotubes under the physical adsorption of biomolecules in the aqueous environment: a molecular dynamics study.

    Science.gov (United States)

    Ajori, S; Ansari, R; Darvizeh, M

    2016-03-01

    The adsorption of biomolecules on the walls of carbon nanotubes (CNTs) in an aqueous environment is of great importance in the field of nanobiotechnology. In this study, molecular dynamics (MD) simulations were performed to understand the mechanical vibrational behavior of single- and double-walled carbon nanotubes (SWCNTs and DWCNTs) under the physical adsorption of four important biomolecules (L-alanine, guanine, thymine, and uracil) in vacuum and an aqueous environment. It was observed that the natural frequencies of these CNTs in vacuum reduce under the physical adsorption of biomolecules. In the aqueous environment, the natural frequency of each pure CNT decreased as compared to its natural frequency in vacuum. It was also found that the frequency shift for functionalized CNTs as compared to pure CNTs in the aqueous environment was dependent on the radius and the number of walls of the CNT, and could be positive or negative.

  10. Relaxation processes and glass transition of confined polymer melts: A molecular dynamics simulation of 1,4-polybutadiene between graphite walls

    Science.gov (United States)

    Solar, M.; Binder, K.; Paul, W.

    2017-05-01

    Molecular dynamics simulations of a chemically realistic model for 1,4-polybutadiene in a thin film geometry confined by two graphite walls are presented. Previous work on melts in the bulk has shown that the model faithfully reproduces static and dynamic properties of the real material over a wide temperature range. The present work studies how these properties change due to nano-confinement. The focus is on orientational correlations observable in nuclear magnetic resonance experiments and on the local intermediate incoherent neutron scattering function, Fs(qz, z, t), for distances z from the graphite walls in the range of a few nanometers. Temperatures from about 2Tg down to about 1.15Tg, where Tg is the glass transition temperature in the bulk, are studied. It is shown that weakly attractive forces between the wall atoms and the monomers suffice to effectively bind a polymer coil that is near the wall. For a wide regime of temperatures, the Arrhenius-like adsorption/desorption kinetics of the monomers is the slowest process, while very close to Tg the Vogel-Fulcher-Tammann-like α-relaxation takes over. The α-process is modified only for z ≤1.2 nm due to the density changes near the walls, less than expected from studies of coarse-grained (bead-spring-type) models. The weakness of the surface effects on the glass transition in this case is attributed to the interplay of density changes near the wall with the torsional potential. A brief discussion of pertinent experiments is given.

  11. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structu...

  12. IMPACT OF DYNAMICAL HYDRATION SHELL AROUND HA PROTEIN ON NONLINEAR CONCENTRATION DEPENDENT T-RAYS ABSORPTION

    Directory of Open Access Journals (Sweden)

    YIWEN SUN

    2013-10-01

    Full Text Available T-rays is sensitive to covalently cross-linked proteins and can be used to probe unique dynamic properties of water surrounding a protein. In this paper, we demonstrate the unique absorption properties of the dynamic hydration shells determined by hemagglutinin (HA protein in terahertz frequency. We study the changes arising from different concentrations in detail and show that nonlinear absorption coefficient is induced by the dynamic hydration water. The binary and ternary component model were used to interpret the nonlinearity absorption behaviors and predict the thickness of the hydration shells around the HA protein in aqueous phase.

  13. Cell Wall Remodeling Enzymes Modulate Fungal Cell Wall Elasticity and Osmotic Stress Resistance.

    Science.gov (United States)

    Ene, Iuliana V; Walker, Louise A; Schiavone, Marion; Lee, Keunsook K; Martin-Yken, Hélène; Dague, Etienne; Gow, Neil A R; Munro, Carol A; Brown, Alistair J P

    2015-07-28

    The fungal cell wall confers cell morphology and protection against environmental insults. For fungal pathogens, the cell wall is a key immunological modulator and an ideal therapeutic target. Yeast cell walls possess an inner matrix of interlinked β-glucan and chitin that is thought to provide tensile strength and rigidity. Yeast cells remodel their walls over time in response to environmental change, a process controlled by evolutionarily conserved stress (Hog1) and cell integrity (Mkc1, Cek1) signaling pathways. These mitogen-activated protein kinase (MAPK) pathways modulate cell wall gene expression, leading to the construction of a new, modified cell wall. We show that the cell wall is not rigid but elastic, displaying rapid structural realignments that impact survival following osmotic shock. Lactate-grown Candida albicans cells are more resistant to hyperosmotic shock than glucose-grown cells. We show that this elevated resistance is not dependent on Hog1 or Mkc1 signaling and that most cell death occurs within 10 min of osmotic shock. Sudden decreases in cell volume drive rapid increases in cell wall thickness. The elevated stress resistance of lactate-grown cells correlates with reduced cell wall elasticity, reflected in slower changes in cell volume following hyperosmotic shock. The cell wall elasticity of lactate-grown cells is increased by a triple mutation that inactivates the Crh family of cell wall cross-linking enzymes, leading to increased sensitivity to hyperosmotic shock. Overexpressing Crh family members in glucose-grown cells reduces cell wall elasticity, providing partial protection against hyperosmotic shock. These changes correlate with structural realignment of the cell wall and with the ability of cells to withstand osmotic shock. The C. albicans cell wall is the first line of defense against external insults, the site of immune recognition by the host, and an attractive target for antifungal therapy. Its tensile strength is conferred by

  14. Small molecule probes for plant cell wall polysaccharide imaging

    Directory of Open Access Journals (Sweden)

    Ian eWallace

    2012-05-01

    Full Text Available Plant cell walls are composed of interlinked polymer networks consisting of cellulose, hemicelluloses, pectins, proteins, and lignin. The ordered deposition of these components is a dynamic process that critically affects the development and differentiation of plant cells. However, our understanding of cell wall synthesis and remodeling, as well as the diverse cell wall architectures that result from these processes, has been limited by a lack of suitable chemical probes that are compatible with live-cell imaging. In this review, we summarize the currently available molecular toolbox of probes for cell wall polysaccharide imaging in plants, with particular emphasis on recent advances in small molecule-based fluorescent probes. We also discuss the potential for further development of small molecule probes for the analysis of cell wall architecture and dynamics.

  15. Proteomic identification of differentially expressed proteins in aortic wall of patients with ruptured and nonruptured abdominal aortic aneurysms

    DEFF Research Database (Denmark)

    Urbonavicius, Sigitas; Lindholt, Jes S.; Vorum, Henrik

    2009-01-01

    To compare the basic proteomic composition of abdominal aortic aneurysm (AAA) wall tissue in patients with nonruptured and ruptured aneurysms.......To compare the basic proteomic composition of abdominal aortic aneurysm (AAA) wall tissue in patients with nonruptured and ruptured aneurysms....

  16. Ser/Thr motifs in transmembrane proteins: conservation patterns and effects on local protein structure and dynamics.

    Science.gov (United States)

    Del Val, Coral; White, Stephen H; Bondar, Ana-Nicoleta

    2012-11-01

    We combined systematic bioinformatics analyses and molecular dynamics simulations to assess the conservation patterns of Ser and Thr motifs in membrane proteins, and the effect of such motifs on the structure and dynamics of α-helical transmembrane (TM) segments. We find that Ser/Thr motifs are often present in β-barrel TM proteins. At least one Ser/Thr motif is present in almost half of the sequences of α-helical proteins analyzed here. The extensive bioinformatics analyses and inspection of protein structures led to the identification of molecular transporters with noticeable numbers of Ser/Thr motifs within the TM region. Given the energetic penalty for burying multiple Ser/Thr groups in the membrane hydrophobic core, the observation of transporters with multiple membrane-embedded Ser/Thr is intriguing and raises the question of how the presence of multiple Ser/Thr affects protein local structure and dynamics. Molecular dynamics simulations of four different Ser-containing model TM peptides indicate that backbone hydrogen bonding of membrane-buried Ser/Thr hydroxyl groups can significantly change the local structure and dynamics of the helix. Ser groups located close to the membrane interface can hydrogen bond to solvent water instead of protein backbone, leading to an enhanced local solvation of the peptide.

  17. Cdc1 removes the ethanolamine phosphate of the first mannose of GPI anchors and thereby facilitates the integration of GPI proteins into the yeast cell wall.

    Science.gov (United States)

    Vazquez, Hector M; Vionnet, Christine; Roubaty, Carole; Conzelmann, Andreas

    2014-11-01

    Temperature-sensitive cdc1(ts) mutants are reported to stop the cell cycle upon a shift to 30°C in early G2, that is, as small budded cells having completed DNA replication but unable to duplicate the spindle pole body. A recent report showed that PGAP5, a human homologue of CDC1, acts as a phosphodiesterase removing an ethanolamine phosphate (EtN-P) from mannose 2 of the glycosylphosphatidylinositol (GPI) anchor, thus permitting efficient endoplasmic reticulum (ER)-to-Golgi transport of GPI proteins. We find that the essential CDC1 gene can be deleted in mcd4∆ cells, which do not attach EtN-P to mannose 1 of the GPI anchor, suggesting that Cdc1 removes the EtN-P added by Mcd4. Cdc1-314(ts) mutants do not accumulate GPI proteins in the ER but have a partial secretion block later in the secretory pathway. Growth tests and the genetic interaction profile of cdc1-314(ts) pinpoint a distinct cell wall defect. Osmotic support restores GPI protein secretion and actin polarization but not growth. Cell walls of cdc1-314(ts) mutants contain large amounts of GPI proteins that are easily released by β-glucanases and not attached to cell wall β1,6-glucans and that retain their original GPI anchor lipid. This suggests that the presumed transglycosidases Dfg5 and Dcw1 of cdc1-314(ts) transfer GPI proteins to cell wall β1,6-glucans inefficiently. © 2014 Vazquez et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  18. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

    Science.gov (United States)

    van der Vaart, Arjan

    2015-05-01

    Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  19. Concentration dependence of dynamic moduli of heat-induced soy protein gels

    NARCIS (Netherlands)

    Renkema, J.M.S.; Vliet, van T.

    2004-01-01

    The concentration dependence of dynamic moduli of soy protein gels was studied for different protein preparations (soy protein isolate), purified glycinin and a -conglycinin rich fraction) at various pHs and salt concentrations. The concentration dependence of the storage modulus of glycinin and

  20. Interaction of a streptococcal cell wall tetraheteroglycan and Salmonella telaviv lipopolysaccharide with polymeric McPC 870 and MOPC 384 mouse IgA myeloma proteins.

    Science.gov (United States)

    Allen, P Z; Pazur, J H

    1984-11-01

    Interactions of polymeric McPC 870 and MOPC 384 mouse IgA myeloma proteins with a streptococcal cell wall tetraheteroglycan (T4-antigen), Salmonella tranoroa lipopolysaccharide (LPS), S. telaviv LPS and its lipid A free polysaccharide were examined by the quantitative precipitin method. Hapten inhibition of myeloma protein precipitation by T4-antigen or S. telaviv LPS indicates a complex anticarbohydrate specificity for 870 and 384 protein combining sites involving several sugars. While the combining site of 870 protein appears to bind alpha-D-mannopyranosyl, alpha-D-galactopyranosyl and alpha-D-glucopyranosyl residues, the combining site of 384 protein can accommodate both the alpha (1----2)-linked glucobiose (kojibiose) and alpha-D-galactopyranosyl but not the alpha-D-mannopyranosyl structure.

  1. Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiments

    Directory of Open Access Journals (Sweden)

    Cushman Mark

    2003-12-01

    Full Text Available Abstract Background Riboflavin synthase catalyzes the transformation of 6,7-dimethyl-8-ribityllumazine into riboflavin in the last step of the riboflavin biosynthetic pathway. Gram-negative bacteria and certain yeasts are unable to incorporate riboflavin from the environment and are therefore absolutely dependent on endogenous synthesis of the vitamin. Riboflavin synthase is therefore a potential target for the development of antiinfective drugs. Results A cDNA sequence from Schizosaccharomyces pombe comprising a hypothetical open reading frame with similarity to riboflavin synthase of Escherichia coli was expressed in a recombinant E. coli strain. The recombinant protein is a homotrimer of 23 kDa subunits as shown by sedimentation equilibrium centrifugation. The protein sediments at an apparent velocity of 4.1 S at 20°C. The amino acid sequence is characterized by internal sequence similarity indicating two similar folding domains per subunit. The enzyme catalyzes the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a rate of 158 nmol mg-1 min-1 with an apparent KM of 5.7 microM. 19F NMR protein perturbation experiments using fluorine-substituted intermediate analogs show multiple signals indicating that a given ligand can be bound in at least 4 different states. 19F NMR signals of enzyme-bound intermediate analogs were assigned to ligands bound by the N-terminal respectively C-terminal folding domain on basis of NMR studies with mutant proteins. Conclusion Riboflavin synthase of Schizosaccharomyces pombe is a trimer of identical 23-kDa subunits. The primary structure is characterized by considerable similarity of the C-terminal and N-terminal parts. Riboflavin synthase catalyzes a mechanistically complex dismutation of 6,7-dimethyl-8-ribityllumazine affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H-pyrimidinedione. The 19F NMR data suggest large scale dynamic mobility in the trimeric protein which may play an important

  2. Staphylococcus aureus Colonization of the Mouse Gastrointestinal Tract Is Modulated by Wall Teichoic Acid, Capsule, and Surface Proteins.

    Directory of Open Access Journals (Sweden)

    Yoshiki Misawa

    2015-07-01

    Full Text Available Staphylococcus aureus colonizes the nose, throat, skin, and gastrointestinal (GI tract of humans. GI carriage of S. aureus is difficult to eradicate and has been shown to facilitate the transmission of the bacterium among individuals. Although staphylococcal colonization of the GI tract is asymptomatic, it increases the likelihood of infection, particularly skin and soft tissue infections caused by USA300 isolates. We established a mouse model of persistent S. aureus GI colonization and characterized the impact of selected surface antigens on colonization. In competition experiments, an acapsular mutant colonized better than the parental strain Newman, whereas mutants defective in sortase A and clumping factor A showed impaired ability to colonize the GI tract. Mutants lacking protein A, clumping factor B, poly-N-acetyl glucosamine, or SdrCDE showed no defect in colonization. An S. aureus wall teichoic acid (WTA mutant (ΔtagO failed to colonize the mouse nose or GI tract, and the tagO and clfA mutants showed reduced adherence in vitro to intestinal epithelial cells. The tagO mutant was recovered in lower numbers than the wild type strain in the murine stomach and duodenum 1 h after inoculation. This reduced fitness correlated with the in vitro susceptibility of the tagO mutant to bile salts, proteases, and a gut-associated defensin. Newman ΔtagO showed enhanced susceptibility to autolysis, and an autolysin (atl tagO double mutant abrogated this phenotype. However, the atl tagO mutant did not survive better in the mouse GI tract than the tagO mutant. Our results indicate that the failure of the tagO mutant to colonize the GI tract correlates with its poor adherence and susceptibility to bactericidal factors within the mouse gut, but not to enhanced activity of its major autolysin.

  3. DNA Topoisomerase II Is Involved in Regulation of Cyst Wall Protein Genes and Differentiation in Giardia lamblia

    Science.gov (United States)

    Lin, Bo-Chi; Pan, Yu-Jiao; Chan, Nei-Li; Li, Tsai-Kun; Wang, Hsin-Chih; Sun, Chin-Hung

    2013-01-01

    The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission. Expression of the cyst wall protein (cwp) genes increases with similar kinetics during encystation. However, little is known how their gene regulation shares common mechanisms. DNA topoisomerases maintain normal topology of genomic DNA. They are necessary for cell proliferation and tissue development as they are involved in transcription, DNA replication, and chromosome condensation. A putative topoisomerase II (topo II) gene has been identified in the G. lamblia genome. We asked whether Topo II could regulate Giardia encystation. We found that Topo II was present in cell nuclei and its gene was up-regulated during encystation. Topo II has typical ATPase and DNA cleavage activity of type II topoisomerases. Mutation analysis revealed that the catalytic important Tyr residue and cleavage domain are important for Topo II function. We used etoposide-mediated topoisomerase immunoprecipitation assays to confirm the binding of Topo II to the cwp promoters in vivo. Interestingly, Topo II overexpression increased the levels of cwp gene expression and cyst formation. Microarray analysis identified up-regulation of cwp and specific vsp genes by Topo II. We also found that the type II topoisomerase inhibitor etoposide has growth inhibition effect on Giardia. Addition of etoposide significantly decreased the levels of cwp gene expression and cyst formation. Our results suggest that Topo II has been functionally conserved during evolution and that Topo II plays important roles in induction of the cwp genes, which is key to Giardia differentiation into cysts. PMID:23696909

  4. Microparticle shape effects on margination, near-wall dynamics and adhesion in a three-dimensional simulation of red blood cell suspension.

    Science.gov (United States)

    Vahidkhah, Koohyar; Bagchi, Prosenjit

    2015-03-21

    We present a 3D computational modeling study of the transport of micro-scale drug carriers modeled as microparticles of different shapes (spherical, oblate, and prolate) in whole blood represented as a suspension of deformable red blood cells. The objective is to quantify the effect of microparticle shapes on their margination, near-wall dynamics and adhesion. We observe that the near-wall accumulation is highest for oblate particles of moderate aspect ratio, followed by spherical particles, and lowest for very elongated prolate particles. The result is explained using micro-scale dynamics of individual particles, and their interaction with red blood cells. We observe that the orientation of microparticles in 3D space and the frequency of their collisions with red blood cells are the key factors affecting their margination. We show that due to repeated collisions with red blood cells in the presence of a bounding wall, the axes of revolution of oblate particles align near the plane of the shear flow, but those of prolate particles shift towards the vorticity axis with a wider distribution. Such specific orientations lead to more frequent collisions and a greater lateral drift for oblate particles than microspheres, but less frequent collisions and a reduced lateral drift for elongated prolate particles, resulting in the observed differences in their near-wall accumulation. Once marginated, the particle shape has an entirely different effect on the likelihood of making particle-wall contacts. We find that marginated prolate particles, due to their alignment along the vorticity axis and large angular fluctuations, are more likely to make contacts with the wall than spherical and oblate particles. We further simulate the adhesion between flowing microparticles and the wall in the presence of red blood cells, and observe that once wall contacts are established, the likelihood of firm adhesion is greater for disk-like particles, followed by elongated prolates, and

  5. PcExl1 a novel acid expansin-like protein from the plant pathogen Pectobacterium carotovorum, binds cell walls differently to BsEXLX1.

    Directory of Open Access Journals (Sweden)

    Miguel Olarte-Lozano

    Full Text Available Microbial expansins act on plant cell walls similarly to plant expansins, albeit their loosening activity levels are tenfold lesser compared to plant expansins. We report the characterization of an expansin-like gene from the plant pathogen Pectobacterium carotovorum, named exl1. PcExl1 is an acidic protein that binds cellulose (Avicel, and weakens filter paper. The acidic nature of PcExl1 confers different binding properties when compared to Bacillus subtilis BsEXLX1, which is a basic protein. PcExl1 binding to wheat cell wall increased when acidic components were depleted, reaching a similar level to the binding to Avicel, indicating that cellulose is the target of PcExl1.

  6. Production of mycobacterial cell wall glycopeptidolipids requires a member of the MbtH-like protein family

    Directory of Open Access Journals (Sweden)

    Tatham Elizabeth

    2012-06-01

    Full Text Available Abstract Background Glycopeptidolipids (GPLs are among the major free glycolipid components of the outer membrane of several saprophytic and clinically-relevant Mycobacterium species. The architecture of GPLs is based on a constant tripeptide-amino alcohol core of nonribosomal peptide synthetase origin that is N-acylated with a 3-hydroxy/methoxy acyl chain synthesized by a polyketide synthase and further decorated with variable glycosylation patterns built from methylated and acetylated sugars. GPLs have been implicated in many aspects of mycobacterial biology, thus highlighting the significance of gaining an understanding of their biosynthesis. Our bioinformatics analysis revealed that every GPL biosynthetic gene cluster known to date contains a gene (referred herein to as gplH encoding a member of the MbtH-like protein family. Herein, we sought to conclusively establish whether gplH was required for GPL production. Results Deletion of gplH, a gene clustered with nonribosomal peptide synthetase-encoding genes in the GPL biosynthetic gene cluster of Mycobacterium smegmatis, produced a GPL deficient mutant. Transformation of this mutant with a plasmid expressing gplH restored GPL production. Complementation was also achieved by plasmid-based constitutive expression of mbtH, a paralog of gplH found in the biosynthetic gene cluster for production of the siderophore mycobactin of M. smegmatis. Further characterization of the gplH mutant indicated that it also displayed atypical colony morphology, lack of sliding motility, altered capacity for biofilm formation, and increased drug susceptibility. Conclusions Herein, we provide evidence formally establishing that gplH is essential for GPL production in M. smegmatis. Inactivation of gplH also leads to a pleiotropic phenotype likely to arise from alterations in the cell envelope due to the lack of GPLs. While genes encoding MbtH-like proteins have been shown to be needed for production of siderophores

  7. Immunological study on the wall proteins of different fruiting portions in Pleurotus ostreatus (Jacq. ex Fr.) Kummer and Agaricus bisporus (Lge.) Sing.

    Science.gov (United States)

    Tedesco, G; Marchi, A; Gerola, F M

    1983-01-01

    Immunological techniques are useful to clarify the sistematic scheme utilized for mushrooms. By comparing the various fruiting portions, a different composition in protein was observed in the cell wall of spores, pileus and stipe. The differences were present both in Agaricus bisporus and in Pleurotus ostreatus. The results indicate that a well definite choice of the utilized portions is necessary for comparative studies. In the Basidiomycetes the meiospores represent the more useful development stage to carry out immunological comparisons.

  8. Modelling Protein Dynamics on the Microsecond Time Scale

    DEFF Research Database (Denmark)

    Siuda, Iwona Anna

    ELNEDIN was therefore proposed as part of the work. Iwona Siuda’s results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins...

  9. Modeling and molecular dynamics simulation of PR-1 protein from ...

    African Journals Online (AJOL)

    Pathogenesis-related (PR) proteins are considered as major weapons in plant's defense tactics against pathogens. The PR-1protein of Solanum tuberosum forms an integral part of the host defense system. We present here the 3D structure of PR-1 protein of S. tuberosum based on homology modeling technique.

  10. Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

    Directory of Open Access Journals (Sweden)

    Xianjun Shen

    Full Text Available How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment. It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.

  11. A benchmark study for the crown-type splashing dynamics of one- and two-component droplet wall-film interactions

    Science.gov (United States)

    Geppert, A.; Terzis, A.; Lamanna, G.; Marengo, M.; Weigand, B.

    2017-12-01

    The present paper investigates experimentally the impact dynamics of crown-type splashing for miscible two- and one-component droplet wall-film interactions over a range of Weber numbers and dimensionless film thicknesses. The splashing outcome is parametrised in terms of a set of quantifiable parameters, such as crown height, top and base diameter, wall inclination, number of fingers, and secondary droplet properties. The results show that the outcome of a splashing event is not affected by the choice of similar or dissimilar fluids, provided the dimensionless film thickness is larger than 0.1. Below this threshold, distinctive features of two-component interactions appear, such as hole formation and crown bottom breakdown. The observation of different crown shapes (e.g. V-shaped, cylindrical, and truncated-cone) confirms that vorticity production induces changes in the crown wall inclination, thus affecting the evolution of the crown height and top diameter. The evolution of the crown base diameter, instead, is mainly dependent on the relative importance of liquid inertia and viscous losses in the wall-film. The maximum number of liquid fingers decreases with increasing wall, film thickness, due to the enhanced attenuation of the effect of surface properties on the fingering process. The formation of secondary droplets is also affected by changes in the crown wall inclination. In particular, for truncated-cone shapes the occurrence of crown rim contraction induces a large scatter in the secondary droplet properties. Consequently, empirical models for the maximum number and mean diameter of the secondary droplets are derived for V-shaped crowns, as observed for the hexadecane-Hyspin interactions.

  12. Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

    Science.gov (United States)

    Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

    2017-01-01

    Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

  13. Vortex dynamics and elliptical structure wake interaction in the proximity of wall using 2-D RANS simulation

    Directory of Open Access Journals (Sweden)

    Arunkumar H. S.

    2018-01-01

    Full Text Available The 2-D numerical study is performed to analyses the flow characteristic behind the elliptical structure placed near the wall for three different gap ratios as 0.25, 0.5, and 1.0. Computational domain and model is initially validated with the unbounded flow over a cylinder without considering wall effect for Reynolds number of 3900. For flow over the cylinder with near wall, computational domain is modelled as Blasius profile is the input to the area of interest. At different gap ratios the effect of boundary layer on vortex shedding is studied with Reynolds number of 1440. By applying different turbulent model for analysis, study the variation in the results and suggest the suitable model for the present type of study. It has been observed that the wall effect is predominant in case of the gap ratio of 0.25 as compared to other gap ratios.

  14. Exploring the common dynamics of homologous proteins. Application to the globin family.

    Science.gov (United States)

    Maguid, Sandra; Fernandez-Alberti, Sebastian; Ferrelli, Leticia; Echave, Julian

    2005-07-01

    We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian network model analysis. After the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe these dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features.

  15. Proteome of cell wall-extracts from pathogenic Paracoccidioides brasiliensis: Comparison among morphological phases, isolates, and reported fungal extracellular vesicle proteins

    Directory of Open Access Journals (Sweden)

    Larissa V.G. Longo

    2014-06-01

    Full Text Available We identified non-covalently linked cell wall proteins from Paracoccidioides brasiliensis yeasts and mycelia, with focus on the yeast pathogenic phase, and correlated them with reported fungal extracellular vesicle proteins. We studied isolates Pb3 and Pb18, which evoke distinct patterns of experimental paracoccidioidomycosis and represent two phylogenetic groups. Proteins were extracted mildly with dithiothreitol, trypsinized, and peptides analyzed by liquid chromatography coupled to high-resolution mass spectrometry. Among 132 yeast-exclusive sequences, 92 were Pb18-exclusive. About 80% of total proteins were classified as secretory, mostly showing non-conventional signals. Extracellular vesicular transportation could be involved, since 60% had orthologs reported in fungal extracellular vesicles.

  16. Heme proteins: the role of solvent in the dynamics of gates and portals.

    Science.gov (United States)

    Scorciapino, Mariano Andrea; Robertazzi, Arturo; Casu, Mariano; Ruggerone, Paolo; Ceccarelli, Matteo

    2010-04-14

    Water plays a pivotal role in the correct functioning of proteins. Hydration is fundamental to their stability and flexibility, to folding process and specific functions, and to protein-protein interactions. In this work, the effects of solvation on proteins dynamics have been investigated by employing molecular dynamics simulations and using myoglobin as a model system. The investigation has been focused on solvent waters residing around/inside the protein, with average times of up to tens of nanoseconds, revealing that these slow waters may have significant effects on biological functioning of the protein. Our study pointed out that water is able to interact with proteins in diverse ways, leading to different kinds of perturbations in their intrinsic dynamic behavior. In particular, for myoglobin it was found that a water molecule can (i) "block" entry/escape of ligands to/from a particular docking site, (ii) act as a "wedge" modulating the dynamics of internal cavities, or (iii) join a "flow" of waters taking a ligand into (or "washing" a ligand away from) the protein interior. The information gathered in this work allowed us to provide a fingerprint of protein solvation state, the hydration sites map, which may represent a novel tool for comparing different forms/species of globular proteins.

  17. Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield.

    Science.gov (United States)

    Bhadra, Pratiti; Pal, Debnath

    2017-04-01

    Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Surface polyethylene glycol conformation influences the protein corona of polyethylene glycol-modified single-walled carbon nanotubes: potential implications on biological performance.

    Science.gov (United States)

    Sacchetti, Cristiano; Motamedchaboki, Khatereh; Magrini, Andrea; Palmieri, Graziana; Mattei, Maurizio; Bernardini, Sergio; Rosato, Nicola; Bottini, Nunzio; Bottini, Massimo

    2013-03-26

    Investigation of the nanoparticle protein corona, the shell of plasma proteins formed around nanoparticles immediately after they enter the bloodstream, is a benchmark in the study of the applications of nanoparticles in all fields of medicine, from pharmacology to toxicology. We report the first investigation of the protein corona adsorbed onto single-walled carbon nanotubes modified with 2 kDa molecular weight polyethylene glycol chains [PEG(2k)-modified SWCNTs or PEG2-SWCNTs] by using a large-scale gel-based proteomics method on biological replicates. More than 240 plasma proteins were selected, and their differences were analyzed among PEG2-SWCNTs differing in surface charge and PEG conformation. The protein corona of PEG2-SWCNTs showed that coagulation proteins, immunoglobulins, apolipoproteins, and proteins of the complement system were among the proteins bound by PEG2-SWCNTs and that their recruitment was independent from the isoelectric point, molecular weight, total hydrophobicity, and number of polyaromatic residues of the proteins. Statistical analysis on protein relative abundance revealed that PEG conformation had a higher influence on the PEG2-SWCNTs' protein corona repertoire than nanotube surface charge. PEG conformation also affected the biological performance of PEG2-SWCNTs. A change in PEG conformation from mushroom to mushroom-brush transition affected the competitive adsorption of the major constituents of the protein corona of PEG2-SWCNTs and promoted shorter blood circulation time, faster renal excretion, and higher relative spleen versus liver uptake of PEG2-SWCNTs. Our data suggest that the protein corona, along with steric stabilization, may mediate the action of PEG conformation on the pharmacokinetic profile of PEG-modified SWCNTs.

  19. Development of a POC test for TB based on multiple immunodominant epitopes of M. tuberculosis specific cell-wall proteins.

    Directory of Open Access Journals (Sweden)

    Jesus M Gonzalez

    Full Text Available The need for an accurate, rapid, simple and affordable point-of-care (POC test for Tuberculosis (TB that can be implemented in microscopy centers and other peripheral health-care settings in the TB-endemic countries remains unmet. This manuscript describes preliminary results of a new prototype rapid lateral flow TB test based on detection of antibodies to immunodominant epitopes (peptides derived from carefully selected, highly immunogenic M. tuberculosis cell-wall proteins. Peptide selection was initially based on recognition by antibodies in sera from TB patients but not in PPD-/PPD+/BCG-vaccinated individuals from TB-endemic settings. The peptides were conjugated to BSA; the purified peptide-BSA conjugates striped onto nitrocellulose membrane and adsorbed onto colloidal gold particles to devise the prototype test, and evaluated for reactivity with sera from 3 PPD-, 29 PPD+, 15 PPD-unknown healthy subjects, 10 patients with non-TB lung disease and 124 smear-positive TB patients. The assay parameters were adjusted to determine positive/negative status within 15 minutes via visual or instrumented assessment. There was minimal or no reactivity of sera from non-TB subjects with the striped BSA-peptides demonstrating the lack of anti-peptide antibodies in subjects with latent TB and/or BCG vaccination. Sera from most TB patients demonstrated reactivity with one or more peptides. The sensitivity of antibody detection ranged from 28-85% with the 9 BSA-peptides. Three peptides were further evaluated with sera from 400 subjects, including additional PPD-/PPD+/PPD-unknown healthy contacts, close hospital contacts and household contacts of untreated TB patients, patients with non-TB lung disease, and HIV+TB- patients. Combination of the 3 peptides provided sensitivity and specificity>90%. While the final fully optimized lateral flow POC test for TB is under development, these preliminary results demonstrate that an antibody-detection based rapid POC

  20. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

    Science.gov (United States)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  1. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: 2H NMR studies on perdeuterated C-phycocyanin.

    Science.gov (United States)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  2. De novo inference of protein function from coarse-grained dynamics.

    Science.gov (United States)

    Bhadra, Pratiti; Pal, Debnath

    2014-10-01

    Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. © 2014 Wiley Periodicals, Inc.

  3. Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution.

    Directory of Open Access Journals (Sweden)

    Brian K Mannakee

    2016-07-01

    Full Text Available The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein's rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces.

  4. Molecular Dynamics Simulations of Protein-Tyrosine Phosphatase 1B. II. Substrate-Enzyme Interactions and Dynamics

    OpenAIRE

    Peters, Günther H.; Frimurer, Thomas M.; Andersen, Jannik N.; Olsen, Ole H.

    2000-01-01

    Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme and substrate flexibility for binding, 3) the electrostatic properties of the enzyme, and 4) the contribution from solvation. The simulations were performed for 1 ns, using explicit water molecules. The last 70...

  5. Protein analysis by dynamic light scattering: Methods and techniques for students

    National Research Council Canada - National Science Library

    Lorber, Bernard; Fischer, Frédéric; Bailly, Marc; Roy, Hervé; Kern, Daniel

    2012-01-01

    Dynamic light scattering (DLS) analyses are routinely used in biology laboratories to detect aggregates in macromolecular solutions, to determine the size of proteins, nucleic acids, and complexes or to monitor the binding of ligands...

  6. Molecular dynamics simulations of interaction between protein-tyrosine phosphatase 1B and a bidentate inhibitor

    National Research Council Canada - National Science Library

    Gui-xia LIU Jin-zhi TAN Chun-ying NIU Jian-hua SHEN Xiao-min LUO Xu SHEN Kai-xian CHEN Hua-liang JIANG

    2006-01-01

    Aim: To investigate the dynamic properties of protein-tyrosine phosphatase (PTP) IB and reveal the structural factors responsible for the high inhibitory potency and selectivity of the inhibitor SNA for PTPIB. Methods...

  7. Endocytosis optimizes the dynamic localization of membrane proteins that regulate cortical polarity.

    Science.gov (United States)

    Marco, Eugenio; Wedlich-Soldner, Roland; Li, Rong; Altschuler, Steven J; Wu, Lani F

    2007-04-20

    Diverse cell types require the ability to maintain dynamically polarized membrane-protein distributions through balancing transport and diffusion. However, design principles underlying dynamically maintained cortical polarity are not well understood. Here we constructed a mathematical model for characterizing the morphology of dynamically polarized protein distributions. We developed analytical approaches for measuring all model parameters from single-cell experiments. We applied our methods to a well-characterized system for studying polarized membrane proteins: budding yeast cells expressing activated Cdc42. We found that a balance of diffusion, directed transport, and endocytosis was sufficient for accurately describing polarization morphologies. Surprisingly, the model predicts that polarized regions are defined with a precision that is nearly optimal for measured endocytosis rates and that polarity can be dynamically stabilized through positive feedback with directed transport. Our approach provides a step toward understanding how biological systems shape spatially precise, unambiguous cortical polarity domains using dynamic processes.

  8. Whey-protein / polysaccharide coacervates : structure and dynamics

    NARCIS (Netherlands)

    Weinbreck, Fanny Chantal Jacqueline

    2004-01-01

    This thesis studied the interactions between food ingredients under acidic conditions (like in yoghurt or in soft drinks for instance). In the chapters 2, 3, and 4, the author investigated the conditions under which a complex was formed between positively charged whey proteins (proteins derived from

  9. Quantitative Fluorescence Microscopy of Protein Dynamics in Living Cells

    NARCIS (Netherlands)

    S.M. Ibrahim (Shehu)

    2006-01-01

    textabstractThe advent of confocal microscopy, fast microcomputers with high storage capacity and, moreover, the availability of fluorescent proteins of various excitation and emission properties have made fluorescence microscopy the method of choice in the study of protein behaviour in living

  10. Computational Fluid Dynamics Modeling of Steam Condensation on Nuclear Containment Wall Surfaces Based on Semiempirical Generalized Correlations

    Directory of Open Access Journals (Sweden)

    Pavan K. Sharma

    2012-01-01

    Full Text Available In water-cooled nuclear power reactors, significant quantities of steam and hydrogen could be produced within the primary containment following the postulated design basis accidents (DBA or beyond design basis accidents (BDBA. For accurate calculation of the temperature/pressure rise and hydrogen transport calculation in nuclear reactor containment due to such scenarios, wall condensation heat transfer coefficient (HTC is used. In the present work, the adaptation of a commercial CFD code with the implementation of models for steam condensation on wall surfaces in presence of noncondensable gases is explained. Steam condensation has been modeled using the empirical average HTC, which was originally developed to be used for “lumped-parameter” (volume-averaged modeling of steam condensation in the presence of noncondensable gases. The present paper suggests a generalized HTC based on curve fitting of most of the reported semiempirical condensation models, which are valid for specific wall conditions. The present methodology has been validated against limited reported experimental data from the COPAIN experimental facility. This is the first step towards the CFD-based generalized analysis procedure for condensation modeling applicable for containment wall surfaces that is being evolved further for specific wall surfaces within the multicompartment containment atmosphere.

  11. Dynamics of domain coverage of the protein sequence universe

    Science.gov (United States)

    2012-01-01

    Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its “dark matter”. Results Here we suggest that true size of “dark matter” is much larger than stated by current definitions. We propose an approach to reducing the size of “dark matter” by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of “dark matter”; however, its absolute size increases substantially with the growth of sequence data. PMID:23157439

  12. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Directory of Open Access Journals (Sweden)

    Murat Cetinbaş

    Full Text Available Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  13. Dataset of the molecular dynamics simulations of bilayers consisting of short amyloidogenic peptide VDSWNVLVAG from Bgl2p–glucantransferase of S. cerevisiae cell wall

    Directory of Open Access Journals (Sweden)

    Anna V. Glyakina

    2016-12-01

    Full Text Available The amyloidogenic peptide VDSWNVLVAG from Bgl2p–glucantransferase of Saccharomyces cerevisiae cell wall and its modifying analog VESWNVLVAG were taken for the construction of four types of bilayers which differ by orientation of the peptides in the layers and of the layers relative to each other. These bilayers were used as starting models for the molecular dynamics (MD at three charge states (neutral, pH3, and pH5. The changes of the fraction of secondary structure during 1 ns simulations were received for 96 MD trajectories. The data article contains the necessary information for the construction of models of β-strands organization in the oligomer structure. These results were used in the associated research article “Structural model of amyloid fibrils for amyloidogenic peptide from Bgl2p–glucantransferase of S. cerevisiae cell wall and its modifying analog. New morphology of amyloid fibrils” (Selivanova et al., 2016 [1].

  14. Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response

    DEFF Research Database (Denmark)

    Bennetzen, Martin V; Larsen, Dorthe Helena; Dinant, Christoffel

    2013-01-01

    -dependent posttranslational modifications (PTMs). To complement our previous analysis of IR-induced temporal dynamics of nuclear phosphoproteome, we now identify a range of human nuclear proteins that are dynamically regulated by acetylation, and predominantly deacetylation, during IR-induced DDR by using mass spectrometry...... to genotoxic insults. Overall, these results present a resource of temporal profiles of a spectrum of protein acetylation sites during DDR and provide further insights into the highly dynamic nature of regulatory PTMs that help orchestrate the maintenance of genome integrity.......Genotoxic insults, such as ionizing radiation (IR), cause DNA damage that evokes a multifaceted cellular DNA damage response (DDR). DNA damage signaling events that control protein activity, subcellular localization, DNA binding, protein-protein interactions, etc. rely heavily on time...

  15. Dynamics of protein-protein interactions studied by paramagnetic NMR spectroscopy

    NARCIS (Netherlands)

    Somireddy Venkata, Bharat Kumar Reddy

    2012-01-01

    Protein-protein interactions play an important role in all cellular processes such as signal transduction, electron transfer, gene regulation, transcription, and translation. Understanding these protein-protein interactions at the molecular level, is an important aim in structural biology. The

  16. Internal dynamics of proteins: short time and long time motions of aromatic sidechains in PTI

    Energy Technology Data Exchange (ETDEWEB)

    Karplus, M.; Gelin, B.R.; McCammon, J.A.

    1980-10-01

    Theoretical approaches to the internal dynamics of proteins are outlined and illustrated by application to the aromatic sidechain motions of tyrosines in the bovine pancreatic trypsin inhibitor. High frequency torsional oscillations are obtained from a molecular dynamics simulation, while the longer time ring rotations are analyzed by use of adiabatic energy minimization and special transition-state trajectory techniques.

  17. Geometric Universality in Brain Allosteric Protein Dynamics: Complex Hydrophobic Transformation Predicts Mutual Recognition by Polypeptides and Proteins,

    Science.gov (United States)

    1986-10-01

    emf -driven RC circuits model the dynamics of ion- conductance behavior of allosteric membrane proteins very well. 50...D. 1985. Advances in the isolation of HTLV-I11 from patients with AIDS and AIDS-related complex and donors at risk. Cancer Res. 45: 45885-45915. 87

  18. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  19. Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR.

    Science.gov (United States)

    Thompson, Matthew K; Ehlinger, Aaron C; Chazin, Walter J

    2017-01-01

    Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples. © 2017 Elsevier Inc. All rights reserved.

  20. Fractal dimensions of soy protein nanoparticle aggregates determined by dynamic mechanical method

    Science.gov (United States)

    The fractal dimension of the protein aggregates can be estimated by dynamic mechanical methods when the particle aggregates are imbedded in a polymer matrix. Nanocomposites were formed by mixing hydrolyzed soy protein isolate (HSPI) nanoparticle aggregates with styrene-butadiene (SB) latex, followe...

  1. The consistency of large concerted motions in proteins in molecular dynamics simulations

    NARCIS (Netherlands)

    de Groot, B.L.; van Aalten, D.M.F.; Amadei, A; Berendsen, H.J.C.

    1996-01-01

    A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the

  2. A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

    Science.gov (United States)

    Chen, Peng; Hu, ShanShan; Zhang, Jun; Gao, Xin; Li, Jinyan; Xia, Junfeng; Wang, Bing

    2016-01-01

    Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures. This paper proposes a dynamic ensemble approach to identify protein-ligand binding residues by using sequence information only. To avoid problems resulting from highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we constructed several balanced data sets and we trained a random forest classifier for each of them. We dynamically selected a subset of classifiers according to the similarity between the target protein and the proteins in the training data set. The combination of the predictions of the classifier subset to each query protein target yielded the final predictions. The ensemble of these classifiers formed a sequence-based predictor to identify protein-ligand binding sites. Experimental results on two Critical Assessment of protein Structure Prediction datasets and the ccPDB dataset demonstrated that of our proposed method compared favorably with the state-of-the-art. http://www2.ahu.edu.cn/pchen/web/LigandDSES.htm.

  3. Proteins associated with the size and expansion rate of the abdominal aortic aneurysm wall as identified by proteomic analysis

    DEFF Research Database (Denmark)

    Urbonavicius, Sigitas; Lindholt, Jes S.; Delbosc, Sandrine

    2010-01-01

    Identification of biomarkers for the natural history of abdominal aortic aneurysms (AAA) holds the key to non-surgical intervention and improved selection for AAA repair. We aimed to associate the basic proteomic composition of AAA wall tissue with the expansion rate and size in patients with AAA....

  4. CONSTRUCTION TECHNOLOGY OF TIMBER-FRAME HOUSES RESISTANT TO DYNAMIC LOADS – STUDY ON MODELS OF EXTERIOR WALLS

    Directory of Open Access Journals (Sweden)

    Marcin Szczepanski

    2015-11-01

    Full Text Available The aim of this paper is to show the numeric representation of experimental studies concerning the behaviour of exterior wall models of a timber-frame house under harmonic loading. A single wall model according to traditional technology of timber-frame house walls (filling with mineral wool was tested. The analysis was conducted for the following frequencies: 0.5 Hz, 1.0 Hz, 2.0 Hz and 5.0 Hz for various values of the specified displacement. A number of hysteresis loops were obtained for each of the tests. Based on them, the damping ratio as well as stiffness were calculated. The skeleton model filled with mineral wool (traditional technology experienced serious damage under larger displacements. The results of the study have been used to propose a numerical model of wall filled with mineral wool. The proposed numerical model is consistent with the results for the values ​​obtained during the experimental study, which proves the correctness of the adopted solution.

  5. Molecular dynamics simulations of protein-tyrosine phosphatase 1B. I. Ligand-induced changes in the protein motions

    DEFF Research Database (Denmark)

    Peters, Günther H. J.; Frimurer, T.M.; Andersen, J.N.

    1999-01-01

    molecular dynamics simulations of PTP1B and PTP1B complexed with a high-affinity peptide DADEpYL, where pY stands for phosphorylated tyrosine. The peptide sequence is derived from the epidermal growth factor receptor (EGFR(988-993)). Simulations were performed in water for 1 ns, and the concerted motions...... in the protein were analyzed using the essential dynamics technique. Our results indicate that the predominately internal motions in PTP1B occur in a subspace of only a few degrees of freedom. Upon substrate binding, the flexibility of the protein is reduced by similar to 10%. The largest effect is found......Activity of enzymes, such as protein tyrosine phosphatases (PTPs), is often associated with structural changes in the enzyme, resulting in selective and stereospecific reactions with the substrate. To investigate the effect of a substrate on the motions occurring in PTPs, we have performed...

  6. Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics

    DEFF Research Database (Denmark)

    Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.

    2000-01-01

    Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. in particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...

  7. Single-Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins.

    Science.gov (United States)

    Gauer, J W; LeBlanc, S; Hao, P; Qiu, R; Case, B C; Sakato, M; Hingorani, M M; Erie, D A; Weninger, K R

    2016-01-01

    Single-molecule FRET measurements have a unique sensitivity to protein conformational dynamics. The FRET signals can either be interpreted quantitatively to provide estimates of absolute distance in a molecule configuration or can be qualitatively interpreted as distinct states, from which quantitative kinetic schemes for conformational transitions can be deduced. Here we describe methods utilizing single-molecule FRET to reveal the conformational dynamics of the proteins responsible for DNA mismatch repair. Experimental details about the proteins, DNA substrates, fluorescent labeling, and data analysis are included. The complementarity of single molecule and ensemble kinetic methods is discussed as well. © 2016 Elsevier Inc. All rights reserved.

  8. Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation

    Directory of Open Access Journals (Sweden)

    Bin Zhang

    2012-10-01

    Full Text Available We present a coarse-grained modeling approach that spans the nanosecond- to minute-timescale dynamics of cotranslational protein translocation. The method enables direct simulation of both integral membrane protein topogenesis and transmembrane domain (TM stop-transfer efficiency. Simulations reveal multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the experimentally observed dependence of protein topology on ribosomal translation rate and protein length. We further demonstrate that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon lateral gate, and it is predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equilibrium and nonequilibrium processes in protein targeting, and it provides insight into the molecular regulation of the Sec translocon.

  9. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

    Science.gov (United States)

    Martinez, N.; Michoud, G.; Cario, A.; Ollivier, J.; Franzetti, B.; Jebbar, M.; Oger, P.; Peters, J.

    2016-09-01

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.

  10. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

    KAUST Repository

    Martinez, N.

    2016-09-06

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.

  11. Similarity in cyst wall protein (CWP) trafficking between encysting Giardia duodenalis trophozoites and CWP-expressing human embryonic kidney-293 cells.

    Science.gov (United States)

    Abdul-Wahid, A; Faubert, G M

    2004-11-19

    Cyst wall proteins 1 and 2 (CWP1 and CWP2) are major constituents of the giardial cyst wall and are expressed with similar kinetics by encysting trophozoites. In the present study, we were interested to determine if the expression of giardial CWPs as heterologous proteins in a higher eukaryotic cell would result in their trafficking across the secretory pathway, as is the case in encysting trophozoites. Recombinant (r)CWP1 and rPro-CWP2 were detected in the lysate and culture media of transfected HEK-293 cells. We then conducted intracellular localization experiments using confocal microscopy and found that the proteins were trafficked in membrane enclosed vesicles across the secretory pathway and released to the culture medium by transfected HEK-293 cells. We then dissected the rCWP1 and rPro-CWP2 molecules to identify the portion(s) responsible for their secretion and found that the putative N-terminal signal peptide was sufficient for directing the secretion of rCWP1, while both the putative N-terminal signal peptide and the 13kDa C-terminal regions were necessary for the secretion of rPro-CWP2 by transfected HEK-293 cells. Taken together, these results demonstrate the degree of conservation of signal peptide recognition between lower and higher eukaryotes.

  12. AtPME3, a ubiquitous cell wall pectin methylesterase of Arabidopsis thaliana, alters the metabolism of cruciferin seed storage proteins during post-germinative growth of seedlings.

    Science.gov (United States)

    Guénin, Stéphanie; Hardouin, Julie; Paynel, Florence; Müller, Kerstin; Mongelard, Gaëlle; Driouich, Azeddine; Lerouge, Patrice; Kermode, Allison R; Lehner, Arnaud; Mollet, Jean-Claude; Pelloux, Jérôme; Gutierrez, Laurent; Mareck, Alain

    2017-02-01

    AtPME3 (At3g14310) is a ubiquitous cell wall pectin methylesterase. Atpme3-1 loss-of-function mutants exhibited distinct phenotypes from the wild type (WT), and were characterized by earlier germination and reduction of root hair production. These phenotypical traits were correlated with the accumulation of a 21.5-kDa protein in the different organs of 4-day-old Atpme3-1 seedlings grown in the dark, as well as in 6-week-old mutant plants. Microarray analysis showed significant down-regulation of the genes encoding several pectin-degrading enzymes and enzymes involved in lipid and protein metabolism in the hypocotyl of 4-day-old dark grown mutant seedlings. Accordingly, there was a decrease in proteolytic activity of the mutant as compared with the WT. Among the genes specifying seed storage proteins, two encoding CRUCIFERINS were up-regulated. Additional analysis by RT-qPCR showed an overexpression of four CRUCIFERIN genes in the mutant Atpme3-1, in which precursors of the α- and β-subunits of CRUCIFERIN accumulated. Together, these results provide evidence for a link between AtPME3, present in the cell wall, and CRUCIFERIN metabolism that occurs in vacuoles. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  13. Dynamics of Nanoparticle-Protein Corona Complex Formation: Analytical Results from Population Balance Equations

    Science.gov (United States)

    Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

    2013-01-01

    Background Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. Method This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. Results The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. Conclusion The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid. PMID:23741371

  14. Dynamics of nanoparticle-protein corona complex formation: analytical results from population balance equations.

    Science.gov (United States)

    Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

    2013-01-01

    Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid.

  15. Is dynamic heterogeneity of water in presence of a protein ...

    Indian Academy of Sciences (India)

    Abstract. Rotational and translational dynamic heterogeneities (DHs) of ambient aqueous solutions of trimethylamine-N-oxide (TMAO) and tetramethylurea (TMU) at several solute concentrations have been inves- tigated and compared. Motional characteristics of water molecules at solute interfaces and in bulk solutions.

  16. Non-interacting surface solvation and dynamics in protein-protein interactions

    NARCIS (Netherlands)

    Visscher, Koen M.; Kastritis, Panagiotis L.|info:eu-repo/dai/nl/315886668; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238

    2015-01-01

    Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo

  17. Structure and Dynamic Properties of Membrane Proteins using NMR

    DEFF Research Database (Denmark)

    Rösner, Heike; Kragelund, Birthe

    2012-01-01

    conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

  18. Molecular modeling of the conformational dynamics of the cellular prion protein

    Science.gov (United States)

    Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

    2014-03-01

    Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

  19. Dynamic disorder can explain non-exponential kinetics of fast protein mechanical unfolding.

    Science.gov (United States)

    Costescu, Bogdan I; Sturm, Sebastian; Gräter, Frauke

    2017-01-01

    Protein unfolding often does not obey a simple two-state behavior. Previous single molecule force spectroscopy studies demonstrated stretched exponential kinetics of protein unfolding under a constant pulling force, the molecular origin of which remains subject to debate. We here set out to extensively sample the mechanical unfolding of ubiquitin and NuG2 by Molecular Dynamics (MD) simulations. Both proteins show kinetics best fit by stretched exponentials, with stretching exponents similar to those found in experiments, even though static disorder is absent in our short MD simulations. Instead, we can ascribe non-exponential kinetics to dynamic disorder, due to conformational fluctuations on the nanosecond timescale. Our study highlights the general role of dynamic disorder in protein kinetics on a broad range of time scales even including those probed in MD simulations. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

    Science.gov (United States)

    Chavent, Matthieu; Duncan, Anna L; Sansom, Mark Sp

    2016-10-01

    Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  1. A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

    Science.gov (United States)

    Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.

    2017-10-01

    Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

  2. Ectopic expression of Capsicum-specific cell wall protein Capsicum annuum senescence-delaying 1 (CaSD1) delays senescence and induces trichome formation in Nicotiana benthamiana.

    Science.gov (United States)

    Seo, Eunyoung; Yeom, Seon-In; Jo, Sunghwan; Jeong, Heejin; Kang, Byoung-Cheorl; Choi, Doil

    2012-04-01

    Secreted proteins are known to have multiple roles in plant development, metabolism, and stress response. In a previous study to understand the roles of secreted proteins, Capsicum annuum secreted proteins (CaS) were isolated by yeast secretion trap. Among the secreted proteins, we further characterized Capsicum annuum senescence-delaying 1 (CaSD1), a gene encoding a novel secreted protein that is present only in the genus Capsicum. The deduced CaSD1 contains multiple repeats of the amino acid sequence KPPIHNHKPTDYDRS. Interestingly, the number of repeats varied among cultivars and species in the Capsicum genus. CaSD1 is constitutively expressed in roots, and Agrobacterium-mediated transient overexpression of CaSD1 in Nicotiana benthamiana leaves resulted in delayed senescence with a dramatically increased number of trichomes and enlarged epidermal cells. Furthermore, senescence- and cell division-related genes were differentially regulated by CaSD1-overexpressing plants. These observations imply that the pepper-specific cell wall protein CaSD1 plays roles in plant growth and development by regulating cell division and differentiation.

  3. Final Report: Regulation and Function of Two Cell Wall protein Genes in Me Dicago Roots and Root Nodules, August 1, 1995 - January 31, 1999

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, James B.

    2000-05-08

    During the period of DOE funding we synthesized several PRP peptides, generated rabbit antisera against two PRP repeats found in early nodulin PRPs, and developed confocal microscopy methods for root immunohistochemistry. Using the antibodies, we completed extensive descriptive studies of PRP deposition in medic and alfalfa roots showing that PRPs deposition is developmentally regulated in roots and spatially restricted within the walls of specific root tissues. Domain-specific antibodies were isolated from polyclonal sera using peptide affinity chromatography and were then used to demonstrate that nodule-specific epitopes are shared by several nodule-specific proteins. The following provides a more detailed summary of this work.

  4. Recombinant human bone morphogenetic protein 2-induced heterotopic ossification of the retroperitoneum, psoas muscle, pelvis and abdominal wall following lumbar spinal fusion

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Raj K. [The George Washington University School of Medicine, Washington, DC (United States); Moncayo, Valeria M.; Pierre-Jerome, Claude; Terk, Michael R. [Emory University School of Medicine, Radiology Department, Musculoskeletal Division, Atlanta, GA (United States); Smitson, Robert D. [Emory University School of Medicine, Atlanta, GA (United States)

    2010-05-15

    A 45-year-old man presented with vertebral collapse at L5 as an initial manifestation of multiple myeloma and underwent spinal fusion surgery using recombinant human bone morphogenetic protein-2 (rhBMP-2). Subsequent computed tomography (CT) scans and X-rays revealed heterotopic ossification of the left psoas muscle, pelvis, and anterior abdominal wall. While the occurrence of heterotopic ossification has previously been reported when rhBMP-2 has been used for spinal fusion surgery, this case demonstrates that it can occur to a much greater degree than previously seen. (orig.)

  5. Controlling transcription fidelity via TATA-binding protein dynamics

    NARCIS (Netherlands)

    Koster, M.J.E.

    2015-01-01

    Transcription underlies all cellular processes and responses to internal and external cues. Deregulation of transcription has implications for the fitness of the cell or organism. During my PhD I have investigated the importance of proper TATA-binding protein (TBP) regulation as a mechanism to

  6. Dynamic modularity in protein interaction networks predicts breast cancer outcome

    DEFF Research Database (Denmark)

    Taylor, Ian W; Linding, Rune; Warde-Farley, David

    2009-01-01

    in biochemical structure were observed between the two types of hubs. Signaling domains were found more often in intermodular hub proteins, which were also more frequently associated with oncogenesis. Analysis of two breast cancer patient cohorts revealed that altered modularity of the human interactome may...

  7. The dynamics of fat, protein and sugar metabolism during walnut ...

    African Journals Online (AJOL)

    Yomi

    Key words: Walnut (Juglans regia L.), fruit development, sugar, fat, protein, invertase. INTRODUCTION. The 'hidden hunger' .... mixture, and then determined by KDY-9820 Kjeldahl apparatus. (Beijing Huawei Science and ... Where, V2, Vl, is the measure value at two measure time; T2 – T1is the days between two measure ...

  8. Dynamic protein assemblies in homologous recombination with single DNA molecules

    NARCIS (Netherlands)

    van der Heijden, A.H.

    2007-01-01

    What happens when your DNA breaks? This thesis describes experimental work on the single-molecule level focusing on the interaction between DNA and DNA-repair proteins, in particular bacterial RecA and human Rad51, involved in homologous recombination. Homologous recombination and its central event

  9. Dynamic expression pattern of kinesin accessory protein in Drosophila

    Indian Academy of Sciences (India)

    In addition, we have found that the DmKAP gene is constitutively expressed in the germline cells and in follicle cells during oogenesis. These cells are also stained using an antibody to KLP68D protein, but mRNA in situ hybridization using KLP64D specific probe has not stained these cells. Together these results proved a ...

  10. Membrane tube formation by motor proteins : forces and dynamics

    NARCIS (Netherlands)

    Koster, Gerbrand

    2005-01-01

    Membrane tubes are ubiquitous within cells. They have a diameter of approximately 50 nanometers, and are formed when a sufficiently large localized force is exerted on a membrane. Important generators of this force are the motor proteins that can move along cytoskeletal filaments. We studied

  11. Protein-enabled layer-by-layer syntheses of aligned, porous-wall, high-aspect-ratio TiO{sub 2} nanotube arrays

    Energy Technology Data Exchange (ETDEWEB)

    Berrigan, John D.; Cai, Ye; Sandhage, Kenneth H. [School of Materials Science and Engineering, Air Force Center of Excellence on Bio-Nano-Enabled Inorganic/Organic Nanocomposites and Improved Cognition (BIONIC), Georgia Institute of Technology, 771 Ferst Drive, Atlanta, Georgia 30332-0400 (United States); Kang, Tae-Sik; Deneault, James R.; Durstock, Michael F. [Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, 45433-7702 (United States)

    2011-05-10

    An aqueous, protein-enabled (biomimetic), layer-by-layer titania deposition process is developed, for the first time, to convert aligned-nanochannel templates into high-aspect-ratio, aligned nanotube arrays with thin (34 nm) walls composed of co-continuous networks of pores and titania nanocrystals (15 nm ave. size). Alumina templates with aligned open nanochannels are exposed in an alternating fashion to aqueous protamine-bearing and titania precursor-bearing (Ti(IV) bis-ammonium-lactato-dihydroxide, TiBALDH) solutions. The ability of protamine to bind to alumina and titania, and to induce the formation of a Ti-O-bearing coating upon exposure to the TiBALDH precursor, enables the layer-by-layer deposition of a conformal protamine/Ti-O-bearing coating on the nanochannel surfaces within the porous alumina template. Subsequent protamine pyrolysis yields coatings composed of co-continuous networks of pores and titania nanoparticles. Selective dissolution of the underlying alumina template through the porous coating then yields freestanding, aligned, porous-wall titania nanotube arrays. The interconnected pores within the nanotube walls allow enhanced loading of functional molecules (such as a Ru-based N719 dye), whereas the interconnected titania nanoparticles enable the high-aspect-ratio, aligned nanotube arrays to be used as electrodes (as demonstrated for dye-sensitized solar cells with power conversion efficiencies of 5.2 {+-} 0.4%). (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Effect of whey protein isolate and β-cyclodextrin wall systems on stability of microencapsulated vanillin by spray-freeze drying method.

    Science.gov (United States)

    Hundre, Swetank Y; Karthik, P; Anandharamakrishnan, C

    2015-05-01

    Vanillin flavour is highly volatile in nature and due to that application in food incorporation is limited; hence microencapsulation of vanillin is an ideal technique to increase its stability and functionality. In this study, vanillin was microencapsulated for the first time by non-thermal spray-freeze-drying (SFD) technique and its stability was compared with other conventional techniques such as spray drying (SD) and freeze-drying (FD). Different wall materials like β-cyclodextrin (β-cyd), whey protein isolate (WPI) and combinations of these wall materials (β-cyd + WPI) were used to encapsulate vanillin. SFD microencapsulated vanillin with WPI showed spherical shape with numerous fine pores on the surface, which in turn exhibited good rehydration ability. On the other hand, SD powder depicted spherical shape without pores and FD encapsulated powder yielded larger particle sizes with flaky structure. FTIR analysis confirmed that there was no interaction between vanillin and wall materials. Moreover, spray-freeze-dried vanillin + WPI sample exhibited better thermal stability than spray dried and freeze-dried microencapsulated samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

    Science.gov (United States)

    Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

    2017-10-01

    Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

  14. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

    Science.gov (United States)

    Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

    2017-10-12

    Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

  15. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

    Science.gov (United States)

    Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

    2016-08-23

    Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering

    Science.gov (United States)

    Shrestha, Utsab R.; Bhowmik, Debsindhu; Mamontov, Eugene; Chu, Xiang-Qiang

    Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the