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Relevant bibliographies by topics / Dynamic conformational equilibrium

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Academic literature on the topic 'Dynamic conformational equilibrium'

Author: Grafiati

Published: 4 June 2021

Last updated: 3 February 2022

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Journal articles on the topic "Dynamic conformational equilibrium"

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Ohno, Shiho, Noriyoshi Manabe, Takumi Yamaguchi, Jun Uzawa, and Yoshiki Yamaguchi. "Ribitol in Solution Is an Equilibrium of Asymmetric Conformations." Molecules 26, no. 18 (2021): 5471. http://dx.doi.org/10.3390/molecules26185471.

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Ribitol (C5H12O5), an acyclic sugar alcohol, is present on mammalian α-dystroglycan as a component of O-mannose glycan. In this study, we examine the conformation and dynamics of ribitol by database analysis, experiments, and computational methods. Database analysis reveals that the anti-conformation (180°) is populated at the C3–C4 dihedral angle, while the gauche conformation (±60°) is seen at the C2–C3 dihedral angle. Such conformational asymmetry was born out in a solid-state 13C-NMR spectrum of crystalline ribitol, where C1 and C5 signals are unequal. On the other hand, solution 13C-NMR h

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Ohhashi, Yumiko, Yoshiki Yamaguchi, Hiroshi Kurahashi, et al. "Molecular basis for diversification of yeast prion strain conformation." Proceedings of the National Academy of Sciences 115, no. 10 (2018): 2389–94. http://dx.doi.org/10.1073/pnas.1715483115.

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Self-propagating β-sheet–rich fibrillar protein aggregates, amyloid fibers, are often associated with cellular dysfunction and disease. Distinct amyloid conformations dictate different physiological consequences, such as cellular toxicity. However, the origin of the diversity of amyloid conformation remains unknown. Here, we suggest that altered conformational equilibrium in natively disordered monomeric proteins leads to the adaptation of alternate amyloid conformations that have different phenotypic effects. We performed a comprehensive high-resolution structural analysis of Sup35NM, an N-te

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Durham, Natasha D., Angela R. Howard, Ramesh Govindan, et al. "Real-Time Analysis of Individual Ebola Virus Glycoproteins Reveals Pre-Fusion, Entry-Relevant Conformational Dynamics." Viruses 12, no. 1 (2020): 103. http://dx.doi.org/10.3390/v12010103.

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The Ebola virus (EBOV) envelope glycoprotein (GP) mediates the fusion of the virion membrane with the membrane of susceptible target cells during infection. While proteolytic cleavage of GP by endosomal cathepsins and binding of the cellular receptor Niemann-Pick C1 protein (NPC1) are essential steps for virus entry, the detailed mechanisms by which these events promote membrane fusion remain unknown. Here, we applied single-molecule Förster resonance energy transfer (smFRET) imaging to investigate the structural dynamics of the EBOV GP trimeric ectodomain, and the functional transmembrane pro

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Ruben, Eliza A., Prafull S. Gandhi, Zhiwei Chen, et al. "19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2." Journal of Biological Chemistry 295, no. 24 (2020): 8227–35. http://dx.doi.org/10.1074/jbc.ra120.013419.

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The conformational properties of trypsin-like proteases and their zymogen forms remain controversial because of a lack of sufficient information on their free forms. Specifically, it is unclear whether the free protease is zymogen-like and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equilibrium from which the ligand selects the optimal fit via conformational selection. Here we report the results of 19F NMR measurements that reveal the conformational properties of a protease and its zymogen precursor in the free form. Using the trypsin-like, clotti

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Cho, Min-Hyung, James O. Wrabl, James Taylor, and Vincent J. Hilser. "Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome." Proceedings of the National Academy of Sciences 117, no. 38 (2020): 23606–16. http://dx.doi.org/10.1073/pnas.1921473117.

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Phosphorylation sites are hyperabundant in the eukaryotic disordered proteome, suggesting that conformational fluctuations play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural–chemical complementarity between the kinase and its protein substrates but also by the free energy difference between the conformational ensembles that are, or are not, recognized by the kinase. To test this hypothesis, we developed a statistical-thermodynamics-based informatics framework, w

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Gouridis, Giorgos, Bianca Hetzert, Kristin Kiosze-Becker, et al. "ABCE1 Controls Ribosome Recycling by an Asymmetric Dynamic Conformational Equilibrium." Cell Reports 28, no. 3 (2019): 723–34. http://dx.doi.org/10.1016/j.celrep.2019.06.052.

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Gutiérrez-de-Terán, Hugo, Xabier Bello, and David Rodríguez. "Characterization of the dynamic events of GPCRs by automated computational simulations." Biochemical Society Transactions 41, no. 1 (2013): 205–12. http://dx.doi.org/10.1042/bst20120287.

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The recent advances in membrane protein crystallography have provided extremely valuable structural information of the superfamily of GPCRs (G-protein-coupled receptors). This has been particularly true for a few receptors whose structure was solved several times under different biochemical conditions. It follows that the mechanisms of receptor conformational equilibrium and related dynamic events can be explored by computational simulations. In the present article, we summarize our recent understanding of several dynamic features of GPCRs, accomplished through the use of MD (molecular dynamic

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Chu, Chia-Chieh, Raphael Plangger, Christoph Kreutz, and Hashim M. Al-Hashimi. "Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site." Nucleic Acids Research 47, no. 13 (2019): 7105–17. http://dx.doi.org/10.1093/nar/gkz498.

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AbstractThe HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find tha

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Weber, Piotr, Piotr Bełdowski, Krzysztof Domino, Damian Ledziński, and Adam Gadomski. "Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations." Entropy 22, no. 4 (2020): 405. http://dx.doi.org/10.3390/e22040405.

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This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes t

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Chen, Wei, Jizhong Lou, Evan A. Evans, and Cheng Zhu. "Observing force-regulated conformational changes and ligand dissociation from a single integrin on cells." Journal of Cell Biology 199, no. 3 (2012): 497–512. http://dx.doi.org/10.1083/jcb.201201091.

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As adhesion molecules, integrins connect a cell to its environment and transduce signals across the membrane. Their different functional states correspond to distinct conformations. Using a biomembrane force probe, we observed real-time reversible switches between bent and extended conformations of a single integrin, αLβ2, on the surface of a living cell by measuring its nanometer-scale headpiece displacements, bending and unbending frequencies, and molecular stiffness changes. We determined the stabilities of these conformations, their dynamic equilibrium, speeds and rates of conformational c

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Dissertations / Theses on the topic "Dynamic conformational equilibrium"

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Preston, Sarah Suzanne. "Metal coordination directed folding of intramolecularly hydrogen-bonded dendrons." The Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=osu1135869971.

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Blanco, Pablo Miguel. "Coupling of binding and conformational equilibria in weak polyelectrolytes. Dynamics and charge regulation of biopolymers in crowded media." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/670053.

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I have carried out this thesis in the Biophysical Chemistry of Macromolecules and Colloids research group of the University of Barcelona. In the recent years, the research group have made significant contributions to the study of the conformational, binding, diffusion and reactivity properties of weak polyelectrolytes and biopolymers. On the one hand, the group has contributed to the design and development of the Site Binding Rotational Isomeric State (SBRIS) model for weak polyelectrolytes. They have also successfully used the SBRIS model to reproduce the complex experimental titration curve

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Timachi, Mohammad Hadi [Verfasser], Lars [Gutachter] Schäfer, and Eckhard [Gutachter] Hofmann. "Exploring conformational dynamics and equilibria of ABC transporters / Mohammad Hadi Timachi ; Gutachter: Lars Schäfer, Eckhard Hofmann ; Fakultät für Chemie und Biochemie." Bochum : Ruhr-Universität Bochum, 2019. http://d-nb.info/1193252431/34.

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Calabrese, Camilla <1987&gt. "Contribution of Non-Covalent Interactions and Electronic Effects on the Conformational Landscape and Tautomeric Equilibria of Molecules and Molecular Complexes: Structural and Dynamical Data from Rotational Spectroscopy." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6984/.

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This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the su

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Hamman, Brian D. "The conformational dynamics and subunit equilibrium of Escherichia coli ribosomal protein L7/L12." Thesis, 1994. http://hdl.handle.net/10125/9378.

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Doebber, Meike Anne. "EPR Analysis of a Two-State Conformational Equilibrium in an N. pharaonis HAMP Domain - Activation/Deactivation of a Signaling Unit"." Doctoral thesis, 2009. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2009032018.

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The photosensitive unit triggering the negative phototaxis in the haloarchaeum Natronomonas pharaonis consists of the receptor sensory rhodopsin II (NpSRII) and its cognate transducer (NpHtrII) in a 2:2 stoichiometry. Upon light excitation, a structural rearrangement in the receptor initiates a displacement/rotation of the transducer helix TM2, which can be considered as starting event for the signal transduction. This signal is further transmitted to the cytoplasmic signaling domain through the signal transduction unit comprising two HAMP domains.Structural information already exists for the

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Mühle, Steffen. "Nanoscale Brownian Dynamics of Semiflexible Biopolymers." Doctoral thesis, 2020. http://hdl.handle.net/21.11130/00-1735-0000-0005-1433-B.

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Book chapters on the topic "Dynamic conformational equilibrium"

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Zocchi, Giovanni. "Statics of DNA Deformations." In Molecular Machines. Princeton University Press, 2018. http://dx.doi.org/10.23943/princeton/9780691173863.003.0002.

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DNA is a deformable molecule. The term “deformable” implies phenomena rooted in the collective behavior of many atoms, and a description based on concepts of continuum and statistical mechanics. Long DNA molecules are an excellent experimental system to study the equilibrium conformations and dynamics of long, flexible molecules. This chapter discusses the following: DNA melting, the zipper model, experimental melting curves, base pairing and base stacking as separate, Hamiltonian formulation of the zipper model, 2 × 2 model, nearest neighbor model, connection to nonlinear dynamics, linear and nonlinear elasticity of DNA, bending modulus and persistence length, measurements of DNA elasticity (short and long molecules), the Euler instability, and the DNA yield transition.

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Beris, Antony N., and Brian J. Edwards. "The Dynamical Theory of Liquid Crystals." In Thermodynamics of Flowing Systems: with Internal Microstructure. Oxford University Press, 1994. http://dx.doi.org/10.1093/oso/9780195076943.003.0016.

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Liquid crystals (LCs) present a state of matter with properties—as the name suggests—intermediate between those of liquids and crystalline solids. Liquid-crystalline materials, as all liquids, cannot support shear stresses at static equilibrium. Their molecules are characterized by an anisotropy in the shape and/or intermolecular forces. Thus, there is the potential for the formation of a separate phase(s), called a “mesophase(s),” where a partial order arises in the molecular orientation and/or location, which extends over macroscopic distances. This partial long-range molecular order, reminiscent of (but not equivalent to) the perfect order of solid crystals, in addition to the material fluidity, is primarily responsible for the many properties which are inherent characteristics of liquid-crystalline phases, such as a rapid response to electric and magnetic fields, anisotropic optical and rheological properties, etc.—see, for examples, the reviews by Stephen and Straley [1974] and Jackson and Shaw [1991], the monographs by de Gennes [1974], Chandrasekhar [1977], and Vertogen and de Jeu [1988], and the edited volumes by Ciferri et al. [1982] and Ciferri [1991]. The variety of the liquid-crystalline macroscopic properties is such that trying to derive a theory capable of describing the principal liquid-crystalline dynamic characteristics can be a very frustrating task if one does not approach the issue in a systematic fashion. Characteristically, the main two theories that have been advanced over the last thirty years for the description of the liquid-crystalline flow behavior—the Leslie/ Ericksen (LE) theory and the Doi theory—are essentially models developed from a set theoretical frame work—continuum mechanics and molecular theory, respectively. Nevertheless, each one of these theories has a limited domain of application. The description of the dynamic liquid-crystalline behavior through the bracket formalism, as seen in this chapter, leads naturally to a single conformation tensor theory with an extended domain of validity. This conformation theory consistently generalizes both previous theories, which can be recovered from it as particular cases. This offers additional evidence that the wealth of inherent information in LCs can only be appropriately handled when pursued in a systematic, fundamental manner.

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Bon Hoa, Gaston Hui, and Carmelo Di Primo. "Application of Pressure Relaxation to the Study of Substrate Binding to Cytochrome P-450cam versus Temperature, Pressure, and Viscosity." In High Pressure Effects in Molecular Biophysics and Enzymology. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195097221.003.0015.

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The pressure-jump relaxation technique is a convenient and interesting means of studying rapid reversible reactions of biological systems. According to the change in reaction volume that accompanies a biochemical process, a rapid pressure change Δp produces a relative equilibrium shift ΔK/K, which is given by ΔlnK = AK/K = — (ΔV°/RT) Δp, where ΔV° is the reaction volume change. If the pressure change has a very short transition time, then relaxation kinetic measurements near equilibrium are possible, allowing the elucidation of reaction mechanisms through the detection of eventual reaction intermediates and the characterization of elementary kinetic and thermodynamic parameters. Our reversible pressure-jump method described in this chapter is capable of producing a sharp pressure change of ±20MPa in less than 3 milliseconds allowing the determination of relaxation rates in the time range of several milliseconds to several minutes at any final pressure up to 400 MPa, and in any viscosity solution. This technique was employed to study the binding kinetics of camphor and its analogues to bacterial cytochrome P-450cam as functions of temperature, pressure, and viscosity. The results obtained are discussed in terms of conformational dynamics of the protein associated with the entry and the exist of water molecules and specific interactions of the substrate1 with the apolar residues in the active site of cytochrome P-450cam. The binding of ligands or substrates to proteins can exhibit multistate kinetic behavior similar to transient-stale enzyme kinetics and isomerizations of proteins. The underlying elementary reaction mechanisms can be elucidated by the use of rapid mixing techniques. Usually a reaction is initiated by mixing the reactants as rapidly as possible, and the approach to equilibrium is monitored. This method has been adapted to the study of enzyme reaction mechanisms under extreme conditions of temperature and pressure (Hui Bon Hoa & Douzou, 1973; Balny et al., 1984). However, this approach is limited by the deadtime, the large amount of sample required, and difficulties in using the apparatus to study viscous solutions, such as Schlieren effects, caused by incomplete mixing in flow experiments. Relaxation techniques overcome these problems by the application of a physical perturbation to a system already at equilibrium.

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Han, Chang Dae. "Rheology of Liquid-Crystalline Polymers." In Rheology and Processing of Polymeric Materials: Volume 1: Polymer Rheology. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195187823.003.0015.

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Liquid crystals (LCs) may be divided into two subgroups: (1) lyotropic LCs, formed by mixing rigid rodlike molecules with a solvent, and (2) thermotropic LCs, formed by heating. One finds in the literature such terms as mesomorphs, mesoforms, mesomorphic states, and anisotropic liquids. The molecules in LCs have an orderly arrangement, and different orders of structures (nematic, smectic, or cholesteric structure) have been observed, as schematically shown in Figure 9.1. The kinds of molecules that form LCs generally possess certain common molecular features. The structural characteristics that determine the type of mesomorphism exhibited by various molecules have been reviewed. At present, our understanding of polymeric liquid crystals, often referred to as liquid-crystalline polymers (LCPs), is largely derived from studies of monomeric liquid crystals. However, LCPs may exhibit intrinsic differences from their monomeric counterparts because of the concatenation of monomers to form the chainlike macromolecules. The linkage of monomers inevitably means a loss of their translational and orientational independence, which in turn profoundly affects the dynamics of polymers in the liquid state. These intramolecular structural constraints are expressed in the flexibility of the polymer chain. Generally speaking, the chemical constitution of the monomer determines the flexibility and equilibrium dimensions of the polymer chain (Gray 1962). Figure 9.2 illustrates the variability of chain conformation (flexible chain, semiflexible chain, and rigid rodlike chain) forming macromolecules. Across this spectrum of chain flexibility, the persistence in the orientation of successive monomer units varies from the extreme of random orientation (flexible chains) to perfect order (the rigid rod). Hence, efforts have been made to synthesize LCPs that consist of rigid segments contributing to the formation of a mesophase and flexible segments contributing to the mobility of the entire macromolecule in the liquid state (Ober et al. 1984). From the point of view of molecular architecture, as schematically shown in Figure 9.3, two types of LCP have been developed: (1) main-chain LCPs (MCLCPs), having the monomeric liquid crystals (i.e., mesogenic group) in the main chain of flexible links, and (2) side-chain LCPs (SCLCPs), having the monomeric liquid crystals attached, as a pendent side chain, to the main chain.

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Conference papers on the topic "Dynamic conformational equilibrium"

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Fatehiboroujeni, Soheil, Sachin Goyal, and Apostol Gramada. "A Method for Identification of the Constitutive Law of Biological Filaments From Their Dynamic Equilibria." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-46776.

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There are several biological filaments that play vital role in cellular processes via twisting and bending deformations. From the double-stranded DNA molecule containing genetic information to the cytoskeletal fibers that provide shape to the cell, biological filaments undergo conformational changes as they perform their biological tasks. Therefore the ability of a filament to deform, which depends on their atomistic structure, is a characteristic property that governs its biological functions. Since there is no direct analytic method to derive the deformability or constitutive law of such fil

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Bidone, Tamara C., Marco A. Deriu, Giacomo Di Benedetto, Diana Massai, and Umberto Morbiducci. "Insights Into the Molecular Mechanisms of Actin Dynamics: A Multiscale Modeling Approach." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53417.

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Actin dynamics, which is at the basis of many fundamental cellular processes as cell migration [1], is governed by the self-assembly and disassembly of actin monomers (G-actin) that, in turn, are determined by the kinetics of ATP hydrolysis and by the local concentrations of Mg2+ and Ca2+ [2]. During cell migration, interactions of the actin filaments (F-actin) with different nucleotide-cation complexes induce local topological rearrangements, because the filament building G-actins undergo conformational shifts between multiple equilibrium states separated by low-energy barriers. For example,

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Kaazempur-Mofrad, Mohammad R., Peter J. Mack, Helene Karcher, Javad Golji, and Roger G. Kamm. "Stress-Induced Mechanotransduction: Some Preliminaries." In ASME 2003 International Mechanical Engineering Congress and Exposition. ASMEDC, 2003. http://dx.doi.org/10.1115/imece2003-43215.

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Mechanical stimuli affect nearly every aspect of cellular function, yet the underlying mechanisms of transduction of force into biochemical signals are not clearly understood. One hypothesis is that forces transmitted via individual proteins, either at the site of cell adhesion to its surroundings or within the stress-bearing members of the cytoskeleton, cause conformational changes that change their binding affinity to other intracellular molecules. This altered equilibrium state can subsequently initiate biochemical signaling cascades of produce immediate structural changes. This paper addre

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Khan, Imad M., and Kurt S. Anderson. "A Robust Framework for Adaptive Multiscale Modeling of Biopolymers Using Highly Parallelizable Methods." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93099.

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For many biopolymers (RNA, DNA, enzymes and proteins) the nature of the molecules interaction within the cell has been determined to be highly a function of its conformational structure. Understanding how to influence and control this structure thus is of critical importance if one wishes to manipulate the intercellular processes of which these biopolymers play such a central role. In molecular dynamics (MD) simulations, a fully atomistic model represents the system at the finest scale and as such captures all the dynamics of the system. If the simulation is permitted to run sufficiently long

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Zheng, Zhi-Ying, Feng-Chen Li, and Qian Li. "Reynolds-Averaged Simulation on Turbulent Drag-Reducing Flows of Viscoelastic Fluid Based on User-Defined Function in FLUENT Package." In ASME 2014 4th Joint US-European Fluids Engineering Division Summer Meeting collocated with the ASME 2014 12th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/fedsm2014-21327.

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A new numerical simulation methodology for turbulent flows of viscoelastic fluid was developed for engineering application purpose based on commercial computational fluid dynamics code FLUENT package. An in-house subroutine was established and embedded into FLUENT code through userdefined function functionalization. In order to benchmark this methodology, numerical simulations on turbulent channel flows of viscoelastic fluid are conducted under different cases with drag reduction rates varied from low level to high level. FENE-P (finitely extensive nonlinear elastic-Peterlin) constitutive mode

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Rone, William S., and Pinhas Ben-Tzvi. "Static Modeling of a Multi-Segment Serpentine Robotic Tail." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-46655.

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This paper presents a generalized method of determining the static shape conformation of a cable-driven serpentine robot. Given a set of desired cable displacements as model inputs, the model calculates the joint angles and cable tensions that result from those displacements. The model’s governing equations are derived from ensuring static equilibrium at each of the robot’s revolute joints, along with compatibility equations ensuring the joint angles result in the desired cable displacements. Elastic, actuation and gravitational loading are included in the model, and the results analyze the re

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