Relevant bibliographies by topics / Proteins - Conformation Dynamics

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Proteins - Conformation Dynamics'

Author: Grafiati
Published: 7 September 2023

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Journal articles on the topic "Proteins - Conformation Dynamics"

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Kang, Hyun-Seo, and Michael Sattler. "Capturing dynamic conformational shifts in protein–ligand recognition using integrative structural biology in solution." Emerging Topics in Life Sciences 2, no. 1 (2018): 107–19. http://dx.doi.org/10.1042/etls20170090.

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In recent years, a dynamic view of the structure and function of biological macromolecules is emerging, highlighting an essential role of dynamic conformational equilibria to understand molecular mechanisms of biological functions. The structure of a biomolecule, i.e. protein or nucleic acid in solution, is often best described as a dynamic ensemble of conformations, rather than a single structural state. Strikingly, the molecular interactions and functions of the biological macromolecule can then involve a shift between conformations that pre-exist in such an ensemble. Upon external cues, suc
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Garaizar, Adiran, Ignacio Sanchez-Burgos, Rosana Collepardo-Guevara, and Jorge R. Espinosa. "Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation." Molecules 25, no. 20 (2020): 4705. http://dx.doi.org/10.3390/molecules25204705.

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Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid–liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, incl
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Brouhard, Gary J., та Luke M. Rice. "The contribution of αβ-tubulin curvature to microtubule dynamics". Journal of Cell Biology 207, № 3 (2014): 323–34. http://dx.doi.org/10.1083/jcb.201407095.

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Microtubules are dynamic polymers of αβ-tubulin that form diverse cellular structures, such as the mitotic spindle for cell division, the backbone of neurons, and axonemes. To control the architecture of microtubule networks, microtubule-associated proteins (MAPs) and motor proteins regulate microtubule growth, shrinkage, and the transitions between these states. Recent evidence shows that many MAPs exert their effects by selectively binding to distinct conformations of polymerized or unpolymerized αβ-tubulin. The ability of αβ-tubulin to adopt distinct conformations contributes to the intrins
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Gormal, Rachel S., Pranesh Padmanabhan, Ravikiran Kasula та ін. "Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies". Proceedings of the National Academy of Sciences 117, № 48 (2020): 30476–87. http://dx.doi.org/10.1073/pnas.2007443117.

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None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-conc
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Mizutani, Tadashi, and Shigeyuki Yagi. "Linear tetrapyrroles as functional pigments in chemistry and biology." Journal of Porphyrins and Phthalocyanines 08, no. 03 (2004): 226–37. http://dx.doi.org/10.1142/s1088424604000210.

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1,19,21,24-tetrahydro-1,19-bilindione is the framework of pigments frequently found in nature, which includes biliverdin IX α, phytochromobilin and phycocyanobilin. 1,19-bilindiones have unique features such as (1) photochemical and thermal cis-trans isomerization, (2) excited energy transfer, (3) chiroptical properties due to the cyclic helical conformation, (4) redox activity, (5) coordination to various metals, and (6) reconstitution to proteins. 1,19-bilindione can adopt a number of conformations since it has exocyclic three double bonds and three single bonds that are rotatable thermally
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Ramirez-Mondragon, Carlos A., Megin E. Nguyen, Jozafina Milicaj, et al. "Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics." International Journal of Molecular Sciences 22, no. 9 (2021): 4619. http://dx.doi.org/10.3390/ijms22094619.

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It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and cl
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Kulkarni, Prakash, Vitor B. P. Leite, Susmita Roy, et al. "Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma." Biophysics Reviews 3, no. 1 (2022): 011306. http://dx.doi.org/10.1063/5.0080512.

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Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs co
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Westenhoff, Sebastian, Elena Nazarenko, Erik Malmerberg, Jan Davidsson, Gergely Katona, and Richard Neutze. "Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches." Acta Crystallographica Section A Foundations of Crystallography 66, no. 2 (2010): 207–19. http://dx.doi.org/10.1107/s0108767309054361.

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Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorpti
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Yang, Jing, Jing Chen, and Zibiao Li. "Structural Basis for the Structure–Activity Behaviour of Oxaliplatin and its Enantiomeric Analogues: A Molecular Dynamics Study of Platinum-DNA Intrastrand Crosslink Adducts." Australian Journal of Chemistry 69, no. 4 (2016): 379. http://dx.doi.org/10.1071/ch15624.

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The discrimination of Pt-GG adducts by mismatch repair proteins, DNA damage-recognition proteins, and translation DNA polymerases was thought to be vital in determining the toxicity, efficacy, and mutagenicity of platinum anti-tumour drugs. Studies on cis-diammine-Pt-GG (from cisplatin and carboplatin) and trans-R,R-diaminocyclohexane (DACH)-Pt-GG indicated that these proteins recognized the differences in conformation and conformational dynamics of Pt-DNA complexes. However, the structural basis of enantiomeric DACH-Pt-GG forms is unclear. Molecular dynamics simulations results presented here
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Li, Haiyan, Zanxia Cao, Guodong Hu, Liling Zhao, Chunling Wang, and Jihua Wang. "Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations." Technology and Health Care 29 (March 25, 2021): 103–14. http://dx.doi.org/10.3233/thc-218011.

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BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models.
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Dissertations / Theses on the topic "Proteins - Conformation Dynamics"

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Ceres, Nicoletta. "Coarse-grain modeling of proteins : mechanics, dynamics and function." Thesis, Lyon 1, 2012. http://www.theses.fr/2012LYO10030.

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Les protéines sont des molécules flexibles, qui accomplissent une variété de tâches cellulaires à travers des mouvements mécaniques et des changements conformationnels encodés dans leur structure tridimensionnelle. Parmi les approches théoriques qui contribuent à une meilleure compréhension de la relation entre structure, mécanique, dynamique et fonction des protéines, les modèles gros-grains sont un outil très puissant. Ils permettent d’intégrer des informations structurales et dynamiques à un coût computationnel réduit, car le traitement explicite des degrés de liberté moins importants est s
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Kragelj, Jaka. "Structure and dynamics of intrinsically disordered regions of MAPK signalling proteins." Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENV060/document.

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Les voies de transduction du signal cellulaire permettent aux cellules de répondre aux signaux de l'environnement et de les traiter. Les voies de transduction de kinases MAP (MAPK) sont bien conservées dans toutes les cellules eucaryotes et sont impliquées dans la régulation de nombreux processus cellulaires importants. Les régions intrinsèquement désordonnées (RID), présentes dans de nombreuses MAPK, n'étaient pas encore structurellement caractérisées. Les RID de MAPK sont particulièrement importantes car elles contiennent des motifs de liaison qui contrôlent les interactions entre les protéi
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Murzycki, Jennifer E. "Probing Protein Dynamics Through Mutational and Computational Studies of HIV-1 Protease: A Dissertation." eScholarship@UMMS, 2006. https://escholarship.umassmed.edu/gsbs_diss/166.

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How proteins undergo conformational changes to bind a ligand is one of the most fundamental questions of protein biology. MD simulations provide a useful computational tool for studying the theoretical movements of protein in solution on nanosecond timescales. The results of these simulations can be used to guide experimental design. By correlating the theoretical models with the results of experimental studies, we can obtain a significant amount of information about protein dynamics. This study represents the application of both computational and traditional experimental techniques to study p
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Abyzov, Anton. "Nuclear Magnetic Resonance Studies of the Dynamics and Thermodynamics of Intrinsically Disordered Proteins." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY026/document.

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Les protéines intrinsèquement désordonnées sont des hétéropolymères très flexibles, impliqués dans des activités cellulaires importantes (transduction du signal, reconnaissance moléculaire, traduction etc.), représentant des cibles potentielles de médicaments contre les maladies neurodégénératives et cancers, et dont les modes dynamiques définissent leur fonction biologique. Même si les états conformationnels qu'elles échantillonnent sont relativement bien connus, ce n'est pas le cas des échelles de temps de la dynamique associée. Dans ce travail nous étudions le comportement conformationnel d
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Link, Justin J. "Ultrafast Protein Conformation Dynamics." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1230584570.

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Dorywalska, Magdalena. "Conformational dynamics of protein synthesis /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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Zang, Chen. "Ultrafast Spectroscopic Study of Protein Conformation Dynamics and Hydration Dynamics." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299481658.

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Bossa, Cecilia. "Conformational fluctuations in proteins. A molecular dynamics based study." Doctoral thesis, La Sapienza, 2005. http://hdl.handle.net/11573/916821.

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Chen, Wei. "Molecular dynamics simulations of binding, unfolding, and global conformational changes of signaling and adhesion molecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28118.

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Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.
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Bruce, Neil John. "Investigating protein conformational change via molecular dynamics simulation." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/investigating-protein-conformational-change-via-molecular-dynamics-simulation(17145939-f643-4b23-bbb9-029cf5489c15).html.

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Accumulation and aggregation of the 42-residue amyloid-[beta] (A[beta]) protein fragment, which originates from the cleavage of amyloid precursor protein by beta and gamma secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the A[beta] sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of A[beta] and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LP
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Books on the topic "Proteins - Conformation Dynamics"

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Livesay, Dennis R. Protein dynamics: Methods and protocols. Humana Press, 2013.

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Subbiah, S. Protein motions. Chaoman & Hall, 1996.

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International Symposium on Structure and Dynamics of Nucleic Acids, Proteins, and Membranes (1986 Riva, Italy). Structure and dynamics of nucleic acids, proteins, and membranes. Plenum Press, 1986.

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Han, Ke-li, Xin Zhang, and Ming-jun Yang, eds. Protein Conformational Dynamics. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-02970-2.

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Rupp, Bernhard. Biomolecular crystallography. Garland Science, 2010.

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Rupp, Bernhard. Biomolecular crystallography. Garland Science, 2010.

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Course on Dynamics and the Problem of Recognition in Biological Macromolecules (2nd 1995 Erice, Italy). Dynamics and the problem of recognition in biological macromolecules. Plenum Press, 1996.

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Xin, Zhang, Ke-li Han, and Ming-jun Yang. Protein Conformational Dynamics. Springer, 2014.

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Xin, Zhang, Ke-Li Han, and Ming-jun Yang. Protein Conformational Dynamics. Springer International Publishing AG, 2016.

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Xin, Zhang, Ke-Li Han, and Ming-jun Yang. Protein Conformational Dynamics. Springer London, Limited, 2014.

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Book chapters on the topic "Proteins - Conformation Dynamics"

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Balasubramaniam, A., S. G. Huang, S. Sheriff, M. Prabhakaran, and V. Renugopalakrishnan. "Solution conformation of neuropeptide Y: 2D NMR and molecular dynamics studies." In Proteins. Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-010-9063-6_11.

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Wüthrich, Kurt. "Conformation of Non-Crystalline Proteins Viewed by NMR." In Structure and Dynamics of Nucleic Acids, Proteins, and Membranes. Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5308-9_2.

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Choi, Ucheor B., Keith R. Weninger, and Mark E. Bowen. "Immobilization of Proteins for Single-Molecule Fluorescence Resonance Energy Transfer Measurements of Conformation and Dynamics." In Intrinsically Disordered Protein Analysis. Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-3704-8_1.

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So, Pui-Kin. "Hydrogen–Deuterium Exchange Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0892-0_10.

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Mao, Youdong. "Structure, Dynamics and Function of the 26S Proteasome." In Subcellular Biochemistry. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-58971-4_1.

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AbstractThe 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal “processor” for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Barth, Marie, and Carla Schmidt. "Quantitative Cross-Linking of Proteins and Protein." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_26.

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AbstractCross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a “light” and a “heavy” cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.
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Tan, Yan-Wen, Jeffrey A. Hanson, Jhih-Wei Chu, and Haw Yang. "Confocal Single-Molecule FRET for Protein Conformational Dynamics." In Protein Dynamics. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-658-0_3.

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Zheng, Wenjun, and Mustafa Tekpinar. "Analysis of Protein Conformational Transitions Using Elastic Network Model." In Protein Dynamics. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-658-0_9.

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Eichinger, Markus, Berthold Heymann, Helmut Heller, Helmut Grubmüller, and Paul Tavan. "Conformational Dynamics Simulations of Proteins." In Computational Molecular Dynamics: Challenges, Methods, Ideas. Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-58360-5_4.

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Hills, Ronald D. "Balancing Bond, Nonbond, and Gō-Like Terms in Coarse Grain Simulations of Conformational Dynamics." In Protein Dynamics. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-658-0_7.

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Conference papers on the topic "Proteins - Conformation Dynamics"

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Karplus, M. "Internal dynamics of macromolecules : Simulations of motion in proteins." In International Conference on Ultrafast Phenomena. Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb1.

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The internal motions of proteins will be discussed. Detailed atom-bases simulations of the native conformation space will be supplemented by simplified models for the full conformation space involved in protein folding.
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Xu, Yangqing, and Gang Bao. "Protein Conformational Changes Under Applied Forces." In ASME 1999 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1999. http://dx.doi.org/10.1115/imece1999-0408.

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Abstract Recent studies confirm that stresses, including that due to gravity, tension, compression, pressure, and shear influence cell growth, differentiation, secretion, movement, signal transduction, and gene expression. Yet, little is known about how cells sense the mechanical stresses or deformations, and convert these mechanical signals into biological or biochemical responses. A possible mechno-chemical coupling mechanism involves protein conformational changes under mechanical forces. Our hypothesis is that mechanical forces can cause large changes of the conformation of proteins, which
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Kazerounian, Kazem, Khalid Latif, Kimberly Rodriguez, and Carlos Alvarado. "ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57243.

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Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this
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Dyer, R. Brian, and Timothy P. Causgrove. "Ultrafast Protein Relaxation: Time-Resolved Infrared Studies of Protein Dynamics Triggered by CO Photodissociation from CO Myoglobin." In International Conference on Ultrafast Phenomena. Optica Publishing Group, 1994. http://dx.doi.org/10.1364/up.1994.tub.4.

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A critical feature of the biological function of heme proteins is the direct coupling of protein motion to the process of binding exogenous ligands to the heme. In carbonmonoxymyoglobin (MbCO), a substantial, specific conformational relaxation is associated with the transition from the ligated to the unligated form of the protein. The analogous tertiary structural changes of the monomer heme subunits of hemoglobin ultimately lead to the R→T quaternary structural transition, the allosteric control mechanism of O2 binding efficiency [1]. We have studied these processes on the earliest timescales
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Lim, Manko, Timothy A. Jackson, and Philip A. Anfinrud. "Ultrafast Near-IR Spectroscopy of Carbonmonoxymyoglobin: the Dynamics of Protein Relaxation." In International Conference on Ultrafast Phenomena. Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb3.

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The conformation of a protein often influences its activity, yielding a structure-function relationship. X-ray diffraction studies have shown that the tertiary structures of ligated and deligated myoglobin (Mb) are somewhat different1. Consequently, dissociation of a ligand from Mb triggers a transition between the two tertiary conformations. The potential energy gradient causing this change is developed at the heme; the iron prefers to be in the plane of the porphyrin in ligated Mb but is displaced 0.5 Å from the plane of the porphyrin in deoxy Mb. The dynamics of this conformational transiti
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Jewel, Yead, Prashanta Dutta, and Jin Liu. "Coarse-Grained Molecular Dynamics Simulations of Sugar Transport Across Lactose Permease." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-52337.

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Sugar (one of the critical nutrition elements for all life forms) transport across the cell membranes play essential roles in a wide range of living organism. One of the most important active transport (against the sugar concentration) mechanisms is facilitated by the transmembrane transporter proteins, such as the Escherichia coli lactose permease (LacY) proteins. Active transport of sugar molecules with LacY proteins requires a proton gradient and a sequence of complicated protein conformational changes. However, the exact molecular mechanisms and the protein structural information involved
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Leeson, D. Thorn, and D. A. Wiersma. "Long-Lived Stimulated Photon Echo Studies of Protein and Glass Dynamics." In Spectral Hole-Burning and Related Spectroscopies: Science and Applications. Optica Publishing Group, 1994. http://dx.doi.org/10.1364/shbs.1994.thb1.

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The dynamical behavior of proteins is often interpreted in terms of conformational substates.1 A protein can assume a large number of slightly different structures, separated by conformational barriers. This view is very similar to the description of glass dynamics in terms of two-level systems.2,3 A two-level system (TLS) represents a group of atoms or molecules which can reside in either of two potential energy wells along a conformational coordinate. At very low temperature the TLS can fluctuate between the two potential energy minima through a tunneling process.
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Maghsoodi, Ameneh, Anupam Chatterjee, Ioan Andricioaei, and Noel Perkins. "An Approximate Model of the Dynamics of the Bacteriophage T4 Injection Machinery." In ASME 2016 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/detc2016-60281.

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Bacteriophage T4 is one of the most common and complex of the tailed viruses that infect host bacteria using an intriguing contractile tail assembly. Despite extensive progress in resolving the structure of T4, the dynamics of the injection machinery remains largely unknown. This paper contributes a first model of the injection machinery that is driven by elastic energy stored in a structure known as the sheath. The sheath is composed of helical strands of protein that suddenly collapse from an energetic, extended conformation prior to infection to a relaxed, contracted conformation during inf
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Cortés, Juan, and Ibrahim Al-Bluwi. "A Robotics Approach to Enhance Conformational Sampling of Proteins." In ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/detc2012-70105.

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Proteins are biological macromolecules that play essential roles in living organisms. Furthermore, the study of proteins and their function is of interest in other fields in addition to biology, such as pharmacology and biotechnology. Understanding the relationship between protein structure, dynamics and function is indispensable for advances in all these areas. This requires a combination of experimental and computational methods, whose development is the object of very active interdisciplinary research. In such a context, this paper presents a technique to enhance conformational sampling of
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Bao, Gang, and Shannon Stott. "Langevin Dynamics of Hinge-Motion in Proteins." In ASME 2000 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2000. http://dx.doi.org/10.1115/imece2000-2634.

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Abstract Many proteins function in mechanically stressful environments. For example, shear flow in blood vessel may exert a force as high as hundreds of piconewtons on an individual selectin-ligand bond. With such a mechanical force, the receptor (selectin) may deform, thereby altering the conformational match between the receptor and the ligand. Although van der Waals forces, electrostatic and hydrophobic interactions are all important, it is often the 3D geometry local to the binding pocket that dictates the characteristics of the bond between the receptor and the ligand. Good conformational
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Reports on the topic "Proteins - Conformation Dynamics"

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Hanke, Andreas. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding. Defense Technical Information Center, 2008. http://dx.doi.org/10.21236/ada483440.

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Markelz, Andrea G. Terahertz Time Domain Spectroscopy of Conformational Dynamics of Sensor Proteins: Basic Research and Pathogen Sensor Development. Defense Technical Information Center, 2004. http://dx.doi.org/10.21236/ada426482.

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