Download or read book Protein Structure and Dynamics Studied by Molecular Dynamics Simulations written by Tim Meyer and published by . This book was released on 2008 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Frontiers in Protein Structure Function and Dynamics written by Dev Bukhsh Singh and published by Springer Nature. This book was released on 2020-07-02 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.

Download or read book Probing Structure and Dynamics of Membrane Proteins by Molecular Dynamics Simulation written by Zoe Li (Ph. D. in pharmaceutics) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics (MD) simulation provides atomistic details of biomolecules’ behaviors and has become a pivotal tool in the study of protein structure, dynamics and drug discovery. In this thesis, MD simulations are used in combination with experimental results to address a variety of biological questions in three protein systems: the 5HT3A serotonin receptor, the acetylcholine binding receptor (AChBP), and the Insig (insulin-induced gene)-Scap (SREBP (sterol regulatory element-binding protein)-cleavage activating protein) complex. The objective of our first system is to investigate the key to generating a stable open structure of the 5HT3A serotonin receptor based on low resolution cryo-electron microscopy structures, which may also apply to other pentameric ligand-gated ion channels (pLGICs). We developed a refined equilibration protocol that involves the rearrangement of transmembrane helices to achieve stable open state structures of the 5-HT3 receptor that allow both water and ion permeation through the channel. Our study underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like state structures of the 5-HT3 receptor. Our second system aims to shed light on the nature of ligand recognition in the pLGICs that are activated upon ligand binding to their extracellular domains. The MD simulation-based absolute binding free energy calculation was carried out to study the electrostatic contribution in the binding of nicotine in a model system (AChBP). Finally, we performed extensive MD simulations on Scap to identify potential binding sites for a previously unknown SREBP activating molecule ammonia and to provide detailed structural mechanisms for how this molecule activates Scap.

Download or read book Proteins written by Charles L. Brooks and published by John Wiley & Sons. This book was released on 2009-09-08 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting a wide-ranging view of current developments in protein research, the papers in this collection, each written by highly regarded experts in the field, examine various aspects of protein structure, functions, dynamics, and experimentation. Topics include dynamical simulation methods, the biological role of atom fluctuations, protein folding, influences on protein dynamics, and a variety of analytical techniques, such as X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. This is part of a series devoted to providing general information on a wide variety of topics in chemical physics in order to stimulate new research and to serve as a text for beginners in a particular area of chemical physics.

Download or read book Protein Dynamics Function and Design written by Oleg Jardetzky and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 3rd Course: Protein Dynamics, Function, and Design. This NATO Advance Study Institute was held in Erice at the Ettore Majorana Centre for Scientific Culture on April 16-28, 1997. The aim of the Institute was to bring together experts applyipg different physical methods to problems of macro molecular dynamics-notably x-ray diffraction, NMR and other forms of spectroscopy, and molecular dynamics simulations. Emphasis was placed on those systems and types of problems-such as mechanisms of allosteric control, signal transmission, induced fit to different ligands with its implications for drug design, and the effects of dynamics on structure determination-where a correlation of findings obtained by different methods could shed the most light on the mechanisms involved and stimulate the search for new approaches. The individual articles represent the state of the art in each of the areas cov ered and provide a guide to the original literature in this rapidly developing field. v CONTENTS 1. Determining Structures of ProteinlDN A Complexes by NMR Angela M. Gronenbom and G. Marius Clore 2. Fitting Protein Structures to Experimental Data: Lessons from before Your Mother Was Born . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Jeffrey C. Hoch, Alan S. Stem, and Peter J. Connolly 3. Multisubunit Allosteric Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 William N. Lipscomb 4. Studying Protein Structure and Function by Directed Evolution: Examples with Engineered Antibodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Andreas Pliickthun 5. High Pressure Effects on Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Download or read book Comparative Studies of Protein Structure and Dynamics by Molecular Dynamics Simulation NMR Spectroscopy and X ray Crystallography written by and published by . This book was released on 1999 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Proteins written by V. Renugopalakrishnan and published by Springer. This book was released on 1991-07-31 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The major goal of 'Expanding Frontiers in Polypeptide and Protein Structural Research' has been to bring the various avenues for the exploration of protein structures to a single forum. The idea of organizing the symposiwn was conceived by one of the editors, V. Renugopalakrislman, during the 9th International Biophysics Congress satellite symposium at Kibbutz Nof-Ginosar, Israel in 1987. It was originally supposed to dwell on 2D NMR and molecular dynamics of polypeptides and proteins. During the earlier part of the last decade, these two approaches began to emerge as powerful tools to probe protein structures at the atomic level in solution. The developments in molecular biology ushered in the capability to design polypeptides and proteins for specific application in science and technology. The emergence of 2D NMR and molecular dynamics was greatly facilitated by contemporary developments in molecular biology and protein engineering. Therefore an international symposiwn devoted exclusively to 2D NMR and molecular dynamics studies of proteins was felt necessary to bring two major approaches in a single forum. In addition to emphasis on 2D NMR and molecular dynamics simulation, the scope of the symposiwn included optical spectroscopy, protein design, and new horizons in protein structure. The symposiwn consisted of five plenary sessions devoted to NMR and optical spectroscopy as probes for protein structure, protein dynamics, computational methods in protein design, and new horizons in protein structure. In addition, five workshops in related areas, viz.

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 851 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

Download or read book Molecular Dynamics and Protein Structure written by Jan Hermans and published by . This book was released on 1985 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.

Download or read book Biomolecular Structure and Dynamics written by G. Vergoten and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.

Download or read book Protein Folding Dynamics and Stability written by Prakash Saudagar and published by Springer Nature. This book was released on 2023-05-27 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.

Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Download or read book Protein Flexibility and Folding written by Leslie A. Kuhn and published by Elsevier Science. This book was released on 2001 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: NMR spin relaxation methods for characterization of disorder and folding in proteins (C. Bracken). Steered molecular dynamics investigations of protein function (B. Isralewitz, J. Baudry, J. Gullingsrud, D. Kosztin, K. Schulten). Intrinsically disordered protein (A. K. Dunker, J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero, J. S. Oh, C. J. Oldfield, A. M. Campen, C. M. Ratliff, K. W. Hipps, J. Ausio, M. S. Nissen, R. Reeves, C. Kang, C. R. Kissinger, R. W. Bailey, M. D. Griswold, Wath Chiu, E. C. Garner, Z. Obradovic). protein flexibility and dynamics using constraint theory (M. F. Thorpe, M. Lei, A. J. Rader, D. J. Jacobs, L. A. Kuhn). Structure and dynamics of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (H. Yan, J. Blaszczyk, B. Xiao, G. Shi, Xinhua Ji). Sampling activated mechanisms in proteins with the activation-relaxation technique (N. Mousseau, P. Derreumaux, G. T. Barkema, R. Maleks). Constructing smooth potential functions for protein folding (G. M. Crippen). Experimental approaches to protein folding based on the concept of a slow hydrogen exchange core (C. Woodward, E. Barbar, N. Carulla, J. Battiste, G. Barany). Structural transitions in neutral and charged proteins in vacuo (G. A. Arteca, O. Tapia). Capture and identification of folding intermediates of cystinyl proteins by cyanylation and mass spectrometry (J. T. Watson, Y. Yang, J. Wu). Solid state NMR measurements of conformation and conformational distributions in the membrane-bound HIV-1 fusion peptide (J. Yang, P. D. Parkanzky, B. A. Khunte, C. G. Canlas, R. Yang, C. M. Gabrys, D. P. Weliky). Continuum solvent molecular dynamics study of flexibility in interleukin-8 (W. Cornell, R. Abseher, M. Nilges, D. A. Case). State of the art in studying protein folding and protein structure prediction using molecular dynamics methods (M. R. Lee, Y. Duan, P. A. Kollman). Evolution of functionality in lattice proteins (P. D. Williams, D. D. Pollock, R. A. Goldstein). The designability of protein structures (R. Helling, Hao Li, R. Mélin, Jonathan Miller, Ned Wingreen, Chen Zeng, C. Tang). Comparing protein structures: a gaussian-based approach to the three-dimensional structural similarity of proteins (G. M. Maggiora, D. C. Rohrer, J. Mestres).

Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 2013-11-27 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...

Download or read book Structure and Dynamics in Protein Function written by Brittany Rose Morgan and published by . This book was released on 2010 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: