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Computational Approaches to Protein Dynamics by Monika Fuxreiter Pdf
The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an
Protein Conformational Dynamics by Ke-li Han,Xin Zhang,Ming-jun Yang Pdf
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.
Frontiers in Protein Structure, Function, and Dynamics by Dev Bukhsh Singh,Timir Tripathi Pdf
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.
Protein Dynamics, Function, and Design by Oleg Jardetzky,Jean-François Lefèvre Pdf
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proteins by Charles L. Brooks,Martin Karplus,B. Montgomery Pettitt Pdf
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.
In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogate molecular level fluctuations. Chapters detail best-practice recipes covering both experimental and computational techniques, reflecting modern protein research. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Dynamics: Methods and Protocols describes the most common and powerful methods used to characterize protein dynamics.
Dancing Protein Clouds: Intrinsically Disordered Proteins in the Norm and Pathology by Vladimir Uversky Pdf
"Dancing protein clouds: Intrinsically disordered proteins in the norm and pathology" represents a set of selected studies on a variety of research topics related to intrinsically disordered proteins. Topics in this update include structural and functional characterization of several important intrinsically disordered proteins, such as 14-3-3 proteins and their partners, as well as proteins from muscle sarcomere; representation of intrinsic disorder-related concept of protein structure-function continuum; discussion of the role of intrinsic disorder in phenotypic switching; consideration of the role of intrinsically disordered proteins in the pathogenesis of neurodegenerative diseases and cancer; discussion of the roles of intrinsic disorder in functional amyloids; demonstration of the usefulness of the analysis of translational diffusion of unfolded and intrinsically disordered proteins; consideration of various computational tools for evaluation of functions of intrinsically disordered regions; and discussion of the role of shear stress in the amyloid formation of intrinsically disordered regions in the brain. Provides some recent studies on the intrinsically disordered proteins and their functions, as well as on the involvement of intrinsically disordered proteins in pthogenesis of various diseases Contains numerous illustrative materials (color figures, diagrams, and tables) to help the readers to delve in the information provided Includes contributions from recognized experts in the field
NMR Spectroscopy for Probing Functional Dynamics at Biological Interfaces by Anirban Bhunia,Hanudatta S Atreya,Neeraj Sinha Pdf
NMR spectroscopy has found a wide range of applications in life sciences over recent decades. Providing a comprehensive amalgamation of the scattered knowledge of how to apply high-resolution NMR techniques to biomolecular systems, this book will break down the conventional stereotypes in the use of NMR for structural studies. The major focus is on novel approaches in NMR which deal with the functional interface of either protein-protein interactions or protein-lipid interactions. Bridging the gaps between structural and functional studies, the Editors believe a thorough compilation of these studies will open an entirely new dimension of understanding of crucial functional motifs. This in turn will be helpful for future applications into drug design or better understanding of systems. The book will appeal to NMR practitioners in industry and academia who are looking for a comprehensive understanding of the possibilities of applying high-resolution NMR spectroscopic techniques in probing biomolecular interactions.
Nuclear Magnetic Resonance Probes of Molecular Dynamics by R. Tycko Pdf
Nuclear Magnetic Resonance Probes of Molecular Dynamics describes the theoretical basis and experimental techniques that make modern NMR spectroscopy a powerful and flexible tool for probing molecular dynamics in chemical, physical, and biochemical systems. Individual chapters, written by leaders in the development and application of NMR from around the world, treat systems that range from synthetic polymers, liquid crystals, and catalysts to proteins and oligonucleotides and techniques that include deuterium NMR, magic angle spinning, multidimensional spectroscopy, and magnetic resonance imaging. A combination of elementary and advanced material makes the book a useful introduction to the field for students at the graduate level as well as an important reference for practising NMR spectroscopists.
Dynamics of Soft Matter by VICTORIA GARCIA SAKAI,Christiane Alba-Simionesco,Sow Hsin Chen Pdf
Dynamics of Soft Matter: Neutron Applications provides an overview of neutron scattering techniques that measure temporal and spatial correlations simultaneously, at the microscopic and/or mesoscopic scale. These techniques offer answers to new questions arising at the interface of physics, chemistry, and biology. Knowledge of the dynamics at these levels is crucial to understanding the soft matter field, which includes colloids, polymers, membranes, biological macromolecules, foams, emulsions towards biological & biomimetic systems, and phenomena involving wetting, friction, adhesion, or microfluidics. Emphasizing the complementarities of scattering techniques with other spectroscopic ones, this volume also highlights the potential gain in combining techniques such as rheology, NMR, light scattering, dielectric spectroscopy, as well as synchrotron radiation experiments. Key areas covered include polymer science, biological materials, complex fluids and surface science.