Collective Langevin Dynamics Of Conformational Motions In Proteins
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Collective Langevin Dynamics Of Conformational Motions In Proteins
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Author : Oliver Lange
language : de
Publisher: Cuvillier Verlag
Release Date : 2006
Collective Langevin Dynamics Of Conformational Motions In Proteins written by Oliver Lange and has been published by Cuvillier Verlag this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with categories.
Collective Langevin Dynamics Of Conformational Motions In Protein
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Author :
language : en
Publisher: Cuvillier Verlag
Release Date : 2006-01-06
Collective Langevin Dynamics Of Conformational Motions In Protein written by and has been published by Cuvillier Verlag this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-01-06 with Science categories.
Functional Domain Motions And Processivity In Bacterial Hyaluronate Lyase
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Author : Harshad Joshi
language : en
Publisher: Universal-Publishers
Release Date : 2010-05-12
Functional Domain Motions And Processivity In Bacterial Hyaluronate Lyase written by Harshad Joshi and has been published by Universal-Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-05-12 with categories.
Processive enzymes are a special class of enzymes which presumably remain attached to their polymeric substrates between multiple rounds of catalysis. Due to this property, the substrate slides along the enzyme and reduces the time for the random diffusional enzyme-substrate encounters thereby increasing the efficiency of these enzymes manifold. Although structural information from many processive enzymes is available, the atomistic details of particularly the substrate sliding process, which is an inherently dynamic process, remain largely unknown. We take first steps to understand the sliding process by investigating a prototypic processive enzyme: Streptococcus Pneumoniae Hyaluronate lyase, a bacterial enzyme that degrades the polysaccharide substrate hyaluronan. Here we have investigated the flexibility of the enzyme as observed from essential dynamics simulations and its relation to the enzyme-substrate interactions by employing several free and enforced molecular dynamics simulations (on sub-microsecond timescale). This way we have identified a coupling between domain motions of the enzyme and the processivity or the sliding phase of the substrate. In the putative mechanism for the substrate translocation phase we observed an energy barrier along the processive direction and it is speculated that this may arise because of the reorientation of the sugar inside the cleft of the protein. This view was supported from the Force probe molecular dynamics simulations and umbrella sampling simulations that were employed to obtain a preliminary free energy profile underlying the mechanism. The observed free energy barrier is low enough to be easily crossed by thermal fluctuations, renderring essential slow collective domain rearrangements as likely rate-limiting factor for the processive cycle. The collective conformational motions of the protein along with particular interactions of individual amino acids may be involved in this translocation phase. Experimental validation along with further computational studies will be useful to understand this complex mechanism.
Protein Interactions
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Author : Volkhard Helms
language : en
Publisher: John Wiley & Sons
Release Date : 2023-02-06
Protein Interactions written by Volkhard Helms and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-02-06 with Science categories.
A fundamental guide to the burgeoning field of protein interactions From enzymes to transcription factors to cell membrane receptors, proteins are at the heart of biological cell function. Virtually all cellular processes are governed by their interactions, with one another, with cell bodies, with DNA, or with small molecules. The systematic study of these interactions is called Interactomics, and research within this new field promises to shape the future of molecular cell biology. Protein Interactions goes beyond any existing guide to protein interactions, presenting the first truly comprehensive overview of the field. Edited by two leading scholars in the field of protein bioinformatics, this book covers all known categories of protein interaction, stable as well as transient, as well as the effect of mutations and post-translational modifications on the interaction behavior. Protein Interactions readers will also find: Introductory chapters on protein structure, conformational dynamics, and protein-protein binding interfaces A data-driven approach incorporating machine learning and integrating experimental data into computational models An outlook on the current challenges in the field and suggestions for future research Protein Interactions will serve as a fundamental resource for novice researchers who want a systematic introduction to interactomics, as well as for experienced cell biologists and bioinformaticians who want to gain an edge in this exciting new field.
Heat Transfer
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Author : Salim Newaz Kazi
language : en
Publisher: BoD – Books on Demand
Release Date : 2015-07-29
Heat Transfer written by Salim Newaz Kazi and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-29 with Technology & Engineering categories.
In the wake of energy crisis due to rapid growth of industries, the efficient heat transfer could play a vital role in energy saving. Industries, household equipment, transportation, offices, etc., all are dependent on heat exchanging equipment. Considering this, the book has incorporated different chapters on heat transfer phenomena, analytical and experimental heat transfer investigations, heat transfer enhancement and applications.
Protein Conformational Dynamics
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Author : Ke-li Han
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-20
Protein Conformational Dynamics written by Ke-li Han and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-01-20 with Medical categories.
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.
Membrane Biomechanics
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Author :
language : en
Publisher: Academic Press
Release Date : 2020-10-23
Membrane Biomechanics written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-10-23 with Science categories.
Membrane Biomechanics, Volume 86, the latest release in the Current Topics in Membranes series, highlights new advances in the field, with this new volume presenting interesting chapters on Lipid bilayers: phase behavior and mechanics, Molecular mechanisms of cell membrane structure modification by omega-3 fatty acids, Mechanical properties of magnetoliposomes, Mechanosensitive ion channels and membrane tension, From cell membrane to the nuclear membrane through modulation of cytoskeleton, Endothelial stiffness in dyslipidemia and aging, Vascular smooth muscle stiffness in aging and vascular disease, Mechanobiology of macrovesicle release and activation, Interplay of membrane cholesterol and substrate on vascular smooth muscle mechanics, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Current Topics in Membranes series Includes the latest information on Membrane Biomechanics
Advances In Protein And Peptide Sciences
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Author : Ben M. Dunn
language : en
Publisher: Bentham Science Publishers
Release Date : 2013-10-30
Advances In Protein And Peptide Sciences written by Ben M. Dunn and has been published by Bentham Science Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-10-30 with Science categories.
Advances in Protein and Peptide Sciences is a book series focused on leading-edge research on the structure, physical properties, and functions of proteins and peptides. The series presents highly cited contributions first published in the journal Current Protein and Peptide Science. Authors of these contributions have updated their work with new experimental data and references following their initial research. Each volume highlights a number of important topics in current research in the field of protein and peptide chemistry and molecular biology, including membrane proteins and their interactions with ligands, computational methods, and proteins in disease and biotechnology.
Single Molecule Dynamics In Life Science
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Author : Toshio Yanagida
language : en
Publisher: John Wiley & Sons
Release Date : 2008-11-24
Single Molecule Dynamics In Life Science written by Toshio Yanagida and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-11-24 with Science categories.
In this first comprehensive resource to cover the application of single molecule techniques to biological measurements, the pioneers in the field show how to both set up and interpret a single molecule experiment. Following an introduction to single molecule measurements and enzymology, the expert authors consider molecular motors and mechanical properties before moving on to the applications themselves. Detailed discussions of studies on protein enzymes, ribozymes and nucleic acids are also included.
Dynamics Of Proteins And Nucleic Acids
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Author : J. Andrew McCammon
language : en
Publisher: Cambridge University Press
Release Date : 1988-04-29
Dynamics Of Proteins And Nucleic Acids written by J. Andrew McCammon and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1988-04-29 with Science categories.
This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plays a crucially important role in biological activity. The authors, both of whom are well known for their work in this field, describe in detail the major theoretical methods that are likely to be useful in the computer-aided design of drugs, enzymes and other molecules. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function. The book will be of interest to graduate students and research workers in structural biochemistry (X-ray diffraction and NMR), theoretical chemistry (liquids and polymers), biophysics, enzymology, molecular biology, pharmaceutical chemistry, genetic engineering and biotechnology.