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Author : Oliver Lange
Publisher : Cuvillier Verlag
Page : 16 pages
File Size : 51,6 Mb
Release : 2006
Category : Electronic
ISBN : 9783865377449
Author : Anonim
Publisher : Cuvillier Verlag
Page : 164 pages
File Size : 49,8 Mb
Release : 2006-01-06
Category : Science
ISBN : 9783736917446
Author : Harshad Joshi
Publisher : Universal-Publishers
Page : 128 pages
File Size : 51,8 Mb
Release : 2010-05-12
Category : Electronic
ISBN : 9781599423203
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.
Author : Volkhard Helms,Olga V. Kalinina
Publisher : John Wiley & Sons
Page : 436 pages
File Size : 51,5 Mb
Release : 2023-02-06
Category : Science
ISBN : 9783527348640
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.
Author : Salim Newaz Kazi
Publisher : BoD – Books on Demand
Page : 408 pages
File Size : 54,7 Mb
Release : 2015-07-29
Category : Technology & Engineering
ISBN : 9789535121466
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.
Author : Anonim
Publisher : Academic Press
Page : 328 pages
File Size : 47,6 Mb
Release : 2020-10-23
Category : Science
ISBN : 9780128210222
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
Author : Ben M. Dunn
Publisher : Bentham Science Publishers
Page : 911 pages
File Size : 45,5 Mb
Release : 2013-10-30
Category : Science
ISBN : 9781608054879
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.
Author : Ke-li Han,Xin Zhang,Ming-jun Yang
Publisher : Springer Science & Business Media
Page : 488 pages
File Size : 46,9 Mb
Release : 2014-01-20
Category : Medical
ISBN : 9783319029702
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.
Author : J. Andrew McCammon,Stephen C. Harvey
Publisher : Cambridge University Press
Page : 256 pages
File Size : 43,9 Mb
Release : 1988-04-29
Category : Science
ISBN : 0521356520
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.
Author : Toshio Yanagida,Yoshiharu Ishii
Publisher : John Wiley & Sons
Page : 347 pages
File Size : 41,6 Mb
Release : 2008-11-24
Category : Science
ISBN : 9783527312887
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.
Author : Paula Marcela Petrone
Publisher : Unknown
Page : 232 pages
File Size : 40,7 Mb
Release : 2009
Category : Electronic
ISBN : STANFORD:36105210231127
Author : M. Doyama,J. Kihara,Mana Tanaka,R. Yamamoto
Publisher : Elsevier
Page : 980 pages
File Size : 55,9 Mb
Release : 2017-01-31
Category : Computers
ISBN : 9781483291475
With advanced materials being in the midst of a widely acknowledged revolution, there is relentless pressure on scientists and engineers to be on the cutting edge of emerging theories and design methodologies. The 379 papers in this two part volume bring together the experience of specialists in the entire field of applications of Materials Science. This multidisciplinary meeting was held to bring together workers in a wide range of materials science and engineering activities who employ common analytical and experimental methods in their day to day work. The results of the meeting are of worldwide interest, and will help to stimulate future research and analysis in this area.
Author : Qiang Cui,Ivet Bahar
Publisher : CRC Press
Page : 432 pages
File Size : 42,7 Mb
Release : 2005-12-12
Category : Medical
ISBN : 9781420035070
Rapid developments in experimental techniques continue to push back the limits in the resolution, size, and complexity of the chemical and biological systems that can be investigated. This challenges the theoretical community to develop innovative methods for better interpreting experimental results. Normal Mode Analysis (NMA) is one such technique. Capable of providing unique insights into the structural and dynamical properties of complex systems, it is now finding a wide range of applications in chemical and biological problems. From the fundamental physical ideas to cutting-edge applications and beyond, this book presents a broad overview of normal mode analysis and its value in state-of-the-art research. The first section introduces NMA, examines NMA algorithm development at different resolutions, and explores the application of those techniques in the study of biological systems. Later chapters cover method developments based on or inspired by NMA but going beyond the harmonic approximation inherent in standard NMA techniques. Normal mode analysis complements traditional approaches with computational efficiency and applicability to large systems that are beyond the reach of older methods. This book offers a unique opportunity to learn from the experiences of an international, interdisciplinary panel of top researchers and explore the latest developments and applications of NMA to biophysical and chemical problems.
Author : Sebastian Doniach
Publisher : Springer Science & Business Media
Page : 400 pages
File Size : 44,9 Mb
Release : 2013-11-22
Category : Science
ISBN : 9781489913494
A number of factors have come together in the last couple of decades to define the emerging interdisciplinary field of structural molecular biology. First, there has been the considerable growth in our ability to obtain atomic-resolution structural data for biological molecules in general, and proteins in particular. This is a result of advances in technique, both in x-ray crystallography, driven by the development of electronic detectors and of synchrotron radiation x-ray sources, and by the development ofNMR techniques which allow for inference of a three-dimensional structure of a protein in solution. Second, there has been the enormous development of techniques in DNA engineering which makes it possible to isolate and clone specific molecules of interest in sufficient quantities to enable structural measurements. In addition, the ability to mutate a given amino acid sequence at will has led to a new branch of biochemistry in which quantitative measurements can be made assessing the influence of a given amino acid on the function of a biological molecule. A third factor, resulting from the exponential increase in computing power available to researchers, has been the emergence of a growing body of people who can take the structural data and use it to build atomic-scale models of biomolecules in order to try and simulate their motions in an aqueous environment, thus helping to provide answers to one of the most basic questions of molecular biology: the relation of structure to function.
Author : Hiqmet Kamberaj
Publisher : Springer Nature
Page : 306 pages
File Size : 46,9 Mb
Release : 2023-07-31
Category : Science
ISBN : 9783031348396
This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.