Download or read book Collective Langevin dynamics of conformational motions in proteins written by Oliver Lange and published by Cuvillier Verlag. This book was released on 2006 with total page 16 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Collective Langevin Dynamics of Conformational Motions in Protein written by and published by Cuvillier Verlag. This book was released on 2006-01-06 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Interactions written by Volkhard Helms and published by John Wiley & Sons. This book was released on 2023-02-06 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Advances in Protein and Peptide Sciences written by Ben M. Dunn and published by Bentham Science Publishers. This book was released on 2013-10-30 with total page 911 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Heat Transfer written by Salim Newaz Kazi and published by BoD – Books on Demand. This book was released on 2015-07-29 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Functional Domain Motions and Processivity in Bacterial Hyaluronate Lyase written by Harshad Joshi and published by Universal-Publishers. This book was released on 2010-05-12 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Single Molecule Dynamics in Life Science written by Toshio Yanagida and published by John Wiley & Sons. This book was released on 2008-11-24 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Membrane Biomechanics written by and published by Academic Press. This book was released on 2020-10-23 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Protein Folding Simulations Combining Self Guided Langevin Dynamics and Temperature Based Replica Exchange written by and published by . This book was released on 2010 with total page 13 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer simulations are increasingly being used to predict thermodynamic observables for folding small proteins. Key to continued progress in this area is the development of algorithms that accelerate conformational sampling. Temperature-based replica exchange (ReX) is a commonly used protocol whereby simulations at several temperatures are simultaneously performed and temperatures are exchanged between simulations via a Metropolis criterion. Another method, self-guided Langevin dynamics (SGLD), expedites conformational sampling by accelerating low-frequency large-scale motions through the addition of an ad hoc momentum memory term. In this work, we combined these two complementary techniques and compared the results against conventional ReX formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All simulations were performed with CHARMM using the PARAM22+CMAP force field and the generalized Born molecular volume implicit solvent model. While SGLD-ReX does not fold up the protein significantly faster than the two conventional ReX approaches, there is some evidence that the method improves sampling convergence by reducing topological folding barriers between energetically similar nearnative states. Unlike MD-ReX and LD-ReX, SGLD-ReX predicts melting temperatures, heat capacity curves, and folding free energies that are closer in agreement to the experimental observations. However, this favorable result may be due to distortions of the relative free energies of the folded and unfolded conformational basins caused by the ad hoc force term in the SGLD model.
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer. This book was released on 2014-01-30 with total page 0 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 Computer Aided Innovation of New Materials II written by M. Doyama and published by Elsevier. This book was released on 2017-01-31 with total page 980 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Statistical Mechanics Protein Structure and Protein Substrate Interactions written by Sebastian Doniach and published by Springer Science & Business Media. This book was released on 2013-11-22 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Methods in Molecular Biophysics written by Nathan R. Zaccai and published by Cambridge University Press. This book was released on 2017-05-18 with total page 710 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current techniques for studying biological macromolecules and their interactions are based on the application of physical methods, ranging from classical thermodynamics to more recently developed techniques for the detection and manipulation of single molecules. Reflecting the advances made in biophysics research over the past decade, and now including a new section on medical imaging, this new edition describes the physical methods used in modern biology. All key techniques are covered, including mass spectrometry, hydrodynamics, microscopy and imaging, diffraction and spectroscopy, electron microscopy, molecular dynamics simulations and nuclear magnetic resonance. Each method is explained in detail using examples of real-world applications. Short asides are provided throughout to ensure that explanations are accessible to life scientists, physicists and those with medical backgrounds. The book remains an unparalleled and comprehensive resource for graduate students of biophysics and medical physics in science and medical schools, as well as for research scientists looking for an introduction to techniques from across this interdisciplinary field.
Download or read book Computational Approaches to Conformational Change and Specificity in Biomolecules written by Paula Marcela Petrone and published by . This book was released on 2009 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Normal Mode Analysis written by Qiang Cui and published by CRC Press. This book was released on 2005-12-12 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Methods in Molecular Biophysics written by Igor N. Serdyuk and published by Cambridge University Press. This book was released on 2007-03-29 with total page 1137 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our knowledge of biological macromolecules and their interactions is based on the application of physical methods, ranging from classical thermodynamics to recently developed techniques for the detection and manipulation of single molecules. These methods, which include mass spectrometry, hydrodynamics, microscopy, diffraction and crystallography, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, are complementary; each has its specific advantages and limitations. Organised by method, this textbook provides descriptions and examples of applications for the key physical methods in modern biology. It is an invaluable resource for undergraduate and graduate students of molecular biophysics in science and medical schools, as well as research scientists looking for an introduction to techniques beyond their specialty. As appropriate for this interdisciplinary field, the book includes short asides to explain physics aspects to biologists and biology aspects to physicists.
Download or read book NIC Symposium 2014 Proceedings written by K. Binder, and published by Forschungszentrum Jülich. This book was released on 2014-03-21 with total page 453 pages. Available in PDF, EPUB and Kindle. Book excerpt:
