Download or read book Comparative Studies of Protein Structure and Dynamics by Molecular Dynamics Simulation NMR Spectroscopy and X ray Crystallography microform written by Marios Philippopoulos and published by National Library of Canada = Bibliothèque nationale du Canada. This book was released on 1999 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Comparative Studies of Protein Structure and Dynamics by written by MARIOS PHILIPPOPOULOS. 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 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 Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Understanding Protein Structure and Dynamics written by Gungor Ozer and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, we have advanced a set of distinct bioinformatic and computational tools to address the structure and function of proteins. Using data mining of the protein data bank (PDB), we have collected statistics connecting the propensity between the protein sequence and the secondary structure. This new tool has enabled us to evaluate new structures as well as a family of structures. A comparison of the wild type staphylococcal nuclease to various mutants using the proposed tool has indicated long-range conformational deviations spatially distant from the mutation point. The energetics of protein unfolding has been studied in terms of the forces observed in molecular dynamics simulations. An adaptive integration of the steered molecular dynamics is proposed to reduce ground state dominance by the rare low energy trajectories on the estimated free energy profile. The proposed adaptive algorithm is utilized to reproduce the potential of mean force of the stretching of decaalanine in vacuum at lower computational cost. It is then used to construct the potential of mean force of this transition in solvent for the first time as to observe the hydration effect on the helix-coil transformation. Adaptive steered molecular dynamics is also implemented to obtain the free energy change during the unfolding of neuropeptide Y and to confirm that the monomeric form of neuropeptide Y adopts halical-hairpin like pancreatic-polypeptide fold.

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 Protein Structure by Distance Analysis written by Henrik Bohr and published by IOS Press. This book was released on 1994 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Download or read book Protein Conformation written by Derek J. Chadwick and published by John Wiley & Sons. This book was released on 2008-04-30 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.

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 Science & Business Media. This book was released on 2013-07-17 with total page 809 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

Download or read book Protein Structure Prediction A Practical Approach written by Michael J. E. Sternberg and published by Oxford University Press, USA. This book was released on 1996-11-28 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure of proteins is a key factor in their biological activity. There is an increasing need to be able to predict the structure of a protein once its amino-acid sequence is known; this book presents practical methods of achieving that ambitious aim, using the latest computer modelling algorithms. - ;The prediction of the three-dimensional structure of a protein from its sequence is a problem faced by an ever-increasing number of biological scientists as they strive to utilize genetic information. The increasing sizes of the sequence and structural databases, the improvements in computing power, and the deeper understanding of the principles of protein structure have led to major developments in the field in the last few years. This book presents practical computer-based methods using the latest computer modelling algorithms. -

Download or read book Protein Structure and Protein Engineering written by Ernst-Ludwig Winnacker and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering has had considerable impact on basic and applied research in biochemistry and molecular biology. It is already in use as a tool in molecular biology, but it is beginning to strongly influence the planning of experiments in biology everywhere, and, with even fur ther-reaching consequences, the appointment politics in research in stitutions and industries. Protein engineering, perhaps more than any other methods of protein analysis and peptide synthesis, has shown that proteins are organic molecules governed by the universal laws of chemistry and physics. How ever, as was the case with other new powerful methods and techniques, protein engineering tempts to an exploration of its limitations and thus generates more questions than it answers. The 39th Mosbacher Colloquium on Protein Structure and Protein Engi neering is not the first conference on this topic and it will not be the last. The important issues are obviously techniques of protein en gineering, examples of application, and the basic framework of protein structure and stability within which reasonable experiments can be de signed; conversely also, what we can learn about protein structure, dynamics, and folding from such experiments. Experiments in this direc tion aim at elucidating the folding code in the long run, but help to exploit the role of individual amino acid residues in catalysis, pro tein stability, and binding specificity in selected proteins now.

Download or read book Recent Developments in Theoretical Studies of Proteins written by Ron Elber and published by World Scientific. This book was released on 1996 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experts provide a unique and broad perspective of the theoretical tools available today to analyze protein structure and function. Topics at the frontier of computational biophysics, such as dynamics and thermodynamics of proteins, reaction path studies, optimization techniques, analytical theories of protein folding, sequence alignment algorithms and electrostatics of proteins are discussed in a pedagogical and complete way. Those entering the field will find the book to be a useful introduction. It will also serve as a complementary text to existing ones that focus on just one of the above subjects.

Download or read book COMPARATIVE QUANTITATIVE GENETICS OF PROTEIN STRUCTURES written by Jose Hleap and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural biology has been long concerned about the emergence of protein structures and the convergence to particular folds. It can be said that protein structures are the realization of genetic information given thermodynamical and biological constraints. Given these properties, let's refer to a structure as a phenotype. As such, protein structures can be analysed as shapes within a geometric morphometrics framework, and as a phenotype in a quantitative genetics framework. Here, I present a robust way to analyse protein structures statistically in either evolutionary or molecular dynamics sampling. I show how General Procrustes Analysis (GPA) can be applied to aligned molecular dynamics snapshots, and provide evidence that the scaling component of GPA is not applicable to protein structures. I also show how analysing protein structures as shapes can give insights into dynamic and evolutionary patterns. Analysing proteins as shapes also gives the possibility to apply known techniques to assess modularity. Traditional techniques have dimensionality limitations. I show how to overcome these limitations and propose a robust way to analyse protein structure modularity. I show how a protein can be partitioned into biologically meaningful clusters, which can be used for description, protein prediction, or analysis of protein dynamics and evolution. The meaning of such modules is discussed further, and a hierarchical model for protein structure modularity is proposed. Also, methods to explore different kinds of modules at different kinds of hierarchy are explored. Finally, given that protein structures are phenotypes, the potential response to selection can be assessed by means of comparative quantitative genetics. I show that traditional comparative approaches have a heavy computational burden, therefore making the analysis infeasible. Nevertheless, similar approaches are developed to efficiently and accurately generate the estimations when the phenotypic variance is partitioned based on repeated measures, using a pooled-within covariance estimation.

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 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.