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 Frontiers in Protein Structure Function and Dynamics written by Dev Bukhsh Singh and published by Springer Nature. This book was released on 2020-07-02 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Computational Protein Design written by Ilan Samish and published by Humana. This book was released on 2016-12-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Download or read book From Protein Sequence to Motion to Function written by Adam Damry and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein dynamics are critical to the structure and function of proteins. However, due to the complexity they inherently bring to the protein design problem, dynamics historically have not been considered in computational protein design (CPD). Herein, we present meta-MSD, a new CPD methodology for the design of protein dynamics. We applied our methodology to the design of a novel mode of conformational exchange in Streptococcal protein G domain B1, producing dynamic variants we termed DANCERs. Predictions were validated by NMR characterization of selected DANCERs, confirming that our meta-MSD framework is suitable for the computational design of protein dynamics. We then performed a thorough NMR characterization of the sequence determinants of dynamics in one DANCER, isolating two mutations responsible for the novel dynamics this protein exhibits. The first, A34F, is responsible for destabilizing the highly stable native G?1 conformation, allowing the protein to sample other conformational states. The second, V39L mediates subtle interactions that stabilize the designed conformational trajectory in the context of the A34F mutation. Together, these results highlight the role of protein plasticity in the development of dynamics and the need for highly accurate computational tools to approach similar design problems. Finally, we present an NMR-based characterization of structural dynamics in a family of related red fluorescent proteins (RFPs) and pinpoint regions of the RFP structure where dynamics correlate to RFP brightness. This overview of the RFP dynamics-function relationship will be used in future projects to perform a computation design of functional dynamics in RFPs.
Download or read book Understanding Protein Dynamics Binding and Allostery for Drug Design written by Guang Hu and published by Frontiers Media SA. This book was released on 2021-06-08 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 The Use of Protein Dynamics in the Study of Protein Conformational Transition and Functionality and Its Relevance in Drug Design written by JoAnne Jean Babula and published by . This book was released on 2020 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: Misregulation of protein signaling pathways is the basis for many human diseases, and thus 95% of Food and Drug Administration approved drugs target proteins. Proteins are dynamic entities which can undergo transitions to reach different conformational states. The conformational state of a protein, or its three-dimensional shape, is intricately linked to functions, such as association with endogenous or exogenous binding partners, or catalysis. Thus, it is of interest to the pharmacological community to understand the mechanisms of protein conformational state transitions in order to better target and control protein functions. In two case studies, I show the importance of understanding protein dynamics in protein function and drug design. In the case of human immunodeficiency virus-1 (HIV-1) protease, a tremendous "open-and-closed" conformational transition is revealed by Molecular Dynamics Simulations (MDS). Through observing the dramatic difference in effectiveness of two Darunavir inhibitor derivatives differentiated by a single atom at locking the protease in the closed conformation, we discovered the residues and mechanism that lead to the protease's conformational transition. This mechanism also explained the significant difference in the binding conformation and binding affinity of these two inhibitors. This study provides insight on how to improve the potency and anti-viral capacity of these compounds. In the second case study, MDS enabled us to observe the conformational transitions of a family of seven isoforms known as the 14-3-3 proteins. Many vital cellular processes involve all or select 14-3-3 isoforms, making this family very difficult to target. Through MDS, I discovered different conformational samplings among these 14-3-3 isoforms which were then validated by SAXS. Subsequently, a FRET-based ligand binding assay was developed which can screen for preferential 14-3-3 isoform binding of endogenous ligands, giving hope that using conformations unique to a 14-3-3 isoform of interest can provide a method for selective drug design
Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2018-03-22 with total page 1489 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012
Download or read book Proteins written by V. Renugopalakrishnan and published by Springer. This book was released on 1991-07-31 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The major goal of 'Expanding Frontiers in Polypeptide and Protein Structural Research' has been to bring the various avenues for the exploration of protein structures to a single forum. The idea of organizing the symposiwn was conceived by one of the editors, V. Renugopalakrislman, during the 9th International Biophysics Congress satellite symposium at Kibbutz Nof-Ginosar, Israel in 1987. It was originally supposed to dwell on 2D NMR and molecular dynamics of polypeptides and proteins. During the earlier part of the last decade, these two approaches began to emerge as powerful tools to probe protein structures at the atomic level in solution. The developments in molecular biology ushered in the capability to design polypeptides and proteins for specific application in science and technology. The emergence of 2D NMR and molecular dynamics was greatly facilitated by contemporary developments in molecular biology and protein engineering. Therefore an international symposiwn devoted exclusively to 2D NMR and molecular dynamics studies of proteins was felt necessary to bring two major approaches in a single forum. In addition to emphasis on 2D NMR and molecular dynamics simulation, the scope of the symposiwn included optical spectroscopy, protein design, and new horizons in protein structure. The symposiwn consisted of five plenary sessions devoted to NMR and optical spectroscopy as probes for protein structure, protein dynamics, computational methods in protein design, and new horizons in protein structure. In addition, five workshops in related areas, viz.
Download or read book Dynamics of Proteins and Nucleic Acids written by J. Andrew McCammon and published by Cambridge University Press. This book was released on 1988-04-29 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Download or read book Nature s Robots written by Charles Tanford and published by OUP Oxford. This book was released on 2003-11-27 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are amazingly versatile molecules. They make the chemical reactions happen that form the basis for life, they transmit signals in the body, they identify and kill foreign invaders, they form the engines that make us move, and they record visual images. All of this is now common knowledge, but it was not so a hundred years ago. Nature's Robots is an authoritative history of protein science, from the origins of protein research in the nineteenth century, when the chemical constitution of 'protein' was first studied and heatedly debated and when there was as yet no glimmer of the functional potential of substances in the 'protein' category, to the determination of the first structures of individual proteins at atomic resolution - when positions of individual atoms were first specified exactly and bonding between neighbouring atoms precisely defined. Tanford and Reynolds, who themselves made major contributions to the golden age of protein science, have written a remarkably vivid account of this history. It is a fascinating story, involving heroes from the past, working mostly alone or in small groups, usually with little support from formal research groups. It is also a story that embraces a number of historically important scientific controversies. Written in clear and accessible prose, Nature's Robots will appeal to general readers with an interest in popular science, in addition to professional scientists and historians of science.
Download or read book Exploring Structure dynamics function Relationship in Proteins Protein written by Karan Pal Kapoor and published by . This book was released on 2015 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Alphafold 3 Understanding Protein Structures written by StoryBuddiesPlay and published by StoryBuddiesPlay. This book was released on 2024-06-09 with total page 69 pages. Available in PDF, EPUB and Kindle. Book excerpt: AlphaFold 3: Unveiling the Protein Universe and Revolutionizing Healthcare Proteins are the fundamental building blocks of life, playing a critical role in every physiological process. But understanding their complex structures has been a longstanding challenge. Enter AlphaFold 3, a revolutionary artificial intelligence system that has unlocked a new era of protein science. This comprehensive guide delves into the fascinating world of proteins and explores how AlphaFold 3 is transforming our understanding and manipulation of these essential molecules. Unveiling Protein Structures with Unprecedented Accuracy AlphaFold 3 utilizes the power of deep learning to predict protein structures with remarkable accuracy, surpassing even the most advanced experimental methods. This breakthrough allows scientists to visualize the intricate three-dimensional shapes of proteins, providing crucial insights into their function and potential roles in health and disease. The Future of Medicine: Personalized Treatments and Early Disease Detection With the ability to predict protein structures, AlphaFold 3 holds immense potential for personalized medicine. By analyzing an individual's unique protein profile, doctors can potentially tailor treatments and identify those at risk for developing certain protein-related diseases. This personalized approach could lead to more effective therapies, earlier intervention, and improved patient outcomes. Beyond Medicine: A Protein-Powered Future The impact of AlphaFold 3 extends far beyond the realm of medicine. Its ability to predict protein structures can benefit various fields, including: Biotechnology and Agriculture: Design of crops with improved resistance to pests and diseases, development of biofuels, and bioremediation strategies. Materials Science and Engineering: Creation of biomimetic materials with unique properties and design of next-generation electronics. Energy Production and Storage: Development of novel enzymes for efficient biocatalysis and exploration of protein-based energy storage solutions. A New Era of Discovery: Unveiling Protein Dynamics and Designing the Future The future of protein science promises even more exciting advancements. By incorporating protein dynamics – how these molecules move and interact – into predictions, AlphaFold 3 can offer a more complete picture of protein function. Additionally, the field of protein design aims to create proteins with entirely new properties, paving the way for groundbreaking innovations in various sectors. Join the Exploration: A Deep Dive into the World of Proteins This guide is just the beginning of your journey into the fascinating world of proteins and AlphaFold 3. As research continues to unlock the secrets of these remarkable molecules, the possibilities for a healthier, more sustainable future are truly limitless.
Download or read book Dynamics Structure and Function of Biological Macromolecules written by Oleg Jardetzky and published by IOS Press. This book was released on 2001 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: A collection of articles looking at modern structural biology, summarizing the applications of physical methods - such as x-ray diffraction, high resolution nuclear magnetic resonance and molecular dynamics - to the study of protein structure and dynamics. There is a review of contemporary thoughts within the field, looking at the mechanisms of alloateric transitions and allosteric control, the transmission of information within protein structures and the role of dynamics in determining the specificity of protein - ligand interactions. There is also a look at future innovations.
