Dynamics and Kinetics in Structural Biology


Book Description

Dynamics and Kinetics in Structural Biology Understand the latest experimental tools in structural biology with this pioneering work Structural biology seeks to understand the chemical mechanisms and functions of biological molecules, such as proteins, based on their atomic structures. Until recently, these structures have been studied only statically, using procedures which deliberately freeze atomic motion. However, freezing eliminates the rapid structural motions so essential to biological activity and function; the molecules are inactive. But with the recent development of X-ray free electron laser (XFEL) sources, efforts to conduct dynamic experiments have expanded using the principles of dynamics and kinetics to capture active biological molecules as they function. Dynamics and Kinetics in Structural Biology promotes the development of these experiments and their successful application. It grounds readers in the foundational principles of dynamics and kinetics; proceeds through extended discussions of experimental procedures and data analysis techniques; and explores experimental frontiers in structural dynamics. The book will aid researchers to gather and interpret cutting-edge data on the dynamic structure of biological molecules, under conditions where they retain their biological functions. Dynamics and Kinetics in Structural Biology offers readers: Authorship by founding figures in the field In-depth presentation of time-resolved X-ray crystallography, solution scattering, and more A pioneering contribution to a rapidly developing field of study Dynamics and Kinetics in Structural Biology is essential reading for graduate students, scientists, researchers and industry professionals engaged in structural studies of biological systems. Industry professionals considering dynamic studies in the development of new product lines will also benefit.




Advanced Molecular Dynamics and Chemical Kinetics


Book Description

A comprehensive, in-depth presentation of theoretical underpinnings and mathematical techniques This is the first book of its kind to combine all the theories of molecular reaction dynamics and chemical kinetics in a single source. It provides a sophisticated treatment of the material that functions both as a professional reference and a high-level text for PhD and postdoctoral researchers. Advanced Molecular Dynamics and Chemical Kinetics offers exceptional, in-depth coverage and includes a complete discussion of the theoretical as well as mathematical presentation of techniques. It features relevant exercises as well as comprehensive coverage of: * Second Quantization * Semiclassical Theory * Quantum Theory of Reaction Rates * Feynman Path Integrals * Wavepacket Propagation and Grid Methods * Photodissociation * Molecular Properties of Solvated Molecules * Quantum Model for Electron Transfer * Electron Transfer Coupling Elements * Proton Transfer Reactions in Solution This is the ideal reference for seasoned professionals in molecular reaction dynamics as well as for younger researchers who may want to enter the field or simply wish to learn more about it. Also available: Introduction to Molecular Dynamics and Chemical Kinetics Gert D. Billing and Kurt V. Mikkelsen




Protein Folding Kinetics


Book Description

First methods book which includes many detailed descriptions Absolutely needed and thus timely for the scientific community Comprises 15% more content and includes the mentioned special features




Mass Spectrometry in Structural Biology and Biophysics


Book Description

The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.




Kinetics and Dynamics


Book Description

"Kinetics and Dynamics" on molecular modeling of dynamic processes opens with an introductory overview before discussing approaches to reactivity of small systems in the gas phase. Then it examines studies of systems of increasing complexity up to the dynamics of DNA. This title has interdisciplinary character presenting wherever possible an interplay between the theory and the experiment. It provides basic information as well as the details of theory and examples of its application to experimentalists and theoreticians interested in modeling of dynamic processes in chemical and biochemical systems. All contributing authors are renowned experts in their fields and topics covered in this volume represent the forefront of today’s science.




Structural Biology in Drug Discovery


Book Description

With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins




Biomolecular Kinetics


Book Description

"a gem of a textbook which manages to produce a genuinely fresh, concise yet comprehensive guide" –Mark Leake, University of York "destined to become a standard reference.... Not just a ‘how to’ handbook but also an accessible primer in the essentials of kinetic theory and practice." –Michael Geeves, University of Kent "covers the entire spectrum of approaches, from the traditional steady state methods to a thorough account of transient kinetics and rapid reaction techniques, and then on to the new single molecule techniques" –Stephen Halford, University of Bristol This illustrated treatment explains the methods used for measuring how much a reaction gets speeded up, as well as the framework for solving problems such as ligand binding and macromolecular folding, using the step-by-step approach of numerical integration. It is a thoroughly modern text, reflecting the recent ability to observe reactions at the single-molecule level, as well as advances in microfluidics which have given rise to femtoscale studies. Kinetics is more important now than ever, and this book is a vibrant and approachable entry for anyone who wants to understand mechanism using transient or single molecule kinetics without getting bogged down in advanced mathematics. Clive R. Bagshaw is Emeritus Professor at the University of Leicester, U.K., and Research Associate at the University of California at Santa Cruz, U.S.A.




Deterministic Kinetics in Chemistry and Systems Biology


Book Description

This book gives a concise overview of the mathematical foundations of kinetics used in chemistry and systems biology. The analytical and numerical methods used to solve complex rate equations with the widely used deterministic approach will be described, with primary focus on practical aspects important in designing experimental studies and the evaluation of data. The introduction of personal computers transformed scientific attitudes in the last two decades considerably as computational power ceased to be a limiting factor. Despite this improvement, certain time-honored approximations in solving rate equations such as the pre-equilibrium or the steady-state approach are still valid and necessary as they concern the information content of measured kinetic traces. The book shows the role of these approximations in modern kinetics and will also describe some common misconceptions in this field.




Methods in Molecular Biophysics


Book Description

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.




Computational Structural Biology


Book Description

This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.