Download or read book A Role for Nuclear Tunneling and Protein Dynamics in Enzyme Catalysis written by Zachary David Nagel and published by . This book was released on 2009 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Dynamics in Enzyme Catalysis written by Judith Klinman and published by Springer. This book was released on 2013-09-14 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Christopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond–Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.

Download or read book Quantum Tunnelling in Enzyme catalysed Reactions written by Rudolf K. Allemann and published by Royal Society of Chemistry. This book was released on 2009 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, there has been an explosion in knowledge and research associated with the field of enzyme catalysis and H-tunneling. Rich in its breath and depth, this introduction to modern theories and methods of study is suitable for experienced researchers those new to the subject. Edited by two leading experts, and bringing together the foremost practitioners in the field, this up-to-date account of a rapidly developing field sits at the interface between biology, chemistry and physics. It covers computational, kinetic and structural analysis of tunnelling and the synergy in combining these methods (with a major focus on H-tunneling reactions in enzyme systems). The book starts with a brief overview of proton and electron transfer history by Nobel Laureate, Rudolph A. Marcus. The reader is then guided through chapters covering almost every aspect of reactions in enzyme catalysis ranging from descriptions of the relevant quantum theory and quantum/classical theoretical methodology to the description of experimental results. The theoretical interpretation of these large systems includes both quantum mechanical and statistical mechanical computations, as well as simple more approximate models. Most of the chapters focus on enzymatic catalysis of hydride, proton and H" transfer, an example of the latter being proton coupled electron transfer. There is also a chapter on electron transfer in proteins. This is timely since the theoretical framework developed fifty years ago for treating electron transfers has now been adapted to H-transfers and electron transfers in proteins. Accessible in style, this book is suitable for a wide audience but will be particularly useful to advanced level undergraduates, postgraduates and early postdoctoral workers.

Download or read book New Trends in Enzyme Catalysis and Biomimetic Chemical Reactions written by Gertz I. Likhtenshtein and published by Springer Science & Business Media. This book was released on 2003 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzyme catalysis is an important and vigorously developing field of basic and applied research, posing challenging problems to biochemists and chemists. This volume embraces modern areas of enzyme catalysis where other books in the field concentrate mainly on kinetic, bioorganic and biochemical aspects of the enzyme catalysis and do not cover biophysical and physicochemical problems. Topics covered include: modern physical and kinetic methods of investigation;contemporary theories of elementary chemical processes in enzymes; structure, dynamics and action mechanism of enzyme active sites; concept of pretransition state; theory of long-range electron transfer and proton translocation;mechanisms of tough biochemical reactions (dinitrogen reduction, light energy conversation, water photooxidation, hydroxilation);the achievements and problems of biomimetic chemical reactions.

Download or read book Enzyme Kinetics Catalysis and Control written by Daniel L. Purich and published by Elsevier. This book was released on 2010-06-16 with total page 915 pages. Available in PDF, EPUB and Kindle. Book excerpt: Far more than a comprehensive treatise on initial-rate and fast-reaction kinetics, this one-of-a-kind desk reference places enzyme science in the fuller context of the organic, inorganic, and physical chemical processes occurring within enzyme active sites. Drawing on 2600 references, Enzyme Kinetics: Catalysis & Control develops all the kinetic tools needed to define enzyme catalysis, spanning the entire spectrum (from the basics of chemical kinetics and practical advice on rate measurement, to the very latest work on single-molecule kinetics and mechanoenzyme force generation), while also focusing on the persuasive power of kinetic isotope effects, the design of high-potency drugs, and the behavior of regulatory enzymes. Historical analysis of kinetic principles including advanced enzyme science Provides both theoretical and practical measurements tools Coverage of single molecular kinetics Examination of force generation mechanisms Discussion of organic and inorganic enzyme reactions

Download or read book On the Role of Enzyme Structure and Structural Dynamics in Lipoxygenase Catalysis written by Cody Addison Marcus Carr and published by . This book was released on 2013 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lipoxygenases are a remarkable class of C-H activating enzymes, cleaving that bond with high specificity and further controlling the reaction with molecular oxygen to form a single fatty acid hydroperoxide product under certain conditions. Glycine max} (soybean) lipoxygenase-1 (SLO), a model system for this two-step reaction, is characterized by a large, nearly temperature-independent kinetic isotope effect (KIE) on the hydrogen-abstraction step. Theoretical modeling of the KIE and its temperature dependence in wild-type SLO and several mutants has provided significant insight into the mechanistic details of this enzyme. We have applied two state-of-the-art biophysical techniques to SLO. In doing so, we have tested the predictions made by the nonadiabatic full tunneling model developed by Hammes-Schiffer and coworkers about substrate-cofactor distances, the dynamics of those distances, and the mechanism by which distal residues affect those distances. A novel application of electron-nuclear double resonance spectroscopy, a pulsed EPR technique, is used to determine not only the electron-nuclear distances but also the variance of those distances in the enzyme-substrate complex, both for wild-type SLO and a single-site mutant (Chapter 2). The experimental substrate-cofactor distance ("donor-acceptor distance") for wild-type SLO is the same as for the mutant, which is counter to model predictions. We have also measured distances for a second substrate carbon and a global minimum distance for substrate hydrogens, which, together, allow us to orient the substrate within the active site. These constraints collectively imply a tightly compressed active site with significant van der Waals overlap and moderately distorted bond geometries, validating qualitative concepts of active-site compaction in this system. The modification of SLO and development of sample conditions for these experiments are also reported. The enormous KIE in a double mutant of SLO, over 500, is partially explained by a crystal structure of that mutant presented herein (Chapter 3). This structure shows a much-expanded active site with no changes in the main chain and minimal changes in side-chain rotamers. The crystal structures of the Ile553 series of SLO mutants are re-examined (Chapter 4). This series shows a progressively greater temperature dependence of their KIEs as the residue size is decreased (Ile→Va→Ala→Gly); we show that this change is correlated with an expanding network of residues that occupy multiple conformers, a distinctly different result than for the double mutant. Finally, large and temperature-independent KIEs in the wild type and a single-site mutant of a cyanobacterial lipoxygenase are reported (Chapter 5). This finding expands the generality of the large, temperature-dependent KIEs in plant, human, and fungal lipoxygenases to include a new biological kingdom. Collectively, these results validate a particular model of lipoxygenase catalysis, illuminate the role of the remainder of the protein in causing that catalysis, and firmly establish ground-state nuclear tunneling as the essential mechanism of C-H activation by lipoxygenase.

Download or read book From Kibbutz Fishponds To The Nobel Prize Taking Molecular Functions Into Cyberspace written by Arieh Warshel and published by World Scientific. This book was released on 2021-10-28 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: What Arieh Warshel and fellow 2013 Nobel laureates Michael Levitt and Martin Karplus achieved — beginning in the late 1960s and early 1970s when computers were still very primitive — was the creation of methods and programs that describe the action of biological molecules by 'multiscale models'. In this book, Warshel describes this fascinating, half-century journey to the apex of science.From Kibbutz Fishponds to The Nobel Prize is as much an autobiography as an advocacy for the emerging field of computational science. We follow Warshel through pivotal moments of his life, from his formative years in war-torn Israel in an idealistic kibbutz that did not encourage academic education; to his time in the army and his move to the Technion where he started in his obsession of understanding the catalytic power of enzymes; to his eventual scientific career which took him to the Weizmann Institute, Harvard University, Medical Research Council, and finally University of Southern California. We read about his unique contributions to the elucidation of the molecular basis of biological functions, which are combined with instructive stories about his persistence in advancing ideas that contradict the current dogma, and the nature of his scientific struggle for recognition, both personal and for the field to which he devoted his life. This is, in so many ways, more than just a memoir: it is a profoundly inspirational tale of one man's odyssey from a kibbutz that did not allow him to go to a university to the pinnacle of the scientific world, highlighting that the correct mixture of persistence, talent and luck can lead to a Nobel Prize.

Download or read book Enzyme Kinetics and Mechanism written by Paul F. Cook and published by Garland Science. This book was released on 2007-03-06 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzyme Kinetics and Mechanism is a comprehensive textbook on steady-state enzyme kinetics. Organized according to the experimental process, the text covers kinetic mechanism, relative rates of steps along the reaction pathway, and chemical mechanism—including acid-base chemistry and transition state structure. Practical examples taken from the literature demonstrate theory throughout. The book also features numerous general experimental protocols and how-to explanations for interpreting kinetic data. Written in clear, accessible language, the book will enable graduate students well-versed in biochemistry to understand and describe data at the fundamental level. Enzymologists and molecular biologists will find the text a useful reference.

Download or read book Structural and Mechanistic Enzymology written by and published by Academic Press. This book was released on 2012-10-22 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: Both strategies for investigation (computational and experimental) in structural and mechanistic Enzymology have developed to some extent independently. However, over the last few years a trend has emerged for strengthening their integration. This combination not only brings together computations and experiments focused on the same enzymatic problems, but also provides complementary insights into the investigated properties and has a powerful synergy effect. This thematic volume of Advances in Protein Chemistry and Structural Biology focuses on the recent success in structural and mechanistic enzymology and has its main emphasis on explaining the enzyme phenomena by using both the experimental and computational approaches. The selected contributions demonstrate how the application of a variety of experimental techniques and modeling methods helps further the understanding of enzyme dynamics, mechanism, inhibition, and drug design. Focuses on the recent success in structural and mechanistic enzymology Has its main emphasis on explaining the enzyme phenomena by using both the experimental and computational approaches Demonstrates how the application of a variety of experimental techniques and modeling methods helps further the understanding of enzyme dynamics, mechanism, inhibition, and drug design

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 Tunnel Effect in Chemistry written by Ronald Percy Bell and published by Springer. This book was released on 2013-11-11 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: The suggestion that quantum-mechanical tunnelling might be a significant factor in some chemical reactions was first made fifty years ago by Hund, very soon after the principles of wave mechanics had been established by de Broglie, Schrodinger and Heisenberg, and similar ideas were put forward during the following thirty years by a number of authors. It was realised from the beginning that such effects would be particularly prominent in reactions involving the movement of protons or hydrogen atoms, and both theoretical and experimental work received a powerful stimulus in the discovery of deuterium in 1932. During the last twenty years theoretical predictions about the tunnel effect have been supported by an increasing body of experimental evidence, derived especially from studies of hydrogen isotope effects. The present book presents an attempt to summarize this evidence and to indicate the main lines of the basic theory. Details of mathematical manipu lation are restricted mainly to Chapter 2 and the Appendices, and many readers may prefer to confine themselves to the results obtained. The main emphasis has been on the kinetics of chemical reactions involving the transfer of protons, hydrogen atoms or hydride ions, although Chapter 6 gives an account of the role of the tunnel effect in molecular spectra, and Chapter 7 makes some mention of tunnelling in solid state phenomena, biological processes and the electrolytic discharge of hydrogen. Only passing references have been made to tunnelling by electrons.

Download or read book Protein Engineering Handbook written by Stefan Lutz and published by John Wiley & Sons. This book was released on 2012-07-31 with total page 1021 pages. Available in PDF, EPUB and Kindle. Book excerpt: Unparalleled in size and scope, this new major reference integrates academic and industrial knowledge into a single resource, allowing for a unique overview of the entire field. Adopting a systematic and practice-oriented approach, and including a wide range of technical and methodological information, this highly accessible handbook is an invaluable 'toolbox' for any bioengineer. In two massive volumes, it covers the full spectrum of current concepts, methods and application areas.

Download or read book Measurement and Analysis of Kinetic Isotope Effects written by and published by Academic Press. This book was released on 2017-09-12 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experimental Analysis of Enzyme Mechanism Using Isotope Effects, Volume 596, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Chapters in this comprehensive update include Measurement of enzyme binding isotope effects, Chemical ligation and isotope labeling to locate dynamic effects, Measurement of heavy enzyme isotope effects, Extracting kinetic isotope effects from a global analysis of reaction progress curves, KIE of metabolic flux and enzymes, Solvent and Primary KIE on Flavin Enzymes, and The Rapid Determination of Primary Deuterium Isotope Effects on Enzyme-Catalyzed Proton Transfer at Carbon in 50/50 HOH/DOD. Readers who are interested in applying or understanding this research will find useful methods currently used for measuring isotope effects on solution and enzyme reactions. Written by pioneers of modern isotope effect research Is the only collection of modern kinetic isotope effect methods currently available

Download or read book Isotope Effects In Chemistry and Biology written by Amnon Kohen and published by CRC Press. This book was released on 2005-11-01 with total page 1092 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of isotope effects has expanded exponentially in the last decade, and researchers are finding isotopes increasingly useful in their studies. Bringing literature on the subject up to date, Isotope Effects in Chemistry and Biology covers current principles, methods, and a broad range of applications of isotope effects in the physical, biolo

Download or read book Theory and Applications of the Empirical Valence Bond Approach written by Fernanda Duarte and published by John Wiley & Sons. This book was released on 2017-02-10 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive overview of current empirical valence bond (EVB) theory and applications, one of the most powerful tools for studying chemical processes in the condensed phase and in enzymes. Discusses the application of EVB models to a broad range of molecular systems of chemical and biological interest, including reaction dynamics, design of artificial catalysts, and the study of complex biological problems Edited by a rising star in the field of computational enzymology Foreword by Nobel laureate Arieh Warshel, who first developed the EVB approach

Download or read book Neurophotonics and Biomedical Spectroscopy written by Robert R. Alfano and published by William Andrew. This book was released on 2018-11-22 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neurophotonics and Biomedical Spectroscopy addresses the novel state-of-the-art work in non-invasive optical spectroscopic methods that detect the onset and progression of diseases and other conditions, including pre-malignancy, cancer, Alzheimer’s disease, tissue and cell response to therapeutic intervention, unintended injury and laser energy deposition. The book then highlights research in neurophotonics that investigates single and multi-photon excitation optical signatures of normal/diseased nerve tissues and in the brain, providing a better understanding of the underlying biochemical and structural changes of tissues and cells that are responsible for the observed spectroscopic signatures. Topics cover a wide array of well-established UV, visible, NIR and IR optical and spectroscopic techniques and novel approaches to diagnose tissue changes, including: label free in vivo and ex vivo fluorescence spectroscopy, Stoke shift spectroscopy, spectral imaging, Resonance Raman spectroscopy, multiphoton two Photon excitation, and more. Provides an overview of the spectroscopic properties of tissue and tissue-light interaction, describing techniques to exploit these properties in imaging Explores the potential and significance of molecule-specific imaging and its capacity to reveal vital new information on nanoscale structures Offers a concise overview of different spectroscopic methods and their potential benefits for solving diagnostic and therapeutic problems

Download or read book Advances in Physical Organic Chemistry written by and published by Elsevier. This book was released on 2004-10-06 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Physical Organic Chemistry provides the chemical community with authoritative and critical assessments of the many aspects of physical organic chemistry. The field is a rapidly developing one, with results and methodologies finding application from biology to solid state physics.