Computational Molecular Dynamics: Challenges, Methods, Ideas
Computational Molecular Dynamics: Challenges, Methods, Ideas

Author: Peter Deuflhard

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 500

ISBN-13: 3642583601

DOWNLOAD EBOOK

On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Nanozymes: Next Wave of Artificial Enzymes
Nanozymes: Next Wave of Artificial Enzymes

Author: Xiaoyu Wang

Publisher: Springer

Published: 2016-07-27

Total Pages: 134

ISBN-13: 3662530686

DOWNLOAD EBOOK

This book describes the fundamental concepts, the latest developments and the outlook of the field of nanozymes (i.e., the catalytic nanomaterials with enzymatic characteristics). As one of today’s most exciting fields, nanozyme research lies at the interface of chemistry, biology, materials science and nanotechnology. Each of the book’s six chapters explores advances in nanozymes. Following an introduction to the rise of nanozymes research in the course of research on natural enzymes and artificial enzymes in Chapter 1, Chapters 2 through 5 discuss different nanomaterials used to mimic various natural enzymes, from carbon-based and metal-based nanomaterials to metal oxide-based nanomaterials and other nanomaterials. In each of these chapters, the nanomaterials’ enzyme mimetic activities, catalytic mechanisms and key applications are covered. In closing, Chapter 6 addresses the current challenges and outlines further directions for nanozymes. Presenting extensive information on nanozymes and supplemented with a wealth of color illustrations and tables, the book offers an ideal guide for readers from disparate areas, including analytical chemistry, materials science, nanoscience and nanotechnology, biomedical and clinical engineering, environmental science and engineering, green chemistry, and novel catalysis.

Computational Catalysis
Computational Catalysis

Author: Aravind Asthagiri

Publisher: Royal Society of Chemistry

Published: 2014

Total Pages: 277

ISBN-13: 1849734518

DOWNLOAD EBOOK

This book presents a comprehensive review of the methods and approaches being adopted to push forward the boundaries of computational catalysis.

Directed Enzyme Evolution: Advances and Applications
Directed Enzyme Evolution: Advances and Applications

Author: Miguel Alcalde

Publisher: Springer

Published: 2017-02-14

Total Pages: 286

ISBN-13: 3319504134

DOWNLOAD EBOOK

This book focuses on some of the most significant advances in enzyme engineering that have been achieved through directed evolution and hybrid approaches. On the 25th anniversary of the discovery of directed evolution, this volume is a tribute to the pioneers of this thrilling research field, and at the same time provides a comprehensive overview of current research and the state of the art. Directed molecular evolution has become the most reliable and robust method to tailor enzymes, metabolic pathways or even whole microorganisms with improved traits. By mirroring the Darwinian algorithm of natural selection on a laboratory scale, new biomolecules of invaluable biotechnological interest can now be engineered in a manner that surpasses the boundaries of nature. The volume is divided into two sections, the first of which provides an update on recent successful cases of enzyme ensembles from different areas of the biotechnological spectrum, including tryptophan synthases, unspecific peroxygenases, phytases, therapeutic enzymes, stereoselective enzymes and CO2-fixing enzymes. This section also provides information on the directed evolution of whole cells. The second section of the book summarizes a variety of the most applicable methods for library creation, together with the future trends aimed at bringing together directed evolution and in silico/computational enzyme design and ancestral resurrection.

Protein Conformational Dynamics
Protein Conformational Dynamics

Author: Ke-li Han

Publisher: Springer Science & Business Media

Published: 2014-01-20

Total Pages: 488

ISBN-13: 3319029703

DOWNLOAD EBOOK

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.

Dynamics in Enzyme Catalysis
Dynamics in Enzyme Catalysis

Author: Judith Klinman

Publisher: Springer

Published: 2013-09-14

Total Pages: 217

ISBN-13: 3642389627

DOWNLOAD EBOOK

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.

Quantum Tunnelling in Enzyme-catalysed Reactions
Quantum Tunnelling in Enzyme-catalysed Reactions

Author: Rudolf K. Allemann

Publisher: Royal Society of Chemistry

Published: 2009

Total Pages: 412

ISBN-13: 0854041222

DOWNLOAD EBOOK

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.

The Sugar Code
The Sugar Code

Author: Hans-Joachim Gabius

Publisher: John Wiley & Sons

Published: 2013-12-06

Total Pages: 600

ISBN-13: 3527644962

DOWNLOAD EBOOK

A reader friendly overview of the structure and functional relevance of natural glycosylation and its cognate proteins (lectins), this book is also one of the few books to cover their role in health and disease. Edited by one of the pioneering experts in the field and written by a team of renowned researchers this resource is a perfect introduction for all students in life and medical sciences, biochemistry, chemistry and pharmacy. Website: WWW.WILEY-VCH.DE/HOME/THESUGARCODE

Combined Quantum Mechanical and Molecular Mechanical Methods
Combined Quantum Mechanical and Molecular Mechanical Methods

Author: Jiali Gao

Publisher:

Published: 1998

Total Pages: 328

ISBN-13:

DOWNLOAD EBOOK

Combined quantum mechanical and molecular mechanical methods (QM/MM) is one of the most promising approaches for quantum mechanical calculations of chemical processes in solution and in enzymes. This book provides an in-depth survey of the methods and applications of these combined techniques in chemistry and biochemistry.