Download or read book Insights into Enzyme Mechanisms and Functions from Experimental and Computational Methods written by and published by Academic Press. This book was released on 2016-08-24 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: Insights into Enzyme Mechanisms and Functions from Experimental and Computational Methods is the latest volume in the popular Advances in Protein Chemistry and Structural Biology series, an essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins, with each thematically organized volume guest edited by leading experts in a broad range of protein-related topics. - Provides cutting-edge developments in protein chemistry and structural biology - Written by authorities in their respective fields - Targeted to a wide audience of researchers, specialists, and students

Download or read book Structural and Mechanistic Enzymology written by and published by Academic Press. This book was released on 2017-07-17 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural and Mechanistic Enzymology, Volume 109, the latest release in the Advances in Protein Chemistry and Structural Biology series, is an essential resource for protein chemists. Chapters in this new volume include Collagenolytic Matrix Metalloproteinase Structure–Function Relationships: Insights from Molecular Dynamics Studies, Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design, Computational Biochemistry-Enzyme Mechanisms Explored, and A Paradigm for C-H Bond Cleavage: Structural and Functional Aspects of Transition State Stabilization by Mandelate Racemase. This series presents new information on protocols and analysis of proteins, with each volume guest edited by leading experts in a broad range of protein-related topics. This volume presents state-of-the-art contributions, providing insights into the relationship between enzyme structure, catalysis, and function. - Provides cutting-edge developments in protein chemistry and structural biology - Features new information about protocols and analysis of proteins - Contains chapters written by authorities in their respective fields - Targeted to a wide audience of researchers, specialists and students

Download or read book Computational Approaches to Biochemical Reactivity written by Gábor Náray-Szabó and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: A quantitative description of the action of enzymes and other biological systems is both a challenge and a fundamental requirement for further progress in our und- standing of biochemical processes. This can help in practical design of new drugs and in the development of artificial enzymes as well as in fundamental understanding of the factors that control the activity of biological systems. Structural and biochemical st- ies have yielded major insights about the action of biological molecules and the mechanism of enzymatic reactions. However it is not entirely clear how to use this - portant information in a consistent and quantitative analysis of the factors that are - sponsible for rate acceleration in enzyme active sites. The problem is associated with the fact that reaction rates are determined by energetics (i. e. activation energies) and the available experimental methods by themselves cannot provide a correlation - tween structure and energy. Even mutations of specific active site residues, which are extremely useful, cannot tell us about the totality of the interaction between the active site and the substrate. In fact, short of inventing experiments that allow one to measure the forces in enzyme active sites it is hard to see how can one use a direct experimental approach to unambiguously correlate the structure and function of enzymes. In fact, in view of the complexity of biological systems it seems that only computers can handle the task of providing a quantitative structure-function correlation.

Download or read book Proceedings of 8th GACM Colloquium on Computational Mechanics written by Tobias Gleim and published by kassel university press GmbH. This book was released on 2019-09-04 with total page 493 pages. Available in PDF, EPUB and Kindle. Book excerpt: This conference book contains papers presented at the 8th GACM Colloquium on Computational Mechanics for Young Scientists from Academia and Industry. The conference was held from August 28th – 30th, 2019 in Kassel, hosted by the Institute of Mechanics and Dynamics of the department for civil and environmental engineering and by the chair of Engineering Mechanics / Continuum Mechanics of the department for mechanical engineering of the University of Kassel. The aim of the conference is, to bring together young scientits who are engaged in academic and industrial research on Computational Mechanics and Computer Methods in Applied Sciences. It provides a plattform to present and discuss recent results from research efforts and industrial applications. In more than 150 presentations, given by young scientists, current scientific developments and advances in engineering practice in this field are presented and discussed. The contributions of the young researchers are supplemented by a poster session and plenary talks from four senior scientists from academia and industry as well as from the GACM Best PhD Award winners 2017 and 2018.

Download or read book Computational Approaches for Studying Enzyme Mechanism Part A written by and published by Academic Press. This book was released on 2016-08-04 with total page 560 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Studying Enzyme Mechanism Part A, is the first of two volumes in the Methods in Enzymology series, focusses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few. - Focuses on computational approaches for studying enzyme mechanism - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Download or read book Computational Approaches for Studying Enzyme Mechanism Part B written by and published by Academic Press. This book was released on 2016-08-03 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study. - Focuses on computational approaches for studying enzyme mechanism - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

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 Molecular Level Atomistic and Structural Insights on Biological Macromolecules Inhibition and Dynamics Studies written by Chandrabose Selvaraj and published by Frontiers Media SA. This book was released on 2024-03-14 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: Everything in a living organism relies on biological macromolecules, which have the role of enzymatic chemical transformations, formation of structures, transportation, catalysis, and regulation of biological processes. They are complex biological structures that require an atomistic understanding. A molecular understanding of biological macromolecules has had a massive impact on the pharmaceutical, biotechnological, and chemical industries. Specifically, new enzymatic structures are being discovered through various experimental and computational methods, by describing an atomistic-level insight into function, mechanism, role in reactions and their inhibition. Those atom-level illustrations are mainly focused through enzyme kinetics, enzyme inhibition, mutational and conformational analysis through quantum mechanical and molecular dynamics methods.

Download or read book Structural and Mechanistic Enzymology written by Christo Christov and published by Academic Press. This book was released on 2012-05-29 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: Other volumes cataloged as a serial, see LCCN: 2009237250

Download or read book Integrative Structural Biology of Proteins and Macromolecular Assemblies Bridging Experiments and Simulations written by Paulo Ricardo Batista and published by Frontiers Media SA. This book was released on 2022-07-26 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Electrostatics based Computational Methods for Understanding Polymerase Mechanism and for Protein Function Annotation written by Ramya Parasuram and published by . This book was released on 2014 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: Knowledge of the active site is the first step to understanding the function of an enzyme. My research encompassed the use of electrostatics-based computational functional site prediction methods, Theoretical Microscopic Anomalous Titration Curve Shapes (THEMATICS) and Partial Order Optimum Likelihood (POOL) to understand the role of active site and distal residues in a polymerase and also to develop a methodology to classify the members of protein superfamilies according to biochemical function and thus to annotate proteins of unknown function. *Role of Active Site and Distal Residues in DNA Polymerase III Alpha* The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue pol III alpha subunit copies DNA accurately, making one error per 105 nucleotide incorporations. The goal of this research is to determine the residues that contribute to this high fidelity and activity of the polymerase subunit. Homology modeling and the computational methods of THEMATICS and POOL are used to predict functionally important amino acid residues. Site-directed mutagenesis and primer extension assays are used to validate these predictions. This and previous work show that the top 15 residues predicted by POOL, which include the three catalytic aspartate residues and seven remote residues, are important for function. Primer extension and thermal denaturation assays were performed to understand better the contribution of these residues to the function of the polymerase. This work has identified ten previously unknown residues, Y340, D405, R390, Y686, R709, K553A, K758, R362, H760 and E688Q, as critical to pol III activity. *Functional Classification of Six-Hairpin Glycosidase Superfamily with Structurally Aligned Local Sites of Activity* There are over 12000 Structural Genomics (SG) protein structures reported in the Protein Data Bank to date. Misannotation rates for SG proteins are estimated to be high since they often are annotated simply by their closest sequence or structural match. We have developed a strategy to predict function reliably and to identify these misannotations. The method POOL is used to predict functionally important residues for members of the Six-hairpin glycosidase superfamily. Starting with the previously characterized members of the superfamily, each functional subclass is shown to exhibit a unique local spatial pattern based on the predictions. These patterns, the chemical signatures associated with each functional type, are used to sort the superfamily according to biochemical function and also to determine whether SG members of this superfamily are correctly or incorrectly annotated. Using this method, we have been able to successfully characterize the six-hairpin glycosidase superfamily and annotate the function of several SG proteins. This work establishes the utility of our electrostatics-based functional residue prediction method in applications to understand enzyme mechanisms and to predict function. The experimental methods can help provide insight to improve the computational methods. Efforts are in progress to automate and optimize the method to enable high-throughput searching for biochemical functional matches across the entire space of known protein 3D structures.

Download or read book Human Genome Structure Function and Clinical Considerations written by Luciana Amaral Haddad and published by Springer Nature. This book was released on 2021-06-07 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a detailed evidence-based overview of the latest developments in how the structure of the human genome is relevant to the health professional. It features comprehensive reviews of genome science including human chromosomal and mitochondrial DNA structure, protein-coding and noncoding genes, and the diverse classes of repeat elements of the human genome. These concepts are then built upon to provide context as to how they functionally relate to differences in phenotypic traits that can be observed in human populations. Guidance is also provided on how this information can be applied by the medical practitioner in day-to-day clinical practice. Human Genome Structure, Function and Clinical Considerations collates the latest developments in genome science and current methods for genome analysis that are relevant for the clinician, researcher and scientist who utilises precision medicine techniques and is an essential resource for any such practitioner.

Download or read book Simulating Enzyme Reactivity written by Inaki Tunon and published by Royal Society of Chemistry. This book was released on 2016-11-16 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: The simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.

Download or read book Proteins written by David M. Leitner and published by CRC Press. This book was released on 2009-09-28 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling can provide a wealth of insight into how energy flow in proteins mediates protein function. Computational methods can also address fundamental questions related to molecular signaling and energy flow in proteins. Proteins: Energy, Heat and Signal Flow presents state-of-the-art computational strategies for studying energy redi

Download or read book Introduction to Bioorganic Chemistry and Chemical Biology written by David Van Vranken and published by Garland Science. This book was released on 2018-10-08 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Bioorganic Chemistry and Chemical Biology is the first textbook to blend modern tools of organic chemistry with concepts of biology, physiology, and medicine. With a focus on human cell biology and a problems-driven approach, the text explains the combinatorial architecture of biooligomers (genes, DNA, RNA, proteins, glycans, lipids, and terpenes) as the molecular engine for life. Accentuated by rich illustrations and mechanistic arrow pushing, organic chemistry is used to illuminate the central dogma of molecular biology. Introduction to Bioorganic Chemistry and Chemical Biology is appropriate for advanced undergraduate and graduate students in chemistry and molecular biology, as well as those going into medicine and pharmaceutical science.

Download or read book Structure and Biophysics New Technologies for Current Challenges in Biology and Beyond written by Joseph D. Puglisi and published by Springer Science & Business Media. This book was released on 2007-03-21 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of articles from the proceedings of the ISSBMR 7th Course: Structure and Biophysics - New Technologies for Current Challenges in Biology and Beyond. This NATO Advanced Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture in June 2005. It presents state of the art information on NMR spectroscopy and its place in the broader field of biophysics.

Download or read book Computational Chemistry Methods in Structural Biology written by and published by Academic Press. This book was released on 2011-09-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. - Essential resource for protein chemists - This volume features articles on Computational Chemistry methods in Structural Biology