Conformational Dynamics Of Large Protein Complexes

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Protein Conformational Dynamics

Author : Ke-li Han,Xin Zhang,Ming-jun Yang
Publisher : Springer Science & Business Media
Page : 488 pages
File Size : 51,6 Mb
Release : 2014-01-20
Category : Medical
ISBN : 9783319029702

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Protein Conformational Dynamics by Ke-li Han,Xin Zhang,Ming-jun Yang Pdf

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.

Targeting Enzymes for Pharmaceutical Development

Author : Nikolaos E. Labrou
Publisher : Humana
Page : 290 pages
File Size : 44,5 Mb
Release : 2020-12-11
Category : Medical
ISBN : 1071601652

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Targeting Enzymes for Pharmaceutical Development by Nikolaos E. Labrou Pdf

This volume explores detailed methods and experimental protocols evaluating the effect of a compound or a mixture of compounds on the action of enzymes that are significant targets in pharmaceuticals. Consisting of three sections, the book delves into recent biocomputing and bioinformatics protocols, state-of-the art modern biophysical, electrophoretic, and chromatographic methods and high-throughput screening approaches, as well as detailed protocols and examples of the inhibition analysis and evaluation of selected enzymes. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Targeting Enzymes for Pharmaceutical Development: Methods and Protocols serves as a vital reference for academics and industry professionals working on expanding our understanding of the wide range of important enzyme targets.

Structure Computation and Dynamics in Protein NMR

Author : N. Rama Krishna,Lawrence Berliner
Publisher : Springer Science & Business Media
Page : 565 pages
File Size : 40,5 Mb
Release : 1999-06-30
Category : Medical
ISBN : 9780306459535

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Structure Computation and Dynamics in Protein NMR by N. Rama Krishna,Lawrence Berliner Pdf

Volume 17 is the second in a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. Volume 16, with the subtitle Modern Techniques in Protein NMR , is the first in this series. These two volumes present some of the recent, significant advances in the biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volume some of the world s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains - vances in two broad categories: I. Large Proteins, Complexes, and Membrane Proteins and II. Pulse Methods. Volume 17 contains major advances in: I. Com- tational Methods and II. Structure and Dynamics. The opening chapter of volume 17 starts with a consideration of some important aspects of modeling from spectroscopic and diffraction data by Wilfred van Gunsteren and his colleagues. The next two chapters deal with combined automated assignments and protein structure determination, an area of intense research in many laboratories since the traditional manual methods are often inadequate or laborious in handling large volumes of NMR data on large proteins. First, Werner Braun and his associates describe their experience with the NOAH/DIAMOD protocol developed in their laboratory.

Protein Conformation

Author : Derek J. Chadwick,Kate Widdows
Publisher : John Wiley & Sons
Page : 282 pages
File Size : 43,6 Mb
Release : 2008-04-30
Category : Science
ISBN : 9780470514153

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Protein Conformation by Derek J. Chadwick,Kate Widdows Pdf

How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.

Simulations in Nanobiotechnology

Author : Kilho Eom
Publisher : CRC Press
Page : 562 pages
File Size : 47,9 Mb
Release : 2011-10-19
Category : Science
ISBN : 9781439835067

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Simulations in Nanobiotechnology by Kilho Eom Pdf

Until the late 20th century, computational studies of biomolecules and nanomaterials had considered the two subjects separately. A thorough presentation of state-of-the-art simulations for studying the nanoscale behavior of materials, Simulations in Nanobiotechnology discusses computational simulations of biomolecules and nanomaterials together. Th

Issues in Computation: 2012 Edition

Author : Anonim
Publisher : ScholarlyEditions
Page : 417 pages
File Size : 40,5 Mb
Release : 2013-01-10
Category : Computers
ISBN : 9781481646345

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Issues in Computation: 2012 Edition by Anonim Pdf

Issues in Computation / 2012 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Computational Chemistry. The editors have built Issues in Computation: 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Computational Chemistry in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Issues in Computation: 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.

Biophysical Techniques in Photosynthesis

Author : Thijs Aartsma,Jörg Matysik
Publisher : Springer Science & Business Media
Page : 520 pages
File Size : 47,8 Mb
Release : 2008-02-01
Category : Science
ISBN : 9781402082504

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Biophysical Techniques in Photosynthesis by Thijs Aartsma,Jörg Matysik Pdf

Since the first volume on Biophysical Techniques in Photosynthesis Research, published in 1996, new experimental techniques and methods have been devised at a rapid pace. The present book is a sequel which complements the publication of the first volume by providing a comprehensive overview of the most important new techniques developed over the past ten years, especially those that are relevant for research on the mechanism and fundamental aspects of photosynthesis.

Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions

Author : Anonim
Publisher : Academic Press
Page : 702 pages
File Size : 49,6 Mb
Release : 2015-10-05
Category : Medical
ISBN : 9780128028469

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Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions by Anonim Pdf

Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions Part A & B, are the latest volumes in the Methods in Enzymology series, continuing the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods centered on the use of Electron Paramagnetic Resonance (EPR) techniques to study biological structure and function. Timely contribution that describes a rapidly changing field Leading researchers in the field Broad coverage: Instrumentation, basic theory, data analysis, and applications

Ubiquitin-dependent Protein Degradation

Author : Anonim
Publisher : Academic Press
Page : 384 pages
File Size : 42,9 Mb
Release : 2019-04-04
Category : Science
ISBN : 9780128186688

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Ubiquitin-dependent Protein Degradation by Anonim Pdf

Ubiquitination and Protein Stability - Part B, Volume 619, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this updated volume presenting interesting chapters written by an international board of authors. Topics of note include chapters on Assays of SUMO protease function in mammalian cells, In vitro analysis of proteasome-associated USP14 activity for substrate degradation and deubiquitylation, Methods to study proteasome regulatory particle assembly, Native mass spectrometry approaches to study the proteasome, Single-molecule methods to study the ubiquitin-proteasome system, Assays for the function of ubiquitin in the mammalian endocytic pathway, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in this series on enzymology

High-field EPR Spectroscopy on Proteins and Their Model Systems

Author : Klaus Möbius,Anton Savitsky
Publisher : Royal Society of Chemistry
Page : 393 pages
File Size : 51,9 Mb
Release : 2009
Category : Medical
ISBN : 9780854043682

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High-field EPR Spectroscopy on Proteins and Their Model Systems by Klaus Möbius,Anton Savitsky Pdf

High-Field EPR Spectroscopy on Proteins and their Model Systems: characterization of Transient Paramagnetic States offers a comprehensive overview of experimental techniques in, and paradigmatic examples of, the application of high-field EPR spectroscopy in biology and chemistry.

Protein Structure, Stability, and Folding

Author : Kenneth P. Murphy
Publisher : Springer Science & Business Media
Page : 258 pages
File Size : 46,6 Mb
Release : 2008-02-04
Category : Science
ISBN : 9781592591930

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Protein Structure, Stability, and Folding by Kenneth P. Murphy Pdf

In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating many of protein stability and dynamics from knowledge of the structure, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of some of this complex area by detailing many of the major techniques in use today.

Protein-Protein Complexes

Author : Martin Zacharias
Publisher : World Scientific
Page : 400 pages
File Size : 42,6 Mb
Release : 2010-05-04
Category : Science
ISBN : 9781908978547

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Protein-Protein Complexes by Martin Zacharias Pdf

Given the immense progress achieved in elucidating protein–protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein–protein interactions from the analysis of protein–protein complex structures and interfaces. What are the driving forces for protein–protein association? How can we extract the mechanism of specific recognition from studying protein–protein interfaces? How can this knowledge be used to predict and design protein–protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein–protein interactions, and how can we influence protein–protein interactions by mutagenesis and small-molecule drugs or peptide mimetics? The book consists of about 15 review chapters, written by experts, on the characterization of protein–protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein–protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein–protein complex structures (docking and homology modeling of complexes, etc.) and design of protein–protein interactions. It serves as a bridge between studying/analyzing protein–protein complex structures (interfaces), predicting interactions, and influencing/designing interactions. Contents: X-ray Study of Protein–Protein Complexes and Analysis of Interfaces (J Janin)A Structural Perspective on Protein–Protein Interactions in Macromolecular Assemblies (R P Bahadur)Energetics of Protein–Protein Interactions (I Jelezarov)Kinetics of Biomacromolecular Complex Formation: Theory and Experiment (G V Pachov et al.)Evolutionary Trace of Protein Functional Determinants (O Lichtarge)Protein–Protein Docking (A Saladin & C Prevost)Data-driven Docking: Using External Information to Spark the Biomolecular Rendez-vous (A S J Melquiond & A M J J Bonvin)High-Resolution Protein–Protein Docking (N London & O Schueler-Furman)Scoring and Refinement of Predicted Protein–Protein Complexes (M Zacharias)Motif-medicated Protein Interactions and Their Role in Disease (H Dinkel & H Sticht)Prediction and Calculation of Protein–Protein Binding Affinities and Mutation Effects (S Fiorucci et al.)Small-molecule Inhibitors of Protein–Protein Interactions (T Berg)Protein Dynamics and Drug Design: The Role of Molecular Simulations (G Morra et al.) Readership: Graduate students and researchers in bioinformatics and computational biology, biophysics, biochemistry, structural biology, and drug design. Keywords:Protein–Protein Interactions;Protein–Protein Complexes;Protein Design;Binding Interface, Protein Evolution;Structural Bioinformatics;Protein Interaction NetworkKey Features:Covers protein–protein interactions at the structural level in great detailDescribes the structure of protein–protein complexes, and also gives insight into the mechanism of complex formation and the forces that drive complex formationCovers to some degree the emerging field of designing new protein–protein interactions, i.e. how to interfere with protein–protein interactions that are of medical importance through drug design

Complementary Strategies to Study Virus Structure and Function

Author : Anonim
Publisher : Academic Press
Page : 349 pages
File Size : 49,6 Mb
Release : 2019-09-13
Category : Science
ISBN : 9780128184578

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Complementary Strategies to Study Virus Structure and Function by Anonim Pdf

Complementary Strategies to Study Virus Structure and Function, Volume 104, the latest release in the Advances in Virus Research series, highlights new advances in the field, with this new volume presenting interesting chapters on X-ray structures from crystals of viral proteins grown in cellula, NMR and SAXS to study protein dynamics and natively disordered viral proteins, Mass spectrometry to study virus particle assembly, Atomic force microscopy to study virus particles, Non-enveloped viruses and interactions with antibodies, Non-enveloped viruses and their mechanism of entry into cells, Structures of enveloped virions by electron cryo-microscopy and cryo-tomography, and many other interesting topics. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Advances in Virus Research series Includes the latest information on virus structure and function

Protein Complex Assembly

Author : Joseph A. Marsh
Publisher : Humana
Page : 506 pages
File Size : 52,5 Mb
Release : 2019-04-15
Category : Science
ISBN : 1493992775

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Protein Complex Assembly by Joseph A. Marsh Pdf

This volume details the importance of multiple experimental techniques and computational methods needed to obtain the comprehensive picture of protein complex structure, dynamics and assembly afforded by the emerging field of integrative structural biology. Chapters guide readers through the broad spectrum of approaches required for a complete representation of protein complexes, including expression and purification, experimental characterization of structure and assembly, and computational methods for identifying protein complexes and modelling their assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein Complex Assembly: Methods and Protocols aims to ensure successful results in the further study of this vital field.

EPR Spectroscopy

Author : Malte Drescher,Gunnar Jeschke
Publisher : Springer Science & Business Media
Page : 247 pages
File Size : 46,9 Mb
Release : 2011-09-06
Category : Science
ISBN : 9783642283475

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EPR Spectroscopy by Malte Drescher,Gunnar Jeschke Pdf

EPR Spectroscopy in Catalysis, by Sabine Van Doorslaer und Damien M. Murphy Radicals in Flavoproteins, by Erik Schleicher und Stefan Weber EPR Spectroscopy in Polymer Science, by Dariush Hinderberger EPR in Protein Science, by Intrinsically Disordered Proteins, by Malte Drescher Site-Directed Spin Labeling of Membrane Proteins, by Enrica Bordignon Structure and Dynamics of Nucleic Acids, by Ivan Krstić, Burkhard Endeward, Dominik Margraf, Andriy Marko und Thomas F Prisner New Directions in Electron Paramagnetic Resonance Spectroscopy on Molecular Nanomagnets, by J. van Slageren