Integrative Structural Biology with Hybrid Methods

Integrative Structural Biology with Hybrid Methods PDF

Author: Haruki Nakamura

Publisher: Springer

Published: 2019-01-08

Total Pages: 272

ISBN-13: 9811322007

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This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.

Scattering Methods in Structural Biology Part B

Scattering Methods in Structural Biology Part B PDF

Author:

Publisher: Elsevier

Published: 2023-01-12

Total Pages: 462

ISBN-13: 0323991823

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Scattering Methods in Structural Biology, Part B, Volume 676 in the Methods in Enzymology serial, highlights advances in the field, presenting chapters on Quality controls, Refining biomolecular structures and ensembles by SAXS-driven molecular dynamics simulations, Data analysis and modelling of small-angle scattering data with contrast variation, Observing protein degradation in solution by the PAN-20S proteasome complex: state-of-the-art and future perspectives of TR-SANS as a complementary tool to NMR, crystallography and Cryo-EM, Extracting structural insights from chemically-specific soft X-ray scattering, Reconstruction of 3D density of biological macromolecules from solution scattering, ATSAS- present state and new developments in computational methods, and much more. Additional chapters cover Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles (FoXSDock and MultiFoXS), Validation of macromolecular flexibility in solution by SAXS, Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes, Application of Molecular Simulation Methods to Analyze SAS Data, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology serial Updated release includes the latest information on Small Angle Scattering Methods for Structural Interpretation

Hybrid Biomolecular Modeling

Hybrid Biomolecular Modeling PDF

Author: Slavica Jonic

Publisher: Frontiers Media SA

Published: 2019-01-24

Total Pages: 128

ISBN-13: 2889456994

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Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.

Computational Structural Biology

Computational Structural Biology PDF

Author: Torsten Schwede

Publisher: World Scientific

Published: 2008

Total Pages: 790

ISBN-13: 9812778780

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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.

Protein Interactions

Protein Interactions PDF

Author: Volkhard Helms

Publisher: John Wiley & Sons

Published: 2022-11-08

Total Pages: 436

ISBN-13: 3527830529

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Protein Interactions A fundamental guide to the burgeoning field of protein interactions From enzymes to transcription factors to cell membrane receptors, proteins are at the heart of biological cell function. Virtually all cellular processes are governed by their interactions, with one another, with cell bodies, with DNA, or with small molecules. The systematic study of these interactions is called Interactomics, and research within this new field promises to shape the future of molecular cell biology. Protein Interactions goes beyond any existing guide to protein interactions, presenting the first truly comprehensive overview of the field. Edited by two leading scholars in the field of protein bioinformatics, this book covers all known categories of protein interaction, stable as well as transient, as well as the effect of mutations and post-translational modifications on the interaction behavior. Protein Interactions readers will also find: Introductory chapters on protein structure, conformational dynamics, and protein-protein binding interfaces A data-driven approach incorporating machine learning and integrating experimental data into computational models An outlook on the current challenges in the field and suggestions for future research Protein Interactions will serve as a fundamental resource for novice researchers who want a systematic introduction to interactomics, as well as for experienced cell biologists and bioinformaticians who want to gain an edge in this exciting new field.

Biological NMR

Biological NMR PDF

Author: A.Joshua Wand

Publisher: Academic Press

Published: 2019-01-03

Total Pages: 440

ISBN-13: 0128138610

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Biological NMR, Part A, the latest release in the Methods of Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on topics such as Protein methyl labeling, Membrane protein expression – yeast, Protein aromatic labeling, His-tag/Metal contamination, Bicelles, nanodiscs and micelles MP host, PTM – phosphorylation, PTM – lipidation, Screening platform for receptor-ligand discovery Solution Spectroscopy, Large protein strategies, NUS data collection/analysis, F19 incl. hydration, ODNP - hydration, Reverse micelle - Hydration Solid State Spectroscopy, SS NMR membrane proteins, SS NMR soluble/aggregate proteins, SS DNP - general, SS NMR nucleic acids, Structure determination and computer analysis, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods of Enzymology series Updated release includes the latest information on the Biological NMR

Structural Biology in Drug Discovery

Structural Biology in Drug Discovery PDF

Author: Jean-Paul Renaud

Publisher: John Wiley & Sons

Published: 2020-01-09

Total Pages: 1367

ISBN-13: 1118900502

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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

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