Scattering Methods in Structural Biology Part B

Scattering Methods in Structural Biology Part B

1st Edition - October 15, 2022

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  • Editor: John Tainer
  • Hardcover ISBN: 9780323991810

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Description

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.

Key Features

  • 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

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

Table of Contents

  • 1. Quality controls
    Jill Trewhalla
    2. Refining biomolecular structures and ensembles by SAXS-driven molecular dynamics simulations
    Jochen S. Hub
    3. Data analysis and modelling of small-angle scattering data with contrast variation
    Cy Jeffries and Andrew Whitten
    4. 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 Frank Gabel
    5. Extracting structural insights from chemically-specific soft X-ray scattering
    Esther W. Gomez
    6. Reconstruction of 3D density of biological macromolecules from solution scattering
    Thomas Grant
    7. ATSAS- present state and new developments in computational methods
    Dmitri Svergun and Haydyn Mertens
    8. Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles (FoXSDock and MultiFoXS)
    Dina Schneidman
    9. Validation of macromolecular flexibility in solution by SAXS
    Michal Hammel
    10. Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes
    Michael Sattler
    11. Application of Molecular Simulation Methods to Analyze SAS Data
    Susan Krueger and Joseph Curtis
    12. From dilute to concentrated solutions of intrinsically disordered proteins: Interpretation and analysis of collected data
    Marie Skepo
    13. Allosteric Inhibitors and drug discovery
    Chris Brosey
    14. SAXS and Fold Prediction
    Susan Tsutakawa
    15. SAXS Data-Assisted Modeling of Multidomain Protein Structures
    Janlin Cheng
    16. FRET methods for ion channels/binding
    Manu Ben-Johny
    17. Interpretation of solution scattering data for Protein Fibrillation
    Bente Vestergaard and Annette Langkilde
    18. Measuring similarity and conformational changes
    Greg Hura
    19. Insights from SAXS on disordered proteins on biological mechanisms: from protein folding to phase separation
    Joshua A. Riback
    20. Lipid/peptide interactions from molecules to microbes
    Georg Pabst

Product details

  • No. of pages: 412
  • Language: English
  • Copyright: © Academic Press 2022
  • Published: October 15, 2022
  • Imprint: Academic Press
  • Hardcover ISBN: 9780323991810

About the Serial Volume Editor

John Tainer

Prof. John A. Tainer trained in X-ray crystallography, biochemistry, and computation. With this foundation, he contributed to structural biochemistry for the biology for DNA repair, reactive oxygen control, the immune response, and other stress responses for >20 years. His NCI-funded papers report robust structural and biophysical measurements to advance understanding of cellular stress responses that are evolutionarily conserved and important in preserving genome stability and preventing diseases in humans. His methods, results, and concepts have stood the test of time: they are often used and cited >30,000 total times. At Scripps, Prof. Tainer created and ran the Scripps NSF Computational Center for Macromolecular Structure along with an NIH P01 on Metalloprotein Structure and Design. He also helped develop and utilize the Scripps share of the NSF San Diego Supercomputer Center. At LBL, he developed and directed the ~$2.9 million/year DOE Program “Molecular Assemblies Genes and Genomics Integrated Efficiently” (MAGGIE) from 2004-2011. At Berkeley, Prof. Tainer designed, developed, and directed the world’s only dual endstation synchrotron beamline SIBYLS (Structurally Integrated BiologY for Life Sciences), used by >200 NIH labs. This unique technology integrates high flux small angle x-ray scattering (SAXS) and macromolecular X-ray crystallography (MX). At SIBYLS his lab develop, optimize, and apply technologies to determine accurate structures, conformations and assemblies both in solution and at high resolution. His lab defined an R-factor gap in MX revealing an untapped potential for insights on nanoscale structures by better modeling of bound solvent and flexible regions. At the University of Texas MD Anderson Cancer Center, Prof. Tainer is joining biochemistry and biophysics to fluorescent imaging measures of protein and RNA interactions on DNA for mechanistic insights. He is integrating these data with cryo-EM, MX and SAXS structures by linking MD Anderson and SIBYLS facilities. As an originator of applying proteins from thermophiles to defining dynamic structures and functional conformations, Prof. Tainer develop methods for measurements on structures including conformations, and assemblies in solution. Prof. Tainer has combined cryo-EM and X-ray structures with biochemistry to define functional assemblies. His lab introduced new equations for analyzing X-ray scattering for flexible macromolecules and complexes. His lab also defined a novel SAXS invariant: the first discovered since the Porod invariant ~60 years ago. The defined parameters quantitatively assess flexibility, measure intermolecular distances, determine data to model agreement, and reduce false positives. Prof. Tainer has a track record of successful collaborations, completing projects, sharing innovating approaches and technologies, developing insights along with new structural data, and providing fundamentally important technologies that improve the ways others do their research. He has benefited from continuous peer-reviewed NCI funding since 1999. NCI support has allowed Prof. Tainer to develop expertise in the methods development and in the structural biology of DNA repair, immune responses, and other stress.

Affiliations and Expertise

Professor and Robert A. Welch Chair in Chemistry, Department of Molecular and Cellular Oncology, The University of Texas, USA

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