Scattering Methods in Structural Biology Part B: Volume 678

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.

Autorentext

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.

Inhalt

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
13. SAXS and Fold Prediction
    Susan Tsutakawa
14. SAXS Data-Assisted Modeling of Multidomain Protein Structures
    Janlin Cheng
15. FRET methods for ion channels/binding
    Manu Ben-Johny
16. Interpretation of solution scattering data for Protein Fibrillation
    Bente Vestergaard and Annette Langkilde
17. Measuring similarity and conformational changes
    Greg Hura
18. Insights from SAXS on disordered proteins on biological mechanisms: from protein folding to phase separation
    Joshua A. Riback
19. Lipid/peptide interactions from molecules to microbes
    Georg Pabst