Small Angle Scattering Part A: Methods for Structural Investigation

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.

1. SAXS foundations and metrics
Robert Rambo
2. Contrast variation sample preparation protocols, experimental procedures, and rudimentary analysis
Lois Pollack
3. Molecular deuteration for neutron scattering
Anthony Patrick Duff
4. Planning, Executing and Assessing the Feasibility of SANS Contrast Variation Experiments
Susan Krueger
5. Technical considerations for small-angle neutron scattering from biological macromolecules
Cy Jeffries and Andrew Whitten
6. Advanced sample environments and capabilities at our synchrotron X-ray beamline with example applications
Melissa Graewert and Dmitri Svergun
7. SEC-SAXS-MALS data acquisition and processing pipeline at SIBYLS
Daniel Rosenberg and Michal Hammel
8. SEC-SAXS: pros and cons, experimental set-up, examples and software developments
Patrice Vachette, Javier Perez and Aurelien Thureau
9. Radiation damage and sample economy for stopped-flow methods in the time regime of millisecond and above
Michael Weiss
10. Stopped-flow-time-resolved SAXS
Henning Tidow and Inokentijs Josts
11. Insights on Temp-jump, time-resolved SAXS
Philip Anfinrud
12. Time-resolved Small-Angle Neutron Scattering (TR-SANS) for structural biology of dynamic systems: history, recent developments, and practical guidelines
Frank Gabel
13. SAXS data collection for Protein Fibrillation
Bente Vestergaard and Annette Langkilde
14. Actin assembly
Kristina Djinovic Carugo
15. SAS induced disulfide bond damage
Edward Snell
16. High pressure SAXS
Richard Gillilan
17. Challenges and opportunities in soft X-ray scattering of biological molecules
Esther W. Gomez
18. Collection of scattering data from lipid membranes and nanodiscs
Lin Yang
19. SANS stealth methods for membrane proteins
Henning Tidow and Inokentijs Josts
20. Predicting solution scattering patterns with explicit-solvent molecular simulations
Jochen S. Hub
21. From dilute to concentrated solutions of intrinsically disordered proteins: Sample preparation and data collection
Marie Skepo
22. Extracting physically-relevant ensemble properties of disordered proteins and other polymers from SAXS data
Joshua A. Riback
23. Determining topological structures of RNA using SAXS
Yun Xing Wang
24. SAS data analyses of polydisperse systems with special emphasis on transient complexes
Pau Bernado and Aamin Sagar
25. FEL samples and data collection
Peter Zwart