Small Angle Scattering Part A: Methods for Structural Investigation

1st Edition, Volume 677 - November 17, 2022
Editor: John Tainer
Language: English
Hardback ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 1 7 9 - 7
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 1 8 0 - 3

Small Angle Scattering, Part A: Methods for Structural Investigation, Volume 675 in the Methods in Enzymology series, highlights new advances in the field, with new chapters in… Read more

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Small Angle Scattering, Part A: Methods for Structural Investigation, Volume 675 in the Methods in Enzymology series, highlights new advances in the field, with new chapters in this updated release including SAXS foundations and metrics, Contrast variation sample preparation protocols, experimental procedures, and rudimentary analysis, Molecular deuteration for neutron scattering, Planning, Executing and Assessing the Feasibility of SANS Contrast Variation Experiments, Technical considerations for small-angle neutron scattering from biological macromolecules, and Advanced sample environments and capabilities at our synchrotron X-ray beamline with example applications.

Additional sections in the book cover SEC-SAXS-MALS data acquisition and processing pipeline at SIBYLS, SEC-SAXS: pros and cons, experimental set-up, examples and software developments, Radiation damage and sample economy for stopped-flow methods in the time regime of millisecond and above, Stopped-flow-time-resolved SAXS, Insights on Temp-jump, time-resolved SAXS, and much more.

Cover
Title page
Table of Contents
Copyright
Contributors
Preface
Chapter One: Advanced sample environments and sample requirements for biological SAXS
Abstract
1: Introduction
2: Correlation between the physical process of the scattering event and sample requirements
3: Automated sample loading robotics
4: Coupling of online purification systems
5: Specialized sample environments
References
Chapter Two: Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis
Abstract
1: Introduction
2: Background: SAXS and CV-SAXS
3: What information can be extracted from CV-SAXS data?
4: Experimental considerations
5: Doing the experiment
6: Examples of information extracted
7: Conclusions and outlook
Acknowledgments
References
Chapter Three: Deuteration for biological SANS: Case studies, success and challenges in chemistry and biology
Abstract
1: Deuteration for small angle neutron scattering
2: Protein SANS
3: Membranes: Sterols and physiologically relevant lipids
4: Deuteration by chemical synthesis
5: Examples of uses of deuteration for neutron scattering
6: Deuteration facilities
7: Deuteration facility use: Costs, feasibility, and quality of the experiment
8: The naming of Isotopologues: A problem for structural biologists, industry, and databases
9: Proposals for the registration of deuterated compounds
10: Concluding remarks
References
Chapter Four: Planning, executing and assessing the validity of SANS contrast variation experiments
Abstract
1: Introduction
2: Experiment planning
3: Data collection and assessment of validity
4: Further data analysis and model refinement
5: Concluding remarks
References
Chapter Five: Technical considerations for small-angle neutron scattering from biological macromolecules in solution: Cross sections, contrasts, instrument setup and measurement
Abstract
1: Introduction
2: Nuclear cross sections
Notes
3: Small angle neutron scattering instruments
4: The measurement approach
5: Summary
Acknowledgments
References
Chapter Six: Size exclusion chromatography coupled small angle X-ray scattering with tandem multiangle light scattering at the SIBYLS beamline
Abstract
1: Introduction
2: Endstation design
3: Sample preparation for SEC-SAXS-MALS
4: Data acquisition
5: Data processing
6: Data validation and analysis
7: Summary and conclusion
Acknowledgments
References
Chapter Seven: SEC-SAXS: Experimental set-up and software developments build up a powerful tool
Abstract
1: Introduction
2: The instrument
3: Data processing
4: Comparative analysis of SEC-SAXS datasets using the various available programs
5: Conclusion
Acknowledgments
References
Chapter Eight: Stopped-flow-time-resolved SAXS for studies of ligand-driven protein dimerization
Abstract
1: Introduction
2: Sample preparation
3: Stopped-flow experiment: The measurement
4: Data analysis and interpretation
5: Singular value decomposition and OLIGOMER analysis of time-resolved SAXS data
6: Fitting a kinetic model to extract rate constants from SF-SAXS data
7: Summary and conclusions
Acknowledgments
References
Chapter Nine: Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines
Abstract
1: Introduction, principles and limitations
2: Examples from diverse classes of biological systems
3: Considerations on sample state and practical guidelines for the design of TR-SANS experiments
4: Conclusions and future perspectives
Acknowledgment
References
Chapter Ten: Protein fibrillation from another small angle: Sample preparation and SAXS data collection
Abstract
1: Introduction
2: General method and safety notes
3: Feasibility, design and optimization
4: The main experiment: SAXS data collection
5: Summary and conclusions
Acknowledgments
References
Chapter Eleven: High-pressure SAXS, deep life, and extreme biophysics
Abstract
1: Introduction
2: Structural effects of pressure on biomolecular systems
3: Pressure dependence of SAXS
4: Methods
5: Summary and conclusions
Acknowledgments
References
Chapter Twelve: Characterization of biological materials with soft X-ray scattering
Abstract
1: Introduction
2: Sample preparation for dry or dehydrated materials
3: Sample preparation for liquids and hydrated solids
4: Storing and transporting samples
5: Mounting samples onto a sample bar
6: Performing NEXAFS experiments
7: Performing RSoXS experiments
8: Opportunities in instrumentation for resonant soft X-ray scattering of biological systems
9: Conclusion and outlook
Acknowledgments
References
Chapter Thirteen: Scattering measurements on lipid membrane structures
Abstract
1: Introduction
2: Information contents in the scattering data
3: General experimental planning considerations
4: Biological membranes
5: Model membrane structures
6: Concluding remarks
References
Chapter Fourteen: Studying integral membrane protein by SANS using stealth reconstitution systems
Abstract
1: Introduction
2: Contrast variation in small-angle neutron scattering (SANS) by selective deuteration of lipids and proteins for use as stealth carrier systems
3: Reconstitution of integral membrane proteins (IMP) into stealth carrier systems/example: Reconstitution of MsbA into stealth nanodiscs
4: SANS data acquisition and analysis of IMP/stealth nanodisc samples
5: Summary and conclusions
Acknowledgments
References
Chapter Fifteen: Predicting solution scattering patterns with explicit-solvent molecular simulations
Abstract
1: Introduction
2: Implicit-solvent methods
3: Explicit-solvent SAS predictions with the WAXSiS method
4: Theory
5: Workflow
6: Practical considerations
7: Summary
References
Chapter Sixteen: From dilute to concentrated solutions of intrinsically disordered proteins: Sample preparation and data collection
Abstract
1: Introduction
2: What is measured during an experiment?
3: Before a measurement
4: Performing a measurement
5: After a measurement
6: Summary and conclusions
Acknowledgments
References
Chapter Seventeen: Deriving RNA topological structure from SAXS
Abstract
1: Introduction
2: Outline of methods and experimental strategies
3: Detailed descriptions of methods and experimental strategies
4: Case studies
5: Summary and conclusions
Acknowledgments
References
Chapter Eighteen: Disentangling polydisperse biomolecular systems by Chemometrics decomposition of SAS data
Abstract
1: Introduction
2: General description of COSMiCS
3: Considerations for SAXS measurements
4: Procedure for COSMiCS decomposition
5: Indications of unreliable/incorrect decomposition and possible solutions
6: Summary and conclusions
Acknowledgments
References

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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Small Angle Scattering Part A: Methods for Structural Investigation

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John Tainer