Workshop 1: Applications of Small Angle Scattering to Structural Biology: An Introduction

Date/Time: Friday, July 29, 2022 @ 8:00 AM PT
Location: ROOM TBA

Portland Marriott Downtown, Portland, Oregon

Organizational Contact: Michal Hammel 

 

     

 

Description

Small angle X-ray and neutron scattering (SAXS/SANS, or SAS) has experienced dramatic growth over the past fifteen years within the structural biology community, emerging as an important and versatile analytical technique for the study of the structure and function of biological macromolecules in solution. Publications that employ the technique on biological macromolecules appear in Pubmed at a rate of ~one per day. Based on this and recent successful workshops at the 2013, 2015, 2016, 2018 and 2020 ACA meetings, we believe the 2022 meeting in Portland will serve as an excellent destination for bringing together SAS experts to prepare students and investigators new to the method for the successful application of this technique. This one-day workshop will provide an introduction to both the theory of the method and best practices common to the field. In addition to synchrotron sources, this workshop will devote content to laboratory X-ray sources.

In contrast to the more intensive SAS courses at synchrotrons around the world that extend across several days, in this proposal we propose a single day of carefully constructed lectures and tutorials to serve as an introduction. This introduction will improve the chances for success in preliminary experiments, draw new people into the field, and elevate the standards for published data and peer-review. The workshop format will include lectures and a selection of hands-on practical exercises. Throughout the workshop the emphasis will be on practical application: knowing how to judge data quality, how to troubleshoot during data collection, and the expectations for a successful experiment and acceptable publication. Students will also learn about aspects of home laboratory data collection, important complementary biophysical techniques for validating your SAXS data, and will be introduced to experiments at national user facilities (synchrotrons and research reactors).

 

Instructors

 

Dr. Hammel is a beamline scientist at the SIBYLS (sector 12.3.1) beamline at the Advanced Light Source, with a focus on biological solution small angle X-ray scattering and synchrotron instrumentation, data collection, and data processing. He is the current co- developer and maintainer of the SAXS software package FoXS for analyzing biological SAS data, which is used by word-wide through WEB based application (https://modbase.compbio.ucsf.edu/foxs/, https://bl1231.als.lbl.gov/bilbomd. He is also developer of semi-automatic SAXS pipeline icoupled with size exclusion chromatography (SEC-SAXS) that allowed remote and mail-in type of data collection at the SIBYLS beamline https://bl1231.als.lbl.gov/htsaxs.

He as a software developer and beamline scientist has written hundreds of pages of tutorials and documentation introducing new and experienced users to different aspects of SAXS data analysis. During his time as a beamline scientist at SIBYLS he has trained hundreds of users both at and away from the beamline in data collection and analysis techniques for BioSAXS. He co-organized Advanced BioSAS workshop at the ACA 2013 and successfully raised the funds for this workshop from industrial partners. He has organized and been instructor for twelve annual SIBYLS bioSAXS workshops from 2009 -2021 which were the parts of Advance Lights Source user meetings. He has been an instructor for the 2018 and 2019 ACA BioSAXS workshops. He has also been extensively involved in the ACA SAS SIG in recent years.

 

Dr. Hopkins is a beamline scientist at the BioCAT (sector 18) beamline at the Advanced Photon Source, with a focus on biological solution small angle X-ray scattering and synchrotron instrumentation, data collection, and data processing. He is the current primary developer and maintainer of the BioXTAS RAW software (https://bioxtas-raw.readthedocs.io/en/latest/) for analyzing biological SAS data, which is used by at least four synchrotron SAXS beamlines, distributed as the primary analysis software with the Xenocs/SAXSLAB homesources, and regularly averages several thousand downloads per year. As a software developer he has written hundreds of pages of tutorials and documentation introducing new and experienced users to different aspects of SAXS data analysis. During his time as a beamline scientist at BioCAT and a postdoc at the Cornell MacCHESS BioSAXS beamline he has trained hundreds of users both at and away from the beamline in data collection and analysis techniques for BioSAXS. He co-organized the 2016 and 2017 MacCHESS BioSAXS workshops and has taught at the 2016, 2017, and 2018 workshops. He has been an instructor for the 2018 and 2019 APS Beyond Rg BioSAXS workshops. He was an organizer and instructor for the 2018 BioCAT BioSAXS workshop and is acting in the same roles at that workshop in November 2019. He was on the organizing committee for the 2018 SAS workshop at the ACA meeting and co-organized the Advanced BioSAS Techniques workshop at the SAS2018 meeting. He has also been extensively involved in the ACA SAS SIG in recent years, currently serving as chair-elect (chair in 2020), as well as being a co-chair for SAS-related sessions at the 2019 and 2020 meetings.

 

Dr. Gillilan co-organized and lectured at the 2013 and 2015 ACA SAS workshops, was on the organizing committee and a lecturer for the 2018 ACA SAS workshop, has run eight introductory BioSAXS workshops at Cornell High Energy Synchroton Source (CHESS), and has trained innumerable scientists in less formal settings both at and away from the beamline in his role as lead scientist for the MacCHESS BioSAXS beamline for the last decade. He has also been extensively involved in the ACA SAS SIG, serving as chair and being co-chair for several SAS related sessions.

 

 

 

Dr. Gupta directs the Johnson Foundation Structural Biology and Biophysics Core Facility at the University of Pennsylvania and has over fifteen years of experience with small angle X-ray and neutron scattering, utilizing both laboratory source and national general user facilities. He has served on the organizing committee and as a lecturer for the 2013, 2015, 2016, and 2018 ACA SAS workshops. He has lectured at eight BioSAXS workshops at CHESS and a similar topical workshop at the NIST Center for Neutron Research (NCNR) in 2011. He has also been extensively involved in the ACA SAS SIG, serving as chair and being co-chair for several SAS related sessions.

 

 
 

Dr. Weiss is a leader of biological Small Angle X-Ray Scattering Group of the Structural Molecular Biology Resource at SSRL in Stanford that operates the state-of-the-art X-ray BioSAXS beamline 4-2 and provides expertise and experimental support for visiting and remote researchers. He organizes biannual 3 to 4 days hand-on training workshops on the application and use of SAXS and diffraction methods in structural biology.

 

 

 

 

Dr. Meisburger is SAS SIG Chair and regularly participate as instructor at the ACA BioSAXS workshops. He is developing novel analyzing tools for size exclusion chromatography coupled SAXS (SEC-SAXS). His development in Single Value Deconvolution application have a significant impact in the determination of solution state of transient protein-protein and protein-DNA complexes.

 

 

 

 

 

Dr. Grant is an Assistant Professor in the Department of Structural Biology at the University at Buffalo Jacob School of Medicine and Biomedical Sciences. He has spoken at and/or co-organized more than two dozen workshops in SAXS and serial crystallography. He is currently the SAS SIG Chair and has chaired and organized several sessions and workshops at the ACA. He is the creator and lead developer of the DENSS software package for the reconstruction of 3D density maps from solution scattering data (https://www.tdgrant.com/denss) and a developer of the OM software package for XFEL data analysis for solution scattering.

 

Schedule 

 Start EndInstructor/Topic 
8:00 8:30 Registration and Software Installation Help; Speaker Introduction
8:30 9:00

Michal Hammel and Greg Hura (ALS)
BioSAS: Basics
Why is SAS helpful? Structure-prediction validation, cryo-EM vs SAXS, characterization of Lipid-nano assembly (vacines).

9:00 9:30

Richard Gillilan (CHESS)
The Scattering Profile
Guinier analysis, concentration, monodispersity, etc.

9:30 10:00

Jesse Hopkins (APS)
Data Analysis: Model-independent Features
Molecular Weight Determination, Invariant Plots and Flexibility, The P(r) function

10:00 10:15 Coffee Break
10:15 12:00

Jesse Hopkins (APS) and Richard Gililan (CHESS)
Tutorial I: Basic Data Analysis: Concentration dependence, radiation damage, calculate a P(r) function, determine Molecular Weight, Dmax, Rg, Volume, etc.…

12:00 1:00

Xenocs /Anton-Paar
Working Lunch - Laboratory Source SAXS
Capabilities and opportunities of laboratory source BioSAXS

1:00 1:30

Kushol Gupta (University of Pennsylvania) + open discussion
Sample Preparation
Sample purification and preparation, aggregation, buffer selection, etc.

1:30 2:00
Steve Meisburger (Cornell)
SEC-SAXS Application and Practical Considerations
2:00 2:30
Kushol Gupta (University of Pennsylvania)
Complementary Biophysical Methods for Sample Assessment 
The importance of supporting biophysical methods including static and dynamic light scattering. 
2:30 3:15
Dina Schneidman-Duhovny (Hebrew University of Jerusalem)
Data Analysis: Model-dependent Analysis of SAS Data 
Calculated scattering profiles from atomic models, Shape reconstruction, Atomistic modeling and defining of system dynamicity using ensemble modeling.
3:00 3:15
Micha Hammel (ALS)
Tutorial II: Calculate, evaluate, and display atomistic ensemble model (FoXS, MultiFOXS, FoXSDock)
3:15 3:30 Coffee Break
3:30 4:30
Thomas Grant (University at Buffalo) and Thomas Weiss (SSRL)
Tutorial 3: Ab initio reconstruction of shape from scattering data.
Calculate, evaluate, and display bead models (DAMMIF/N) and electron density models (DENSS)
4:30 5:00
Greg Hura (ALS)
High throughput SAXS - screening technique 
Structural similarity map by comparing SAXS profiles
5:00 5:30
Thomas Weiss (SSRL)
Publishing SAS data
Best practices for data presentation, validation, and supporting information
5:30  

Conclusion