The Advanced Photon Source
a U.S. Department of Energy Office of Science User Facility

Workshop on biological science opportunities provided by the APS Upgrade

Macromolecular X-ray crystallography (MX) is the most powerful method for structure determination of biological molecules. Last year 91% of all new Protein Data Bank deposits (10,121) were solved using X-rays, and over 90% of these were determined using synchrotron radiation. MX is essential for basic, biomedical and environmental research, drug discovery and biotechnology. In the US, the APS is the largest and the most productive light source for MX. The APS upgrade (APS-U) to a multi-bend achromat (MBA) lattice will deliver the ultimate X-ray source that will radically transform MX capabilities. The brilliant, micron-size, stable X-ray beams will become routinely available to a large number of users at more than a dozen MX stations 24 hrs/day, 200 days/year. Advanced MX methods at APS-U beamlines utilizing microcrystals will allow static, dynamic and time resolved macromolecular studies at unmatched speed and scale, wide range of temperatures (10 – 350 K), providing high-resolution and atomic insight. The APS-U integrated suites of experimental and computational capabilities will examine biological molecules at subnanometer to millimeter length, on time scales from picoseconds to seconds and at different temperatures and pressures. This will make APS-U a powerful one-of-a-kind tool for structural biology.

The specific advantages of APS-U X-ray source are (i) highly parallel X-ray beams that will be essential to study large macromolecular complexes at high resolution, (ii) increased brightness that will allow beamlines to deliver intense micrometer sized beams, resulting in a 100-fold improvement in signal-to-noise, (iii) increased brightness at high energy that can be exploited to  reduce primary radiation damage due to escape of photoelectrons that cause most of the damage from the X-ray beam footprint, and (iv) high-speed detectors that will allow a reduction of secondary radiation damage at room temperature by using very short exposures to  “out-run” free-radical diffusion.  The source will also be ideal to exploit macromolecular systems in situ and in cellulo.

In a context where new technologies for structure determination emerge, such as free electron lasers and cryo-electron microscopy, this workshop will explore how these future structural biology resources can be used to address grand challenges in biology for predictive understanding of the relationship between the genome, structure, function, and interactions important for research relevant to DOE energy, biological and environmental missions, and NIH human health and well-being missions.

MX APS-U Workshop Organizing Committee
Member Facility/University
Erin Adams U. Chicago
Paul Adams UC Berkeley
Brian Davison ORNL
Robert Fischetti ANL
Andrzej Joachimiak ANL
Philippe Noirot ANL
Todd Yeates UCLA
MX APS-U Workshop Agenda

Argonne National Laboratory, August 20-21, 2018, Bldg. 446 Auditorium

Day 1 - August 20

Talks 15 Minutes + Q&As
7:50 – 8:00 AM Welcome & Workshop Goals Philippe Noirot
8:00 – 10:00 AM Session 1 – Hard X-Rays and Future Trends in Structural Biology Chairperson: Robert Fischetti and Andrzej Joachimiak
8:00 - 8:20 Hard X-Rays at APS-U Stephen Streiffer, ANL
8:20 - 8:40 Serial Millisecond Crystallography at Micro-Focus Monochromatic and Poly-Chromatic Beamlines Wei Liu, ASU
8:40 - 9:00 Serial Crystallography: A New Data Collection Paradigm Ed Latmann, Hauptman-Woodward MRC
9:00 - 9:20 Painting with X-Rays: Flexible Beam Shapes for Optimal Data Quality James Holton, ALS/LBNL
9:20 - 10:00 Discussion Discussion participant: Gayle Woloschak, Northwestern U.
10:00 – 10:30 AM Coffee break  
10:30 – 12:30 PM Session 2 – Emerging Technologies
Chairperson: Todd Yeates
10:30 – 10:50 Electric-Field Stimulated Protein Mechanics Rama Ranganathan, UChicago
10:50 – 11:10 Time-Resolved X-Ray Experiments: From the Synchrotron to the XFEL and Back Michael Thompson, UCSF
11:10 – 11:30 Optimizing Serial Crystallography Experiments with Live Diffraction Data Analysis Artem Lyubimov, SSRL
11:30 – 11:50 Challenges in Diffuse X-Ray Scattering from Protein Crystals Michael Wall, LANL
11:50 – 12:30 Discussion Discussion participants: Jose Rodriguez, UCLA; Aina Cohen, SLAC (remote attendee)
12:30 – 1:30 PM Lunch  
1:30 – 3:30 PM Session 3 – Future Needs for Structural Biology in Plant, Microbiome and Environmental Sciences Chairperson: Paul Adams
1:30 – 1:50 X-Ray Crystallography and Spectroscopy for Studying Metalloenzymes Junko Yano, LBNL
1:50 – 2:10 Molecular Mechanisms of Biofilm Signaling: Observing Receptors and Enzymes in Action Holger Sondermann, Cornell
2:10 – 2:30 From “Omics” to Function: Deciphering Poorly Annotated Genomes with Structural Biology Michelle O’Malley, UCSB
2:30 – 2:50 Understanding Plant Cell Wall Architecture and Chemistry by Real-Time Imaging Shi-You Ding, U Michigan
2:50 – 3:30 Discussion Discussion participant: Crysten Blaby-Haas, BNL
3:30 – 4:00 PM Coffee Break  
4:00 – 6:00 PM Session 4 - Future Needs for Structural Biology in Biomedical and Microbiome Research Chairperson: Erin Adams
4:00 – 4:20 Imaging and Imagining Bacterial Flagella Eric Sundberg, U Maryland
4:20 – 4:40 Synthetic Antibodies and Nanobodies for Structural Biology Tim Springer, Harvard U.
4:40 – 5:00 Membrane Proteins: Reaching for High-Hanging Fruits Heather Pinkett, Northwestern U.
5:00 – 5:20 Microbial Structural Biology Sean Crosson, UChicago
5:20 – 6:00 Discussion Discussion participant: Engin Ozkan, UChicago
7:00 PM Dinner (on your own)  

Day 2 - August 21

8:00 – 10:00 AM Session 5 – Future Needs for Structural Biology in Bioenergy and Synthetic Biology Research Chairperson: Brian Davison
8:00 - 8:20 High Throughput Strategies for Enzyme Discovery and Evolution Carrie Eckert, UC Boulder
8:20 - 8:40 Plant Systems Biology Research for Bioenergy Crop Improvement: Progress and Gaps Udaya Kalluri, ORNL
8:40 - 9:00 The Study of Multi-Functional Enzymes Remains Challenging Today Mike Himmel NREL
9:00 - 9:20 Using Neutrons to Probe Biomass and Biomembrane Structures Brian Davison, ORNL
9:20 - 10:00 Discussion Discussion participant: Ian Blabby, BNL
10:00 – 10:30 AM Coffee break  
10:30 – 12:30 PM Session 6 – Attendees Discuss and Summarize Workshop Findings Chairpersons: All committee members
10:30 – 10:55 Session 1 - Hard X-Rays and Future Trends in Structural Biology  
10:55 – 11:20 Session 2 - Emerging Technologies  
11:20 – 11:45 Session 3 - Future Needs for Structural Biology in Plant, Microbiome and Environmental Sciences  
11:45 – 12:10 Session 4 - Future Needs for Structural Biology in Bioenergy and Synthetic Biology Research  
12:10 – 12:35 Session 5 - Future Needs for Structural Biology in Biomedical and Microbiome Research  
12:30 – 1:30 PM Lunch  
1:30 – 3:30 PM Report writing  
4:00 PM Adjourn  


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