The Doudna group, explained in their recent paper, “Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a” combine SAXS with Cryo-Em to show the C-terminal binding domain is sufficient for Cas12a inhibition. CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. The inhibitor AcrVA4 uses a previously undescribed strategy to recognize the L. bacterium Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. Their findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.


doudna paper.png


figure Allosteric activation paper.png

In the Marletta group’s recent paper, “Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy” they corroborate the structural elongation of the particle observed in cryo-EM using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO. Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. They determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains.


SIBYLScovers.png

Date: October 2 - 3, 2019 Location: Building 33 at Lawrence Berkeley National Laboratory, Berkeley, CA

Building / ROOM : 33-306

This two-day workshop will cover frontiers in biological SAXS and will provide participants with software tutorial sessions for biological SAXS in addition to hands-on training in experimental techniques. The latest advances in SAXS studies on biological systems will be discussed with a particular focus on dynamic and flexible structures in biomolecules, membrane protein scattering, and complementary methods in crystals and in solution. Updates on current developments of software for SAXS analysis and solution structure modeling will be illustrated.

The first day of the workshop will begin with a brief run-through on current updates. Greg Hura and Michal Hammel, Berkeley Lab’s SAXS beamline scientists, will introduce the capabilities of the mail-in program at SIBYLS and the future of high-throughput and SEC-SAXSat the SIBYLS Beamline. Distinguished speakers will contribute to the basis of the workshop over the two days by sharing complementary experimental approaches and modeling techniques. This will provide for a flux of ideas among workshop participants and inspire new perspectives for future data analysis. The second day will be dedicated to practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Enrollment is limited to 30 participants. 





Inquires: Kathryn Burnett

Registration: Registration is now open. To attend the workshop you need to REGISTER for the 2019 ALS user meeting. When you register, indicate that you plan to attend the “10th Annual SIBYLS bioSAXS Workshop”.

SCHEDULE : October 2nd, 2019

Building / ROOM : 33-306

Day 1: BioSAXS Workflow

8:30-8:40 Introduction to the SIBYLS team and Workshop Agenda (Hammel)

8:40 - 9:20 Key Note - Mark Glover (Uni. Alberta) Building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time

9:20 - 10 SAXS basics (G. Hura)

10 - 10:20 Break

10:20 - 12:20pm HT-SAXS, details of collection, getting intensity vs q (Burnett and Hura)

12:20 - 1:30 Lunch

1:30 - 2:30 SEC-SAXS-MALS, details of collection, getting intensity vs q (Hammel and Rosenberg)

2:30 - 3:00 ALS and beamline tour (SIBYLS team)

3:00 - 3:30 Analysis of SEC-SAXS-MALS (Hammel)

3:30- 3:50 Break

3:50 - 4:10 Ben Horst ( UC Berkeley) Allosteric activation of the NO receptor soluble guanylate cyclase revealed by cryo-EM and SAXS

4:10 - 4:30 Lauren Carter (University of Washington) De novo protein design validated by SAXS

4:30 - 4:45 Soumya Remesh (NCI) Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling

4:45 - 5 Curtis Hodge (LBNL) Functionalized Nanocage for Antibody Display

October 3rd, 2019 Day 2: Beyond Shapes with SAXS

8:30 - 9:15 HT-SAXS examples (Hura)

9:20 - 10 Special SEC-SAXS-MALS tools with RAW and Evolving SVD (Hammel)

10 - 10:20 Break

10:20 - 12:20pm User posed problem

12:20 - 1:30 Lunch

1:30 -2:00 SAXS modeling, BILBOMD, FoXS etc… (Hammel)

2:00-5:00 Hands on practical

After implementing many upgrades made possible by IDAT support, the SIBYLS beamline has enabled the collection of data for over 50 laboratories in 2019 (so far). High impact results have begun to be reported in journals using the new high throughput and size exclusion coupled SAXS (HT and SEC-SAXS) capabilities. Representative results include those from the Baker laboratory at University of Washington. The Baker laboratory is the leading de-novo protein design laboratory in the world and relies heavily on SAXS capabilities provided through IDAT funding. Results will undoubtedly impact synthetic biology projects of relevance to DOE-BER. In addition, DOE seeks to leverage scientific scale to accomplish missions that could not be accomplished by single PI laboratories.



Recently in Science:

De novo design_baker Paper.png

Environmentally triggered conformational changes can now be programmed by de novo protein design as shown through SAXS data collected at the SIBYLS beam line 12.3.1 with IDAT support. The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. The Baker lab designed homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells.



Read more about it here:

Scott E. Boyken, Mark A. Benhaim, Florian Busch, Mengxuan Jia, Heejun Choi, Jason C. Klima, Zibo Chen, Carl Walkey, Alexander mileant, Aniruddha Sahasrabuddhe, Kathry Y. Wei, Edgar A Hodge, Sarah Byron, Alfredo Quijano-Rubio, Banumathi Sankaran, NeilP king, Jennifer Lippincott-Schwartz, Vicki H. Wysocki, Kelly K. Lee, David Baker De novo design of tunable, pH-driven conformational changes Science 17 May 2019: Vol. 364, Issue 6441, pp. 658-664 DOI: 10.1126/science.aav7897

WebAppWide.png

SIBYLS is pleased to announce SAXS Frameslice, a new Webapp for merging frame sliced SAXS data. The Webapp was designed by Dave Shin with the purpose of improving your SAXS calculations by averaging the intensities of different regions of your data from multiple images of the same sample. With this Webapp you can:

  • Determine the limits of radiation-induced aggregation or damage, and adjust your data accordingly (particularly for the guinier region of your data).

  • Remove data points from either end of your data.

  • Improve signal to noise ratios, particularly at the Wide-angle region of your data.

Date: May 9th 2019

Location: Advanced Light Source at Lawrence Berkeley National Laboratory, Berkeley, CA

Building 6, conference room #2202

SAXS_board.JPG This one-day workshop for current and future SIBYLS users will provide participants with software tutorial sessions for biological SAXS. The latest advances in SAXS studies on biological systems will be discussed with particular focus on advances in synchrotron scattering techniques, modeling of dynamic and flexible structures, and integrating bioSAXS analysis within high resolution structures.
Updates on current developments of software for SAXS analysis pertaining to structural biology will be reviewed.

We will begin with a brief run-through on current updates. Greg Hura, Berkeley Lab’s SAXS Beamline Scientist will introduce the future of high throughput. Michal Hammel, another one of Berkeley Lab’s SAXS Beamline Scientists, will present current developments in size exclusion chromatography coupled SAXS (SEC-SAXS) and give a talk about integrating high-resolution models in the SAXS modeling. Students and postdocs are encouraged to bring their own SAXS data collected at SIBYLS. We will provide an opportunity for participants to present and discuss their projects with the group. If you are interested in discussing your SAXS project, please email Kathryn Burnett. This will provide for a flux of ideas among workshop participants, and inspire new perspectives for future data analysis. During the afternoon session we will provide practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Organizers: SIBYLS



Inquires: Kathryn Burnett

Limited to 30 participants.

Registration: Registration is now open. To attend the workshop you need to send an email to Kathryn Burnett

Lunch is provided.

SCHEDULE :

May 9, 2019 12:00 pm - 5:00 pm

Building 6, conference room #2202

12:00 - 1:30 pm Greg Hura and Michal Hammel Working lunch and introductions

1:30 - 2:30 pm Greg Hura and Michal Hammel Tour of the ALS, both SAXS and MX end stations

2:30 - 3:00 pm Scott Classen “Crystallographic Options at the ALS”

3:00 - 3:40 pm Michal Hammel and Daniel Rosenberg “Size Exclusion Coupled SAXS issues”

3:40 - 4:20 pm Greg Hura and Kathryn Burnett “High-throughput SAXS issues”

4:20 - 5:00 pm Hands on User Projects

**figintro.jpg Date: October 3 - 4, 2018 Location: Advanced Light Source at Lawrence Berkeley National Laboratory, Berkeley, CA

Building 33 room 306

The two-day workshop, held during ALS user meeting, will provide participants with software tutorial sessions for biological SAXS in addition to hands-on training in experimental techniques. The latest advances in SAXS studies on biological systems will be discussed with particular focus on advances in synchrotron scattering techniques, modeling of dynamic and flexible structures, bioSAXS with membrane protein, and integrating bioSAXS analysis within cryo-EM imaging.
Updates on current developments of software for SAXS analysis pertaining to structural biology will be reviewed.

The first day of the SIBYLS annual workshop will focus on applied science while the second day will focus more on practical tutorials.

We will begin with a brief run-through on current updates. Greg Hura, Berkeley Lab’s SAXS Beamline Scientist will introduce the future of high throughput. Three keynote speakers: Walter Chazin (Vanderbilt), Thomas Weiss (SLAC, Stanford) and Steve Meisburger (Princeton), will continue Dr. Hura’s discussion by elaborating on the basics of SAXS and the fascinating integration of bioSAXS in integrative structural biology. Michal Hammel, another one of Berkeley Lab’s SAXS Beamline Scientists, will present current developments in size exclusion chromatography coupled SAXS (SEC-SAXS) and give a talk about integrating high-resolution models in the SAXS modeling. Other distinguished speakers from the SIBYLS user community: Chris Brosey (MD Anderson) , Fatma Zehra Yildiz (Harvard) and George Ueda (University of Washington) will contribute to the basis of the workshop over the two days by sharing complementary experimental approaches and modeling techniques. Screen Shot 2018-07-19 at 2.35.35 PM.png

For the second day, students and postdocs are encouraged to bring their own SAXS data collected at SIBYLS. During the morning session, we will provide an opportunity for participants to present and discuss their projects with the group. If you are interested in presenting, please email Kathryn Burnett. This will provide for a flux of ideas among workshop participants, and inspire new perspectives for future data analysis.

The afternoon session will be dedicated to practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Enrollment is limited to 30 participants. 



Organizers: Michal Hammel, Greg Hura



Inquires: Kathryn Burnett

Registration: Registration is now open. To attend the workshop you need to REGISTER for the 2018 ALS user meeting. When you register, indicate that you plan to attend the “9th Annual SIBYLS bioSAXS Workshop”.

SCHEDULE :

October 3rd, 2018 Building 33 room 306

8:45 am Michal Hammel and Greg Hura “Welcoming remarks”

9:00 am Greg Hura (LBL) “Redefining frontier in bioSAXS”

10:00 am Break

10:20 am Walter Chazin (Vanderbilt) “Redefining of protein dynamicity by integrating NMR and SAXS”

11:00 am Steve Meisburger (Princeton) “Redefining of bioSAXS by the SEC-SAXS approach and SVD deconvolution”

11:40 am Michal Hammel (LBL) “Integrative structural modeling by combining crystallography, SAXS and X-ray tomography”

12:00 pm Lunch and Exhibitors—ALS Patio and Exhibitor Tent

1:30 pm Beamline tour and demonstration, Greg Hura and Daniel Rosenberg, LBNL

2:20 pm Thomas Weiss ( SLAC) “Overview on the workflows and how we do SAXS at SSRL”

3:00 pm Break

3:20 pm Chris Brosey (MD Anderson) “Using High-Throughput SAXS to Illuminate Allosteric Landscapes and Advance Drug Discovery”

3:50 pm Fatma Zehra Yildiz (Harvard) “TBD”

4:20 pm George Ueda (Washington Uni) “Computational design of self-assembling cyclic protein homo-oligomers”

4:40 pm Soumya Remesh (LBL) “HU multimerization shift controls nucleoid compaction as seen through SAXS and X-ray tomography”

5:00 pm Gather for Evening Session—Building 50 Auditorium

October 4th, 2018

9:00 am Short students presentations followed by an open discussion

10:00 am Break

10:15 am Greg Hura: “SAXS analysis part 1”

11:15 am Michal Hammel: “SEC-SAXS data processing and SVD deconvolution”

12:00 am Lunch and Exhibitors—ALS Patio and Exhibitor Tent

1:00 pm Greg Hura, “SAXS Analysis part 2”

1:30 pm Michal Hammel “Tools for modeling flexibility in proteins using SAXS data”

2:00 pm Greg Hura “SAXS Similarity Maps”

2:20 pm Practical session with Mentors

5:00 pm Closing comments: Michal Hammel and Greg Hura

We are pleased to announce the 8th annual SIBYLS bioSAXS workshop as part of the Advanced Light Source 2017 User Meeting:

Date: October 3 - 4, 2017

Location: Advanced Light Source at Lawrence Berkeley National Laboratory, Berkeley, CA

Description:

The 8th annual SIBYLS bioSAXS workshop will cover frontiers in Biological SAXS. The two-day workshop will provide participants with software tutorial sessions for biological SAXS in addition to hands-on training in experimental techniques. The latest advances in SAXS studies on biological systems will be discussed with particular focus on advances in synchrotron scattering techniques, dynamic and flexible structures in biomolecule, membrane protein scattering, and complementary methods in crystals and in solution. Updates on current developments of software for SAXS analysis pertaining to structural biology will be illustrated.

The first day of the workshop will begin with a brief run-through on current updates. Greg Hura, Berkeley Lab's SAXS Beamline scientist at SIBYLS, will introduce the capabilities of the new detector and the future of high throughput SAXS at the SIBYLS Beamline 12.3.1. The keynote speaker, John Tainer from MD Anderson Cancer Center in Houston, will continue Dr. Hura's discussion by elaborating on the basics of SAXS.

Michal Hammel, another one of Berkeley Lab's SAXS Beamline Scientists, will give a talk about SAXS modeling, SAXS profile computations using FOXS, and calculations of SAXS shape.

Other distinguished speakers (TBD), will contribute to the basis of the workshop over two days by sharing complementary experimental approaches and modeling techniques. This will provide for a flux of ideas among workshop participants, and inspire new perspectives for future data analysis. The second day of the workshop will be dedicated to practical hands-on exercises.

Enrollment is limited to 30 participants.

Organizers: Michal Hammel, Greg Hura

Inquires: Kathryn Burnett

Registration: Early registration is open until September 18th. When you register, indicate that you plan to attend the "Biological Small-Angle X-Ray Scattering (SAXS)" workshop. Here is the link to REGISTER for the 2017 Advanced Light Source User Meeting. 

WORKSHOP SCHEDULE:

Tuesday, October 3rd 

12:20 Lunch (ALS Patio and Exhibitor Tent)

14:00 Welcoming Remarks: Michal Hammel, LBNL (Bldg 2, rm 100B)

14:15 John Tainer, M.D. Anderson Cancer Center

          "Making macromolecular structures speak"

15:00 Coffee Break  

15:15 Greg Hura, LBNL 

          "What is going on with the SIBYLS Beamline?"

16:00 Kathryn Burnett, LBNL: Mail-in SAXS at SIBYLS

16:20 Michal Hammel and Daniel Rosenberg, LBNL: SEC SAXS at SIBYLS

17:00 End of first day's workshop

Wednesday, October 5th (Building 2, room 100B)

9:00   Short presentations followed by open discussion

10:00 Coffee Break

10:15 Beamline tour and demonstration, Greg Hura and Tad Ogorzalek, LBNL

11:15 Greg Hura: SAXS Analysis

12:00 Lunch (ALS patio and Exhibitors Tent)

13:00 Henry Tang, LBNL 

          "Conformational Change Analysis with SAXS"

13:30 Soumya Remesh, LBNL

          "Tools for modeling flexibility in proteins using SAXS data"

14:00 Practical session with Mentors 

16:45 Closing comments: Michal Hammel, LBNL

17:00 End of BioSAXS workshop

 

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