Recently in SAXS Category

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

Are you looking to apply your skills in Integrative Structural Biology to the development of new approaches to explore organization of functional bacterial chromosome? The SIBYLS Group at Lawrence Berkeley National Laboratory is seeking a Postdoctoral Fellow in the field of Integrative Structural Biology. For more details on the position, please see the pdf document below….

LBNL NCI job description

protein_heatmap5-01.png

Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. The authors of this paper created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. These methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.


Yen-Ting Lai1, Greg L. Hura, Kevin N. Dyer, Henry Y. H. Tang, John A. Tainer and Todd O. Yeates Designing and defining dynamic protein cage nanoassemblies in solution 14 Dec 2016:Vol. 2, no. 12

In this paper, the authors show that CRY1, a protein coding gene that activates circadian gene expression and metabolic states and circadian oscillators, binds directly to the PAS domain core of CLOCK:BMAL1. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24 hr periodicity of gene expression. Integrative modeling and solution X-ray scattering studies (conducted at the SIBYLS beamline 12.3.1) irrefutably position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. This study is significant for understanding the clock mechanism as fundamental for the development and application of therapies for circadian-related disorders.

SAXS_Profile_CLOCK _centered.png

SAXS profile of CRY1:CLOCK:BMAL1 repressive complex.

(A) Scattering traces of CRY1:CLOCK:BMAL1 ternary complex (CCB) at different con- centrations are shown. These scattering plots were merged to generate the dataset as the input for FoXSDock. (B) Guinier analysis of CCB shows little or no aggregation of sample. SAXS-calculated molecular weight of the ternary complex is 113 kDa. (C) Kratky plot shows the CCB complex indicates a folded mass with an elongated shape. (D) PDB of FoXSDock HADDOCK driven model that is among the top 20 nearly degenerate docking structures, χ = 2.74.


Michael AK, Fribourgh L, Chelliah Y, Sandate C, Hura GL, Schneidman-Duhovny, Tripathi SM, Takahashi JS, Partch CL “Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1” PNAS 2017 Jan 31, doi:10.1073/pnas.1615310114

Tip link filaments convey force and gate inner-ear hair-cell transduction channels to mediate perception of sound and head movements. Cadherin-23 and protocadherin-15 form tip links through a calcium-dependent interaction of their extracellular domains made of multiple extracellular cadherin (EC) repeats. These repeats are structurally similar, but not identical in sequence, often featuring linkers with conserved calcium-binding sites that confer mechanical strength to them. In a paper recently published in Nature Communications the Sotomayor lab reports the X-ray crystal structures of human protocadherin-15 EC8-EC10 and mouse EC9-EC10, which show an EC8-9 canonical-like calcium-binding linker, and an EC9-10 calcium-free linker that alters the linear arrangement of EC repeats. Molecular dynamics simulations and small-angle X-ray scattering experiments support this non-linear conformation. Simulations also suggest that unbending of EC9-10 confers some elasticity to otherwise rigid tip links. The new structure provides a first view of protocadherin-15’s non- canonical EC linkers and suggests how they may function in inner-ear mechanotransduction, with implications for other cadherins.

nat_comm_highlight_sm.png

Araya-Secchi R, Neel BL, Sotomayor M. “An elastic element in the protocadherin-15 tip link of the inner ear.” Nat Commun 2016 Nov 18 ;7

We are pleased to announce the 7th annual SIBYLS bioSAXS workshop:

SYBILS homepage image-1.png

Date: October 4th - 5th, 2016

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

Description:

The 7th 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 speakers, Frank Gabel (IBS, Grenoble), Haydyn Mertens (EMBL, Hamburg), and Robert Rambo (Diamond, Oxford) will continue Dr. Hura’s discussion by elaborating on the basics of SAXS.

Michal Hammel, another SAXS Beamline Scientist at SIBYLS, will give a talk about SAXS modeling, SAXS profile computations using FOX, and calculations of SAXS shape.

Other distinguished speakers, (TBD), 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 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: Registration is now open. To attend the workshop you need to REGISTER for the 2016 Advanced Light Source User Meeting. When you register, indicate that you plan to attend the “7th Annual SIBYLS bioSAXS Workshop”.

SCHEDULE :

Tuesday, October 4th (Building 2, Rm 100B)

12:20 Lunch (ALS Patio and Exhibitor Tent)

14:00 Welcoming Remarks: Michal Hammel, LBNL

14:15 Frank Gabel, IBS, Grenoble

15:00 Coffee Break

15:15 Haydyn Mertens, EMBL, Hamburg

16:00 Coffee Break

16:15 John Tainer, The University of Texas M.D. Anderson Cancer Center, Houston

16:30 Update on SAXS at SIBYLS : Greg Hura, LBNL

16:45 Mail-in SAXS at SIBYLS : Kathryn Burnett, LBNL

17:00 End of first day’s workshop

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

9:00 Short presentations followed by open discussion

10:30 Coffee Break

10:45 Robert Rambo, Diamond Light Source, Oxford

12:00 Lunch (ALS patio and Exhibitors Tent)

13:00 Practical session with mentors (Greg Hura, Michal Hammel, Robert Rambo, Haydyn Martens, Frank Gabel)

16:45 Closing comments, Michal Hammel, LBNL

17:00 End of BioSAXS workshop

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