Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. In this paper the authors define molecular pathways linking AIF’s active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF’s central β-strand to modulate a hydrophobic border at the dimerization interface, and (2) an interaction network links AIF’s FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. This knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.

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Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA. “Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.” Structure 2016 Dec 06 ;24(12)

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.

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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

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The BioSAXS workshop at the ALS User Meeting on October 4th and 5th was a big success. The workshop was filled to capacity with attendees coming from many different regions of the US. Participants were given detailed information about the range and capabilities of our new Pilatus detector and the future upgrades to the SIBYLS beamline. The latest advances in SAXS studies on biological systems were discussed, along with updates on current developments of software for SAXS analysis. The afternoon of the second day of the workshop was dedicated to practical hands-on SAXS analysis.

We would like to extend special thanks to our illustrious speakers; Haydyn Martens (EMBL,Hamburg), Frank Gabel (IBS, Grenoble), Robert Rambo (Diamond Light Source, Oxford) and John Tainer (M.D. Anderson Cancer Center, Houston) for their informative talks. Thanks also to Subrata Dutta, Henry Tang, Mitra Sayantan, Rahul Banerjee and Ryan Spencer for presenting their SAXS related projects, facilitating some lively, illuminating conversation. And, of course, thanks to everyone who attended.

For those who were not able to attend this year, we look forward to seeing you in October 2017 for the 8th Annual BioSAXS workshop. In the meantime, be sure to take advantage of our Mail-in HTSAXS program and check out all the different SAXS analysis tools that you can download from our website.

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

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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

The facilities and staff at the SYBILS beamline contributed to this breakthrough study exploring the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain.

Exploring the Repeat Protein Universe structures.png

Naturally occurring proteins—chains of amino acids that fold into functional, three-dimensional shapes—are believed to represent just a small fraction of the universe of all possible permutations of amino-acid sequences and folds. How can we begin to systematically sift through those permutations to find and engineer from scratch (de novo) proteins with the characteristics desired for medical, environmental, and industrial purposes? To address this question, a team led by researchers from the Institute for Protein Design at the University of Washington have published a landmark study that used both protein crystallography and small-angle x-ray scattering (SAXS) at the ALS to validate the computationally designed structures of novel proteins with repeated motifs. The results show that the protein-folding universe is far larger than realized, opening up a wide array of new possibilities for biomolecular engineering.

Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. “Exploring the repeat protein universe through computational protein design.” Nature 2015 Dec 24 ;528(7583)link

Our new pixel array detector, a Pilatus3 2M from dectris, arrived at LBNL on July 27, 2015 and was installed on the SAXS endstation at SIBYLS beamline 12.3.1. The first user data was collected on August 19, 2015.

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2015 workshop participants.jpgOur 6th annual SIBYLS bioSAXS workshop “Frontiers in biological SAXS” was a huge success. A big thank you to all of you who attended and a special thanks to our fabulous speakers:

  • Robert Rambo, Principal Beamline Scientist for the solution state SAXS beamline B21 at the Diamond Light Source, Oxfordshire, UK

  • John J. Tanner, Professor of Biochemistry, University of Missouri-Columbia

  • Chris Brosey, Postdoc with Tom Ellenberger’s Lab, Washington University in St. Louis

  • Carrie Partch, Assistant Professor in Physical and Biological Sciences, University of California - Santa Cruz

  • Samuel Bouyain, Associate Professor, School of Biological Sciences, University of Missouri - Kansas City

  • Dina Schneidman, Postdoc with Sali Lab, University of California, San Francisco

We look forward to another successful workshop in Fall 2016!

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