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

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SIBYLS has installed new robotics that halve the time it takes to collect a full 96-well plate, from approximately 5 hours to 2.5 hours per plate (with the potential to collect a plate in 10 minutes over the coming year). We believe this will be a game changer for many reasons. We will be able to accommodate more users per week, enable new screening methods, and have more time to offer SEC-coupled SAXS and time resolved SAXS. In addition to the new robotics, we have improved instruments for higher data quality. Our new monitor of transmitted beam intensity should greatly reduce buffer subtraction errors. We have also replaced the windows for lower background. In completing these upgrades, the stage is now set for increased sample to detector distance providing access to lower q (an upgrade that will occur sometime during the summer).

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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.

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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

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.

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