Recently in Science:


Structure determination of gold nanoparticles (AuNPs) is necessary for understanding their physical and chemical properties, but only one AuNP larger than 1 nanometer in diameter [a 102-gold atom NP (Au102NP)] has been solved to atomic resolution. Whereas the Au102NP structure was determined by x-ray crystallography, other large AuNPs have proved refractory to this approach. Here, we report the structure determination of a Au68NP at atomic resolution by aberration-corrected transmission electron microscopy, performed with the use of a minimal electron dose, an approach that should prove applicable to metal NPs in general. The structure of the Au68NP was supported by small-angle x-ray scattering and by comparison of observed infrared absorption spectra with calculations by density functional theory.

read about it here:

Azubel M, Koivisto J, Malola S, Bushnell D, Hura GL, Koh AL, Tsunoyama H, Tsukuda T, Pettersson M, Häkkinen H, Kornberg RD. “Nanoparticle imaging. Electron microscopy of gold nanoparticles at atomic resolution.” Science 2014 Aug 22 ;345(6199):909-12 link

We are pleased to announce the 5th annual SIBYLS bioSAXS workshop “Frontiers in biological SAXS”


Date: October 7-8, 2014 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA

Small angle scattering (SAS) is experiencing a dramatic increase in popularity within the structural biology community. The availability of synchrotron radiation, low-noise detectors, powerful computing hardware, and better algoritms, has made the technique accessible to a much larger audience than ever before. At the same time, biologists are investigating ever more complex systems that pose increasing challenges to conventional crystallography. The latest advances in SAXS studies on biological systems will be reported and discussed in 2 days workshop by invited experts with focus on following four topics (see program). 1) Advances in Synchrotron Scattering technique 2) Dynamic & Flexible Structures in Biomolecules 3) Membrane Protein Scattering 4) Complementary Methods in Crystals and in Solution

The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. Participants will also receive updates on current development of software dedicated to analyze SAXS for structural biology. Half day of the workshop will be dedicated for data processing by workshop participants. Enrollment is limited to 30 participants. 

Organizers: Michal Hammel, Greg Hura

Inquires: Jane Tanamachi

Registration: To attend “Frontiers in biological SAXS” you need register for the 2014 Advanced Light Source Users’ Meeting. ALS user meeting will be held at Berkeley Lab beginning Monday, October 6. “Frontiers in biological SAXS” will begin Thuesday October 7th and continue through Wednesday October 8th. When you registering, you must indicate “Frontiers in biological SAXS”

Tuesday, October 7th LBNL Building 2 , room 100B

11:30 Lunch at the ALS patio

12:30 Welcoming Remarks Michal Hammel and Greg Hura “Frontiers in biological SAXS”

12:45 Lois Pollack, Cornell Univesity

13:15 Edward Snell, Hauptman-Woodward Institute

13:45 Lokesh Gakhar, University of Iowa

14:15 Coffee Break

14:30 Greg Hura, LBNL

15:00 Dina Schneidman, University California, San Francisco “SAXS based modelling of proteins with long disordered fragments”

15:30 Sherry Wang, National Cheng Kung University, Taiwan “Molecular architecture and stepwise assembly of IL-33 signaling complex”

16:00 Michal Hammel LBNL “A molecular switch in nucleoid compaction dictates bacterial pathogenicity”

16:30 TBD

17:00 TBD

Wednesday, October 8th LBNL Building 2 , room 100B

9:00 Michal Hammel, LBNL “Data reduction and processing tutorial”

10:30 Coffee Break

10:45 Greg Hura “Data reduction and processing tutorial”

12:00 Lunch Break at the ALS patio

13:00 - till late Practical session with Mentors (Greg Hura, Michal Hammel, Dina Schneidman, Sherry Wang)

A new publication is available that describes practical aspects of collecting High-throughput SAXS data at the SIBYLS beamline, with a focus on challenging low concentration samples. Additional practical advice is laid out with respect to interpreting the resulting data.

Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer JA, Hura GL. “High-throughput SAXS for the characterization of biomolecules in solution: a practical approach.” Methods Mol. Biol. 2014;1091:245-58. link

The SIBYLS beamline was instrumental in providing key structural data for two recent publications exploring the dynamic nature of DNA repair.


The Mre11‐Rad50 complex is highly conserved, yet the mechanisms by which Rad50 ATP‐driven states regulate the sensing, processing and signaling of DNA double‐strand breaks are largely unknown. Here we design structure‐based mutations in Pyrococcus furiosus Rad50 to alter protein core plasticity and residues undergoing ATP‐driven movements within the catalytic domains. With this strategy we identify Rad50 separation‐of‐function mutants that either promote or destabilize the ATP‐bound state. Crystal structures, X‐ray scattering, biochemical assays, and functional analyses of mutant PfRad50 complexes show that the ATP‐induced ‘closed’ conformation promotes DNA end binding and end tethering, while hydrolysis‐induced opening is essential for DNA resection. Reducing the stability of the ATP‐bound state impairs DNA repair and Tel1 (ATM) checkpoint signaling in Schizosaccharomyces pombe, double‐strand break resection in Saccharomyces cerevisiae, and ATM activation by human Mre11‐Rad50‐Nbs1 in vitro, supporting the generality of the P. furiosus Rad50 structure‐based mutational analyses. These collective results suggest that ATP‐dependent Rad50 conformations switch the Mre11‐Rad50 complex between DNA tethering, ATM signaling, and 5′ strand resection, revealing molecular mechanisms regulating responses to DNA double‐strand breaks.

read more in the full articles…

Deshpande RA, Williams GJ, Limbo O, Williams RS, Kuhnlein J, Lee J-H, Classen S, Guenther G, Russell P, Tainer JA, Paull TT. “ ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.” EMBO J. 2014 Feb 3.


Shibata A, Moiani D, Arvai AS, Perry J, Harding SM, Genois M-M, Maity R, van Rossum-Fikkert S, Kertokalio A, Romoli F, Ismail A, Ismalaj E, Petricci E, Neale MJ, Bristow RG, Masson J-Y, Wyman C, Jeggo PA, Tainer JA. “DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities.” Mol Cell. 2014 Jan 9;53(1):7-18.

Young researchers are encouraged to apply for the Cancun conference “Dynamic Structures in DNA Damage Responses and Cancer” from the 12-15th February, 2014. We expect that there will be lively discussions on both methods and results during the sessions and good opportunities to interact with top colleagues. To inspire your productive discussions the conference venue has breath taking views of the Caribbean Sea and a great beach to enjoy with colleagues. There are a few spots to join the conference and some for late breaking talks so if you or your group members would appreciate this intimate and informative meeting on dynamic structures in DNA damage responses and cancer, then we would encourage you to APPLY. We are putting together many of the people driving advances under one roof to make this a meeting that will prove uniquely productive and informative for those working in this area and seeking collaborators. Although you may have a busy schedule we aim to make this meeting worth your taking the time to participate by directly aiding research progress and collaborations.

Greg Hura and colleagues developed and applied nanogold labels for DNA complexes with proteins examined by small angle X-ray scattering (SAXS) to follow DNA conformations acting in error detection by the mismatch repair (MMR) system in solution. This technique can examine short or long pieces of DNA and in most solution conditions, including those closest to cellular environments. This technique is expected to be useful for many biologically important systems involving DNA complexes and conformations. In this manuscript the authors reveal DNA bending followed by straightening by the repair protein MutS at the site of a mismatch as a suitable mechanism for error detection and signaling needed to avoid mutations and cancers and to control microbial stability and evolution in response to environmental stress.


Mismatch DNA bending by MutS and straightening in the presence of ATP. Contour plots of the distribution of DNA ends are visualized by placing the structural information from the crystal structure of MutS/DNA on the same scale as the distance and pop- ulation information from the P(Dij) distributions. The P(Dij) distributions from 71-bp DNA in the presence of MutS (left) and the presence of MutS and excess ATP (right) set contour levels. The widest part of the distribution is the width of the gold nanocrystal. DNA of the crystal structure has been ex- tended to 71 bp for the MutS/DNA complex and replaced by straight DNA for the ATP model.

For all the details please check out the full manuscript:

Hura GL, Tsai C-L, Claridge SA, Mendillo ML, Smith JM, Williams GJ, Mastroianni AJ, Alivisatos AP, Putnam CD, Kolodner RD, Tainer JA. “DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals.” Proceedings of the National Academy of Sciences. 2013 Oct 7.

We are pleased to announce the 4th annual SIBYLS bioSAXS workshop.

Date: October 8-9, 2013 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA


The SIBYLS team will host a workshop with strong emphasis on experimental aspects of Small Angle X-ray Scattering techniques in structural biology. The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. The latest advances in SAXS studies on biological systems will be reported and discussed by invited experts including our keynote speakers Prof. Peter Moore (Yale), Pau Bernando (CNRS France) and John Tainer (Scripps). Also planned are presentations on solution structure modeling techniques for proteins, RNA, DNA-protein complexes. The second day of the workshop will be dedicated for processing of workshop participant data previously collected at SIBYLS.

Participants will receive updates on current software dedicated to analyze SAXS for structural biology:

Enrollment is limited to 30 participants.

More details

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