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SSRL Headlines Vol. 10, No. 7  January, 2010


Contents of this Issue:

  1. Science Highlight — A Crystal Structure of HIV-1 Capsid Proteins Shows Flexibility Necessary for Capsid Assembly
  2. Science Highlight — Researchers Visualize and Measure the Morphological Phases of Platinum Nanocrystals
  3. Science Highlight — A Very High-resolution Crystal Structure of a SUMO-like Domain in a Yeast Rad60 Protein
  4. Operations Resume after Storm-related Power Outage
  5. Todd Martinez Named 2010 National Security Science and Engineering Faculty Fellow by DoD
  6. Decorated with Electric Current, Nanoribbons Align with Expectations
  7. 48th ICFA Advanced Beam Dynamics Workshop on Future Light Sources
  8. User Research Administration
  9. Fresh Food Delivered to Bldg. 120 Kitchen Every Weekday

1.  Science Highlight — A Crystal Structure of HIV-1 Capsid Proteins Shows Flexibility Necessary for Capsid Assembly
       (contact: C.D. Stout,

hiv-capsid figure
Superposition of multiple copies of the HIV-1 CA hexamer.
The genome of the human immunodeficiency virus (HIV-1) is bundled inside a capsid composed of about 1,500 copies of the viral Capsid Assembly (CA) protein. These proteins first assemble into substructures, each with six proteins, and these substructures come together to create the cone-shape casing of the virus. Disruption of capsid formation is a natural target for HIV therapies, and knowing the atomic structure of the CA proteins in the capsid would be useful for drug development. However, inherent flexibility in these molecules makes obtaining quality crystals difficult.

A team of researchers led by Mark Yeager, from The Scripps Research Institute have solved the crystal structure of the hexameric CA protein substructure at 2.7 Å. To obtain their crystals, they used more stable subunits obtained by crosslinking the proteins at sites suggested by a 9 Å electron microscopy structure. They collected data using SSRL Beam Line 7-1 and solved the structure using molecular replacement. Their structure shows that the N-terminal domains are packed tightly in the center of the hexameric structure, but the C-terminal domains on the outside have more structural variability. This flexibility is probably necessary to allow the hexamers to assemble into the cone-like shape.

This research will aid discoveries of new capsid-targeted therapeutic agents against HIV-1 using structure-based drug design. This work was published in the June 11, 2009, issue of Cell.

To learn more about this research see the full scientific highlight

2.  Science Highlight — Researchers Visualize and Measure the Morphological Phases of Platinum Nanocrystals
       (contacts: M.F. Toney,; R.D. Tilley,

highlight figure
TEM images of platinum nanoparticles obtained from high concentration reactions.
Crystals of different sizes and shapes have different functional properties. This is certainly true in the case of platinum nanocrystals, which can be used to increase catalytic reactions including hydrogen cell fuel oxidation. Understanding crystallization processes will allow researchers to fine-tune the shape, size, and quality of crystals for specific, tailored applications.

An international team of researchers led by Richard Tilley from Victoria University in Wellington, New Zealand investigated the crystallization process of platinum nanocrystals. They set up reactions with two precursor concentrations (low and high) and took measurements over time. Real time in situ x-ray diffraction (XRD), using SSRL Beam Line 7-2, measured the crystallinity of the nanocrystals during the reactions, while transmission electron microscopy (TEM) revealed the morphology of the crystalline material. Combining the information from these two techniques allowed the researchers to discern the processes of crystallization.

The researchers found that the low concentration reactions create slow-growing, faceted crystals by laying down each platinum atomic layer in a thermodynamically controlled manner. In striking contrast, the high concentration reactions are kinetically controlled and go through distinct morphological phases over time, starting with a cuboctahedral faceted structure, growing into quasi-octapods, further evolving through simultaneous growth and dissolution of different parts of the nanocrystals into etched-octapods, and finally becoming porous nanocrystals.

The researchers conclude that combining the TEM and in situ XRD techniques creates a powerful tool for understanding crystal growth and structure. This research was published in the October 14, 2009, issue of the Journal of the American Chemical Society.

To learn more about this research see the full scientific highlight

3.  Science Highlight — A Very High-resolution Crystal Structure of a SUMO-like Domain in a Yeast Rad60 Protein
       (contacts: J.J.P. Perry,; J.A. Tainer,

highlight figure
The crystal structure of Rad60 SLD2.
DNA is a relatively stable molecule, but it can be damaged by chemicals generated inside our cells or by radiation originating from outside our cells. Significant amounts of DNA damage can lead to rapid-aging, cancer, and other diseases, so the cell has a fleet of enzymes that specialize in combating this daily wear-and-tear. One important group of DNA repair enzymes is the Rad60 family of proteins that is highly conserved from yeast to humans. Sequence analysis determined that Rad60 proteins contain two functional domains that are similar to the small ubiquitin modifier (SUMO) domain. The SUMO domain is used by the cell as a molecular tag that is covalently attached to target proteins, to alter their functions and/or cellular localization. The presence of SUMO-like domains suggests that Rad60 proteins can interact with proteins involved the SUMO pathway.

To determine the similarities between Rad60 and SUMO, a research team led by structural biologist John Tainer and geneticist Nick Boddy from The Scripps Research Institute used SSRL Beam Line 11-1 to solve a very high-resolution (0.97 Å) crystal structure of one of the SUMO-like domains of Rad60 from fission yeast. When comparing to a previously known structure of SUMO, the researchers found that the backbones of the two domains were well conserved, but most of the surface features were not. Since the enzyme would interact with other proteins through surface interactions, this suggests that Rad60 does not interact with the same set of proteins, nor undergoes covalent attachment to target proteins. However, one exception was a conserved surface feature known to be important for interactions with a specific factor (Ubc9) in the SUMO pathway, which functions to promote SUMOylation of target proteins. The researchers followed up on this observation with yeast genetics experiments performed in Nick Boddy's laboratory. They found that mutating this Ubc9 binding feature and hence, inhibiting Rad60's modulation of Ubc9, made cells more susceptible to DNA damage, which confirms that it is critical to Rad60 function.

This study is the first to explore the structure of SUMO-like proteins in detail. Defining how the SUMO pathway is used in DNA repair will aid our understanding of many diseases, including cancer, Alzheimer's, Parkinson's, and Huntington's. This research was published in the May 1, 2009, issue of Nature Structural and Molecular Biology.

To learn more about this research see the full scientific highlight

4.   Operations Resume after Storm-related Power Outage
       (contacts: C. Knotts,; B. Bozorg-Chami,

Due to severe storms in the area during the week of January 18th, SLAC experienced a site-wide power outage that lasted several days. Since that time, staff have worked to restore critical services, ensure safe working conditions, restore beam in SPEAR3 and restart user operations. Most beam lines resumed operations early during the last week of January. The accelerator physics tests scheduled for January 25-26 were canceled and returned to users who lost beam time during the outage.

We extend our thanks to staff, especially the Facilities staff, for all their hard work to restore these services as safely and efficiently as possible. We also acknowledge and appreciate our scientific users for their patience. We are compiling suggestions to improve future emergency communications and coordination based on lessons learned from this recent experience. Please contact Cathy Knotts or Behzad Bozorg-Chami to share your thoughts or feedback.

As a reminder in the event of future emergencies, please make a note of SLAC emergency information hotline: 1-877-447-SLAC/1-877-447-7522. SSRL users should also consult the SPEAR3 status website or the SPEAR3 status line at 650-926-BEAM / 650-926-2326 for updated information related to SSRL SPEAR3 and user operations.

5.   Todd Martinez Named 2010 National Security Science and Engineering Faculty Fellow by DoD

T. Martinez
T. Martinez
Earlier this week the Department of Defense (DoD) announced the selection of 11 distinguished university faculty scientists and engineers forming the 2010 class of its National Security Science and Engineering Faculty Fellowship (NSSEFF) program. NSSEFF provides grants to top-tier researchers from U.S. universities to conduct unclassified, basic research that may transform DoD's capabilities in the long term. The eleven fellows named will each be awarded up to $4.2 million over 5 years. Todd Martinez, Professor of Photon Science (SLAC National Accelerator Laboratory) and Department of Chemistry at Stanford University, will receive funding for his research in theoretical and computational design of light-and force-driven molecular materials (see Martinez' research interests at: Zachary J. Lemnios, Director, Defense Research and Engineering states, "These distinguished researchers have a demonstrated record of success in fields of strategic importance to the DoD. Their NSSEFF work will not only contribute to preparing DoD and the nation for an uncertain future, but will also develop the necessary high quality science, technology, engineering and mathematics talent that will be essential to the department's continued success." Read the press release and see the complete list of fellows at the Department of Defense website.


6.   Decorated with Electric Current, Nanoribbons Align with Expectations
       Based on SLAC Today Article by Olga Kuchment

(Image courtesy Hailin Peng.)
A substance predicted to shrink electronics and give quantum physicists a new tabletop toy behaves pretty much as its designers expected.

Last month in the journal Nature Materials, SLAC's Photon Science Directorate researchers and their coworkers at Materials Science Engineering, Stanford University, confirmed how electric current moves on tiny ribbons of a topological insulator, a material that insulates in its bulk but conducts unusually well on the surface. The work resulted from a close collaboration between the research groups of Stanford researcher Yi Cui, and Zhi-Xun Shen and Shoucheng Zhang of the Stanford Institute for Materials and Energy Science (SIMES). Some of the ARPES measurements supporting these results were performed on Beam Line 5-4 at SSRL.

"Electrical current properties are very difficult to study in a typical bulk sample of these topological insulators," said Shen, Director of SIMES, a joint Stanford/SLAC institute. "By making very small nanoribbons we were able to study the unique surface properties."

In extremely thin ribbons of the compound bismuth selenide, the large ratio of edges to innards makes the material's coolest properties easy to detect. Electrons running on the nanoribbon surface flow especially smoothly, act as though they have no mass, and have a set spin-at least when the ribbons are immersed in frigid liquid helium. In principle, the properties could extend to room temperature.

"It opens up a lot of future applications," said SIMES physicist and co-author Yulin Chen. The material could be a boon to spintronics, a technology that uses electron spin to store information. The applications of spintronics include miniscule computer chips and sensors, and quantum computing. Read more at:

7.   48th ICFA Advanced Beam Dynamics Workshop on Future Light Sources
       (contacts: J. Galayda,; J. Corlett,; T. Raubenheimer,

The 48th ICFA Advanced Beam Dynamics Workshop on Future Light Sources will be held at SLAC March 1-5, 2010. The workshop series on future light sources is the flagship event of the ICFA sub-panel on Future Light Sources. It intends to review and discuss modern accelerator-based light sources for wavelengths ranging from the infrared to x-rays. The workshop program will consist of plenary talks and working group sessions. Working groups will be dedicated to critical issues of scientific needs for future light sources, ERL, FEL, storage ring, and novel light source concepts, as well as to the essential technologies of high brightness electron sources, synchronization, high resolution beam diagnostics, undulators, x-ray beam line optics and detectors.

Attendance will be limited to 150 people. Additional information and registration details are available at the workshop website:

8.   User Research Administration
       (contacts: C. Knotts,, and L. Dunn,


    February 2 is the deadline for submitting Macromolecular Crystallography Beam Time Requests for the March through May 2010 scheduling period.

    February 15 is the deadline for submitting new X-ray/VUV Beam Time Requests for the third scheduling period (mid May through July 2010). (New proposals submitted for the December 1, 2009 deadline are currently being peer reviewed; ratings should be distributed within the next weeks or two)

    Submit requests by logging into our user portal at:


    The next proposal deadlines coming up are April 1 for Macromolecular Crystallography and June 1 for X-ray/VUV. For more information on proposal submittal see:


    Please submit an End-of-Run Summary after each scheduled experiment at SSRL. Comments on your experience at SSRL are extremely important to us, and we need your feedback to meet our mission requirements, including assessment and reporting. This form can be submitted through the user portal at:

9.   Fresh Food Delivered to Bldg. 120 Kitchen Every Weekday
       (contacts: M. Steger,; C. Knotts,

In response to user suggestions, a pilot program to provide fresh food to users and staff is underway. The SLAC cafe has installed a deli-type refrigerator in the Building 120 kitchen near the User Administration offices. Cafe staff restock the refrigerator with fresh salads, sandwiches, yogurt parfaits, cookies etc., every weekday. A limited number of entree items that can be heated in the microwave or oven are also available all at competitive price. The payment collection container is located adjacent to the refrigerator (no change available). Check out these fresh food options the next time you need a snack while at SSRL. We would appreciate your feedback on this pilot program.


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 29 January 2010
Content Owner: L. Dunn
Page Editor: L. Dunn