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SSRL Headlines Vol. 9, No. 11  May, 2009


Contents of this Issue:

  1. Science Highlight — Bromine-rich Tips of Calcified Crab Claws as Model for Biomaterials
  2. Science Highlight — Visualizing Brain Metals in Health and Disease
  3. Science Highlight — Potential Implications for Cataract Formation - Redox Changes at the Sulfur Atom of Methionine
  4. JCSG Update
  5. A 35th Anniversary for X-ray Science at SLAC
  6. Joint SSRL/LCLS Annual Users' Meeting and Workshops, October 19-21, 2009
  7. SLAC to Join New Energy Frontier Research Efforts
  8. House Science Committee Staff Tour SLAC
  9. SSRL User Admin Update
  10. Photon Science-Related Workshops, Conferences and Schools
  11. New Luxury Hotel and Restaurant Adjacent to SLAC Site

1.  Science Highlight — Bromine-rich Tips of Calcified Crab Claws as Model for Biomaterials
       (contact: R. Scott,

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The tips of crab pincers are made of a very hard material, allowing the crab to fight and forage for food without wearing down their tools. Made mostly of proteins, the tip is known to be bromine-rich instead of calcium-rich, but the biochemical structure and mechanical properties were mostly unknown. Understanding this hard material made by crabs may lead to development of materials made by humans for use in a variety of purposes that require a small, fracture-resistant tool.

A team led by Robert Schofield of the University of Oregon and Robert Scott of the University of Georgia in Athens studies the material of crab claw tips. They found that the uncalcified, bromine-rich material is harder and stiffer than normal arthropod cuticle that lacks heavy elements and much more resistant to fracture than the calcified material in other parts of the crab.

Theorizing that the resistance to fracture comes from the arrangement of bromine atoms in the protein structure, the team collaborated with SSRL scientist Matthew Latimer to analyze the distribution and environment of bromine atoms in the crab claw tip. Using x-ray microscopy and spectroscopy at SSRL Beam Line 9-3, they found the bromine is evenly dispersed and likely bonds to phenyl rings, suggesting that a bromotyrosine moiety may be central to the special properties of this material. They hypothesize that either the bromine stiffens the material by creating more cross-links between the protein residues or the presence of the heavy atoms dampens energies created in impacts through their high electron densities. The results are published in the June issue of the Journal of Structural Biology.

To learn more about this research see the full scientific highlight at:

2.  Science Highlight — Visualizing Brain Metals in Health and Disease
       (contact: H. Nichol,

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Metals such as iron, copper, and zinc are critical for brain function, where they serve various roles, such as enzyme cofactors or neurotransmitters. Because the metal atoms can be reactive and cause cell damage, their locations and concentrations are tightly controlled. This control can be lost in some neurodegenerative diseases. Diseases like Alzheimer's dementia and Parkinson's disease are either caused by or lead to increased metal in areas of the brain, while others, like Menkes disease, are characterized by decreased concentrations of metals. Spinocerebellar ataxia (SCA) refers to a group of degenerative disorders that cause uncoordinated movement. Some cases of SCA are linked to abnormal metal concentrations in the brain, but the specific patterns associated with various forms of the disorder are unknown.

A research group led by Helen Nichol from the University of Saskatchewan used SSRL Beam Line 10-2 to compare the concentrations of iron, copper, and zinc metals in various regions of normal and SCA-affected brain tissues. The recently upgraded beam line allows measurement of the concentration of multiple metals in the same whole tissue sample using a rapid scanning x-ray fluorescence imaging technique.

In the March 24 issue of the journal Cerebellum, the researchers report areas of both higher or lower metal concentrations in the SCA brain compared to the control. Part of the basal ganglia had more iron. Part of the brainstem lacked copper. Part of the cerebellum lacked iron. Some of these results were consistent with findings from other experiments, while other observations highlight areas warranting further study. The rapid scanning XRF technique this team pioneered will be useful in future research of SCAs and other neurodegenerative diseases.

To learn more about this research see the full scientific highlight at:

3.  Science Highlight — Potential Implications for Cataract Formation - Redox Changes at the Sulfur Atom of Methionine
       (contact: P. Kennepohl,

highlight figure
In a similar way to your old pick-up truck rusting in the driveway, your body experiences a continuous battle against the elements. A constant barrage of oxidative stress attacks your cells and their constituent parts, including proteins. Like rust-proof paint on your vehicle, you have defense mechanisms that seek to prevent damage before it starts. But also like your trusty truck, once a weakness in the armor presents itself, it can spread rapidly - and often unnoticed - until you suddenly discover significant damage. Numerous diseases, as well as aging itself, are linked to uncontrolled oxidative processes that lead to irreversible damage and ultimately death. Understanding these oxidative processes may lead toward stopping and possibly even reversing damage.

Over the last decade, extensive studies of oxidative damage to proteins have shown that certain amino acids are more susceptible to oxidation than others. Methionine (MetS) is easily oxidized into its sulfoxide form (MetSO). This damaged form is readily reduced back to its natural form by enzymes, but sometimes it can build up and become further oxidized to sulfone (MetSO2), for which there is no easy way back to its original MetS form. MetS oxidation plays an important role in age-related cataracts. The most abundant protein in the eye lens, a-crystallin, aggregates and causes a marked decrease in the transparency of the lens - eventually leading to blindness. These protein aggregates show signs of oxidative damage, especially through oxidized forms of MetS. Long-term UV light exposure has been shown to increase oxidation of a-crystallin at methionine residues.

A research team led by Pierre Kennepohl of the University of British Columbia explored the basic photochemical processes of MetS that may lead to damage in lens proteins such as a-crystallin. This study, which relied heavily on x-ray absorption spectroscopy studies of the sulfur atoms (at the sulfur K-edge), performed at SSRL's BL6-2, showed that light-driven processes can lead to MetS oxidation but also to beneficial reductive processes that transform MetSO back to MetS. Which of these reaction directions is stronger is directly linked to the presence of dioxygen (O2). The crystalline lens is usually free of O2, ensuring that oxidative damage can be reversed when our eyes our exposed to light. However, lens levels of O2 are believed to increase with age, thus acquiring the conditions that allow age-related cataracts to form. These studies suggest that controlling the permeability of the crystalline lens towards dioxygen could prevent age-related cataracts. So the surface of the eye lens may, in fact, be quite similar to the rust-proof paint on your pickup. It may work well at first, but over time it can fail, allowing rust to set in. This work was published in the February 18 issue of the Journal of the American Chemical Society.

To learn more about this research see the full scientific highlight at:

4.   JCSG Update
       (contacts: A. Deacon,; H-J. Chiu,

The Joint Center for Structural Genomics (JCSG) was established in 1999, as a consortium that initially involved Stanford Synchrotron Radiation Lightsource (SSRL), The Scripps Research Institute (TSRI, the lead institution), the University of California at San Diego (UCSD), and the Genomics Institute of the Novartis Research Foundation (GNF). The JCSG is one of the four large-scale structural genomics production centers that are currently funded by the NIH Institute of General Medical Sciences (NIGMS) Protein Structure Initiative (PSI). The major goal of JCSG has been to develop and integrate innovative technologies into a highly efficient production pipeline for protein structure determination and during the current phase to continue development while using the pipeline for high throughput study of the structure and function of proteins of biological significance. The protein targets that are being actively investigated at the JCSG include members of large protein families that have no or very little structural coverage, proteins from metagenomes including the Global Ocean Sampling survey and the human gut microbiome, and all proteins from the T. maritima genome.

The Structure Determination Core (SDC) of JCSG is based at SSRL, and is responsible for crystal screening, structure determination, structure refinement, PDB deposition and some functional studies within the JCSG pipeline. At SDC, all protein crystals are initially screened and their diffraction properties are evaluated using the automation features available on SSRL macromolecular crystallography beam lines. Thus, the best crystal of each protein target is selected for MAD data collection. The process is very efficient; for example, during the period of May 2008 to April 2009, the JCSG collected 285 MAD/SAD data sets of which 86% had structures determined (i.e. 245 solved structures) that translated to 216 unique protein structures. In addition, many high resolution native data sets and anomalous data sets used to identify and locate the unknown bound metals in JCSG structures were also collected over this same period. As of 05/20/2009, JCSG had screened over 100,000 crystals using the SSRL structural biology beam lines equipped with the Stanford AutoMounter (SAM), had solved 945 structures and had deposited 838 structures in the PDB. On April 23-24 2009, over 80 JCSG consortium members, close collaborators, members from the Scientific Advisory Board and representatives of the NIH NIGMS PSI program met together for the JCSG's 8th annual meeting in La Jolla, California. The presentations in the meeting included the progress reports for the last year, and future challenges and planning sessions for the next phase of the PSI (PSI: High Throughput Structural Biology).
TM0574dimRNA Structure yir029hex Structure TM0021_trimerADP Structure

5.   A 35th Anniversary for X-ray Science at SLAC
       May 4, 2009 SLAC Today Article by Shawne Workman

April 1974 drawing of plans for the first Stanford Synchrotron Radiation Project beam lines.
Thirty-five years ago the Stanford Synchrotron Radiation Project - the precursor to today's Stanford Synchrotron Radiation Lightsource - began operations. The SLAC archives note that SSRP was the world's first synchrotron radiation hard x-ray lightsource based on an electron storage ring. SSRP science launched with five experimental stations sharing SLAC's first x-ray beam line.

For more about the SSRP, see the SLAC Archives and History Office SSRP timeline and photo gallery.

6.   Joint SSRL/LCLS Annual Users' Conference and Workshops, October 19-21, 2009
       (contact: C. Knotts,
User Mtg banner

Make plans to attend the 2009 SSRL/LCLS Users' Conference, October 19-21, 2009. The meeting will have plenary talks, a joint poster session, workshops, and vendor exhibits. This year Sebastien Boutet (, Katherine Kantardjieff (, Richard W. Lee ( and Donghui Lu ( are co-chairing the conference. Stay tuned for more information which will be posted on the meeting web site as it becomes available.

7.   SLAC to Join New Energy Frontier Research Efforts
       May 18, 2009 SLAC Today Article by Michael Wall

The Department of Energy has funded 46 new projects that will investigate ways to make the U.S. energy economy greener and more secure. SLAC will contribute substantially to at least three of these Energy Frontier Research Centers.

Each of the 46 EFRCs, which the White House announced April 27, will receive between two and five million dollars per year for five years-a total DOE commitment of $777 million. One project, run out of the National Renewable Energy Laboratory in Golden, Colorado, will use the Stanford Synchrotron Radiation Lightsource at SLAC to help identify more efficient materials for solar energy conversion. Another, based at Oak Ridge National Laboratory, will try to find new ways to develop super-strong, radiation-tolerant materials, with possible applications in energy infrastructure. The Oak Ridge center will employ SLAC's Linac Coherent Light Source in this effort. Read more at:

8.   House Science Committee Staff Tour SLAC
       May 29, 2009 SLAC Today Article by Shawne Workman

SLAC Members of the House Science Committee staff hear about SLAC science from SSRL Senior Staff Scientist Uwe Bergman. (Photo by Nicholas Bock.)
Yesterday afternoon, four staff members from the House Science Committee visited SLAC for a tour of science programs and facilities across the lab. After a luncheon with the SLAC Executive Council, the group made stops and heard presentations at the SLAC linac, Stanford Synchrotron Radiation Lightsource, Linac Coherent Light Source and the Kavli Institute for Particle Astrophysics and Cosmology. The visiting science committee members were: physicist and former American Physical Society fellow Adam Rosenberg, professional staff member for the Energy and Environment Subcommittee of the Full House Committee on Science and Technology; Jetta Wong, who handles Civilian Research, Development and Demonstration Programs at the Department of Energy; Margaret Caravelli, from the Science and Technology Committee's Republican Staff Chief Counsel; and Professional Staff Member Elizabeth Chapel.

9.   SSRL User Admin Update
      (contacts: C. Knotts,; L. Dunn,

The next deadline for beam time proposals on our macromolecular crystallography beam lines is July 1, 2009. Beam time eligibility for proposals submitted for this deadline begins fall 2009. For more information see:

Reminder: SSRL's current experimental run will end the morning of Monday, August 10. We expect to resume user operations in late October 2009

As always, we appreciate feedback on your data collection experience at SSRL. We have tried to make it easier for users to review scheduled experiments and to provide feedback by adding End of Run Summary forms to our user portal, see:

Pulse Summer School Thumbnail
PULSE School
10.   Photon Science-Related Workshops, Conferences and Schools

11.   New Luxury Hotel and Restaurant Adjacent to SLAC Site

The Rosewood Sand Hill, a luxury hotel and spa owned by Stanford and situated on 16 acres of university land just west of SLAC, celebrated its grand opening April 2. Rosewood Sand Hill has 123 rooms, suites and villas.

The complex also includes a new restaurant, Madera, which features an open artisan wood-burning kitchen, extensive wine list, comfortably elegant ambiance, picturesque views, indoor and outdoor dining, and two private dining rooms with terraces and cozy fireplaces. This Menlo Park restaurant is open daily for breakfast, lunch and dinner and for Sunday brunch as well.


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 MAY 2009
Content Owner: L. Dunn
Page Editor: L. Dunn