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SSRL Headlines Vol. 8, No. 5  November, 2007


Contents of this Issue:

  1. Science Highlight — Tuning the Properties of Iron-Sulfur Clusters in Proteins
  2. Science Highlight — A Step Toward Understanding High-Temperature Superconductors
  3. Call for User Publications, Awards, Invited Lectures
  4. JCSG Celebrates Its 500th Structure
  5. Planning Any International Shipments?
  6. Holiday Shutdown
  7. User Administration Update

1.  Science Highlight — Tuning the Properties of Iron-Sulfur Clusters in Proteins
       (contacts: B. Hedman, hedman@ssrl.slac.stanford; K.O. Hodgson,; E.I. Solomon,

Proteins containing iron-sulfur clusters are ubiquitous in nature and catalyze one-electron transfer processes. These proteins have evolved into two classes that have large differences in their electrochemical potentials: high potential iron-sulfur proteins (HiPIPs) and bacterial ferredoxins (Fds). The role of the surrounding protein environment in tuning these redox potentials has been a persistent puzzle in the understanding of biological electron transfer. Although high potential iron-sulfur proteins and ferredoxins have the same iron-sulfur structural motif, there are large differences in their electrochemical potentials. HiPIPs react oxidatively at physiological potentials, while Fds are reduced. Sulfur K-edge x-ray absorption spectroscopy (XAS; measured at SSRL Beam Line 6-2) has been used to uncover the substantial influence of hydration on this variation in reactivity, in a collaborative effort led by Stanford Chemistry and Photon Science researchers. The study showed that the Fe-S covalency (a measure of the electronic overlap of the sulfur and iron orbitals forming the bonds within the clusters) is much lower in natively hydrated Fd active sites than in HiPIPs, but increases upon water removal; similarly, HiPIP covalency decreases when reversibly unfolded, exposing an otherwise hydrophobically shielded active site to water. These results demonstrate that the Fe-S covalency determined from the sulfur-K XAS data is a direct experimental marker of the local electrostatics due to H-bonding. Studies on related model compounds and accompanying density functional theory calculations support a correlation between Fe-S covalency and ease of oxidation, which suggests that differential hydration accounts for most of the difference between Fd and HiPIP reduction potentials. This raises the intriguing possibility that oxidation/reduction potentials can be regulated by protein/protein and protein/DNA interactions that effect cluster hydration.
Schematic representation of the common active-site iron-sulfur cluster structural motif.

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

2.  Science Highlight — A Step Toward Understanding High-Temperature Superconductors        (contacts: D.H. Lu,; Z.-X. Shen,

a, Underdoped sample with Tc = 75 K. b, Underdoped sample with Tc = 92 K. c, Overdoped sample with Tc = 86 K. At 10 K above Tc there exists a gapless Fermi arc region near the node. [see larger image and more detailed caption at Nature].
Scientists can make high-temperature superconductors, but they don't have a good theory for how they work. Understanding high-temperature superconductors will have significant impact on the modern condensed matter theory, and may someday allow scientists to design room-temperature superconductors. SLAC Photon Science and Stanford Professor Z.-X. Shen and colleagues, working at SSRL's Beam Line 5-4, recently made observations that will help shape the theory. Their results are published in the Nov. 1 issue of Nature.

Certain materials become superconductors-that is, losing all resistance to electric current-when they become colder than their transition temperature. So far, the warmest transition temperature recorded is minus 164 degrees Fahrenheit. Below the transition temperature, the electrons pair up. This pairing reduces the energy of the electrons. The strength of pairing is characterized as a superconducting gap in the single particle excitation spectrum, which is found below the transition temperature in both conventional and high-temperature superconductors.

In high-temperature superconductors, scientists also observe a gap above the transition temperature, called the pseudogap. So far it has been unclear whether the two gaps are unrelated, or if the pseudogap is a precursor to the superconducting gap. Using angle-resolved photoemission spectroscopy to measure the energy gap at different temperatures and momenta, Shen and colleagues found that the pseudogap and the superconducting gap coexist and exhibit different temperature dependence. Therefore, the two gaps seem to have different origins. This should provide an important step toward unveiling the mystery of the pseudogap phenomena. To learn more about this research see the full scientific highlight at:

3.   Call for User Publications, Awards, Invited Lectures
       (contacts: L. Dunn,

In preparation for a key program review of SSRL by the DOE Office of Basic Energy Sciences and for our Annual NIH, NCRR/Biomedical Technology Program (BTP) Progress Report, SSRL needs your support. Please provide us, by December 5, with a list of publications, major awards and invited lectures for work based at least in part on use of SSRL resources for years 2005-2007. Please send your list of publications by email to or by using the web form at: Please also flag those that you view as being "high profile, high impact" with a sentence explaining the impact.

Lists of publications reported to SSRL to date and sample acknowledgment statements can be found at:

Biochemistry and Cell Biology December cover image (85: 537-542 (2007)). Inset image: Synchrotron X-ray fluorescence mapping reveals the asymetric distribution of iron in an intact Xenopus laevis oocyte. Image: Popescu et. al, University of Saskatchewan Background image: Human breast cancer cells MCF-7 immunostained for microtubules (alpha-tubulin) in green and transcription factor Sp1 in red, with nuclei in blue. Image provided by Shihua He, University of Manitoba. Science October 19 cover image (318, 430 (2007)). Structure of a gold nanoparticle in which the central atoms are packed in a decahedron, surrounded by additional layers of gold atoms in unanticipated geometries. Gold atoms, gold; sulfur atoms, blue; carbon atoms, white; oxygen atoms, red; the superimposed red mesh depicts the electron-density distribution determined by x-ray crystallography. Image: Pablo D. Jadzinsky and Guillermo Calero. Molecular Cell October 12 cover image (28, 41 (2007)). The high-resolution structure of the mammalian endoplasmic reticulum Hsp90 chaperone GRP94 with bound ATP. The extent to which a common mechanism applies to all Hsp90 chaperones has been controversial. In cytosolic Hsp90s, ATP binding results in N-terminal dimerization that is critical for ATP hydrolysis and subsequent chaperone function. Dollins et al. show that nucleotide-bound GRP94 adopts a conformation that precludes N-terminal dimerization yet demonstrate GRP94-catalyzed ATPase activity using kinetic analyses, suggesting that nucleotide binding is not the major driving force for catalytically productive conformational changes.

4.   JCSG Celebrates Its 500th Structure
      SLAC Today article by Elizabeth Buchen

Ashley Deacon loads samples of crystallized proteins into an automated sample mounting system.
On October 29, the Joint Center for Structural Genomics (JCSG)-in which SLAC plays an integral role-celebrated a major milestone as it deposited its 500th unique protein structure into the Protein Data Bank (PDB). A protein's 3D structure dictates its function-including how it interacts with other proteins, how it catalyzes chemical reactions and how it might be inhibited or activated by drugs. By determining structures representative of large protein families from a wide range of genomes, the JCSG seeks to illuminate key aspects of biology, chemistry and medicine that span from neurodegenerative disease to human evolution.

The process of depositing a protein structure into the PDB begins with the Bioinformatics Core (based at the University of California San Diego and the Burnham Institute for Medical Research) selecting the targets to be investigated and the Crystallomics Core (based at The Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation) producing soluble proteins that are then crystallized. Researchers at SLAC's Stanford Synchrotron Radiation Laboratory (SSRL) then use x-ray diffraction to map out the atomic structure of each crystallized protein. This Structure Determination Core (SDC) group determines the 3D structures and deposits the structural coordinates and diffraction data into the PDB, where they are freely available to the scientific community.

"Together, the Institutes in our consortium have established a very effective pipeline," said SLAC's Ashley Deacon, who leads the SDC. "We have developed new technologies and automated the various steps of the process to scale up not only production, but also to increase the efficiency, lower the cost and increase the quality of the structures determined."

SSRL has contributed to the development of robotic hardware to process and evaluate the crystal samples, enabling fast sample turn-around at the beam lines, and has generated novel software programs for high through-put structure determination. "Because the beam line is fully automated, we can control almost every step in our experiment from any computer," said Jessica Chiu, who manages crystal screening and data collection activities at SDC. "We can be at home, or in another country, and still screen crystals around the clock. This allows us to attain maximal throughput at the beam lines with minimal human intervention."

The determination of 500 structures is a tremendous accomplishment, and a testament to the talented scientific team and to the success of their automated, highly efficient operation. "We've doubled the rate at which we solve new structures since 2005," Deacon reported, "and we're still getting faster. But we won't compromise quality. The best way to speed things up is to get the best quality data you possibly can."

More information on all of the structures solved and deposited by the JCSG can be found at the JCSG Structure Gallery.

JCSG is funded by the NIH National Institute of General Medical Sciences, Protein Structure Initiative U54GM074898.

5.   Planning Any International Shipments?
       (contacts: C. Knotts,; L. Dunn,

There are new procedures related to international shipments, so please contact us in advance if you are planning to ship samples, equipment or other scientific items from SSRL to a location outside of the US following your beam time at SSRL (for example, to return dewars to a collaborator or your home institution).

6.   Holiday Shutdown
Please note that SSRL will close for the holiday break at 4 pm on Friday, December 21. User operations will resume on most beam lines around noon on Wednesday, January 2. Users shipping samples for beam time which begins on January 2 are encouraged to ship these so that they arrive before December 21.

7.   User Administration Update
      (contact: C. Knotts,

Macromolecular Crystallography Proposals due December 1: If you are interested
in submitting a proposal for the December 1, 2007 deadline for time on macromolecular crystallography beam lines, see:

X-ray/VUV Beam Time Requests due December 7: Please submit your requests for X-ray/VUV beam time for the February-May 2008 scheduling period.

Start your holiday shopping on your next visit to SSRL: When you check in for beam time, check out our Texas Orange t-shirts commemorating the first joint SSRL and LCLS users' conference. On sale now - just $10 - while supplies last. See Michelle Steger Bldg. 120, Rm. 219.


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: 3 DEC 2007
Content Owner: L. Dunn
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