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SSRL Headlines Vol. 6, No. 1  July, 2005


Contents of this Issue:

  1. Science Highlight — Elastic Gateway in Ion Channel Discovered
  2. Science Highlight — Old Wines in a New Barrel
  3. First Operation of a SPEAR3 Beam Line at 500 mA and Summer Shutdown Update
  4. NIGMS Announces Funding for Second Phase of Protein Structure Initiative
  5. SSRL Users' Organization Executive Committee Update
  6. Report from BES Program Review of SSRL
  7. Nominations for the Spicer Young Investigator Award and Lytle Award Due August 15
  8. Upcoming SR-Related Meetings, Conferences and Workshops at SLAC
  9. LCLS Science Team Leaders Meet at SSRL
  10. 25 Years of Pioneering Insertion Devices
  11. Promoting Synchrotron-Related Science

1.  Science Highlight — Elastic Gateway in Ion Channel Discovered
      (contact: Senyon Choe,

kir figure
Ion channels in our cells generate the nerve impulses that enable the heart to beat, the body to move, and sensation and thought to occur. Scientists from the Salk Institute for Biological Studies have identified a tiny flexible gateway that controls the rapid-fire opening and closing of a family of ion channels through which nerve-triggering potassium ions flow in and out of cells of the body. Malfunctions in the channels leads to several human diseases, including epilepsy, cardiac arrhythmias and muscle disorders. To pinpoint the parts of the ion channel structure that are important for it to function normally, Senyon Choe, Paul Slesinger and colleagues compared two types of "Kir" channels that have a unique closure device at one end that seems to control the movement of potassium in heart cells. Using painstaking detective work involving crystallography at SSRL, molecular biology and electrophysiology, the Salk team revealed that the closure device is formed from structures called G-loops that surround the "mouth" of the ion channel on the inside of the cell membrane. The researchers suspect that the G-loop complex operates like an elastic cuff that is closed in the resting position and expands to allow potassium ions out of the cell. The findings were published in the March 1, 2005 issue of Nature Neuroscience. Kir channels are important in medicine because they appear to have crucial roles in brain seizures including epilepsy, abnormal heart beats (heart arrhythmias), hyperactivity and developmental disorders. In 2001, researchers showed that Andersen's syndrome, a rare genetic disease involving cardiac arrhythmias, muscle paralysis and abnormal growth, is triggered by a mutation in the Kir2 channel.

To learn more about this research see:

2.  Science Highlight — Old Wines in a New Barrel
      (contacts: Stéphane Richard,; Joseph Noel,

Orf2 Figure
Using x-ray diffraction data collected on Beam Line 9-2 at SSRL, and other beam lines at the ESRF and BNL, scientists at The Salk Institute for Biological Studies discovered the three-dimensional structure of a protein that bacteria use to make biologically active compounds. By effectively engineering this protein, scientists may be able to create new drugs with therapeutic properties. The bacterial protein, known as Orf2, contains a previously unknown structure shaped like a barrel. "Looking at the protein's structure is like opening up a clock and understanding how all the parts fit together and work in unison," said Joseph Noel, co-author of a June 16 Nature publication on the research. Orf2 is one of a small number in a recently isolated family of proteins that create compounds with anti-microbial, anti-cancer, anti-viral, anti-inflammatory, and anti-oxidant properties. "We currently use the protein as a surrogate chemist, allowing it to catalyze chemical reactions that would be difficult or impossible to do with traditional chemistry," said Noel. This allows the researchers to slightly modify existing chemicals, which may lead them to discover new drugs. "We hope to use and engineer the protein to create novel compounds," said co-investigator Stéphane Richard.

To learn more about this research see:

3.   First Operation of a SPEAR3 Beam Line at 500 mA and Summer Shutdown Update
      (contact: Piero Pianetta,

During the July 18-19, 2005 Accelerator Physics period, a significant milestone towards operating beam lines at 500 mA was achieved. On Monday evening, SPEAR3 was successfully
SPEAR3 500mA first beam line operation
Screen Shot showing BL 6-2 open at 500 mA - click for large version
operated at 500 mA with all insertion device gaps closed for the first time. The following day, Beam Line 6-2, which was rebuilt for operation at high current last year, was opened and successfully operated at a current of 500 mA. Rocking curve measurements and radiation surveys were conducted on BL6-2 at 25, 100, 200, 300, 400, and 500 mA. These measurements were made using both the Si(111) and Si(333) reflections to observe any changes in the rocking curve widths due to power loading on the monochromator crystals. At 500 mA, the power on the first LN-cooled monochromator crystal was calculated to be 1580 Watts with a peak power density of 14.4 Watt/mm2. No major problems with the beam line optics were encountered and no concerns resulted from the radiation surveys. Overall, the monochromator performance was significantly better than anticipated from our modeling studies. We will continue to work on both the safety and operational aspects to enable 500 mA operations sometime during the 2006 run. Towards this effort our experimental run has been extended by one day to allow further machine studies for 500 mA operations.

Immediately following this final day of machine physics on August 1, summer shutdown activities will begin in earnest. During this shutdown, scheduled from August 2-November 28, 2005, significant beam line development and construction activities will be undertaken, including construction for the new BL12 alcove and associated chicane lattice installation and upgrades to BL10, BL9 and BL7. These beam lines will be available for users after upgrades and commissioning are completed. For BL10-1, BL10-2 and BL9-3, this is expected by mid-December 2005; BL9-1 and BL9-2 by January 2006. BL7-3 is expected to be available for users by February 2006, with BL7-1 and 7-2 a bit later in early 2006. A preliminary copy of 2006 user operations schedule can be found at:

Deadlines related to beam time requests and new proposals are also posted on the website:

4.   NIGMS Announces Funding for Second Phase of Protein Structure Initiative
      (contact: Ashley Deacon,

The National Institute of General Medical Sciences recently announced the funding for the second phase of the Protein Structure Initiative. Building on the successful pilot phase which was initiated in 2000, the new program will target larger numbers of proteins for structure determination and will also start to address more challenging classes of proteins. The program consists of four large-scale production-oriented structural genomics centers and six specialized centers which focus on technology development. SSRL and its scientific staff are involved in one Center of each type.

The Joint Center for Structural Genomics (directed by Ian Wilson, D.Phil., D.Sc., of The Scripps Research Institute in La Jolla, CA) has been funded as one of the large-scale centers. The Structure Determination Core of the JCSG, based at SSRL, will receive ~$15M over 5 years and is one of the principal activities of the JCSG. SSRL is also involved in the Center for High-Throughput Structural Biology (led by George DeTitta, Ph.D., Hauptman-Woodward Medical Research Institute, Buffalo, NY) whose funding was also announced as one of the specialized technology development centers. This center involves the collaborative efforts of the Hauptman-Woodward Institute, the University of Rochester, Cornell University, Stanford Synchrotron Radiation Laboratory, University of Washington, University of Pittsburgh, and Ontario Cancer Institute.

5.   SSRL Users' Organization Executive Committee Update
      (contacts: Glenn Waychunas, SSRLUOEC Chair,; Joy Andrews, SSRLUOEC Vice Chair,

The SSRL Users' Organization Executive Committee (SSRLUOEC) met on July 11. The agenda included an update from SSRL Director Keith Hodgson, a presentation on future scientific opportunities with SPEAR3 including pulsed beam for time structure experiments by Jo Stöhr, a preliminary discussion of top-up injection led by Bob Hettel, an update from Glenn Waychunas on user activism, plans for the next annual SSRL Users' Meeting by Joy Andrews, and an update on user outreach, communications, user administration by Cathy Knotts. Users are encouraged to nominate colleagues to serve on the SSRLUOEC (nominations due by September 30; ballots will then be issued and new representatives elected on October 17). Users are also encouraged to attend the annual Users' Meeting on October 17-18 and to participate in SSRLUOEC meetings; the next SSRLUOEC meeting will immediately follow the Users' Meeting on October 18. Minutes of SSRLUOEC meetings are posted on the user SSRLUO website:

6.   Report from BES Program Review of SSRL
      (contact: Keith Hodgson,

SSRL recently received a very positive report of the Department of Energy's Basic Energy Sciences (BES) review of SSRL that took place in February. Reviewers commented enthusiastically on the quality of the science and efficiency of the facility. In his cover letter, BES Scientific User Facilities Division Director Dr. Pedro Montano congratulated the SSRL staff "for the outstanding operation of SSRL," stating that "the SPEAR3 transition was a success," "the success of SPEAR3 upgrade is a major accomplishment," and that "SSRL is a well-run facility that adds real value to the research community." The review panel also noted several areas of concern including career development path for scientific staff. We would like to thank our users for their continued support of SSRL and the outstanding science that they produce, both factors in contributing to the excellence of this peer review.

7.   Nominations for the Spicer Young Investigator Award and Lytle Award Due August 15
      (contact: Cathy Knotts,

We encourage you to nominate individuals for the Spicer Young Investigator Award. The award was established in 2004 to honor Bill Spicer (1929-2004), one of the original founders of the Stanford Synchrotron Radiation Laboratory. This award recognizes important technical or scientific accomplishments that benefited from, or are beneficial to, the SSRL. The award is open to senior graduate students and those within seven years of entry into their professional scientific field. The award will consist of a certificate and $1,000 as well as waived registration and travel support to participate in the 2005 Annual SSRL Users' Meeting on October 17-18, when the award will be announced. Nominations in the form of a letter or email message summarizing the technical or scientific contributions of the candidate must be submitted before the August 15, 2005 deadline to Cathy Knotts. Nominations should include the candidate's curriculum vitae and publications; supporting letters are also encouraged.

Users are equally encouraged to nominate candidates for the 2005 Farrel W. Lytle Award which consists of a certificate and $1,000 (awardee names are added to a plaque displayed in the SSRL User Research Administration Office). All SSRL users and staff are eligible for this award. Nominations will be reviewed and the recipient selected by members of the SSRL Users' Organization Executive Committee. The Award will be presented at the Users' Meeting dinner on Monday, October 17, 2005. Nominations summarizing the individual's contributions and why they should be recognized through this award must be submitted before the August 15, 2005 deadline to Cathy Knotts.

8.   Upcoming SR-Related Meetings, Conferences and Workshops at SLAC

FEL2005: Over 200 scientists, engineers and managers of the FEL project teams
FEL Mtg Announcement
as well as prospective x-ray laser experimenters will participate in FEL2005, which will be held at the Frances C. Arrillaga Alumni Center at Stanford University on August 20-26, 2005. Program, registration and other details are available at the conference website:

SMB School
SSRL SMB Summer School: Apply by August 1 to participate in the SSRL Structural Molecular Biology Summer School on September 12-15, 2005. This school will highlight the use and applications of X-ray Absorption Spectroscopy (XAS) and Macromolecular Crystallography (MC) in the study of biological systems.

32nd Annual SSRL Users' Meeting: As mentioned above, SSRL's Users' Meeting will be held at SLAC on October 17-18, 2005. The meeting will feature sessions on x-ray absorption spectroscopy, structural genomics, ultrafast science and a sampling of materials research from other DOE labs. There will also be a young
Users Mtg Announcement
investigators session and a poster session, with awards for outstanding graduate student posters (the cost of the awards dinner will also be waived for graduate students participating in the poster competition). Several workshops will be offered in conjunction with the Users' Meeting including biological and materials small angle x-ray scattering, and soft x-ray science at LCLS. Details about the full list of workshops will be posted to the Users' Meeting site in the coming weeks.

9.   LCLS Science Team Leaders Meet at SSRL
      (contacts: John Arthur,; Jerry Hastings,

At the recommendation of the LCLS Scientific Advisory Committee (SAC), the community of scientists that last year submitted Letters of Intent to develop programs at LCLS has been organized into groups reflecting the five Science Thrust Areas which encompass the range of proposed LCLS science. Each of these five groups has selected a Team Leader and one or more Co-Team Leaders, who will work closely with LCLS and LUSI staff to make sure that LCLS will be able to best address the Science Thrust Areas.

The Science Team Leaders have agreed to meet quarterly at SSRL to discuss LCLS and LUSI issues. The most recent meeting took place on June 29-30. At this meeting the Team leaders received an update on LCLS progress and plans for LUSI. They discussed the intricate relationships between LCLS, LUSI, SSRL, and the Science Teams, and the roles that each will play in developing the unique science capability of LCLS. All agreed that open and timely communication between all parties will be the key to building a successful facility, and that the primary responsibility for enabling this communication lies within the LUSI project.

The next meeting of the Science Team Leaders will take place October 18-19, immediately after the SSRL Users' Meeting.

10.   25 Years of Pioneering Insertion Devices
        (contact: Herman Winick,

To mark the 25th anniversary of the first permanent magnet undulator to be used for synchrotron radiation research (implemented at SSRL in collaboration with LBNL), some of those who contributed to the design, construction and
From Left: Boyce, Yang, Winick, Hoyer and Chin with 
characterization gathered recently around the magnet itself, which is on display on the SSRL experimental floor. The concept for this magnet was the brainchild of Klaus Halbach (1925-2000) of LBNL. The mechanical design was done by LBNL engineers Egon Hoyer and John Chin, now retired. The electronic controls for varying the gap and compensating the end fields were done by John Yang, who recently retired from SSRL. The spectrum from this device was characterized by George Brown (former SSRL Faculty), Teresa Troxel, and Herman Winick of SSRL along with Zahid Hussain and Eberhard Umbach at LBNL. Due to the success of these devices, many third generation synchrotron radiation sources were built starting in the late 1980's (the latest of these is the SPEAR3 storage ring at SSRL/SLAC).

11.   Promoting Synchrotron-Related Science

Ongoing communication about the benefits that research involving synchrotron radiation may ultimately provide is vitally important to SSRL and the other synchrotron light sources. With your help we can be far more effective in communicating the importance of SR-related science in general and your research in particular. We are always interested in receiving input on published papers and theses that are based at least in part on work done at SSRL. Please see for publications lists and appropriate acknowledgement statements for SSRL and our funding facilities. We especially encourage you to let us know in advance of publishing breakthrough research results (contact Cathy Knotts,, 650-926-3191). Moreover, whenever your institution puts out a press release on your synchrotron-related research, it will be tremendously helpful if some mention of the light source(s) that you collected data at is included. This will give SR-based research more visibility and the press release will likely be posted to, but again - please let us know in advance of the release date. We look forward to working with users and their home institutions to promote user research to a broader audience.

You can keep up to date with news related to light-source research and developments from around the globe by signing up for the News Flash feature at See to subscribe.


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: 31 JUL 2005
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