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SSRL Headlines Vol. 5, No. 2  August, 2004


Contents of this Issue:

  1. Science Highlight — Resurrecting the Dead and the Deadly
  2. Science Highlight — Understanding the Role of Thiolate Ligation in Nature's Hydroxylating Heme Enzymes
  3. SPEAR3 Receives DOE Excellence in Project Acquisition Award
  4. SSRLUOEC and SSRL Plan Annual Users' Meeting and Workshops, October 20-26
  5. LCLS Division Formed at SLAC
  6. Report on the ICFA Future Light Sources Subpanel on XFEL Short Bunch Measurement and Timing
  7. Educating Scientists in the Use of SR Techniques - the SMB 2004 Summer School
  8. SSRL Proposal Review Panel and NIH SMB Advisory Committee Meetings
  9. User Research Administration Announcements

1.  Science Highlight — Resurrecting the Dead and the Deadly
      (contact: Ian A. Wilson, )

Researchers have literally unearthed clues as to why the 1918 influenza pandemic was so deadly. The 1918 influenza pandemic ranks as the largest and most destructive outbreak of an infectious disease, killing 20 to 40 million people worldwide. Using fragments of the flu genome from Alaskan victims preserved by permafrost and army autopsy tissues, James Stevens and Ian Wilson of the Scripps Research Institute in La Jolla, California and their collaborators have assembled genes from the 1918 flu virus.

The Scripps researchers then cloned, expressed and crystallized the viral protein, called hemagglutinin (HA) and utilized SSRL's macromolecular crystallography beam lines to reveal the coils, stalks and heads that make up HA's structure. The intricate structure helps explain why the 1918 flu virus was unusually virulent. HA is the most abundant protein on the virus's surface and as such is the main target for the immune system to try to defend against infection. For the virus, HA is also very important because it binds to human lung cells and enables the virus to get internalized into the cell inside sacs called vesicles. Once inside, HA changes shape to help the viral membrane fuse to the vesicle membrane allowing for infection to proceed. While 1918 HA appeared to be at the base of the evolutionary tree of human viruses, its structural analysis shows that it is actually more closely related to avian (bird) forms.

Two features of the structure particularly stand out in potentially contributing to the extraordinarily high infectivity and mortality rates observed in 1918. The receptor binding site (for the virus to attach to human cells) is narrow and is only a single mutation away from a known swine-avian virus. The mutation makes the binding site slightly larger, which could increase affinity for human cells. The researchers also observed two previously unseen basic patches (histidine rich) which may boost HA infectivity when it fuses to the vesicle membrane in order to escape and replicate itself inside human cells. One of the patches is found only in avian forms of HA, "providing tantalizing evidence of a direct jump of this virus from birds to the human na´ve population," said the researchers. To learn more about this recent article in Science, see: html or

2.  Science Highlight — Understanding the Role of Thiolate Ligation in Nature's Hydroxylating Heme Enzymes
      (contact: Michael T. Green,

Chloroperoxidase is one of a large class of heme proteins that play important roles in a number of physiological processes, including xenobiotic metabolism, neurological development, blood pressure control, and immune defense. These heme protein systems all have the ability to oxygenate saturated hydrocarbons under ambient conditions, a process which is chemically quite challenging, and hence is also of industrial importance. Recently, extended x-ray absorption fine structure (EXAFS) spectroscopy experiments conducted at SSRL by Michael Green (Pennsylvania State University) and his coworkers have been used to provide the first structural characterization of the oxygen intermediate of chloroperoxidase. The results demonstrate that the intermediate is a protonated ferryl species, which is in contrast to the widely accepted porphyrin-radical cation model. These results have important implications for understanding the mechanism of numerous heme enzymes, and EXAFS is one of the only methods that could provide this type of structural information on the intermediate. To learn more about this recent article in Science, see: html or

3.  SPEAR3 Receives DOE Excellence in Project Acquisition Award
       (contact: Keith Hodgson,

The SPEAR3 project management team was awarded the Excellence in Acquisition Award by DOE Secretary Abraham at the Fourth Annual DOE Project Management Awards ceremony on Friday, August 13, in Washington, D.C. The Annual Project Management Awards pay tribute to those teams who have achieved outstanding results through resourceful, innovative thinking and implementation. Tom Elioff, Bob Hettel, Richard Boyce and Hanley Lee traveled to Washington D.C. to accept the award but were quick to praise the staff back at home for their help in seeing the project through to completion. According to Boyce, "The entire SPEAR3 project team deserves credit for the successful culmination of 4 years of intense effort and dedication which resulted in the remarkable accomplishment of meeting the extremely tight installation schedule and exceeding our first beam-to-users goal." SPEAR3 was a project jointly funded by DOE and NIH with DOE providing the management oversight and review. For more information see:

4.  SSRLUOEC and SSRL Plan Annual Users' Meeting and Workshops, October 20-26

On July 30, the SSRL Users' Organization Executive Committee (SSRLUOEC) met with SSRL management to discuss a number of topics, including planning the 2004 Users' Meeting. The 31st Annual SSRL Users' Meeting on October 20-22 will feature presentations to help users incorporate new technology and make the most of SPEAR3 beam time as well as sessions on spectroscopy, scattering and diffraction; reports from SSRL staff and young investigators; and a special session on the history and future of photoemission in memory of W. E. Spicer.
Please register at: http://www-

Users are encouraged to submit abstracts for poster presentations by September 24. Graduate students, in particular, are encouraged to participate in the meeting and in the graduate student poster competition. Registration fees are significantly discounted for students, and the cost to attend the awards dinner will be waived for students submitting posters.

Three concurrent workshops will be held before the annual Users' Meeting on Wednesday, October 20, 2004:
  1. Modern Valence Band Photoemission Spectroscopy - A Legacy of W. E. Spicer and a Powerful Tool for Materials
  2. High Throughput Screening/Macromolecular Crystallography
  3. Experimental Methods of X-ray Scattering Workshop
A Workshop in Ultrafast Science and LCLS Experiments at SSRL is being planned for October 25-26, 2004. The workshop will begin with a joint session on Monday morning followed by breakout sessions for each of the five thrust areas chosen for the first phase of the LCLS science program on Monday afternoon and Tuesday morning.
  • Atomic, molecular and optical physics
  • High energy density states of matter
  • Optical pump-x-ray probe studies in chemistry, biology and materials science
  • Diffraction imaging of single objects approaching atomic scale resolution
  • Coherent x-ray scattering for the study of dynamics (X-ray photon correlation spectroscopy)
The workshop will end with a joint session on Tuesday afternoon. The workshop will focus on the scientific goals and technical needs as well as experimental specifications. This workshop is open to all users (and potential future users interested in learning more about how to participate in LCLS and utilize this new technology).

Nominations for the 2004 Farrel W. Lytle Award are due before September 10. The Lytle Award is presented annually at the Users' Meeting to recognize important technical or scientific accomplishments in synchrotron radiation-based science and to foster collaboration and efficient use of beam time among users and staff at the Stanford Synchrotron Radiation Laboratory (SSRL).

Nominations for the SSRL Users' Organization Executive Committee Election are due before September 24. Users are encouraged to nominate candidates for the 7 vacancies in 2005; ballots will be prepared and circulated electronically in late September, and the election results will be announced at the Users' Meeting awards dinner on Thursday, October 21.

For more details regarding the upcoming Users' Meeting see:

5.  LCLS Division Formed at SLAC
       (contacts: John Galayda,

To construct the world's first x-ray free electron laser, SLAC has created a new Linac Coherent Light Source (LCLS) Division and named John Galayda as its Associate Director. After three years of planning the LCLS facility in collaboration with scientists at UCLA, LANL, LLNL, ANL and BNL, Galayda will oversee the construction phase, guiding the project's growth from the drawing board into a new national user facility. The LCLS Division will operate alongside the existing divisions at SLAC from initial setup and equipment procurements in 2004-2005 through construction in 2005-2008. If all goes as scheduled and the system is brought online in 2009, users from around the world may apply to perform experiments using this new x-ray source. It is anticipated that user access will utilize the general user model pioneered by SSRL on SPEAR. An initial set of instruments is currently being defined (see item 4. above). The LCLS is a technology with unprecedented potential that will push into new experimental frontiers.

However, before the LCLS comes online there have been, and will continue to be, reviews and approvals along the way to keep the project on track. A second DOE construction management (Lehman) review was held August 10-12, with the purpose of reviewing all aspects of the project's design and long-lead procurement plans - technical, conventional construction, cost, schedule, management, and ES&H to determine the project's readiness for Critical Decision 2b (CD-2b, Approve Performance Baseline) and CD-3a (Approve Start of Long-Lead Procurement). Comments made at the closeout session were very favorable; the reviewers were impressed with the progress made thus far and had relatively minimal concerns. Dr. Patricia Dehmer, DOE Associate Director for BES, indicated that there is very strong support in Washington to ensure the on time and successful completion of the LCLS. For more information on the LCLS see:

6.  Report on the ICFA Future Light Sources Subpanel on XFEL Short Bunch Measurement and Timing
       (contact: Jerry Hastings,

The ICFA Future Light Sources Subpanel has sponsored a number of workshops focusing on accelerator issues critical to the development of free electron lasers that will operate in the hard x-ray regime. The LCLS has jointly organized several of these with the European XFEL project centered at DESY in Hamburg Germany. The most recent present workshop held July 26-30 focused on issues that will be critical to the optimal utilization of the short pulses (~ 100 fs) that these machines will deliver: measurement of the electron and photon bunch lengths and the timing systems for the accelerator and the synchronization of experimental lasers to the FEL photon beam. Approximately 50 participants from all over the world gathered at SLAC for the 5-day event.

The program allowed significant time for discussion and also featured highlight presentations which included new ideas for distributed timing systems based on using lasers and optical fibers as compared to conventional coaxial distribution systems based on quartz crystal oscillators as the master clock. There was also focus on electron beam bunch length diagnostics where electro-optic sampling at the SPPS facility at SLAC has recently demonstrated time resolution below 300 fs, with the clear possibility of extending this down to ~ 50 fs. Also discussed were ideas of using the x-ray photon beam to excite carriers in semiconductors and inserting this material as an active element in a laser interferometer. The discussion on these issues was lively.

Further details of the workshop can be found at:

7.  Educating Scientists in the Use of SR Techniques - the SMB 2004 Summer School
       (contact: Serena DeBeer George,

The fourth in a series of structural molecular biology (SMB) summer schools was held at SSRL August 16-20. The school focused on the following synchrotron-based techniques: x-ray absorption spectroscopy, small angle x-ray scattering, and macromolecular crystallography, and the application of these techniques to biological problems. The summer school opened with introductory talks on synchrotron radiation and beam line optics. Three days of lectures followed, providing an introduction to each of the three techniques, as well as covering basic theory, experimental considerations, and applications. The lecture portion was followed by a day and a half of rotating practical sessions, giving the students hands-on experience in data collection and analysis. This year's summer school was attended by 23 students and was led by a team of 18 tutors (all of whom are recognized experts in their field). The lectures and practical sessions were enthusiastically received by the participants, and we hope to build on the success of this year's summer school to make next year's an even bigger success.

8.  SSRL Proposal Review Panel and NIH SMB Advisory Committee Meetings
       (contacts: Keith Hodgson,; Britt Hedman,

The Proposal Review Panel (PRP) met for the 56th time July 30-31, 2004. The PRP plays a critical role in the peer-reviewed proposal process as well as providing strategic advice and guidance on SSRL's programs and long-range planning. Several presentations were made during this meeting including: SSRL Director's Report (Keith Hodgson), Beam Line/Operations Update (Britt Hedman, Piero Pianetta), SSRLUO Executive Committee Report (Benjamin Bostick), User Administration (Cathy Knotts), and LCLS (John Galayda). The PRP reviewed 22 new proposals and considered a number of proposal extension requests. At the closing session on Saturday, PRP Chair Russ Chianelli (UTEP) recognized the outstanding results related to the SPEAR3 upgrade, beam line development, and user support. The SSRL NIH Structural Molecular Biology Advisory Committee also met on Saturday, July 31, to review activities and discuss strategies for the future.

9.  User Research Administration Announcements
       (contacts: Cathy Knotts,; Lisa Dunn,

New Proposals Due November 1 (X-ray/VUV) and December (MC): If your current proposal is getting close to its expiration date or if you are planning to conduct new experiments, consider submitting a new X-ray and VUV proposal by the November 1, 2004 deadline or a new Macromolecular Crystallography proposal by the December 1, 2004 deadline. Proposals submitted by these dates will be peer reviewed, rated, and eligible for beam time in spring 2005. For more information of the proposal submittal, review and scheduling process, visit:


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 AUG 2004
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