Previous Editions__________________________________________________________________________SSRL Headlines Vol. 10, No. 4 October, 2009__________________________________________________________________________
Contents of this Issue:
All of the biologically produced methane comes from methanogenic archaea
bacteria. These methanogens produce methane using an enzyme called
methyl-coenzyme M reductase. MCR's complex reaction requires a reduced nickel
cofactor in the enzyme's active site. Researchers have proposed two competing
theories of the enzyme's mechanism that differ in the chemistry of the first
step of the reaction.
A group of researchers led by SSRL's Ritimukta Sarangi used Beam Line 9-3 to
acquire structural information for the MCR's reaction intermediates to
determine which mechanistic theory is correct. Overcoming difficulties due to
MCR's sensitivity to oxygen, the researchers used a combination of Ni K-edge
x-ray absorption spectroscopic (XAS) studies and density functional theory
(DFT) calculations to find the electronic and geometric properties of various
enzyme-intermediate complexes.
Through these experiments, the researchers identified which of the proposed
mechanistic theories is correct. They also found that certain traits of the
nickel cofactor help stabilize the potentially unstable reaction intermediates.
This work was published in the April issue of the journal Biochemistry.
User Operations resumed at SSRL this week following our annual three-month
shutdown period. The shutdown was carefully orchestrated to complete concurrent
and tightly scheduled back-to-back projects both safely and on time. Our thanks
to the many people who have worked tremendously hard to ensure the success of
these updates to the SPEAR3 storage ring, the beam lines and the facility in
general.
A test of 200 milliamp operations occurred during the final two weeks of the
FY2009 experimental run and we have approval to continue operating at that
current during the fall portion of our FY2010 run. To further our goal of
achieving an optimal blend of higher current, beam stability and quality user
data, tests will be conducted at currents up to 500 milliamps during scheduled
accelerator physics periods this fall when SSRL users are not collecting data.
During these AP periods, SSRL staff will characterize beam line performance and
run experiments with control samples to better understand any changes that
occur as the intensity is increased. At the same time, Radiation Protection
staff will conduct careful radiological surveys of the beam line shielding to
ensure safe operations at the elevated current.
In the words of SSRL Acting Director Piero Pianetta, "With the completion of
the SPEAR3 Beam Line Upgrade project in 2009, we are back to our full
complement of 25 fully operational beam lines with two more that will be
brought into operation during the coming year. These additional beam lines will
enable us to increase the number of users who can to perform science at SSRL
and help alleviate some of the oversubscription rates that we have been
experiencing over the past several years.
The large number of users who will cycle through SSRL on a daily basis to
conduct more than 500 experiments during the first scheduling period alone,
present a challenge to ensure that the work is properly planned and that
hazards are identified and mitigated. Starting this past year, we have worked
to improve the SSRL user processes to make sure they are well aligned to Work
Planning and Control. For the coming run we will implement a process that will
provide additional pre-run oversight to our users in an effort to help identify
any hazards that might have otherwise slipped through the cracks. In addition,
we have added personal protective equipment, or PPE, stations at strategic
places around the lab and at each beam line so that safety glasses, gloves,
sharps containers etc. are readily available.
I am looking forward to a safe and productive run in FY2010 as well as working
hard with users and staff to identify opportunities that will bring new and
exciting programs to the laboratory".
see operating and beam line schedules at:
The SSRL/LCLS Users' Meeting and Workshops wrapped up on Thursday, October 22.
More than 250 participants from around the world attended the activities over
the 5-day event, which updated users on facility capabilities and performance
at SLAC, highlighting 35 years of fantastic research at the Stanford
Synchrotron Radiation Lightsource, the start of commissioning-with-user science
at Linac Coherent Light Source and the importance of user safety while using
SLAC x-ray facilities.
"The SSRL/LCLS Users' Meeting and Workshops is a way to get users to come
together and talk about what they are doing," said SLAC physicist Sebastien
Boutet, one of the program chairs for the event.
The event launched with a pre-meeting symposium on Sunday, October 18,
"Advances in Lightsource Science-Past, Present and Future," in honor of SLAC
Photon Science and Stanford Applied Physics Professor Sebastian Doniach, who
served as the founding Director of the Stanford Synchrotron Radiation
Lightsource (then called the Stanford Synchrotron Radiation Project).
Thirty-five years later, SSRL continues to produce fantastic results (see
article 4 below).
After the Monday morning overview talks, the presentations moved to more
specific presentations by SSRL and LCLS users. "The scientific talks are
highlights of what users have achieved during the past year," said SSRL Senior
Staff Scientist and meeting co-organizer Donghui Lu. Two such talks were given
by Yulin Chen, who at the meeting received the Spicer Award for his work in
material sciences on topological insulators; and Leslie Jimison who accepted
the Klein Award for her materials science research on semiconducting polymers.
see also SLAC Today article at:
Doniach was one of the key players in adapting SLAC's SPEAR ring for use as a
light source, and from 1973 to 1977 served as the first Director of SSRL.
According to the event organizer, Prof. Aharon Kapitulnik, Stanford, Doniach
also made important contributions in condensed matter physics, superconductors
and biophysics.
The symposium, titled "Advances in Light Source Science-Past, Present and
Future," covered a similarly wide range of topics. Nine presenters from around
the world gave talks on everything from the Doniach Phase Diagram-an important
model in condensed matter physics-to the role of physics in biology and
medicine.
"Seb is a real pioneer," Kapitulnik said. "The symposium provided a great
opportunity to honor him."
The SSRL Users' Organization Executive Committee (SSRLUOEC) met on October 20
immediately following the annual Users' Meeting. Newly elected representatives
to the 2009-10 SSRLUOEC were announced during the Tuesday morning session by
incoming chair Katherine Kantardjieff (CSU Fullerton) and again at the SSRLUOEC
meeting for anyone who may have missed the earlier announcement. New members
include: Junko Yano (LBNL) representing Bio Spectroscopy/Bio SAXS; David Singer
(UC Berkeley/LBNL) for Environmental/Geoscience; Matthew Sazinsky (Pomona
College) for Macromolecular Crystallography; Aaron Lindenberg (Stanford
University) for Ultrafast Science; R. Joseph Kline (NIST) for Materials Science
and Leslie Jimison (Stanford University) as
a graduate student representative. The next SSRLUOEC meeting will be scheduled
soon and users are invited to participate to discuss any issues or suggestions
they have. Information on SSRLUOEC members and activities are posted at:
http://www-ssrl.slac.stanford.edu/userresources/ssrluo/ssrluo.html
Researchers at the Stanford Synchrotron Radiation Lightsource have helped
resolve the structures of 73 proteins involved in the metabolic processes of
Thermotoga maritima, a heat-loving bacterium found in deep-sea thermal
vents.
The work is part of a larger study conducted by the Joint Center for Structural
Genomics and collaborators to reconstruct the organism's central metabolic
network-a complex system that encompasses more than 478 different proteins.
Published in the September 18 issue of Science, the study is the most
comprehensive of its kind ever completed. The results could help explain how
metabolic networks evolve, and could help drive further research in both
medicine and energy science.
After screening the samples, researchers used the SSRL protein crystallography
beam to create x-ray diffraction patterns of the crystallized proteins.
Analyzing the patterns, they were able to determine each protein's
three-dimensional structure. Researchers at the Burnham Institute for Medical
Research then combined the SSRL data with 358 protein structures determined
using computer modeling techniques, creating a map of how the different
proteins interact with other molecules.
"We have complete coverage for all the pathways that perform all of the
organism's essential functions," said SSRL Senior Staff Scientist Ashley
Deacon, core leader for the JCSG Structure Determination Core. Read more at:
Winick, who is Assistant Director Emeritus at SSRL and Professor Emeritus in
the Applied Physics and SLAC Photon Science Departments at Stanford University,
will receive the prize February 14 at the American Physical Society's general
meeting in Washington, D.C. He will share the award with City College of New
York physicist Joseph Birman and National Science Foundation Elementary
Particle Physics Program Director Moishe Pripstein.
The award is named for Andrei Sakharov, a Russian physicist and Nobel laureate
who campaigned extensively against nuclear proliferation in the former Soviet
Union. The prize was first given in 2006 to Cornell University physicist and
Soviet exile Yuri Orlov, who, in the 1970s and 80s, was imprisoned and
subsequently deported for criticizing human rights violations by the Soviet
government.
"It is humbling to get a prize for which the previous winners were such
incredible people, who took such serious risks and endured such serious
punishments," Winick said. "Here I am in a free country, speaking my mind and
trying to help these people with no thought of repercussions against me." Read
more at:
X-ray/VUV Beam Time requests for the February-May 2010 scheduling period are
due by November 15. Log into the User Portal to submit requests.
December 1 is the next deadline for submitting new X-ray, VUV and
Macromolecular Crystallography standard proposals. For more information on
proposal deadlines, instructions, and forms see:
Time is reserved on many beam lines for rapid access proposals. A full listing
of the Rapid Access applications is available at:
It is with sadness that we report that Peter Boyd, owner of Boyd Technologies
and a former SSRL duty operator, passed away last month. Peter was a well-liked
duty operator at SSRL in the 1990's who often used his excellent machining
skills to help many users with sample holders and modifications. He
subsequently left SSRL to start his own business machining a variety of sample
holders, tools and ion chambers for synchrotron beam x-ray absorption and
scattering experiments with customers at both SSRL and the ALS. We are saddened
by his death and will miss him. For those of you who remember Peter,
condolences can be sent to MaryBeth Boyd at Boyd Technologies, PO Box 95,
Manchester, CA 95459.
It is extremely important that users not only inform us whenever work conducted
at SSRL results in a publication, but also acknowledge SSRL and our funding
agencies in each publication. User help is needed to keep current records on
publications including refereed journal papers, conference proceedings, book
chapters and theses, invited lectures and major awards and patents based at
least in part on work conducted at SSRL. This information allows SSRL to
demonstrate scientific achievements and productivity when responding to
requests sent out by the Department of Energy and the National Institutes of
Health.
This information can be submitted anytime via email message to Lisa Dunn or
Cathy Knotts or via the reference submission form at:
For recent publications lists and the proper acknowledgement statements see:
__________________________________________________________________________
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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