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SSRL Headlines Vol. 6, No. 11 June, 2006
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Contents of this Issue:
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1. Science Highlight —
Chemists Discover how Nature Makes Medicine
(contact:
C.L. Drennan, cdrennan@mit.edu)
After years of wondering how organisms managed to create medically valuable
natural products, like antibiotics and anti-fungal agents, chemists have
discovered the surprisingly simple secret by shining x-ray light on the
problem. MIT and Harvard researchers used crystallography beam lines at the
Stanford Synchrotron Radiation Laboratory and the Advanced Light Source in
Berkeley for their research.
They determined the atomic structure of an iron-dependent halogenase, the
enzyme SyrB2, from the plant pathogen Pseudomonas syringae. This enzyme
catalyzes the chlorination of threonine during biosynthesis of the anti-fungal
agent syringomycin, a natural-product antibiotic. This provides one example of
how an enzyme can coax a reaction to generate medically valuable halogenated
natural products. The products include antibiotics, anti-tumor agents and
fungicides, and they are challenging to synthesize in a laboratory. The
crystallography study revealed in this case how the specific structure at the
iron-containing active site of the enzyme (the site responsible for the
chemical reaction) provides information that can help in understanding how the
chemical process takes place.
|
| Crystal structure of the non-heme iron halogenase
SyrB2. |
The structure revealed a novel coordination for iron that contains a chloride
ion together with two histidine amino acids, a deviation from the way an iron
atom is normally held in an enzyme's active site of this kind in that it does
not contain a carboxylate-containing amino acid. The position of the
surrounding amino acids indicate that the structure has more room at the active
site, enough space for the chloride to enter and bind to the iron as part of
the chemical reaction.
"Now that we have the enzyme's structure and figured out how it works, it makes
sense. But it's not what we would have predicted," said Catherine Drennan of
MIT. "Things are usually not this simple, but there's an elegant beauty in this
simplicity," one that might help chemistry labs gain the enzyme's capabilities.
To learn more about this research see the full technical highlight at:
http://www-ssrl.slac.stanford.edu/research/highlights_archive/SyrB2.html
2. Science Highlight —
Protecting against DNA Invasion
(contact:
G. Balendiran, gbalendiran@coh.org)
| | 
|
| |
Dimer of C.BclI structure.
| |
X-ray studies conducted at SSRL have shed light on a sword-and-shield type of
defense used by bacteria to protect themselves from viral attacks. This new
knowledge could prove significant to medical research on human cancers caused
by a similar defense mechanism gone awry.
Researchers from the City of Hope cancer research and treatment center in
Duarte, California, determined the crystal structure of the protein that
controls this defense system in bacteria called Bacillus
caldolyticus. Unless
stopped, viral DNA slips into bacterial DNA, where it gets copied many times
over, and then destroys its host. To protect bacterial cells, the control
protein ensures the proper ratio between two enzymes, the "swords" and the
"shields." The sword enzyme slashes invading viral DNA into useless pieces. The
shield enzyme adds a protective layer to bacterial DNA, so the sword will not
cut its master. Too few shields lead to bacterial cell death, and too many
shields protect the viral DNA as well.
The crystal structure of the control protein uncovers the presence of a
helix-turn-helix (HTH) motif which has the potential to bend B-DNA. The
structural study also revealed amino acid residues that are most likely
involved in the DNA interaction. The proposed model suggests that the protein
adjusts the levels of the defense enzymes (swords and shields) by sliding along
the bacterial DNA, bending and changing its shape to turn on or off the
respective genes.
To learn more about this research see the full technical highlight at:
http://www-ssrl.slac.stanford.edu/research/highlights_archive/cbcli.html
3.
SPEAR3 Fast Orbit Feedback Milestone Achieved in June
(contact:
R. Hettel, hettel@slac.stanford.edu)
On June 14, the SSRL Accelerator Systems Department commissioned an improved
system designed to stabilize electron beam orbit in a frequency bandwidth
approaching 100 Hz. The Fast Orbit Feedback System replaces the slower
version, which corrects the orbit every few seconds, and that has been in use
since SPEAR3 became operational. The new system acquires electron orbit and
photon beam position data and updates the orbit correction magnets at a 4 kHz
rate using a high speed distributed processing network. The system is
effective in suppressing beam motion up to a few 10s of Hz caused by magnet
support girder vibration, traffic near the SPEAR3 complex, and, most notably,
disturbances arising from user-controlled insertion device changes. Work is
continuing to improve and optimize fast orbit feedback performance.
4. Register for SSRL Summer Workshops in the
Structural Biology Sciences
July 28-30, 2006: Workshop on Small-Angle X-ray Scattering and Diffraction
Studies in Structural Biology. Organized by Hiro Tsuruta, Thomas Weiss and
Marc Niebuhr (SSRL), this workshop will provide hands-on training on
experimental techniques, software tutorial sessions primarily for solution
x-ray scattering studies, and talks on recent applications. Several shifts of
beam time have been allocated for short periods of data collection by workshop
participants. Register at:
http://www-ssrl.slac.stanford.edu/conferences/workshops/saxs2006/index.php
August 4, 2006: SSRL Crystallography Remote Access Workshop. There are still a
few slots remaining for this workshop which will be held at the
Hauptman-Woodward Medical Research Institute in Buffalo, NY on August 4.
Organizers Aina Cohen and Clyde Smith (SSRL), and Edward Snell (HWI) are
planning an agenda that will start with lectures and a live demonstration of
remote access data collection followed by two hands-on training sessions.
Attendees will learn about the beam line and software developments and how to
successfully complete all stages of a remote access experiment.
For more information and to register see:
http://smb.slac.stanford.edu/public/news/workshops/SSRL-HWI-2006/
5. Call for Nominations for Klein, Spicer and
Lytle Awards
Please take a few moments to consider nominating your colleagues for one or
more of the following awards which will be presented at the 33rd Annual SSRL
Users' Meeting, October 12-13, 2006:
- Klein Professional Development Award due August 1
- Spicer Young Investigator Award due August 1
- Lytle Award due August 15
Earlier this year, the SSRL Users' Organization Executive Committee (SSRLUOEC)
established a Scientific Development Award to honor Melvin P. Klein
(1921-2000), a pioneer at the forefront of accomplishments in NMR, EPR, and
x-ray absorption spectroscopy who was dedicated to the pursuit of the structure
of the Mn complex characterized by the interplay of these methods. The Melvin
P. Klein Scientific Development Award will be given to an undergraduate or
graduate student to disseminate scientific results based on work performed at
SSRL. The award (up to $1,000) will reimburse a student to present their work
at a scientific conference during the following year. The recipient will be
selected by a user subcommittee based on a nomination package which should
include a letter of recommendation from the advisor; an abstract written by the
candidate describing the experiment and scientific results (not to exceed 300
words); and information on when and where the work is to be presented.
Nominations must be received by August 1. Additional instructions and
information on making a donation toward this award are available at:
http://www-ssrl.slac.stanford.edu/kleinaward.html
Submit nominations for the William E. Spicer Young Investigator Award by August
1. The Spicer Award was established in 2004 to honor Bill Spicer (1929-2004),
one of the original founders of the Stanford Synchrotron Radiation Project.
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 PhDs within seven years of entry into their professional
scientific field. The award consists of a certificate and $1,000 as well as
waived registration and travel support to make a presentation at SSRL33 on
October 12-13. Nominations in the form of a letter or email summarizing the
technical or scientific contributions of the candidate must be sent to Cathy
Knotts (knotts@slac.stanford.edu) before August 1. Nominations should include
the candidate's CV and publications; supporting letters are also encouraged.
http://www-ssrl.slac.stanford.edu/spiceraward.html
Submit nominations for 2006 Farrel W. Lytle Award by August 15. The Lytle Award
was established by the SSRLUOEC to promote 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 SSRL. The
award consists of a certificate and $1,000. All SSRL users and staff are
eligible for this award. The recipient will be selected by the SSRLUOEC, and
the award will be presented at the SSRL33 awards dinner on Thursday, October
12, 2006. Nominations summarizing the individual's contributions and why they
should be recognized through this award must be sent before the August 15
deadline to Cathy Knotts (knotts@slac.stanford.edu):
http://www-ssrl.slac.stanford.edu/lytleaward.html
6.
Stanford Board of Trustees Committee Visits SLAC
 |
| Tour Stop at BL 11-1 |
The Committee on
Academic Policy, Planning and Management of the Stanford Board
of Trustees visited SLAC on Wednesday, June 14. After hearing an overview of
the SLAC scientific program by SLAC Director Jonathan Dorfan and remarks by
KIPAC Director Roger Blandford on the Particle Astrophysics and Cosmology
Program, they toured the site, including brief stops at three SSRL beam lines
where they heard from Keith Hodgson, Jennifer Leisch and Gordon Brown about the
role of synchrotron-related science in pharmaceutical drug discovery, research
towards a hydrogen economy and efforts aimed at restoring our polluted
environment, respectively.
7.
Secretary of Energy Bodman Speaks to DOE Employees
 |
| Secretary Bodman |
On Wednesday, June 14, Department of Energy Secretary Samuel Bodman reached out
to all 116,000 Department of Energy (DOE) federal and contractor employees via
live broadcast to express his appreciation for the work behind a number of
remarkable DOE achievements over the past year and to discuss future challenges
and opportunities within the organization. Secretary Bodman also stressed the
importance of a safe workplace. For a full transcript of his remarks see:
http://today.slac.stanford.edu/a/2006/06-16.htm
8.
Summer Public Science Lectures at SLAC and Stanford University
 |
|
The Thinker, 1880-1881. Promised gift to the Iris & B. Gerald
Cantor Center for Visual Arts at Stanford University |
Kavli Institute for Particle Astrophysics and Cosmology (KIPAC) astrophysicist
Sarah Church will give a SLAC public lecture, "Whispers of the Big Bang", on
Tuesday, June 27, at 7:30 p.m. in the SLAC Panofsky Auditorium.
http://today.slac.stanford.edu/a/2006/06-16.htm
On Tuesday, August 29, Sean Brennan (SSRL) will give the next lecture in the
series on "A Comet on Earth: Results from the Stardust Mission."
Uwe Bergmann (SSRL) will give a talk titled "Archimedes: Ancient Text Revealed
with X-ray Vision on Thursday, August 3, as part of a series of outdoor science
lectures held this summer at the Stanford Cantor Arts Center. Parking, museum
entrance and lectures are free. Visitors can explore the Cantor Center starting
at 5 p.m. and then migrate outside to hear scientists talk in lay terms about
their research starting at 7 p.m. For the full schedule and directions see:
http://news-service.stanford.edu/news/2006/june21/summer-062106.html
http://museum.stanford.edu/visit/visit_MapDirections.html
9.
More SSRL News for a Wider Audience
Several months ago, SLAC began distributing an electronic daily newsletter,
SLAC Today. With additional communications staff, we are able to feature more
articles about SSRL activities written for the general public in SLAC Today as
well as in this monthly newsletter. See the following for some of the more
recent articles. To subscribe to SLAC Today, visit
http://today.slac.stanford.edu/subscribe.asp
 |
| Beam Line 7-2
monochromator. |
Cool Running for SSRL. As SSRL prepares to turn up the juice to 500 mA,
engineers are busily upgrading components to handle the increased power. Key
among these components are the monochromators, devices that allow researchers
to fine-tune the x-ray beams to the needs of the experiment. Read more at
http://today.slac.stanford.edu/feature/monochromators.asp
Why the Aluminum Foil? Perhaps you've noticed that physicists seem to love
aluminum foil. Give them a high-precision, expensive vacuum chamber and what do
they do with it? Wrap the whole thing like leftovers. The real story, of
course, is more complicated than an arbitrary love for shiny things. Foil is
used for many things in the lab, and it turns out that when it comes to vacuum
chambers, aluminum foil is crucial to developing an ultra-high vacuum. Read
more at
http://today.slac.stanford.edu/feature/tin-foil.asp
10.
Macromolecular Crystallography Proposals due July 1
(contact:
L. Dunn, lisa@slac.stanford.edu)
July 1, 2006 is the next deadline for submitting macromolecular crystallography
proposals. Proposals submitted in July will be eligible for beam time
beginning in November 2006. For more information see Proposal Submittal and
Scheduling Procedures for Macromolecular Beam Lines at SSRL.
http://www-ssrl.slac.stanford.edu/users/user_admin/guide.html
11.
Photon Science Job Opportunities
A number of positions are currently available at the LCLS, LUSI and SSRL.
Please refer to the Photon Science Job Openings page for more information about
these job opportunities.
http://www-ssrl.slac.stanford.edu/photonscience/jobs.html
__________________________________________________________________________
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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