Previous Editions__________________________________________________________________________SSRL Headlines Vol. 10, No. 7 January, 2010__________________________________________________________________________
Contents of this Issue:
A team of researchers led by Mark Yeager, from The Scripps Research Institute
have solved the crystal structure of the hexameric CA protein substructure at
2.7 Å. To obtain their crystals, they used more stable subunits obtained
by
crosslinking the proteins at sites suggested by a 9 Å electron microscopy
structure. They collected data using SSRL Beam Line 7-1 and solved the
structure using molecular replacement. Their structure shows that the
N-terminal domains are packed tightly in the center of the hexameric structure,
but the C-terminal domains on the outside have more structural variability.
This flexibility is probably necessary to allow the hexamers to assemble into
the cone-like shape.
This research will aid discoveries of new capsid-targeted therapeutic agents
against HIV-1 using structure-based drug design. This work was published in the
June 11, 2009, issue of Cell.
To learn more about this research see the full scientific highlight
An international team of researchers led by Richard Tilley from Victoria
University in Wellington, New Zealand investigated the crystallization process
of platinum nanocrystals. They set up reactions with two precursor
concentrations (low and high) and took measurements over time. Real time in
situ x-ray diffraction (XRD), using SSRL Beam Line 7-2, measured the
crystallinity of the nanocrystals during the reactions, while transmission
electron microscopy (TEM) revealed the morphology of the crystalline material.
Combining the information from these two techniques allowed the researchers to
discern the processes of crystallization.
The researchers found that the low concentration reactions create slow-growing,
faceted crystals by laying down each platinum atomic layer in a
thermodynamically controlled manner. In striking contrast, the high
concentration reactions are kinetically controlled and go through distinct
morphological phases over time, starting with a cuboctahedral faceted
structure, growing into quasi-octapods, further evolving through
simultaneous
growth and dissolution of different parts of the nanocrystals into
etched-octapods, and finally becoming porous nanocrystals.
The researchers conclude that combining the TEM and in situ XRD
techniques creates a powerful tool for understanding crystal growth and
structure. This research was published in the October 14, 2009, issue of the
Journal of the American Chemical Society.
To learn more about this research see the full scientific highlight
To determine the similarities between Rad60 and SUMO, a research team led by
structural biologist John Tainer and geneticist Nick Boddy from The Scripps
Research Institute used SSRL Beam Line 11-1 to solve a very high-resolution
(0.97 Å) crystal structure of one of the SUMO-like domains of Rad60 from
fission yeast. When comparing to a previously known structure of SUMO, the
researchers found that the backbones of the two domains were well conserved,
but most of the surface features were not. Since the enzyme would interact with
other proteins through surface interactions, this suggests that Rad60 does not
interact with the same set of proteins, nor undergoes covalent attachment to
target proteins. However, one exception was a conserved surface feature known
to be important for interactions with a specific factor (Ubc9) in the SUMO
pathway, which functions to promote SUMOylation of target proteins. The
researchers followed up on this observation with yeast genetics experiments
performed in Nick Boddy's laboratory.
They found that mutating this Ubc9 binding feature and hence, inhibiting
Rad60's modulation of Ubc9, made cells more susceptible to DNA damage, which
confirms that it is critical to Rad60 function.
This study is the first to explore the structure of SUMO-like proteins in
detail. Defining how the SUMO pathway is used in DNA repair will aid our
understanding of many diseases, including cancer, Alzheimer's, Parkinson's, and
Huntington's. This research was published in the May 1, 2009, issue of Nature
Structural and Molecular Biology.
To learn more about this research see the full scientific highlight
Due to severe storms in the area during the week of January 18th, SLAC
experienced a site-wide power outage that lasted several days. Since that time,
staff have worked to restore critical services, ensure safe working conditions,
restore beam in SPEAR3 and restart user operations. Most beam lines resumed
operations early during the last week of January. The accelerator physics tests
scheduled for January 25-26 were canceled and returned to users who lost beam
time during the outage.
We extend our thanks to staff, especially the Facilities staff, for all their
hard work to restore these services as safely and efficiently as possible. We
also acknowledge and appreciate our scientific users for their patience. We are
compiling suggestions to improve future emergency communications and
coordination based on lessons learned from this recent experience. Please
contact Cathy Knotts or Behzad Bozorg-Chami to share your thoughts or feedback.
As a reminder in the event of future emergencies, please make a note of SLAC
emergency information hotline: 1-877-447-SLAC/1-877-447-7522. SSRL users
should also consult the SPEAR3 status website
http://www-ssrl.slac.stanford.edu/talk_display.html or the SPEAR3 status
line at 650-926-BEAM / 650-926-2326 for updated information related to
SSRL SPEAR3 and user operations.
see:
http://www.defense.gov/releases/release.aspx?releaseid=13267
Last month in the journal Nature Materials, SLAC's Photon Science
Directorate researchers and their coworkers at Materials Science Engineering,
Stanford University, confirmed how electric current moves on tiny ribbons of a
topological insulator, a material that insulates in its bulk but conducts
unusually well on the surface. The work resulted from a close collaboration
between the research groups of Stanford researcher Yi Cui, and Zhi-Xun Shen and
Shoucheng Zhang of the Stanford Institute for Materials and Energy Science
(SIMES). Some of the ARPES measurements supporting these results were
performed on Beam Line 5-4 at SSRL.
"Electrical current properties are very difficult to study in a typical bulk
sample of these topological insulators," said Shen, Director of SIMES, a joint
Stanford/SLAC institute. "By making very small nanoribbons we were able to
study the unique surface properties."
In extremely thin ribbons of the compound bismuth selenide, the large ratio of
edges to innards makes the material's coolest properties easy to detect.
Electrons running on the nanoribbon surface flow especially smoothly, act as
though they have no mass, and have a set spin-at least when the ribbons are
immersed in frigid liquid helium. In principle, the properties could extend to
room temperature.
"It opens up a lot of future applications," said SIMES physicist and co-author
Yulin Chen. The material could be a boon to spintronics, a technology that uses
electron spin to store information. The applications of spintronics include
miniscule computer chips and sensors, and quantum computing. Read more at:
The 48th ICFA Advanced Beam Dynamics Workshop on Future Light Sources will be
held at SLAC March 1-5, 2010. The workshop series on future light sources is
the flagship event of the ICFA sub-panel on Future Light Sources. It intends to
review and discuss modern accelerator-based light sources for wavelengths
ranging from the infrared to x-rays. The workshop program will consist of
plenary talks and working group sessions. Working groups will be dedicated to
critical issues of scientific needs for future light sources, ERL, FEL, storage
ring, and novel light source concepts, as well as to the essential technologies
of high brightness electron sources, synchronization, high resolution beam
diagnostics, undulators, x-ray beam line optics and detectors.
Attendance will be limited to 150 people. Additional information and
registration details are available at the workshop website:
http://www-conf.slac.stanford.edu/icfa2010/
February 2 is the deadline for submitting Macromolecular Crystallography Beam
Time Requests for the March through May 2010 scheduling period.
February 15 is the deadline for submitting new X-ray/VUV Beam Time Requests for
the third scheduling period (mid May through July 2010). (New proposals
submitted for the December 1, 2009 deadline are currently being peer reviewed;
ratings should be distributed within the next weeks or two)
Submit requests by logging into our user portal at:
The next proposal deadlines coming up are April 1 for Macromolecular
Crystallography and June 1 for X-ray/VUV. For more information on proposal
submittal see:
Please submit an End-of-Run Summary after each scheduled experiment at SSRL.
Comments on your experience at SSRL are extremely important to us, and we need
your feedback to meet our mission requirements, including assessment and
reporting. This form can be submitted through the user portal at:
https://www-ssrl.slac.stanford.edu/URAWI
In response to user suggestions, a pilot program to provide fresh food to users
and staff is underway. The SLAC cafe has installed a deli-type refrigerator in
the Building 120 kitchen near the User Administration offices. Cafe staff
restock the refrigerator with fresh salads, sandwiches, yogurt parfaits,
cookies etc., every weekday. A limited number of entree items that can be
heated in the microwave or oven are also available all at competitive price.
The payment collection container is located adjacent to the refrigerator (no
change available). Check out these fresh food options the next time you need a
snack while at SSRL. We would appreciate your feedback on this pilot program.
__________________________________________________________________________
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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