Structure of
a DNA
clamp–loader complex
by Dan Krotz
Sliding clamps are ring-shaped proteins
that encircle DNA and enable polymerases—enzymes that
replicate DNA—to relax and regain their hold on DNA
strands without losing their place, despite the considerable
torque that results from the production of double-helical
DNA. In addition to their role in DNA replication, sliding
clamps are also involved in several other processes that require
a mobile contact on DNA. Hoping to shed light on this important
but still poorly understood mechanism, a trio of researchers
from Berkeley and New York have obtained the crystal structure
of a sliding clamp in complex with a clamp loader assembly
that is "powered" by the hydrolysis of ATP. The
researchers found a spiral structure in the clamp loader with
a striking correspondence to the grooves of the DNA double
helix. The crystal structure suggests a simple explanation
for how interaction with the double helix triggers ATP hydrolysis
and the release of the sliding clamp. Full
story.
Publication about this research: G.D.
Bowman, M. O'Donnell, and J. Kuriyan, "Structural Analysis
of a eukaryotic sliding DNA clamp–clamp loader complex,"
Nature 429, 724 (2004).
Contact: John Kuriyan, kuriyan@berkeley.edu
Secretary of
Energy
Spencer Abraham visits ALS
Secretary Abraham made a return visit
to the ALS on Tuesday, July 7. Accompanied by Berkeley Lab
Deputy Director Pier Oddone and the Lab's Director-to-be Steven
Chu, the Secretary toured the ALS and listened to a presentation
by David Attwood (Materials Sciences Division) about recent
research using extreme ultraviolet (EUV) lithography and its
application to developing small, powerful semiconductors.
Abraham was also shown the imaging of
proteins at the Macromolecular Crystallography Facility. Gerry
McDermott (Physical Biosciences Division) illustrated the
prospect of a leukemia-fighting drug via the characterization
of a protein that regulates white blood cell production. And
Physical Biosciences Division Director Graham Fleming noted
the Lab's collaboration with the Howard Hughes Medical Institute,
whose two beamlines are studying biomedically important molecules
as a framework for understanding how molecules function and
interact. An extended
article on the visit can be found online.
Steven Chu (center) at the
Macromolecular Crystallography beamline with (from left)
Pier Oddone, Secretary Abraham, and Gerry McDermott.
Small-molecule
crystallography
beamline commissioned
A revolution in material-synthesis techniques—requiring
the ability to verify the crystal structures produced—is
the driving force behind the need for a massive capacity for
obtaining structural solutions of small-molecule systems with
small crystal sizes. In these materials, the number of atoms
per unit cell is too great for powder techniques and the size
of the crystals is too small to be obtained using single-crystal
laboratory systems. The combination of an ALS bend-magnet
source at Beamline 11.3.1 together with simple, brightness-preserving,
compact optics provides the intense x-ray radiation necessary
for studies of crystals that, because they are extremely small
or weakly diffracting, would be difficult or impossible to
study on standard laboratory systems. The beamline has been
successfully commissioned and will be available to general
users beginning August 1.
Structure of Cr(NH3)6•CuCl5
obtained from a 40 x 15 x 10 µm crystal with a resolution
of 0.75 Å.
Beamline 11.3.1 has been designed for
small-molecule crystallography with an energy range of 6–17
keV (2.07–0.73 Å) and a flux at the sample position
of 1010 photon/s at 16 keV. The beam size is 280
x 90 µm and can be collimated to 100 x 100 µm.
The Beamline 11.3.1 endstation can accommodate
a wide variety of experiments, ranging from single-crystal
diffraction to high-pressure powder studies. The diffraction
patterns are recorded with the newly available Bruker SMART
7000 CCD, with a four-port readout APEX-II detector coupled
to a 20-cm-diameter (14- x 14-cm active area) fiber-taper
optic. The fast readout of the detector (1.3 s for a 512-
x 512-pixel image) and typical exposure times of 0.5 seconds
per frame provide high-throughput data collection with high
resolution (0.75 Å). Cryocooling of the crystals (down
to 100 K) enables the use of high-intensity synchrotron radiation
for characterizing small crystals and unique crystals that
are difficult to grow. Data collected are processed using
the new APEX-II software for integrating the intensities of
the diffracted x rays and for converting the intensities to
crystallographic structure factors.
ALS Beamline 11.3.1 is supported by the
U.S. Department of Energy, Office of Basic Energy Sciences
at Lawrence Berkeley National Laboratory under Contract No.
DE-AC03-76SF00098.
Contact: Sirine Fakra, SFakra@lbl.gov
SAC meeting highlights
environmental research
The ALS Scientific Advisory Committee (SAC), which is
charged with advising Berkeley Lab and ALS management on issues
relating to ALS operations, resource allocation, and strategic
planning, met June 15–16. Environmental research at
the ALS got top billing on the agenda. Satish Myneni (Princeton
University) gave a presentation on "Understanding the
Dynamics of Environmental Processes," followed by Matthew
Marcus (ALS) on "Micro-XAFS with Micro-XRD." After
a short break, Hoi-Ying Holman (Earth Sciences Division) and
David Shuh (Chemical Sciences Division) provided the committee
with updates on activities at Beamlines 1.4 and 11.0.2, respectively.
A talk by Ernest Majer (Earth Sciences Division) closed out
the morning presentations. The afternoon session included
discussion of a proposal for a new protein crystallography
superbend beamline from APIC (Advanced Protein Crystallography
Industrial Consortium) and a report on Proposal Study Panel
(PSP) issues by Neville Smith (ALS). On the second day, committee
members tackled a review of protein crystallography Beamline
5.0.2 and conducted a freewheeling discussion on recent strategic
planning efforts, including a report on last month's Users'
Executive Committee (UEC) retreat by UEC Chair Dennis Lindle.
Current
members of the advisory committee are listed online.
Contact: Ben Feinberg, B_Feinberg@lbl.gov
ALS Doctoral
Fellowship
winners announced
 The
ALS is extremely pleased to announce this year's winners of
ALS Doctoral Fellowships: Christopher Cappa (University of
California, Berkeley), physical chemistry; Yulin Chen (Stanford
University), spin-resolved photoemission spectroscopy; Henry
Fu (University of California, Berkeley), correlated electron
physics; Johnathon Holroyd (Montana State University), physics/magnetic
materials; Timothy Learmonth (Boston University), physics;
John Strachan (Stanford University), condensed matter physics/magnetism;
Michelle Weinberger (University of California, Los Angeles),
physical/materials chemistry; and Feng Wang (University of
Michigan), solid state physics.
These exceptional Ph.D. students have
been selected to perform a major part of their thesis work
at the ALS during a one-year appointment covering the 2004
- 2005 academic year. For Yulin Chen and Feng Wang, this will
be a continuation of their fellowship grants from last year.
Congratulations to all eight!
The selection committee consisted of
Sam Bader (Argonne National Laboratory and SAC Chair), Dennis
Lindle (University of Nevada, Las Vegas, and UEC Chair), Anders
Nilsson (Stanford University), Zahid Hussain (ALS), and Neville
Smith (ALS). Detailed
information about the fellowships, along with links to
frequently asked questions and the application form, can be
found online.
Contact: Zahid Hussain, ZHussain@lbl.gov
2004 ALS Users'
Meeting update
 General
information, meeting deadlines, and online registration for
this year's ALS Users' Meeting, to be held at Berkeley Lab
October 18–20, is now available on the Users'
Meeting Web site. The early registration deadline is Friday,
October 1. Information about accommodations
for meeting participants in local hotels is also available
online.
The deadline for submitting abstracts
for oral and poster presentations is Wednesday, September
15. See instructions
for online submissions.
This year, ten focused workshops will
follow the end of the formal Users' Meeting program beginning
Tuesday, October 19, through Wednesday, October 20. The workshop
topics and their organizers are as follows:
Actinide Spectroscopy at the
ALS
David Shuh and Jim Tobin
Advances in Crystallographic
Data Analysis and Acquisition
Christine Trame
Magnetic Nanostructures, Interfaces,
and New Materials: Theory, Experiment, and Applications
Elke Arenholz and Yves Idzerda
Nanoscience at Synchrotrons
Franz Himpsel and Louis J. Terminello
New Complex Materials for Synchrotron
Science
Byron Freelon and R. Ramesh
New Directions in Hard X-Ray
Spectroscopy and Spectromicroscopy
Matthew Marcus
Photon-In and Photon-Out X-Ray
Spectroscopy in Material Sciences, Environmental Energy, and
Chemical Analysis
Jonathan Denlinger and Jinghua Guo
X-Ray Microscopy: Advances and
Challenges
Carolyn Larabell and Mark LeGros
What's Behind the Shielding?
An ALS Accelerator Tutorial
David Robin
Modern Valence Band Photoemission
Spectroscopy: The Legacy of W.E. Spicer and a Powerful Tool
for Materials (Joint ALS-SSRL workshop to be held
at SSRL)
Ingolf Lindau, Piero Pianetta, Zhi-Xhu Shen, and Neville Smith
Interested participants are encouraged
to contact the workshop leaders directly for more detailed
information about workshop agendas and speakers.
Contact: alsum@lbl.gov |
