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Protein
Crystallography Newsletter
Volume 1, No. 7, August 2009
In
this issue:
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Continuing
Education Webinar
Small
Angle X-ray Scattering Analysis Techniques for Proteins
Presenter: Tom McNulty
September 30th at 3:30 PM EDT
(19:30 GMT)
Click
here to register |
FR-E+
DW SuperBright dual wavelength
rotating anode X-ray generator.
PDF guide to
installing a cryo nozzle. Click
here to open.
Dr. Garib
Murshudov of the University of York presenting a paper about
BALBES at ecm25 (top) and ecm25 participants enjoying the street
life of Istanbul (bottom).
The End of
Overeating: How to Curb the Insatiable American Appetite by
David Kessler.
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Crystallography
in the news
August
20, 2009. A team of researchers, lead by Prof. Jamie Cate at UC
Berkeley, have for the first time captured elusive nanoscale
movements of ribosomes
at work, shedding light on how these cellular factories take
in genetic instructions and amino acids to churn out proteins.
August 19, 2009. Case Western Reserve University School of
Medicine has received a $4
million grant from the National Institute of Biomedical
Imaging and Bioengineering, a division of the National
Institutes of Health (NIH), to fund the Case Center for
Synchrotron Biosciences.
August 17, 2009. Researchers at the University of Virginia
Health System, led by Prof. Wladek Minor, determined the
structure of the enzyme
protein BA2930, which is produced by the bacteria
responsible for anthrax.
August 13, 2009. Presearchers at the European Molecular Biology
Laboratory (EMBL) in Heidelberg, Germany, have identified a
whole family
of proteins capable of a direct response to the activation
of PARP1 by DNA damage.
August 3, 2009. Led by crystallographer Eric Gouaux of the
Vollum Institute at Oregon Health & Science University, a
team of researchers solved the structure of an ion
channel membrane protein in the closed conformation.
Synchrotron
quality data in your home laboratory
When you need to collect data immediately, the Rigaku
FR-E+ SuperBright™ X-ray generator delivers the flux of a
2nd generation beam line in your home lab, allowing you to
examine crystals at home that previously required a trip to the
synchrotron. Extremely high flux in a small beam enables
screening of poor crystals, where no diffraction would be
observed with a conventional X-ray generator or sealed tube
source. The FR-E+ can collect full data sets on difficult
samples and solve previously intractable structures.
Why wait for beam time at the synchrotron? The unique anode
design, combined with a patented 70 micron anode focal spot,
provides unrivaled intensities. Owners routinely collect high
resolution data on their FR-E+ and have often reported
collecting better data on their FR-E+ than they have from a
synchrotron beamline. One customer even told us that the FR-E+
has "changed the way we do crystallography". As the
only commercially available rotating anode X-ray generator with
a dual wavelength (DW) option, FR-E+ DW users employ longer
wavelengths (like Cr or Co) to collect phasing information for
rapid de novo structure determinations. For maximum
performance, a VariMax optic has been designed for each available
wavelength to provide a beam with ideal properties for
unparalleled performance.
Request a copy of the FR-E+
SuperBright brochure.
SAXS
analysis techniques for proteins
Rigaku
Life Sciences Webinar Series continues on September 30th. In
this webinar presented by Tom McNulty, we will explore the
application of small angle X-ray scattering (SAXS) techniques to
study non-crystalline macromolecular samples in solution,
including proteins, DNA and RNA, viruses and biological fibers.
Click
here to register.
Useful
links for crystallography
BALBES
- a system for solving protein structures from molecular
replacement. A unique feature is that it contains a specifically
designed internal database tailored from the PDB. All entries of
the PDB have been analyzed according to sequence identities and
three dimensional similarity; only non-redundant sets of protein
structure are stored with entries clustered into hierarchical
trees based on sequence alignment. The internal database is
updated from the PDB on a monthly basis. BALBES can be
downloaded or you can run it on the BALBES server. Long, F.,
Vagin, A., Young, P., Murshudov, G. N. "
BALBES: a molecular replacement pipeline" Acta
Cryst, D64; 125-134 (2008).
Selected
recent crystallographic papers
BioXTAS RAW, a software program for high-throughput automated
small-angle X-ray scattering data reduction and preliminary
analysis. S. Nielsen, K. Toft, D. Snakenborg, M. Jeppesen, J.
Jacobsen, B. Vestergaard, J. Kutter and L. Arleth. J.
Appl. Cryst.
42 (2009).
Characterization of gadolinium complexes for SAD phasing in
macromolecular crystallography: application to CbpF. R. Molina,
M. Stelter, R. Kahn and J. Hermoso. Acta
Cryst. D65, 823-831 (2009).
Cross-linking of protein crystals as an aid in the generation of
binary protein-ligand crystal complexes, exemplified by the
human PDE10a-papaverine structure. O. Andersen, D. Schönfeld,
I. Toogood-Johnson, B. Felicetti, C. Albrecht, T. Fryatt, M.
Whittaker, D. Hallett and J. Barker.
Acta
Cryst. D65, 872-874 (2009).
Handling cell-parameter errors in crystallographic data. J.
Haestier.
J.
Appl. Cryst.
42 (2009).
Simulation of small-angle X-ray scattering from thylakoid
membranes. J. Kirkensgaard, J. Holm, J. Larsen and D. Posselt.
J.
Appl. Cryst. 42, 649-659 (2009).
Slow cooling of protein crystals. M. Warkentin and R. Thorne.
J.
Appl. Cryst.
42 (2009).
To scavenge or not to scavenge: that is the question. E. Nowak,
A. Brzuszkiewicz, M. Dauter, Z. Dauter and G. Rosenbaum.
Acta
Cryst. D65, 1004-1006 (2009).
Book
review: The End of Overeating: Taking Control of the
Insatiable American Appetite by David
Kessler
I came across this book just before hitting the
road for the summer conferences. The author was the commissioner
of the FDA under Bush (41) and Clinton. What I found most
interesting about The End of Overeating is how well the author mapped
out my own personal journey with the problem of overeating.
Basically, this book describes how the American food industry
has found that a combination of fat, sugar and salt in the right
proportions is nearly as addictive to all mammals as cocaine. If
you like Chili's you better not read the book. By mixing these
three natural ingredients in ways that do not occur in nature,
Americans have created a diet that is unsustainable and
addictive. Furthermore, Kessler contrasts the American style of
eating, often in a car, to the French and Japanese, where meals
are based on quality food, presentation and often lengthy
affairs. Of course, the portions are also usually somewhat
smaller in these foreign countries.
What finally made me decide to recommend this book is that I was
at a conference with nearly unlimited food, breakfast buffet,
pastries at mid-morning, lunch buffet, afternoon snacks, dinner
buffet and late night snacks. At lunch a young, German student
asked me "do Americans always eat like this?" All one
had to do was look around at the other students and visitors to
know the answer was that the majority do. Ironically, by the end
of the week the German student had adopted our bad habits,
several plates piled with food and a muffin at every break. In
the end the author suggests that - unlike other addictions -
food is one we cannot do without. In order to deal with it, we
have to realize food is not our friend. That is not to say we
can't we enjoy a piece of cake once in a while ... but that is
just it, once in a while.
For further reading:
The
Big Oyster: History on the Half Shell by Mark Kurlansky.
This book provides a history of New York City from the point of
its estuaries oyster beds. An interesting side story is how the
abundance of cheap food became the American way.
In
Defense of Food by Michael Pollan. A great book that first
defines "food" and some simple rules for finding
"food".
I promise to review a book relevant to structural biology next
month.
Joseph D. Ferrara, Ph.D.
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