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Protein
Crystallography Newsletter
Volume 1, No. 8, September 2009
In
this issue:
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Continuing
Education Webinar
High-Throughput
Structural
Biology at the JCSG
Presenter: Dr. Ian Wilson
October 28th at 12:00 PM EDT
(16:00 GMT)
Click
here to register |
How
many crystals have you missed? Protein crystals in heavy
precipitate imaged (visible top and UV bottom) with the new Rigaku
Minstrel HT UV system.
CCP4
Study Weekend (6th - 8th January 2010)
"From Crystal to Structure with CCP4"
Click on image
or here
to take the one question survey.
Textbook of
Structural Biology
by Anders Liljas, et al.
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Crystallography
in the news
September
2, 2009. New York University chemists, lead by Prof. Nadrian
Seeman, have created three-dimensional
DNA structures, by using single-stranded sticky ends that link
double helices in DNA triangles that point in different
directions, a breakthrough bridging the molecular world to the
world where we live.
September 2, 2009. Boron-based
compounds trick a biomedical protein. University of Oregon
team, lead by Prof. Shih-Yuan Liu, used X-ray crystallography to
demonstrate that specially synthesized boron compounds are readily
accepted in biologically active enzymes.
September 3, 2009. Vanderbilt chemists, led by Prof. Billy Hudson,
have identified a unique chemical bond that holds together type IV
collagen dimer molecules. The sulfilimine
(N=S) bond has never been observed in biological molecules
before, but is responsible for the strength of these collagen
networks in all animals from sea sponges to humans.
September 13, 2009. Brookhaven National Laboratory biologist Dr.
Dax Fu reports a high-resolution X-ray crystallography view of zinc
transport protein that reveals shape-shifting atomic
interactions suggesting a mechanism and possible drug targets.
September 21, 2009. Rice University biochemists are developing a
system of "evolutionary
forecasting" to better understand the mechanisms of
antibiotic resistance with the goal of showing which sets of genes
a pathogen will modify to become drug-resistant.
New
high-throughput crystal imaging system
New
from Rigaku, the Minstrel™
HT UV imaging system is the world's first high-throughput UV
imaging and protein crystal monitoring system. Built upon the
platform of Rigaku's state-of-the-art imaging and analysis system,
the Minstrel
HT UV employs both visible and UV fluorescence microscopy to
successfully detect crystals where visible imaging alone falls
short and to monitor crystal growth by distinguishing protein
crystals from non-protein crystals, such as salt. Employing a 5.1
megapixel CCD, with a single optical train for superior optical
quality, this new automated system offers the highest available
optical resolution for combined visible and UV spectrum imaging
systems. The instrument features polarization and both
monochromatic & color imaging in visible spectrum. With
multi-slice capability, and combined image capability, the Minstrel
HT UV ensures that all features within a drop can be clearly
observed.
In the Minstrel
HT UV, an ultraviolet microscope is mated with a patent
pending ultraviolet light emitting diode (LED) illumination
source (bright and dark field), called Clean Light Technology™,
providing minimal UV exposure and adding no additional heat to the
well. Clean Light Technology eliminates photo damage and has no
impact on resulting X-ray diffraction data quality. The wavelength
of the LED is matched to the absorption peak of tryptophan, which
is one of the fluorescing amino acids found in almost all protein
crystals. This allows for definitive detection of protein crystals
within opaque or heavily precipitated drops and eliminates time
spent screening or optimizing around salt crystals, thereby
increasing your productivity and the reliability of the
experimental results.
Request a copy of the Minstrel
HT UV brochure.
Lab
Spotlight: What is P-CUBE?
P-CUBE
is an EU-funded project, coordinated and managed by Prof. Markus
G. Grütter and Dr. Jutta Tatzel respectively, that offers free
access to infrastructures for the European science community in
structural biology.
The first project within the Seventh Framework Program that brings
together research, networking and service activities, P-CUBE
offers exciting cutting edge technologies in contemporary
structural biology and provides access to: high-throughput cloning
and expression technologies in prokaryotic and eukaryotic cells,
high-throughput crystallization facilities, the DARPin-selection
methodology, ESPRIT technology, and advanced light microscopy.
Service and access to these infrastructures are free of charge for
scientists all across Europe from now until March 2013.
Useful
links for crystallography
COPS
(Classification Of Protein Structures) web server is a
next-generation web application that provides fast and intuitive
access to the entire set of currently available protein
structures. COPS organizes structural domains by quantified
structural similarities which can be visualized immediately with
Jmol. Additionally, structural biologists can employ iCOPS to
classify their own structures.
Selected
recent crystallographic papers
Three-Dimensional
Structural View of the Central Metabolic Network of Thermotoga
maritima. Y. Zhang, I. Thiele, D. Weekes, Z. Li, L.
Jaroszewski, K. Ginalski, A. Deacon, J. Wooley, S.A. Lesley, I.A.
Wilson, B. Palsson, A. Osterman, and A. Godzik.
Science
Vol. 325, 5947, 1544-1549 (2009).
Optics: Ultrafast X-ray photography. Margaret M. Murnane and
Jianwei Miao. Nature
460, 1088-1090 (2009).
Structure of a tetrameric MscL in an expanded intermediate state.
Z. Liu, C.S. Gandhi and D.C. Rees. Nature
461, 120-124 (2009).
Engineering of recombinant crystallization chaperones. Shohei
Koide. Current
Opinion in Structural Biology Vol. 19, 4,
449-457 (2009).
Book
review: Textbook
of Structural Biology
by A. Liljas, L. Liljas, J. Piskur, G.n Lindblom,
P. Nissen and M. Kjeldgaard
As
promised, this review is of a book directly relevant to structural
biology … just check out the title. I started this book not
knowing what level of prior experience the reader needed.. After
reading the first few chapters, I concluded that the reader had
better have an organic chemistry, biology and crystallography
course under their belts, since advanced concepts are introduced
without description. I read the book and I realized that this text
provides a well thought out and reasonably current survey of
structural biology.
The first four chapters introduce structural biology, protein and
DNA structure, as well as lipids and membrane structure. The
remaining twelve chapters describe, in great detail, the current
state of the art in structural biology, including: enzymes, DNA
replication and recombination, transcription, protein synthesis
and translation, protein folding and degradation, membrane
proteins, signal transduction, cell motility and transport,
cell-cell interactions, the immune system, viruses and the
evolution of macromolecules. The last chapter on macromolecule
evolution is particularly interesting in that this year is the
150th anniversary of the publication of On the Origin of Species.
Each chapter is elucidated with structures from the recent
literature as well as historical examples where appropriate. Each
protein is provided with its PDB code so it very easy to study a
given structure in depth. However, this is also my one complaint,
as the reader is forced to go to the PDB to find references for
the structures.
There are six appendices on diverse topics such as energetics,
fold comparison, prediction of conformation, assignment of
function, protein modification and a current list of Nobel
laureates. The main text is 484 pages with well written prose. I
enjoyed reading this book and recommend it for an advanced level
class in structural biology or as a current reference text.
I have preordered my copy of Biomolecular Crystallography:
Principles, Practice, and Application to Structural Biology by
Bernhard Rupp, so look for a review of that book here in October
or November. Finally, I am pleased to report that Sean B. Carroll,
an author reviewed here in the past, now has a monthly column in
the New York Times titled "Remarkable
Creatures"
Joseph D. Ferrara, Ph.D.
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