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Protein Crystallography Newsletter
Volume 5, No. 8, August 2013
Crystallography in the news
In this issue:
Crystallography in the news
Upcoming event
Product spotlight: Rigaku Reagents
Lab spotlight: Fromme lab
Useful links for crystallography
Science video of the month
Survey of the month
Monthly crystallographic papers
Book review
Upcoming Event
The 47th course of the
International School of Crystallography
Structural Basis of Pharmacology: Deeper
Understanding of Drug Discovery Through
Crystallography
Erice, Sicily: 30 May - 8 June 2014
August 1, 2013. Researchers at the University of Alberta have collaborated to create
antibodies for a leading prion study in Switzerland and created a 3-D image showing
where those antibodies bind to the prion molecule. That will help design the next
steps to a cure for diseases such as bovine spongiform encephalopathy (BSE).
August 6, 2013. Researchers have achieved dynamic, atomic-scale views of a protein,
aquaporin zero (AQP0), needed to maintain the transparency of the lens in the human
eye. The work, funded in part by the National Institutes of Health, could lead to new
insights and drugs for treating cataracts and a variety of other health conditions.
August 8, 2013. In an advance that will help scientists design and engineer proteins, a
team including researchers from SLAC National Accelerator Laboratory and Stanford
Univ. has found a way to identify how protein molecules flex into specific atomic
arrangements required to catalyze chemical reactions essential for life. The achieve​
ment uses a new computer algorithm to analyze data from X-ray studies of crystallized
proteins. Scientists were able to identify cascades of atomic adjustments that shift
protein molecules into new conformations.
August 22, 2013. Some day, designer metal-binding proteins could catalyze chemical
reactions unseen in nature for industrial and medical applications. Unfortunately, these
proteins are difficult to create from scratch. Now, using computational design,
researchers have generated a novel metal-binding protein by incorporating an unnatural
amino acid with a taste for metals.
August 26, 2012. In 1961, Alexander Rich—along with David Davies, Watson, and Crick
—hypothesized that the RNA known as poly (rA) could form a parallel-stranded double
helix. Fifty years later, scientists from McGill University successfully crystallized a short
RNA sequence, poly (rA)11, and used data collected at the Canadian Light Source
(CLS) and the Cornell High Energy Synchrotron to confirm the hypothesis of a poly (rA)
double-helix.
August 27, 2013. Of a family of fireproof materials known as brominated flame
retardants (BFRs), TBBPA is one of the most widely used. Dr Linda Birnbaum, and her
NIH team, focused their attention on TBBPA using X-ray crystallography. The ability of
TBBPA to bind to and inhibit an enzyme that metabolises oestrogen (oestrogen
sulfotransferase) could result in the body having too much oestrogen.
If you have never been to a crystallography school in
Erice, you are missing one of the most wonderful
experiences of your professional career. Top-notch
speakers and an almost perfect location make for an
unforgettable time. A trip to Erice should be on any
crystallographer's bucket list.
Diseases, from bacterial and viral infections to cancer
to chronic maladies, are still among the greatest
problems for mankind despite tremendous progress in
genetics, biology, and chemistry. The purpose of this
course is dual: 1) It will provide a review of the
fundamentals and the application of crystallography
to drug design, and an evaluation of the technology
at the present state. 2) It will review the progress in
this field and summarize the application and results to
current field of interest.
Interested candidates should register using this
Product spotlight: Rigaku Reagents
Rigaku has acquired the consumable crystallization
business from Emerald Bio.
We will continue to produce the high quality products
that Emerald has become known for and will extend
the product line with some exciting new products,
under the name of Rigaku Reagents, Inc.
Interested candidates should register using this
form by November 30, 2013.
Lab in the Spotlight
The line of Wizard screens is one of the most popular
product lines in the global crystallization market. When
you do get a hit on a commercial screen, you can use
the EZ-Screen Builder, to custom design your
optimization screen online, and receive a 96 deep well
block in via FedEx.
Ask for more information.
Lab in the spotlight: Fromme group
Professor Petra Fromme
Department of Chemistry and Biochemistry
Arizona State University, Tempe, AZ
The research in Prof. Fromme's group focuses on the structural
biochemistry and biophysics of membrane proteins. There are two
major biological fields of interest: photosynthesis and infectious diseases.
Fromme lab
Survey of the Month
The work on photosynthesis includes the investigation of the structure and function of
the large membrane protein complexes involved in the primary processes of photo​
synthesis and the development of an artificial oxygen evolving complex in DNA
nanocages, and is part of the ASU Center for Bio-Inspired Solar Fuel production. A
special focus for their studies is the structure and function of the large bio-solar energy
converters, Photosystem I, Photosystem II, and the ATP-Synthase, an enzyme that
functions as a molecular motor. They also use time-resolved femtosecond nano​
crystallo​
g raphy to determine a molecular movie of water splitting. Another exciting
project deals with transport processes across membranes, with a special focus on
transport into cell organelles.
The work on important viral, bacterial and human membrane proteins is the focus of
the ASU Center for Membrane Proteins in Infectious Diseases led by Prof. Fromme. The
center involves a collaboration of eleven groups at ASU. They have selected fifty
target proteins that play important roles in the infection cycle. The work involves new
method development for expression, purification, biophysical characterization,
crystallization and structure determination of the membrane proteins.
Useful links: Membrane proteins of known structure
Professor Stephen White's group, located in the
Department of Physiology and Biophysics in the School of
Medicine of the University of California at Irvine, works on
biophysical problems related to the folding and stability of membrane proteins. His
group maintains the Membrane Proteins of Known Structure, a current list of
membrane protein structures determined by X-ray and electron diffraction with links to
the Protein Data Bank and other useful sites.
Selected recent crystallographic papers
Generation of functional antibodies for mammalian membrane protein crystallography.
Hino, Tomoya; Iwata, So; Murata, Takeshi. Current Opinion in Structural Biology.
Aug2013, Vol. 23 Issue 4, p563-568. 6p. http://dx.doi.org/10.1016/j.sbi.2013.04.007.
A strategy to select suitable physicochemical attributes of amino acids for protein fold
recognition. Sharma, Alok; Paliwal, Kuldip K.; Dehzangi, Abdollah; Lyons, James; Seiya
Imoto; Satoru Miyano. BMC Bioinformatics. 2013, Vol. 14 Issue 1, p1-11. 11p. 2
Diagrams, 17 Charts. http://dx.doi.org/10.1186/1471-2105-14-233.
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and
binding sites. Full Text Available By: Cereto-Massagué, Adrià; Ojeda, María José;
Joosten, Robbie P.; Valls, Cristina; Mulero, Miquel; Josepa Salvado, M.; Arola-Arnal,
Anna; Arola, Lluís; Garcia-Vallvé, Santiago; Pujadas, Gerard. Journal of Cheminformatics.
2013, Vol. 5 Issue 1, p1-9. 9p. 3 Color Photographs, 1 Diagram, 4 Charts.
http://dx.doi.org/10.1186/1758-2946-5-36.
Ligand/kappa-opioid receptor interactions: Insights from the X-ray crystal structure.
Martinez-Mayorga, Karina; Byler, Kendall G.; Yongye, Austin B.; Giulianotti, Marc A.;
Dooley, Colette T.; Houghten, Richard A. European Journal of Medicinal Chemistry.
Aug2013, Vol. 66, p114-121. 8p. http://dx.doi.org/10.1016/j.ejmech.2013.05.021.
Aug2013, Vol. 66, p114-121. 8p. http://dx.doi.org/10.1016/j.ejmech.2013.05.021.
Synthesis, spectral, X-ray crystallography, electrochemistry, DNA/protein binding and
radical scavenging activity of new palladium(II) complexes containing triphenylarsine.
Kalaivani, P.; Prabhakaran, R.; Kaveri, M.V.; Huang, R.; Staples, R.J.; Natarajan, K.
Inorganica Chimica Acta. Aug2013, Vol. 405, p415-426. 12p.
http://dx.doi.org/10.1016/j.ica.2013.06.038.
Clustering procedures for the optimal selection of data sets from multiple crystals in
macromolecular crystallography. Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron,
Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So;
Evans, Gwyndaf. Acta Crystallographica: Section D. Aug2013, Vol. 69 Issue 8, p16171632. 16p. http://dx.doi.org/10.1107/S0907444913012274.
http://www.surveymonkey.com/s/rigaku
Science Video
RapiData: Program Overview
MORPH-PRO: a novel algorithm and web server for protein morphing. Castellana, Natalie
E.; Lushnikov, Andrey; Rotkiewicz, Piotr; Sefcovic, Natasha; Pevzner, Pavel A.; Godzik,
Adam; Vyatkina, Kira. Algorithms for Molecular Biology. 2013, Vol. 8 Issue 1, p1-9. 9p.
http://dx.doi.org/10.1186/1748-7188-8-19.
A prototype direct-detection CCD for protein crystallography. Green, Katherine S.;
Szebenyi, Doletha M. E.; Boggs, Kasey; Bredthauer, Richard; Tate, Mark W.; Gruner,
Sol M. Journal of Applied Crystallography. Aug2013, Vol. 46 Issue 4, p1038-1048. 11p.
http://dx.doi.org/10.1107/S0021889813016592.
Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0:
Protonation states and hydration structure in the free-form. Ohnishi, Yuki; Yamada,
Taro; Kurihara, Kazuo; Tanaka, Ichiro; Sakiyama, Fumio; Masaki, Takeharu; Niimura,
Nobuo. BBA - Proteins & Proteomics. Aug2013, Vol. 1834 Issue 8, p1642-1647. 6p.
http://dx.doi.org/10.1016/j.bbapap.2013.05.012.
This weeklong crash course is designed to introduce
participants to the best and latest equipment and
techniques for macromolecular X-ray crystallography.
The students also get to meet and learn from the
leading developers of software in the field, and then
actually use the NSLS beamlines to collect data. The
course is offered by Brookhaven Labs Biology and
National Synchrotron Light Source departments, and
reflects an educational component of the PXRR
(Macromolecular Crystallography Research
Resource), funded jointly by the National Center for
Research Resources a branch of the National
Institutes of Health (NIH) and the U.S. Department of
Energy's Office for Biological & Environmental
Research.
Combining crystallography and EPR: crystal and solution structures of the multidomain
cochaperone DnaJ. Barends, Thomas R. M.; Brosi, Richard W. W.; Steinmetz, Andrea;
Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten; Seidel,
Ralf; Shoeman, Robert L.; Zimmermann, Sabine; Bittl, Robert; Schlichting, Ilme;
Reinstein, Jochen. Acta Crystallographica: Section D. Aug2013, Vol. 69 Issue 8, p15401552. 13p. http://dx.doi.org/10.1107/S0907444913010640.
Structure and function of Hip, an attenuator of the Hsp70 chaperone cycle. Li, Zhuo;
Hartl, F Ulrich; Bracher, Andreas. Nature Structural & Molecular Biology. Aug2013, Vol.
20 Issue 8, p929-935. 7p. 1 Chart, 6 Graphs. http://dx.doi.org/10.1038/nsmb.2608.
Mitigation of X-ray damage in macromolecular crystallography by submicrometre line
focusing. Finfrock, Y. Zou; Stern, Edward A.; Alkire, R. W.; Kas, Joshua J.; EvansLutterodt, Kenneth; Stein, Aaron; Duke, Norma; Lazarski, Krzysztof; Joachimiak,
Andrzej. Acta Crystallographica: Section D. Aug2013, Vol. 69 Issue 8, p1463-1469. 7p.
http://dx.doi.org/10.1107/S0907444913009335.
Integrated biophysical approach to fragment screening and validation for fragmentbased lead discovery. Leonardo Silvestre, Hernani; Blundell, Thomas L.; Abell, Chris;
Ciulli, Alessio. Proceedings of the National Academy of Sciences of the United States of
America. 8/6/2013, Vol. 110 Issue 32, p12984-12989. 6p.
http://dx.doi.org/10.1073/pnas.1304045110.
On the role of surface composition and curvature on biointerface formation and
colloidal stability of nanoparticles in a protein-rich model system. Orts-Gil, Guillermo;
Natte, Kishore; Thiermann, Raphael; Girod, Matthias; Rades, Steffi; Kalbe, Henryk;
Thünemann, Andreas F.; Maskos, Michael; Österle, Werner. Colloids & Surfaces B:
Biointerfaces. Aug2013, Vol. 108, p110-119. 10p.
http://dx.doi.org/10.1016/j.colsurfb.2013.02.027.
Structure-Based Design of Covalent Siah Inhibitors. Stebbins, John L.; Santelli, Eugenio;
Feng, Yongmei; De, Surya K.; Purves, Angela; Motamedchaboki, Khatereh; Wu, Bainan;
Ronai, Ze'ev A.; Liddington, Robert C.; Pellecchia, Maurizio. Chemistry & Biology.
Aug2013, Vol. 20 Issue 8, p973-982. 10p.
http://dx.doi.org/10.1016/j.chembiol.2013.06.008.
The X-ray Crystal Structure of Mannose-binding Lectin-associated Serine Proteinase-3
Reveals the Structural Basis for Enzyme Inactivity Associated with the Carnevale,
Mingarelli, Malpuech, and Michels (3MC) Syndrome. Yongqing, Tang; Wilmann, Pascal
G.; Reeve, Shane B.; Coetzer, Theresa H.; Smith, A. Ian; Whisstock, James C.; Pike,
Robert N.; Wijeyewickrema, Lakshmi C. Journal of Biological Chemistry. 8/2/2013, Vol.
288 Issue 31, p22399-22407. 9p. http://dx.doi.org/10.1074/jbc.M113.483875.
X-ray diffraction details water's path through a cell pore. Smart, Ashley G. Physics
Today. Aug2013, Vol. 66 Issue 8, p16-17. 2p. http://dx.doi.org/10.1063/PT.3.2068.
Today. Aug2013, Vol. 66 Issue 8, p16-17. 2p. http://dx.doi.org/10.1063/PT.3.2068.
On the reproducibility of protein crystal structures: five atomic resolution structures of
trypsin. Liebschner, Dorothee; Dauter, Miroslawa; Brzuszkiewicz, Anna; Dauter,
Zbigniew. Acta Crystallographica: Section D. Aug2013, Vol. 69 Issue 8, p1447-1462.
16p. http://dx.doi.org/10.1107/S0907444913009050.
Phase determination of the crystal structure factor by measuring rocking curves from a
polar crystal. Negishi, Riichirou; Fukamachi, Tomoe; Jongsukswat, Sukswat; Hirano,
Kenji; Hirano, Keiichi; Kawamura, Takaaki. Journal of Applied Crystallography. Aug2013,
Vol. 46 Issue 4, p1216-1218. 3p. http://dx.doi.org/10.1107/S0021889813011564.
Book review:
OS X Mountain Lion: The Missing Manual
By David Pogue
O'Reilly Media, 2012, ISBN-13: 978-1449330279, 888 pages
I went to Amazon to look for a book and my landing page displayed this title. I like
what Pogue has to say about technology and this seemed like a good book to read.
Actually, it is a great book. I once heard Jerry Pournelle say that the great thing about
Mac OS X is the fact it takes only a few minutes to figure out whether you can do
something or not, whereas with the other major desktop OS it can take much, much
longer. This book demonstrates that OS X is very feature rich and contradicts
Pournelle's statement because there are so many really, really useful features in OS X
that are not obvious, ones that you really need once you learn about them.
The author fulfills what he set out to do, which is to provide the missing manual for OS
X. Frankly, the chapter on Spotlight alone is worth the purchase price. After finishing
the second chapter, I bought the upgrade to 10.8. After finishing the chapter on
security I decided the next computer I buy for home will be a Mac. Also, the editions
for Snow Leopard and Mountain Lion would have saved me a lot of money, time and
grief had I known about them when I switched to Mac OS three years ago. I've
bought a number of apps that I probably did not need because the functionality was
buried in the OS somewhere.
I do have one negative comment. I bought this as an ebook for my Kindle and that
was a mistake. The Kindle does not know how to display ⌘ properly. Sometimes it is
displayed, but more often than not it is replaced with a space or, worse, overlayed
with the symbol to the right. I have the Kindle app on my MacBook, so I read the
book there when convenient. This actually had a very positive effect. I could switch
from the Kindle reader to the OS and try out whatever I was reading. I found this
positive reinforcement very beneficial in committing keystrokes to memory.
Another important feature of the Kindle version is that everything is hyperlinked, so
you can bounce around or use another great feature: www.missingmanuals.com,
where you can access The Missing CD-ROM for this book. The book's index is massive,
taking up 25% of the book itself, making it easy to find specific items. There are
sidebars with the titles "Gem in the Rough", "Note", "Tip", "Power User Clinic," and
others. These provide details beyond the main text and are quite useful.
The book is divided into eight sections: Introduction, The OS X Desktop, Programs in
OS X, The Components of OS X, The Technologies of OS X, OS X Online, Appendices
and Index. As I mentioned earlier, the chapter on Spotlight is very illuminating, and
even details the query language available, which allows for intelligent searching. Here's
one neat trick I learned: ⌘-space takes you to Spotlight. Enter a formula, for example
sin(pi), and you get the answer. Spotlight is a basic scientific calculator. If you type a
word, look down a bit and hover over the "Look Up" entry, the dictionary entry
appears.
OS X is capable of taking dictation (Chapter 5), but it requires one to upload their
contact list to Apple. I haven't tried it yet, because I cringe at the thought of
uploading my contacts, but I would be curious to hear about your experiences with
dictation.
Chapter 11 is chock full of useful stuff. Calendar has a feature that will display a
document at a specific time, which is great for reminding you what you should be
doing right now. Preview is far more powerful than I realized, especially in the way it
handles PDFs. In fact, I am going to see if I can jettison Acrobat and all other utilities
I've acquired for handling PDFs and live with Preview alone. If you turn on
TimeMachine it will make backups of critical files to your main disk when your backup
drive is not connected. TimeMachine is so easy to use there is no longer an excuse for
being among the 96% of people who don't back up their files.
Chapter 13 covers security, and Mac OS X provides plenty of that by default. However,
Chapter 13 covers security, and Mac OS X provides plenty of that by default. However,
I learned I can enhance security significantly. I have already activated FileVault and will
add a boot password. There is one command program not described that is extremely
useful: purge. Execute this from a terminal and your Mac's memory is cleared of
rubbish. Do this once or twice week and you won't have to reboot except for
updates. Now if I can just get Calendar to activate this every day at 0200.
Before I close, here is another great time saver: hold down any character key for a
second or so and an accented character selection dialog appears. Pick a number and
you are done. I could go on and on about things I learned about OS X, but you really
need to get the latest version of OS X, 10.8, and this book to take advantage of the
rich features. Or you can spend all your free time poking around and figuring it out for
yourself.
Joseph D. Ferrara
Chief Science Officer
Rigaku Corporation
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