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Protein
Crystallography Newsletter
Volume 5, No. 10, October 2013
In
this issue:
Letters to the Editor
Crystallography Times welcomes comments to be published on issues relevant to structural biology. This month marks our first letter from an incredulous reader:
I read with some amusement the results from you last newsletter quiz. How many of the participants did in-house crystallography before cryocrystallography? Capillary mounting—painful, damaged crystals, increased background, bad for plates, absorption problems, not good for small
crystals...Data—
suffered radiation
decay and generally required two or more data sets to get a complete set. In short, all of the technology listed in the survey would be useless if your crystal was small or died in the beam.
Just my 2 cents.
John Rose Ph.D., Associate Professor
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Product in the Spotlight
 Rigaku's popular Minstrel HT series
Lab in the Spotlight
 Soybean Lipoxygenase L-1 at 1.4 Å Resolution
Crystallization WebinarCapillary counter-diffusion methods for protein crystallization: Screening and crystal improvement
Dr. José A. Gavira
Laboratorio de Estudios Cristalográficos
IACT, (CSIC - UGR)
Avd. de las Palmeras, 4
18100 Armilla (Granada), Spain
Tuesday, Nov. 12th, 2013
8:00am PST (16:00 GMT) |  |
Dr. Jose Gavira will give a scientific presentation in
the Rigaku Crystallization Webinar series on November 12th, 2013, 8:00am Pacific Standard Time. The webinar is open to
all. Register here.
Survey of the Month
http://www.surveymonkey.com/s/rigaku
Last Month's Survey Rate your level of agreement with the following statement: I would use covalent modification of macromolecules with a fluorescence probe, to detect the binding of individual components in a complex during crystallization, if such a product was available.
Professor Stephen Curry leads a round-table discussion on Austrian-born British molecular biologist Max Perutz, who won a Nobel
Prize in 1962 for discovering the structure of hemoglobin. Scientists who worked with
him discuss his legacy alongside footage and previously unseen interviews. Perutz founded the MRC Laboratory of Molecular Biology (LMB) at Cambridge University in the postwar years, where he was the prominent figure in a group of brilliant scientists. Having worked under JD Bernal, the pioneer in X-ray crystallography, Perutz also fostered the talents of his student Francis Crick alongside post-doc James Watson, who worked in his Cambridge lab before the pair discovered the structure of DNA.
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Crystallography
in the news
October 2, 2013. Highlighting an important but unexplored area of evolution, scientists at The Scripps Research Institute (TSRI),
led by Prof. Peter E. Wright, have found evidence that, over hundreds of millions of years, an essential protein, dihydrofolate reductase (DHFR), has evolved chiefly by changing how it moves rather than by changing its basic molecular structure.
October 9, 2013. To get a better idea of the rise and significance of X-ray crystallography, have a look at this short animated film made by 12foot6 for the Royal Institution (RI) as part of a project funded by the Science and Technology Facilities
Council to celebrate the centenary of the technique.
October 9, 2013. This year's Nobel Prize in Chemistry recognizes three researchers who helped bring dynamism to
the study of large molecules like proteins. Martin Karplus, Michael Levitt, and Arieh Warshel started studying how to simulate the activity that goes on inside a protein back in the 1970s, when computing power was extremely hard to come by.
October 9, 2013. To date, 28 Nobel Prizes have been awarded to projects related to
crystallography. 2013 marks the 120th anniversary of the birth of Max von Laue, who won the first of those awards in 1914 for discovering that X-rays can be diffracted by crystals.
October 15, 2013. Arapaima gigas is the largest—and evolutionarily, one of the oldest—fish species living within the lakes of the Amazon River basin. A team of researchers based at the Lawrence Berkeley National Laboratory interested in determining how this fish evolved to coexist so successfully with the vicious predatory piranha observed the response of microscopic collagen layers using small-angle X-ray scattering (SAXS).
October 18, 2013. Scientists at the University of Washington have been trying to decipher the complex structure of an enzyme that "exhibits behavior similar to that of an enzyme key in the development of AIDS from an HIV infection" for the last decade. Gamers playing spatial game Foldit have managed to collectively determine the enzyme's structure in a mere ten days.
October 21, 2013. Recognition of the role of protein structure changes in signaling has driven a proliferation of techniques to detect the shifts. Pfizer and Roche think they have found a better way and have invested in Biodesy, the California-based startup behind the second-harmonic generation (SHG) method. Pfizer and Roche were joined by 5AM Ventures in a $15 million Series A financing round that will give Biodesy the cash to further develop and commercialize its technology.
Product spotlight: Minstrel HT and Minstrel HT UV
The Minstrel HT and HT UV are automated high-throughput ultraviolet and visible crystal imaging and protein crystal monitoring systems that automatically image crystallization experiments and link images with crystallization conditions.
Minstrel HT and Minstrel HT UV provide unattended image acquisition, providing an objective history of the experiment. A fully integrated system for temperature controlled incubation, inspection, and analysis of protein crystallization plates, each installation is comprised of one Minstrel HT/HT UV imaging station and either one or two Gallery HT incubator storage systems. They are the perfect systems for labs that are working on difficult conditions, such as membrane proteins, where the crystal may be invisible in LCP with visible light.
Ask for more information.
View the product video.
Lab in the
spotlight: Wladek Minor laboratory
Wladek Minor Laboratory
Professor Wladek Minor
Department of Molecular Physiology and Biological Physics
University of Virginia
The Minor laboratory studies macromolecular structure with an aim toward in-depth understanding of structure-function relationships. X-ray diffraction analysis is their primary research tool, but they also employ other physical and biochemical methods of analysis. The program emphasizes two broad
themes: crystallographic studies on molecules of immediate interest, and methodology development. Most of the macromolecules that they have under study relate to one or more of a few broad biological areas: cellular signal transduction and metalloproteins. The same systems have been chosen as subjects for methodology development. The methodology development includes the development of various crystallographic tools that
comprise the HKL package.
The Minor lab currently has almost twenty members ranging from postdoctoral
research associates to lab technicians to visiting faculty.
Useful link: Protein crystallography course
Prof. Randy Read organized a series of lectures for a
macromolecular crystallography course that was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB. The content of the course is available online.
Selected
recent crystallographic papers
A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel. Cao, Hui-Ling; Sun, Li-Hua; Li, Jian; Tang, Lin; Lu, Hui-Meng; Guo, Yun-Zhu; He, Jin; Liu, Yong-Ming; Xie, Xu-Zhuo; Shen, He-Fang; Zhang, Chen-Yan; Guo, Wei-Hong; Huang, Lin-Jun; Shang, Peng; He, Jian-Hua; Yin, Da-Chuan. Acta Crystallographica: Section D. Oct2013, Vol. 69 Issue 10, p1901-1910. 10p. http://dx.doi.org/10.1107/S0907444913016296.
Classification of protein crystallisation images using texture-based statistical features. Lekamge, B. M. Thamali; Sowmya, Arcot; Mele, Katarina; Fazio, Vincent J.; Newman, Janet. AIP Conference Proceedings. Oct2013, Vol. 1559 Issue 1, p270-276. 7p. 1 Black and White Photograph, 2 Charts. http://dx.doi.org/10.1063/1.4825019.
Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography. Round, Adam; Brown, Elizabeth; Marcellin, Romain; Kapp, Ulrike; Westfall, Corey S.; Jez, Joseph M.; Zubieta, Chloe. Acta Crystallographica: Section D. Oct2013, Vol. 69 Issue 10, p2072-2080. 9p. http://dx.doi.org/10.1107/S0907444913019276.
Structure and Dynamics of the N-Terminal Domain of the Cu(l) Binding Protein CusB. Ucisik, Melek N.; Chakravorty, Dhruva K.; Merz Jr., Kenneth M. Biochemistry. 10/1/2013, Vol. 52 Issue 39, p6911-6923. 13p. http://dx.doi.org/10.1021/bi400606b.
Graphene as a protein crystal mounting material to reduce background scatter. Wierman, Jennifer L.; Alden, Jonathan S.; Kim, Chae Un; McEuen, Paul L.; Gruner, Sol M. Journal of Applied Crystallography. Oct2013, Vol. 46 Issue 5, p1501-1507. 7p. http://dx.doi.org/10.1107/S002188981301786X.
The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. Meilleur, Flora; Munshi, Parthapratim; Robertson, Lee; Stoica, Alexandru D.; Crow, Lowell; Kovalevsky, Andrey; Koritsanszky, Tibor; Chakoumakos, Bryan C.; Blessing, Robert; Myles, Dean A. A. Acta Crystallographica: Section D. Oct2013, Vol. 69 Issue 10, p2157-2160. 4p. http://dx.doi.org/10.1107/S0907444913019604.
Improving experimental phases for strong reflections prior to density modification. Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J. Acta Crystallographica: Section D. Oct2013, Vol. 69 Issue 10, p2039-2049. 11p. http://dx.doi.org/10.1107/S0907444913018167.
Fragment-based discovery of focal adhesion kinase inhibitors. Grädler, Ulrich; Bomke, Jörg; Musil, Djordje; Dresing, Verena; Lehmann, Martin; Hölzemann, Günter; Greiner, Hartmut; Esdar, Christina; Krier, Mireille; Heinrich, Timo. Bioorganic & Medicinal Chemistry Letters. Oct2013, Vol. 23 Issue 19, p5401-5409. 9p. http://dx.doi.org/10.1016/j.bmcl.2013.07.050.
Protein dynamics: Shake it up, baby. Finkelstein, Joshua M. Nature Chemical Biology. Oct2013, Vol. 9 Issue 10, p600-600. 1p. http://dx.doi.org/10.1038/nchembio.1344.
Optimization and control of crystal shape and size in protein crystallization process. Liu, Jing J.; Hu, Yang D.; Wang, Xue Z. Computers & Chemical Engineering. Oct2013, Vol. 57, p133-140. 8p. http://dx.doi.org/10.1016/j.compchemeng.2013.04.022.
Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): Insights from kinetic and crystallographic studies. Chittori, Sagar; Simanshu, Dhirendra Kumar; Banerjee, Sanchari; Murthy, Ambika Mosale Venkatesh; Mathivanan, Subashini; Savithri, Handanahal Subbarao; Murthy, Mathur Ramabhadrashastry Narasimha. BBA - Proteins & Proteomics. Oct2013, Vol. 1834 Issue 10, p2036-2044. 9p. http://dx.doi.org/10.1016/j.bbapap.2013.05.020.
Structure and nucleic acid binding activity of the nucleoporin Nup157. Hyuk-Soo Seo; Blus, Bartlomiej J.; Janković, Nina Z.; Blobel, Günter. Proceedings of the National Academy of Sciences of the United States of America. 10/8/2013, Vol. 110 Issue 41, p16450-16455. 6p. http://dx.doi.org/10.1073/pnas.1316607110.
Binding of the N-Terminal Domain of the Lactococcal Bacteriophage TP901-1 CI Repressor to Its Target DNA: A Crystallography, Small Angle Scattering, and Nuclear Magnetic Resonance Study. Frandsen, Kristian H.; Rasmussen, Kim K.; Jensen, Malene Ringkjøbing; Hammer, Karin; Pedersen, Margit; Poulsen, Jens-Christian N.; Arleth, Lise; Leggio, Leila Lo. Biochemistry. 10/1/2013, Vol. 52 Issue 39, p6892-6904. 13p. http://dx.doi.org/10.1021/bi400439y.
Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer. Yee-Wai Cheung; Kwok, Jane; Law, Alan W. L.; Watt, Rory M.; Kotaka, Masayo; Tanner, Julian A. Proceedings of the National Academy of Sciences of the United States of America. 10/1/2013, Vol. 110 Issue 40, p15967-15972. 6p. http://dx.doi.org/10.1073/pnas.1309538110.
Chaperone machines for protein folding, unfolding and disaggregation. Saibil, Helen. Nature Reviews Molecular Cell Biology. Oct2013, Vol. 14 Issue 10, p630-642. 13p. http://dx.doi.org/10.1038/nrm3658.
Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase. Pica, Andrea; Merlino, Antonello; Buell, Alexander K.; Knowles, Tuomas P. J.; Pizzo, Elio; D'Alessio, Giuseppe; Sica, Filomena; Mazzarella, Lelio. Acta Crystallographica: Section D. Oct2013, Vol. 69 Issue 10, p2116-2123. 8p. http://dx.doi.org/10.1107/S0907444913020507.
Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop.
Harijan, Rajesh K.; Kiema, Tiila R.; Karjalainen, Mikael P.;
Janardan, Neelanjana; Murthy, M. R. N.; Weiss, Manfred S.;
Michels, Paul A. M.; Wierenga, Rik K. Biochemical Journal. 10/1/2013, Vol. 455 Issue 1, p119-135. 17p. http://dx.doi.org/10.1042/BJ20130669.
Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states. Sander, Bodo; Tria, Giancarlo; Shkumatov, Alexander V.; Kim, Eun-Young; Grossmann, J. Günter; Tessmer, Ingrid; Svergun, Dmitri I.; Schindelin, Hermann. Acta Crystallographica: Section D. Oct2013, Vol. 69 Issue 10, p2050-2060. 11p. http://dx.doi.org/10.1107/S0907444913018714.
Interactive visualization tools for the structural biologist. Porebski, Benjamin T.; Ho, Bosco K.; Buckle, Ashley M. Journal of Applied Crystallography. Oct2013, Vol. 46 Issue 5, p1518-1520. 3p. http://dx.doi.org/10.1107/S0021889813017858.
Book
review:
Small Angle X-ray and Neutron Scattering from Solutions of Biological Macromolecules
by Dmitri I. Svergun, Michel H. J. Koch, Peter A Timmins, Roland P. May
Pogue
Oxford University Press, Oxford, 2013, ISBN 978-0-19-963953-3
The authors set out to provide a modern textbook on the application of small angle scattering (SAS) to biological macromolecules and have succeeded. The layout allows for note-taking in the wide margins, but I did not partake since my copy was signed by one of the authors. The heavy math associated with Fourier transforms and spherical harmonics is placed in the first two appendices so crystallographers, who should be well versed in these methods, can go right to the core of the topic and neophytes can absorb all this information in one nice bundle. Throughout the book, caveats associated with the SAS technique are provided that will help prevent novice users from making fatal or dumb mistakes. The authors also provide numerous examples for the reader and supply the names of various programs in the ATSAS package that would apply to that case.
The book is divided into four major parts: Theory and Experiment; Data Analysis Methods; Biological Applications of Solution SAS; and
Appendices. I've mentioned two of the four appendices already. The other two cover interactions between spherical molecules, and web resources.
Part 1 is further divided into chapters on scattering, instrumentation and, importantly, experimental setup and data processing. Part II covers analysis of data from monodisperse and polydisperse/interacting systems. Part III, which is the part that seems to be most needed by the community, covers static studies, kinetic and perturbation studies, analysis of interparticle interactions, and hybrid methods.
There is a Conclusions and Future Prospects section that provides a short retrospective and prospective on SAS. I hope everyone reads this section, as it also alludes to both the limitations and promise of
SAS.
I received a first printing of this book, and there are
few typographical/typesetting errors. The authors have set up a
web page where the community can input errata so that subsequent printings
will be errorless.
Here are a few items I've picked up recently to expand my thinking:
The Great Courses: Civil Liberties and the Bill of Rights by John E. Finn. The last time I took a course on constitutional law, I was in high school, three chief justices ago. This course was a great update on the rights provided through the 1st, 4th, 5th and 6th amendments and the later 14th amendment (not part of the Bill of Rights, actually). The only disappointment is that it stopped with the decisions of 2005 and a lot has happened since then.
Just to show I am not averse to learning about other continents, I picked a copy of Savage Continent: Europe in the Aftermath of World War II by Keith Lowe. I heard an interview with the author on NPR and it sounds like I will gain a new appreciation for post-war Europe. SPIE was having a sale on "field guides," three for two, and I couldn't pass up Special Functions for Engineers by Larry C. Andrews, Image Processing by Khan M. Iftekharuddin and Abdul A. Awwal and Probability, Random Processes and Random Data Analysis by Larry C. Andrews and Ronald L. Philips. A quick perusal shows these will be handy books to have on the shelf.
Joseph D. Ferrara
Chief Science Officer
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