Crystallography in the news

April 2, 2014. A technology developed by Cornell scientists that prepares proteins for X-ray crystallography has made its way into the world marketplace: ADC Inc., a maker of scientific instruments located just outside Ithaca, has licensed the high-pressure cryocooler, called HPC-201, and has just fulfilled its first order to a research center in Japan.

April 3, 2014. Diamond Light Source, the UK's national synchrotron science facility, is celebrating an important milestone this month as a 2-year project to design and build a highly specialized in-vacuum X-ray detector for its new long wavelength life science beamline enters the commissioning phase. Beamline I23, which is currently under construction as part of Diamond's Phase III development, is the Long Wavelength Macromolecular Crystallography beamline and is optimized for operation in the wavelength range 1.5 to 4Å.

April 8, 2014. The structure of a key part of the machinery that allows cells to divide has been identified by researchers at the University of California, Davis, opening new possibilities for throwing a wrench in the machine and blocking runaway cell division in cancer. The structure of kinesin-5 allows for targeting it to treat various forms of cancer.

April 15, 2014. Sun Hur, assistant professor of biological chemistry and molecular pharmacology at Harvard Medical School, has been studying RIG-I and other members of the innate cellular antiviral response for some time. She has provided a structural rationale for how ubiquitin helps RIG-I do its job, and how that might help keep the immune system from getting out of hand.

April 15, 2014. Professor Joseph Ng from the University of Alabama in Huntsville has an experiment that is set to fly to the International Space Station (ISS) that could shed new light on the roles enzymes play in biological processes. The experiment, Protein Crystals for Neutron Crystallography (PC4NC), studies an enzyme inorganic pyro­phosphatase (IPPase).

April 21, 2014. An experiment just launched into orbit by a team of Caltech researchers could be an important step toward understanding a devastating neurodegenerative disease. Led by Pamela Bjorkman, Max Delbrück Professor of Biology, the project will investigate whether the huntingtin protein can form crystals in microgravity aboard the ISS, crystals that are crucial for understanding the molecular structure of the protein.

April 22, 2014. A protein phosphatase, called PP5, is scheduled to be launched to the ISS. Richard E. Honkanen, professor of biochemistry in the University of South Alabama College of Medicine and the lead researcher on the PP5 project, said the protein is considered a validated target for anti-tumor drug development.

April 22, 2014. A landmark study from The University of Queensland has described the ultimate act of sacrifice and survival, in the plant world. The research sheds light on how the plant immune system, encompassing a pair of proteins, provides resistance against common plant diseases. When these proteins are disturbed by an infection, the infected cell dies allowing for the immunity of the entire plant.

April 24, 2014. A team led by scientists at The Scripps Research Institute (TSRI) working with the International AIDS Vaccine Initiative (IAVI) has discovered a new vulnerable site on the HIV virus. The newly identified site can be attacked by human antibodies in a way that neutralizes the infectivity of a wide variety of HIV strains.

Product spotlight: Rigaku Remote

Rigaku's RigakuRemote offers the ability to remotely monitor the status of a single crystal X-ray system from anywhere you can get an internet connection. It provides real-time updates of the state of your instrumentation, including video of the crystal and enclosure. Also included are current information about the scans being collected, and a JPEG view of the last diffraction image collected.

iOS and Android versions
RigakuRemote supports remote monitoring on both iOS and Android devices using a native app. The app allows you to connect to multiple instruments, so that you can easily monitor the status of your entire lab.

Web version
RigakuRemote also supports a web-based version, written using standard HTML and Javascript, that allows you to monitor the status of your instrumentation from any computer with a web browser.

Ask for more information.

Professor Adrian Goldman
Leadership Chair in Membrane Biology
Astbury Centre for Structural Molecular Biology
School of Biomedical Sciences
University of Leeds

Adrian's research group focuses on understanding interactions in or near the membrane. They are interested in bacterial autotransporter secretion and the host-pathogen interactions that lead to disease; in cell signalling in the RET tyrosine kinase receptor system; and in integral membrane pumps and channels, such as the T. maritima pyrophosphatase that they solved in 2012.

Current major projects include:

     •  Structure-function studies of integral membrane pyrophosphatases
     •  Understanding how trimeric autotransporters work
     •  Bacterial evasion of complement
     •  The mechanism of the RET tyrosine kinase

SBKB - The Structural Biology Knowledgebase is a free, comprehensive resource produced by collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG). The site offers you an easy way of keeping abreast of developments both by the PSI and more generally in the fields of structural genomics and structural biology. The SBKB serves as a continually updated portal to research data and other resources from the PSI. NPG provides a monthly update with synopses of important research advances, recent additions to a categorized library of research articles, as well as news and events in structural biology. You can register to receive a monthly email newsletter and subscribe to RSS feeds.

'Unconventional' Coordination Chemistry by Metal Chelating Fragments in a Metalloprotein Active Site. Martin, David P.; Blachly, Patrick G.; Marts, Amy R.; Woodruff, Tessa M.; De Oliveira, César A F.; Andrew McCammon, J.; Tierney, David L.; Cohen, Seth M. Journal of the American Chemical Society. 4/9/2014, Vol. 136 Issue 14, p5400-5406. 7p. http://dx.doi.org/10.1021/ja500616m.

Capturing the Hemoglobin Allosteric Transition in a Single Crystal Form. Shibayama, Naoya; Sugiyama, Kanako; Tame, Jeremy R. H.; Sam-Yong Park. Journal of the American Chemical Society. 4/2/2014, Vol. 136 Issue 13, p5097-5105. 9p. http://dx.doi.org/10.1021/ja500380e.

Characterization of the effects of phosphorylation by CK2 on the structure and binding properties of human HP1β. Munari, Francesca; Gajda, Michal Jan; Hiragami-Hamada, Kyoko; Fischle, Wolfgang; Zweckstetter, Markus. FEBS Letters. Apr2014, Vol. 588 Issue 7, p1094-1099. 6p. http://dx.doi.org/10.1016/j.febslet.2014.02.019.

Crystal and Solution Structure Analysis of FhuD2 from Staphylococcus aureus in Multiple Unliganded Conformations and Bound to Ferrioxamine-B. Podkowa, Krzysztof J.; Briere, Lee-Ann K.; Heinrichs, David E.; Shilton, Brian H. Biochemistry. 4/1/2014, Vol. 53 Issue 12, p2017-2031. 15p. http://dx.doi.org/10.1021/bi401349d.

Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center. Ohnuma, Takayuki; Umemoto, Naoyuki; Nagata, Takuya; Shinya, Shoko; Numata, Tomoyuki; Taira, Toki; Fukamizo, Tamo. BBA - Proteins & Proteomics. Apr2014, Vol. 1844 Issue 4, p793-802. 10p. http://dx.doi.org/10.1016/j.bbapap.2014.02.013.

Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans. Thiruselvam, Viswanathan; Sivaraman, Padavattan; Kumarevel, Thirumananseri; Ponnuswamy, Mondikalipudur Nanjappagounder. Biochemical & Biophysical Research Communications. Apr2014, Vol. 446 Issue 4, p945-951. 7p. http://dx.doi.org/10.1016/j.bbrc.2014.03.036.

Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation. Bojar, Daniel; Martinez, Jacobo; Santiago, Julia; Rybin, Vladimir; Bayliss, Richard; Hothorn, Michael. Plant Journal. Apr2014, Vol. 78 Issue 1, p31-43. 13p. http://dx.doi.org/10.1111/tpj.12445.

Crystallization and preliminary X-ray analysis of a novel type of lipolytic hydrolase from Bacillus licheniformis. Ju, Hansol; Pandian, Ramesh; Kim, Kyungmin; Kim, Kyeong Kyu; Kim, T. Doohun. Acta Crystallographica: Section F, Structural Biology Communications. Apr2014, Vol. 70 Issue 4, p473-475. 3p. http://dx.doi.org/10.1107/S2053230X14004142.

Crystallization and preliminary X-ray crystallographic analysis of importin-α from Neurospora crassa. Bernardes, Natalia E.; Takeda, Agnes A. S.; Freitas, Fernanda Z.; Bertolini, Maria Célia; Fontes, Marcos R. M. Acta Crystallographica: Section F, Structural Biology Communications. Apr2014, Vol. 70 Issue 4, p501-504. 4p. http://dx.doi.org/10.1107/S2053230X14005068.

Crystallizing Membrane Proteins in the Lipidic Mesophase.Experience with Human Prostaglandin E2 Synthase 1 and an Evolving Strategy. Li, Dianfan; Howe, Nicole; Dukkipati, Abhiram; Shah, Syed T.A.; Bax, Benjamin D.; Edge, Colin; Bridges, Angela; Hardwicke, Phil; Singh, Onkar M. P.; Giblin, Ged; Pautsch, Alexander; Pfau, Roland; Schnapp, Gisela; Wang, Meitian; Olieric, Vincent; Caffrey, Martin. Crystal Growth & Design. Apr2014, Vol. 14 Issue 4, p2034-2047. 14p. http://dx.doi.org/10.1021/cg500157x.

Integrative computational modeling of protein interactions. Rodrigues, João P. G. L. M.; Bonvin, Alexandre M. J. J. FEBS Journal. Apr2014, Vol. 281 Issue 8, p1988-2003. 16p. http://dx.doi.org/10.1111/febs.12771.

Mechanisms, kinetics, impurities and defects: consequences in macromolecular crystallization. McPherson, Alexander; Kuznetsov, Yurii G. Acta Crystallographica: Section F, Structural Biology Communications. Apr2014, Vol. 70 Issue 4, p384-403. 20p. http://dx.doi.org/10.1107/S2053230X14004816.

Modeling and control of crystal shape in continuous protein crystallization. Kwon, Joseph Sang-Il; Nayhouse, Michael; Christofides, Panagiotis D.; Orkoulas, Gerassimos. Chemical Engineering Science. Apr2014, Vol. 107, p47-57. 11p. http://dx.doi.org/10.1016/j.ces.2013.12.005.

Preliminary crystallographic analysis of the ankyrin-repeat domain of Arabidopsis thaliana AKT1: identification of the domain boundaries for protein crystallization. Chaves-Sanjuán, Antonio; Sánchez-Barrena, María José; González-Rubio, Juana María; Albert, Armando. Acta Crystallographica: Section F, Structural Biology Communications. Apr2014, Vol. 70 Issue 4, p509-512. 4p. http://dx.doi.org/10.1107/S2053230X14005093.

Preparation, crystallization, and preliminary crystallographic analysis of wild-type and mutant human TREM-2 ectodomains linked to neurodegenerative and inflammatory diseases. Kober, Daniel L.; Wanhainen, Kelsey M.; Johnson, Britney M.; Randolph, David T.; Holtzman, Michael J.; Brett, Tom J. Protein Expression & Purification. Apr2014, Vol. 96, p32-38. 7p. http://dx.doi.org/10.1016/j.pep.2014.01.015.

Progress in crystallization of major histocompatibility complex class I in vertebrates. Feng, Lei; Sun, Mingwei; Dong, Songpeng; Gao, Feng-Shan. Chinese Science Bulletin. Apr2014, Vol. 59 Issue 12, p1308-1316. 9p. http://dx.doi.org/10.1007/s11434-014-0211-z.

Protein Crystal Shape and Size Control in Batch Crystallization: ComparingModel Predictive Control with Conventional Operating Policies. Kwon, Joseph Sang-II; Nayhouse, Michael; Christofides, Panagiotis D.; Orkoulas, Gerassimos. Industrial & Engineering Chemistry Research. Apr2014, Vol. 53 Issue 13, p5002-5014. 13p. http://dx.doi.org/10.1021/ie400584g.

Structural biology: Making protein crystals fly. Doerr, Allison. Nature Methods. Apr2014, Vol. 11 Issue 4, p366-367. 2p. http://dx.doi.org/10.1038/nmeth.2913.

Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography. Amano, Yasushi; Yamaguchi, Tomohiko; Tanabe, Eiki. Bioorganic & Medicinal Chemistry. Apr2014, Vol. 22 Issue 8, p2427-2434. 8p. http://dx.doi.org/10.1016/j.bmc.2014.03.001.

Structure and closure of connexin gap junction channels. Oshima, Atsunori. FEBS Letters. Apr2014, Vol. 588 Issue 8, p1230-1237. 8p. http://dx.doi.org/10.1016/j.febslet.2014.01.042.

Structure and protective efficacy of the Staphylococcus aureus autocleaving protease EpiP. Kuhn, Misty L.; Prachi, Prachi; Minasov, George; Shuvalova, Ludmilla; Ruan, Jiapeng; Dubrovska, Ievgeniia; Winsor, James; Giraldi, Monica; Biagini, Massimiliano; Liberatori, Sabrina; Savino, Silvana; Bagnoli, Fabio; Anderson, Wayne F.; Grandi, Guido. FASEB Journal. Apr2014, Vol. 28 Issue 4, p1780-1793. 14p. http://dx.doi.org/10.1096/fj.13-241737.

Structure of a Class C GPCR Metabotropic Glutamate Receptor 1 Bound to an Allosteric Modulator. Huixian Wu; Chong Wang; Gregory, Karen J.; Gye Won Han; Hyekyung P. Cho; Yan Xia; Niswender, Colleen M.; Katritch, Vsevolod; Meiler, Jens; Cherezov, Vadim; Conn, P. Jeffrey; Stevens, Raymond C. Science. 4/4/2014, Vol. 344 Issue 6179, p58-58. 1/3p. http://dx.doi.org/10.1126/science.1249489.

The role of protein dynamics in GPCR function: insights from the β₂AR and rhodopsin. Manglik, Aashish; Kobilka, Brian. Current Opinion in Cell Biology. Apr2014, Vol. 27, p136-143. 8p. http://dx.doi.org/10.1016/j.ceb.2014.01.008.

Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases. Kožíšek, Milan; Lepšík, Martin; Grantz Šašková, Klára; Brynda, Jirí; Konvalinka, Jan; Rezácová, Pavlína. FEBS Journal. Apr2014, Vol. 281 Issue 7, p1834-1847. 14p. http://dx.doi.org/10.1111/febs.12743.

Weak protein-ligand interactions studied by small-angle X-ray scattering. Tuukkanen, Anne T.; Svergun, Dmitri I. FEBS Journal. Apr2014, Vol. 281 Issue 8, p1974-1987. 14p. http://dx.doi.org/10.1111/febs.12772.

X-ray crystal structure of voltage-gated proton channel. Takeshita, Kohei; Sakata, Souhei; Yamashita, Eiki; Fujiwara, Yuichiro; Kawanabe, Akira; Kurokawa, Tatsuki; Okochi, Yoshifumi; Matsuda, Makoto; Narita, Hirotaka; Okamura, Yasushi; Nakagawa, Atsushi. Nature Structural & Molecular Biology. Apr2014, Vol. 21 Issue 4, p352-357. 6p. http://dx.doi.org/10.1038/nsmb.2783.

Book review: Particle and Particle Systems Characterization:
                      Small Angle Scattering (SAS) Applications
     by Wilfried Gille
     CRC Press, Boca Raton, 2014, 336 pages, ISBN: 978-1466581777.

The author set out to present the applications of small angle scattering for particle systems. He has created a handbook of equations for dealing with chord length distributions; that is, the distributions of all lengths from one point on the surface of a particle to another point on the surface of a particle. There are many graphs and graphics to describe the various subtopics. Mathematica code examples are also provided. The book seems to be directed at scientists who might be studying two-phase systems and writing their own code to do so.

This book is divided into ten chapters: (1) Scattering experiments and structure functions, particles and the correlation of function of small-angle scattering, (2) Chord length distribution densities of selected elementary geometric figures, (3) Chord length distributions of infinitely long cylinders, (4) Particle-to-particle interference - a useful tool, (5) Scattering patterns and structure functions of Boolean models, (6) The "Dead Leaves" model, (7) Tessellations, fragment particles and puzzles, (8) Volume fraction of random two-phase samples for fixed order range L from γ(r,L), (9) Interrelations between the moments of the chord length distributions of random two-phase systems, and (10) Exercises on problems of particle characterization: examples.

The actual printing of my copy leaves much to be desired. It seems as if CRC was trying to conserve paper and ink: long equations are forced to fit on one line at the expense of making them barely readable. The inlining of equations in the main text also makes for difficult reading. I have discussed this with the publisher and have been told this is not normal.

Book review: The Sixth Extinction: An Unnatural History

     by Elizabeth Kolbert
     Henry Holt and Co, New York, 2014, 321 pages, ISBN: 978-0805092998.

I heard an interview with the author on NPR in late December and preordered my copy for February delivery. I finally got around to reading it now. The timing may be fortuitous, though, as the latest Intergovernmental Panel on Climate Change report is due out soon.

Kolbert paints a pretty bleak picture of the future. She spends considerable time studying several extinct species and the cause of their demise in the first part of the book. The extinction timeline is interspersed with species undergoing extinction now and species long gone. Some, like mastodons, seem to have died a slow death at human hands, while the great auk was clearly wiped out by humans. Species that died out a long time ago, like the ammonites and dinosaurs, are given their due.

Next, Kolbert explores the Anthropocene, or modern, era. She looks at the acidifying oceans, which has an impact on shelled creatures and reefs. She spends a couple of chapters examining how deforestation is changing the climate and causing "relaxation of species," a polite term describing the reduction of the number of species in an area as it is cut off from larger areas by manmade structures such as roads. Kolbert then looks at the Columbian exchange, which has had the effect of flattening the earth into one supercontinent again, exchanging species between places in a manner that could not have happened at such great speed without man.

She also describes how humans have been trying to save species like the Sumatran rhino through breeding programs, takes a look at how Homo sapiens did in the Neanderthals and, finally, at saving the DNA of species for posterity.

I tend to be an optimist. I would like to think "Don't worry. As long we keep exploring [other planets], humanity is going to survive," but I think the quote by Richard Leakey ("Homo sapiens might not only be the agent of the sixth extinction, but also risks being one of its victims") is more appropriate.

On the lighter side:

Life by Keith Richards and James Fox, Little, Brown and Co., New York, 2010, 576 pages, ISBN: 978-0316034418. Sex, drugs and rock-n-roll in no particular order other than chronological. I recommend having an iPod with Forty Licks on it so you can listen to the songs as the author describes the creation of the music.

Dance of the Reptiles: Rampaging Tourists, Marauding Pythons, Larcenous Legislators, Crazed Celebrities, and Tar-Balled Beaches: Selected Columns by Carl Hiaasen, 2014, Vintage, New York, 416 pages, ISBN: 978-0345807021. This book contains classic columns by Hiaasen from the Miami Herald on various topics over the last couple of decades. I now know where Mr. Hiaasen gets his ideas for his novels. The adage "truth is stranger than fiction" applies here.