Crystallography Newsletter Volume 8, No. 08, August 2016 Crystallography in the news

In this issue: August 1, 2016. It's not the job of researchers to become experts in public relations – that's why universities have press offices. However, more scientists now see the need to Rigaku X-ray forum control their own press. That demand has led to the emergence of an online tool for Crystallography in the news managing the practice: a free site called Kudos, which aims to help researchers maximize the reach and impact of their papers on social media, and measure the effects of their Survey of the month efforts. Last month's survey Product spotlight August 3, 2016. Mike Kent, a researcher in Sandia National Laboratories' Biological and Videos of the month Engineering Sciences Center, is studying a protein called Nef involved in HIV progression. He and his collaborators have developed a new hybrid method to study this HIV protein Lab in the spotlight that compromises the immune system. The method also could work on many other Upcoming events proteins that damage cellular processes and cause diseases. Useful link August 7, 2016. Bryan Chakoumakos, a researcher at the Department of Energy's Oak Recent crystallographic papers Ridge National Laboratory, has been elected fellow of the American Crystallographic Book review Association. Chakoumakos, who leads the Structure of Matter group in the Quantum Condensed Matter Division, has been recognized by the association for his excellence in research, service and leadership in the world of crystallography. Rigaku Oxford Diffraction invites all users of Rigaku equipment August 8, 2016. The Ueno group at Tokyo Institute of Technology has developed a new to join us on our X-ray forum strategy in which two different organometallic iridium (Ir) and palladium (Pd) metal complexes are immobilized into a single protein cage of apo-ferritin to construct a protein- based microcompartment.

August 9, 2016. Study finds enzyme "cannibalizes" itself to perform an essential reaction. LipA, in an unusual chemical arrangement, removes the sulfur from an iron-sulfur cluster that it already contains. The finding could have long-term applications in medicine and agriculture, and is also generally significant within biochemistry research, since solving the LipA mystery suggests a means by which other enzymes use sulfur in similar settings.

August 12, 2016. Dieter Bromme, of the University of British Columbia, describes a faster way to find medicines hiding in nature. Affinity crystallography identifies new, potent inhibitors of an enzyme involved in osteoporosis.

August 15, 2016. In a new study, researchers from the Cambridge Crystallographic Data www.rigakuxrayforum.com Centre (CCDC) and the U.S. Department of Energy's (DOE's) Argonne National Laboratory have teamed up to capture neon within a porous crystalline framework.

Here you can find discussions about software, general crystallography issues and more. It’s August 17, 2016. Researchers from Lawrence Berkeley National Laboratory uncovered the also the place to download the latest version of molecular mechanism that activates a bacterium's pathogenic genes. The key, they found, E. coli Pro was in the way DNA is packaged. By studying the up close, the research team Rigaku Oxford Diffraction’s CrysAlis software determined that the interaction between the DNA and the HU proteins was triggering for single crystal data processing. gene expressions that resulted in pathogenicity.

We look forward to seeing you on there soon. August 22, 2016. The Department of Chemistry, B Borooah College, organised an outreach programme of the International Union of Crystallography on August 20. The Survey of the month main theme of the event is to promote crystallography education among the students of the North-East and also to share the information that India is hosting the 24th International Union of Crystallography Congress from August 21, 2017, at Hyderabad.

August 24, 2016. Enhanced interrogation is coming to molecular structure studies in the form of MOFs, or metal-organic frameworks. These sturdy crystalline networks hold uncooperative molecules still while they are doused with X-rays. But resorting to MOFs doesn't stretch, distort, or break molecules. It merely keeps them still for analysis by means of X-ray crystallography or nuclear magnetic resonance spectroscopy.

August 25, 2016.Two specific classes of calcium channel blockers, commonly prescribed for patients with heart diseases, develop separate therapeutic effects based on their actions at varied sites on the calcium channel molecule. This discovery was made through the use of X-ray crystallography.

August 25, 2016. Rice University structural biologist Yizhi Jane Tao and geneticist Weiwei Zhong have won a prestigious National Institutes of Health R01 grant to study how the Orsay virus infects a specific worm. They hope to reveal universal details about how viruses infect the intestine of animals, including humans, and how to fight them. The five- year award for $1.25 million will help the researchers continue their study of the Orsay virus.

Product spotlight: XtalCheck

The XtalCheck system is an automated tool for performing in situ crystallography experiments on your existing X-ray diffraction system. Protein crystallography often requires screening large numbers of crystals to identify samples that are suitable for X-ray diffraction experiments. Specifically, crystallographers usually loop and cryo-freeze samples for X-ray screening to identify whether the sample contains a protein or salt and to evaluate diffraction resolution, mosaicity and other crystal parameters. This iterative process of mounting and screening of many samples is time consuming and rarely automated. The XtalCheck system addresses this bottleneck by automating diffraction data collection for crystals directly from SBS format crystallization plates. For more >

Last month's survey

Rigaku's XtalCheck system for automated in situ crystallography

Lab in the spotlight

Prof. Elspeth Garman Professor of Molecular Biophysics University of Oxford Videos of the month The Garman group focuses on improving methods for structural Funny video biology and particularly for Macromolecular Crystallography (MX) to enable problems not previously accessible to structure solution to be tackled. This work currently includes studies on 100K and room temperature (RT) radiation damage, modelling the 3-D distribution of absorbed dose during an MX experiment, and the accurate quantitative analysis of the trace elements in proteins using microbeam Proton Induced X-ray Emission (microPIXE). The group also solves protein structures, one of the most recent being arylamine N-acetyltransferase from Mycobacterium tuberculosis.

If your latest research proposal was turned down, we have the perfect video to cheer you up.

Science video

Useful link

Growing Crystals That Will Make Your Crystallographer Happy A Case of Crystal Clarity by Elspeth Garman Paul D. Boyle, Department of Chemistry, Western University

Usually when we want to see the structure and shape of objects we can look at them with our eyes or, if the Practically every chemist knows the necessity of recrystallization as a method of objects are quite small, through light microscopes. purification. What is less well known, however, is methods by which "X-ray quality" However, really tiny things like the proteins in our crystals may be obtained. The purpose of this monograph is to briefly and informally bodies can't be seen with visible light. Instead we use outline some of the methods which can be used to obtain single crystals suitable for X-ray a technique called X-ray crystallography to determine diffraction studies. the structure and shape of these objects.

Selected recent crystallographic papers

To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent. Dahanayake, Jayangika N.; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R. Molecular Simulation. Aug2016, Vol. 42 Issue 12, Upcoming events p1001-1013. 13p. DOI: 10.1080/08927022.2016.1139108.

JASIS, September 7 – 9, 2016 in Chiba, Japan Conformational Changes and Flexibility of DNA Devices Observed by Small-

Angle X-ray Scattering. Bruetzel, Linda K.; Gerling, Thomas; Sedlak, Steffen M.; International Soft Matter Conference Walker, Philipp U.; Zheng, Wenjun; Dietz, Hendrik; Lipfert, Jan. Nano Letters. Aug2016, (ISMC2016), September 12 – 16, 2016 in Vol. 16 Issue 8, p4871-4879. 9p. DOI: 10.1021/acs.nanolett.6b01338. Grenoble, France

Accurate optimization of amino acid form factors for computing small-angle X- International Small-Angle Scattering Conference ray scattering intensity of atomistic protein structures. Tong, Dudu; Yang, Sichun; (SAS), September 13 – 18, 2016 in Berlin, Lu, Lanyuan. Journal of Applied Crystallography. Aug2016, Vol. 49 Issue 4, p1148-1161. Germany 13p. DOI: 10.1107/S1600576716007962.

See full list > In situ identification and absolute separation of small molecules by single crystal X-ray diffraction in metal-organic frameworks. Gao, Heng Ya; Zhang, Le; Yan, Chang Sheng; Meng, Li Na; Li, Jian Qiang; Meng, Pan Pan; Gong, Le Le; Luo, Feng. CrystEngComm. 8/7/2016, Vol. 18 Issue 29, p5429-5433. 5p. DOI: 10.1039/c6ce01085g.

SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. Schindler, Christina E.M.; de Vries, Sjoerd J.; Sasse, Alexander; Zacharias, Martin. Structure. Aug2016, Vol. 24 Issue 8, p1387-1397. 11p. DOI: 10.1016/j.str.2016.06.007.

Group 12 complexes of 2,6-bis([(2-pyridinylmethyl)thio]methyl)pyridine: Synthesis and characterization by X-ray crystallography and proton NMR. Carra, Bradley J.; Till, Stephanie N.; VanGundy, Robert A.; Pike, Robert D.; Bebout, Deborah C. Polyhedron. Aug2016, Vol. 114, p278-285. 8p. DOI: 10.1016/j.poly.2015.12.038.

Computational Simulation of the Activation Cycle of Gα Subunit in the G Protein Cycle Using an Elastic Network Model. Kim, Min Hyeok; Kim, Young Jin; Kim, Hee Ryung; Jeon, Tae-Joon; Choi, Jae Boong; Chung, Ka Young; Kim, Moon Ki. PLoS ONE. 8/2/2016, Vol. 11 Issue 8, p1-20. 20p. DOI: 10.1371/journal.pone.0159528.

Structural modeling of G-protein coupled receptors: An overview on automatic web-servers. Busato, Mirko; Giorgetti, Alejandro. International Journal of Biochemistry & Cell Biology. Aug2016 Part B, Vol. 77, p264-274. 11p. DOI: 10.1016/j.biocel.2016.04.004.

Discovery of pyrido[3,4-g]quinazoline derivatives as CMGC family protein kinase inhibitors: Design, synthesis, inhibitory potency and X-ray co?crystal structure. Esvan, Yannick J.; Zeinyeh, Wael; Boibessot, Thibaut; Nauton, Lionel; Théry, Vincent; Knapp, Stefan; Chaikuad, Apirat; Loaëc, Nadège; Meijer, Laurent; Anizon, Fabrice; Giraud, Francis; Moreau, Pascale. European Journal of Medicinal Chemistry. Aug2016, Vol. 118, p170-177. 8p. DOI: 10.1016/j.ejmech.2016.04.004.

Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase. Villa, Fabrizio; Simon, Aline C.; Ortiz Bazan, Maria Angeles; Kilkenny, Mairi L.; Wirthensohn, David; Wightman, Mel; Matak-Vinkov?c, Dijana; Pellegrini, Luca; Labib, Karim. Molecular Cell. Aug2016, Vol. 63 Issue 3, p385-396. 12p. DOI: 10.1016/j.molcel.2016.06.009.

Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules. Caterino, Marco; Petruk, Ariel A.; Vergara, Alessandro; Ferraro, Giarita; Marasco, Daniela; Doctorovich, Fabio; Estrin, Dario A.; Merlino, Antonello. Dalton Transactions: An International Journal of Inorganic Chemistry. 8/14/2016, Vol. 45 Issue 30, p12206-12214. 9p. DOI: 10.1039/c6dt01685e.

2.4 Å resolution crystal structure of human TRAP1 , the Hsp90 paralog in the NM mitochondrial matrix. Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun; Chang, Changsoo; Tsai, Francis T. F.; Lee, Sukyeong. Acta Crystallographica Section D: Structural Biology. Aug2016, Vol. 72 Issue 8, p904-911. 7p. DOI: 10.1107/S2059798316009906.

Monitoring conformational heterogeneity of the lid of DnaK substrate-binding domain during its chaperone cycle. Banerjee, Rupa; Jayaraj, Gopal Gunanathan; Peter, Joshua Jebakumar; Kumar, Vignesh; Mapa, Koyeli. FEBS Journal. Aug2016, Vol. 283 Issue 15, p2853-2868. 16p. DOI: 10.1111/febs.13769.

On Ramachandran angles, closed strings and knots in protein structure. Si Chen; Antti J Niemi. Journal of Physics: D Applied Physics. 8/10/2016, Vol. 49 Issue 31, p1-1. 1p. DOI: 10.1088/0022-3727/49/31/315401.

Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin. Ju Yaen Kim; Masato Nakayama; Hiroshi Toyota; Genji Kurisu; Toshiharu Hase. Journal of Biochemistry. Aug2016, Vol. 160 Issue 2, p101- 109. 9p. DOI: 10.1093/jb/mvw016.

Mechanism of substrate specificity of phosphatidylinositol phosphate kinases. Yagmur Muftuoglu; Yi Xue; Xiang Gao; Dianqing Wu; Ya Ha. Proceedings of the National Academy of Sciences of the United States of America. 8/2/2016, Vol. 113 Issue 31, p8711-8716. 6p. DOI: 10.1073/pnas.1522112113.

High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits. Schiebel, Johannes; Krimmer, Stefan G.; Röwer, Karine; Knörlein, Anna; Wang, Xiaojie; Park, Ah Young; Stieler, Martin; Ehrmann, Frederik R.; Fu, Kan; Radeva, Nedyalka; Krug, Michael; Huschmann, Franziska U.; Glöckner, Steffen; Weiss, Manfred S.; Mueller, Uwe; Klebe, Gerhard; Heine, Andreas. Structure. Aug2016, Vol. 24 Issue 8, p1398-1409. 12p. DOI: 10.1016/j.str.2016.06.010.

Collision-free configuration-spaces in macromolecular crystals. Chirikjian, Gregory S.; Shiffman, Bernard. Robotica. Aug2016, Vol. 34 Issue 8, p1679-1704. 26p. DOI: 10.1017/S0263574715001046.

Profile of James M. Berger. Viegas, Jennifer. Proceedings of the National Academy of Sciences of the United States of America. 8/9/2016, Vol. 113 Issue 32, p8885-8887. 3p. DOI: 10.1073/pnas.1610739113.

Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology. Hahn, Alexander; Parey, Kristian; Bublitz, Maike; Mills, Deryck J.; Zickermann, Volker; Vonck, Janet; Kübrandt, Werner; Meier, Thomas. Molecular Cell. Aug2016, Vol. 63 Issue 3, p445-456. 12p. DOI: 10.1016/j.molcel.2016.05.037.

Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115. Nakamichi, Yusuke; Oiki, Sayoko; Mikami, Bunzo; Murata, Kousaku; Hashimoto, Wataru. Protein Journal. Aug2016, Vol. 35 Issue 4, p300-309. 10p. DOI: 10.1007/s10930-016- 9673-y.

Crystal structure of 5-[(4-carboxybenzyl)oxy]-isophthalic acid. Faizi, Md. Serajul Haque; Ahmad, Musheer; Ali, Akram; Potaskalov, Vadim A. Acta Crystallographica: Section E. Aug2016, Vol. 72 Issue 8, p1219-1222. 9p. DOI: 10.1107/S2056989016011762.

Synthesis, characterization, X-ray crystallography analysis, and catalytic activity of bis(2-pyridylmethyl)amine copper complexes containing coupled pendent olefinic arms in atom transfer radical addition (ATRA) reactions. Bussey, Katherine A.; Cavalier, Annie R.; Mraz, Margaret E.; Oshin, Kayode D.; Sarjeant, Amy; Pintauer, Tomislav. Polyhedron. Aug2016, Vol. 114, p256-267. 12p. DOI: 10.1016/j.poly.2015.12.043.

Capturing neon – the first experimental structure of neon trapped within a metal-organic environment. Wood, Peter A.; Sarjeant, Amy A.; Yakovenko, Andrey A.; Ward, Suzanna C.; Groom, Colin R. Chemical Communications. 8/21/2016, Vol. 52 Issue 65, p10048-10051. 4p. DOI: 10.1039/c6cc04808k.

Book review

This month's theme is women in science. I came across Unlocking the Clubhouse listening to Fresh Air and Rise of the Rocket Girls listening to Science Friday, both on NPR. I highly recommend fathers of young girls read both books as they give insight into overcoming the "but you're a girl" mentality of many people.

Unlocking the Clubhouse: Women in Computing by Jane Margolis and Allan Fisher, 2002, MIT Press, Cambridge, 182 pages, ISBN: 978-0262632690.

This is a report on how computer science has become male dominated over the last 30 years. The authors' analysis suggests this started in the 1980s with the first widespread distribution of home computers like the TRS-80, Commodore 64 and Apple II. They further suggest that these computers wound up in the hands of boys, mostly, since the machines provided a release for less social boys that more social girls did not need. The authors followed several cohorts through the computer science program at Carnegie Mellon University and found that the women tended to lose confidence more quickly than their male counterparts. The loss of confidence and failure to become part of the male culture caused a large dropout rate. Finally, the authors looked at how CMU reversed these trends by first teaching practical applications of computer science, providing a more gender neutral environment and improving teaching. The result is much higher retention and matriculation rates for women in the computer science program at CMU.

My takeaway lesson from this book is that fathers need to work with their daughters in the same way they work with boys in terms of teaching the basics: how use computers, program them and take them apart and put them back together.

Rise of the Rocket Girls: The Women Who Propelled Us, From Missiles to the Moon to Mars Nathalia Holt, 2016, Little, Brown and Co., New York, 352 pages, ISBN: 978-0316338929.

This book is a history of the women at the Jet Propulsion Laboratory. I have often asked myself why it's called the JPL: the only thing the lab had to do with jet propulsion was the design of rocket motors to launch heavy bombers off aircraft carriers during WWII. The reason the word "jet" is used and not "rocket" has to do with the wider defense community's belief that rockets were a bad idea at the time of JPL's birth in the late 1930s. Everything JPL has done since has involved getting objects into space and monitoring them once there.

Before electronic computers became commonplace, "human computers" were the machines that generated the algorithms and performed the calculations needed to predict the motions of the planets, construct buildings, etc. Macie Roberts, the manager of Computers at JPL, created a team made up entirely of talented young women. They were engineers and scientists, some with degrees and some without. These pioneering women calculated the yields of rocket propellants and trajectories for the original Corporal and Sargent rockets for the Army to the first American satellite, Explorer, for Mercury, Gemini, Apollo manned programs, and the host of subsequent satellites from Mariner and Viking to Voyager and beyond. First they used slide rules and tables, then Fridon calculators. When electronic computers came into the picture they became the first coders, first in assembly and then FORTRAN.

The author shows how the principles that allowed women to succeed as scientists that were outlined in Unlocking the Clubhouse could work, long before the studies were done at Carnegie Mellon University.

Review by Joseph D. Ferrara, Ph.D. Deputy Director, X-ray Research Laboratory, Rigaku

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