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Rigaku Crystallography Newsletter
Volume 7, No. 4, April 2015
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In this issue:


Survey of the month

April 2015 survey

survey



Science videos of the month
Alexander McPherson presented the Fankuchen Award lecture at the 2013 ACA meeting in Honolulu, HI

video

McPherson's lecture was titled, "Let Us Now Praise Famous Men". Richard E. Dickerson received the 2013 ACA Fankuchen Award, but he was unable to travel to the ACA meeting.

video



Upcoming events

• RapiData Collection and Structure Solving, May 3 – 8, 2015 in Menlo Park, CA, USA.

• 61st Benzon Symposium: “Structural Biology on the Move”, August 24 – 27, 2015 in Copenhagen, Denmark. Abstract deadline is May 1, 2015.

See full list >


Last month's survey

Many scientists like to cook, supposedly because it is an experiment that you can eat.

For the readers of this newsletter, it would be interesting to know what percentage find cooking rewarding and fun.

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Crystallography in the news

April 2, 2015. Researchers led by Min Guo at Scripps Research Institute Florida report they have used X-ray crystallography to determine how borrelidin jams its protein target, threonyl-tRNA synthetase. The structural insights could enable drug developers to massage the molecule, which also has potent antifungal, antimalarial, and anticancer properties, into a viable therapeutic.

April 7, 2015. Researchers from the School of Medicine at The University of Texas Health Science Center at San Antonio today revealed the molecular structure of the cytotoxin from Mycoplasma pneumoniae, a widespread, highly contagious bacterium that infects the lungs.

April 9, 2015. Scientists at Texas Biomedical Research Institute in San Antonio are receiving funding from the National Institutes of Health in the form of a $2.36 million R01 grant over the next five years to focus efforts on exploring and developing a novel mechanism of Filovirus detection using llama antibodies.

April 13, 2015. Scientists from Jülich, Grenoble, Frankfurt and Moscow uncovered the atomic structure of KR2, a light-driven transporter for sodium ions that had only recently been discovered. Based on the structural information the team then identified a simple way to turn KR2 from a sodium into a potassium pump.

April 15, 2015. G protein coupled receptors (GPCRs) are essential drug targets for therapeutic intervention. Biased ligand signaling is a new approach to GPCR drug discovery. The concept is simply promoting selective interaction of the receptor through a smaller number of proteins than it normally interacts with.

April 17, 2015. An editorial in Nature Chemical Biology is critical of the data quality in the Protein Structure Database (PDB). It emphasized that while structural biology advances have democratized access to biomolecular snapshots, high standards must be maintained to ensure their utility.

April 20, 2015. Scientists at the University of York have identified problems with nearly half of the structural data on carbohydrate molecules available to the scientific community.

April 21, 2015. Research teams led by Edward Yu of Iowa State University and the Ames Laboratory have described the structures of two proteins they believe pump antibiotics from bacteria, allowing the bacteria to resist medications. One of the protein pumps, known as MtrF, is believed to be the mechanism that allows gonorrhea bacteria to resist certain antibiotics.

April 23, 2015. With a sophisticated X-ray analysis, a US-German team of scientists has solved the molecular structure of an important regulator for blood pressure in the human body.

April 30, 2015. Rigaku Corp. today announced that the acquisition of Agilent’s X-Ray diffraction business was completed. From April 30, ex-XRD group in Agilent is combined with Rigaku’s single-crystal X-ray business to form a new business unit, Rigaku Oxford Diffraction.


Product spotlight: ACTOR: Automated crystal transport orientation and retrieval robot

ACTOR™ is a proven commercial solution for automating routine crystal screening and data collection at both synchrotron beam lines and home laboratories. Compatible with almost any goniometer and detector combination, the ACTOR eliminates much of the physical handling of samples required during crystal screening and data collection.

Rapid automatic crystal screening
ACTOR allows you to screen up to 30 samples per hour. Adding automation to your structure solution pipeline also complements the high throughput needed for fragment-based screening projects and structural genomics programs. ACTOR enables you to quickly screen many crystals for optimal diffraction qualities and cryo-conditions and includes ranking software to assist you in comparing samples and finding the best crystals for data collection.

ACTOR

Visit Rigaku.com for more information about ACTOR.


Lab spotlight: The Vrielink Group

Alice Vrielink
Professor of Structural Biology
School of Biomedical Biomolecular and Chemical Sciences
University of Western Australia

The Vrielink Group

The Vrielink group members are primarily interested in the structural aspect of enzyme function and mechanism, as well as understanding the structural factors underlying gene transcription. In the area of enzyme function their work can be divided into two main categories: redox catalysis in flavoenzyme oxidases and substrate channeling in multifunctional enzymes. In the transcription field they are pursuing structural and biophysical studies on a number of important factors governing transcription elongation. In addition, they are pursuing ultra-high resolution crystallographic studies of protein folding, stability and interactions with prosthetic groups.

The Vrielink Group

 


Useful link: 3-D Method Aids Study of Proteins

Researchers from the Universitat Autònoma de Barcelona’s Institute of Biotechnology and Biomedicine (IBB) and the University of Warsaw have developed AGGRESCAN3D, a new computational method that allows studying the structure of folded globular proteins and their propensity for forming toxic protein aggregates. Read more >


Useful link: International Union of Crystallography Server

The International Union of Crystallography is a non-profit scientific union serving the worldwide interests of crystallographers and other scientists employing crystallographic methods.

This server supplies information on crystallography from the IUCr, and pointers to other information services of interest to crystallographers.


Selected recent crystallographic papers

Crystal Structure and Prediction. Thakur, Tejender S.; Dubey, Ritesh; Desiraju, Gautam R. Annual Review of Physical Chemistry. 2015, Vol. 66, p21-42. 19p. DOI: 10.1146/annurev-physchem-040214-121452.

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Lyubimov, Artem Y.; Murray, Thomas D.; Koehl, Antoine; Araci, Ismail Emre; Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Cohen, Aina E.; Soltis, S. Michael; Baxter, Elizabeth L.; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Berger, James M. Acta Crystallographica: Section D. Apr2015, Vol. 71 Issue 4, p928-940. 13p. DOI: 10.1107/S1399004715002308.

Multifunctional cellulolytic auxiliary activity protein HcAA10-2 from Hahella chejuensis enhances enzymatic hydrolysis of crystalline cellulose. Ghatge, Sunil; Telke, Amar; Waghmode, Tatoba; Lee, Yuno; Lee, Keun-Woo; Oh, Doo-Byoung; Shin, Hyun-Dong; Kim, Seon-Won. Applied Microbiology & Biotechnology. Apr2015, Vol. 99 Issue 7, p3041-3055. 15p. DOI: 10.1007/s00253-014-6116-6.

Radiation decay of thaumatin crystals at three X-ray energies. Liebschner, Dorothee; Rosenbaum, Gerold; Dauter, Miroslawa; Dauter, Zbigniew. Acta Crystallographica: Section D. Apr2015, Vol. 71 Issue 4, p772-778. 7p. DOI: 10.1107/S1399004715001030.

Time-lapse anomalous X-ray diffraction shows how Fe2+ substrate ions move through ferritin protein nanocages to oxidoreductase sites. Pozzi, Cecilia; Di Pisa, Flavio; Lalli, Daniela; Rosa, Camilla; Theil, Elizabeth; Turano, Paola; Mangani, Stefano. Acta Crystallographica: Section D. Apr2015, Vol. 71 Issue 4, p941-953. 13p. DOI: 10.1107/S1399004715002333.

A Fluorescent Probe for Imaging p53—MDM2 Protein—Protein Interaction. Liu, Zhenzhen; Miao, Zhenyuan; Li, Jin; Fang, Kun; Zhuang, Chunlin; Du, Lupei; Sheng, Chunquan; Li, Minyong. Chemical Biology & Drug Design. Apr2015, Vol. 85 Issue 4, p411-417. 7p. DOI: 10.1111/cbdd.12434.

Luciferin and derivatives as a DYRK selective scaffold for the design of protein kinase inhibitors. Rothweiler, Ulli; Eriksson, Jonas; Stensen, Wenche; Leeson, Frederick; Engh, Richard A.; Svendsen, John S. European Journal of Medicinal Chemistry. Apr2015, Vol. 94, p140-148. 9p. DOI: 10.1016/j.ejmech.2015.02.035.

A practical kit for micro-scale application of the ceiling crystallisation method. Adawy, Alaa; Corbeek, Wil; de Ronde, Erik; van Enckevort, Willem J. P.; de Grip, Willem J.; Vlieg, Elias. CrystEngComm. 2015, Vol. 17 Issue 13, p2602-2605. 4p. DOI: 10.1039/c4ce01814a.

Integrative, dynamic structural biology at atomic resolution—it's about time. van den Bedem, Henry; Fraser, James S. Nature Methods. Apr2015, Vol. 12 Issue 4, p307-318. 12p. DOI: 10.1038/nmeth.3324.

A Primer to Single-Particle Cryo-Electron Microscopy. Cheng, Yifan; Grigorieff, Nikolaus; Penczek, Pawel A.; Walz, Thomas. Cell. Apr2015, Vol. 161 Issue 3, p438-449. 12p. DOI: 10.1016/j.cell.2015.03.050.

You are lost without a map: Navigating the sea of protein structures. Lamb, Audrey L.; Kappock, T. Joseph; Silvaggi, Nicholas R. BBA - Proteins & Proteomics. Apr2015, Vol. 1854 Issue 4, p258-268. 11p. DOI: 10.1016/j.bbapap.2014.12.021.

Structural classification of steroid-binding sites on proteins by coarse-grained atomic environment and its correlation with their biological function. Hori-Tanaka, Yasuha; Yura, Kei; Takai-Igarashi, Takako; Tanaka, Hiroshi. Steroids. Apr2015, Vol. 96, p81-88. 8p. DOI: 10.1016/j.steroids.2015.01.015.

Palladium(II) complexes of anthraquinone-based As–O–As type and Se–O–Se type bipodands. Synthesis, X-ray crystallography and catalytic properties. Mariappan, Kadarkaraisamy; Ragothaman, Janani Sindhu; Balasubramanian, Vinothini; Hoffman, Mariah; Alaparthi, Madhubabu; Sykes, Andrew G. Inorganica Chimica Acta. Apr2015, Vol. 429, p46-50. 5p. DOI: 10.1016/j.ica.2014.12.028.

Taking a closer look for a broader view: combining powder diffraction with electron crystallography for a better understanding of modulated structures. Palatinus, Lukáš. Acta Crystallographica: Section B, Structural Science, Crystal Engineering & Materials. Apr2015, Vol. 71 Issue 2, p125-126. 2p. DOI: 10.1107/S2052520615005910.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography. Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N.; Nishida, Clinton R.; Ortiz de Montellano, Paul R. Journal of Biological Chemistry. 4/17/2015, Vol. 290 Issue 16, p10000-10017. 18p. DOI: 10.1074/jbc.M114.627935.

High-pressure protein crystallography of hen egg-white lysozyme. Yamada, Hiroyuki; Nagae, Takayuki; Watanabe, Nobuhisa. Acta Crystallographica: Section D. Apr2015, Vol. 71 Issue 4, p742-753. 12p. DOI: 10.1107/S1399004715000292.

X-ray crystallography-promoted drug design of carbonic anhydrase inhibitors. Ivanova, Jekaterina; Leitans, Janis; Tanc, Muhammet; Kazaks, Andris; Zalubovskis, Raivis; Supuran, Claudiu T.; Tars, Kaspars. Chemical Communications. 4/28/2015, Vol. 51 Issue 33, p7108-7111. 4p. DOI: 10.1039/c5cc01854d.

High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Fukuda, Yohta; Inoue, Tsuyoshi. Chemical Communications. 4/18/2015, Vol. 51 Issue 30, p6532-6535. 4p. DOI: 10.1039/c4cc09553g.

Achieving grazing-incidence ultra-small-angle X-ray scattering in a laboratory setup. Zheng, Nan; Yi, Zhiyong; Li, Zhenzhen; Chen, Ran; Lai, Yuqing; Men, Yongfeng. Journal of Applied Crystallography. Apr2015, Vol. 48 Issue 2, p608-612. 5p. DOI: 10.1107/S1600576715001752.

Modeling the ComD/ComE/ comcde interaction network using small angle X-ray scattering. Sanchez, Dyana; Boudes, Marion; Tilbeurgh, Herman; Durand, Dominique; Quevillon-Cheruel, Sophie. FEBS Journal. Apr2015, Vol. 282 Issue 8, p1538-1553. 16p. DOI: 10.1111/febs.13240.

Nebula: reconstruction and visualization of scattering data in reciprocal space. Reiten, Andreas; Chernyshov, Dmitry; Mathiesen, Ragnvald H. Journal of Applied Crystallography. Apr2015, Vol. 48 Issue 2, p604-607. 4p. DOI: 10.1107/S1600576715001788.

Antibacterial properties and atomic resolution X-ray complex crystal structure of a ruthenocene conjugated β-lactam antibiotic. Lewandowski, Eric M.; Skiba, Joanna; Torelli, Nicholas J.; Rajnisz, Aleksandra; Solecka, Jolanta; Kowalski, Konrad; Chen, Yu. Chemical Communications. 4/11/2015, Vol. 51 Issue 28, p6186-6189. 4p. DOI: 10.1039/c5cc00904a.

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy. Langkilde, Annette E.; Morris, Kyle L.; Serpell, Louise C.; Svergun, Dmitri I.; Vestergaard, Bente. Acta Crystallographica: Section D. Apr2015, Vol. 71 Issue 4, p882-895. 14p. DOI: 10.1107/S1399004715001674.


Book review:

What Should We Be Worried About?: Real Scenarios That Keep Scientists Up at Night
(Edge Question Series), edited by John Brockman, Harper Perennial, New York, 2014, 528 pages, ISBN: 978-0062296238.

This Idea Must Die: Scientific Theories That Are Blocking Progress
(Edge Question Series), edited by John Brockman, Harper Perennial, New York, 2015, 592 pages, ISBN: 978-0062374349.

John Brockman, founder of the Edge Foundation, a web-based think tank, edited both of these books. Each year he asks a large group of people—many of them members of the Edge Foundation—the question for the year. Each book is a collection of short essays that answer the title question from thinkers in many fields. Several are from authors that have been reviewed here in the past, including Sean Carroll, Steven Pinker, Charles Seife, Nicholas Nassim Taleb and Sherry Turkle, so some of the answers may be familiar to you. Each essay is accompanied by a short bio of the author and the title, or titles, of some recent book.

The first book came to me as a recommendation from Amazon. I picked up the second book after hearing an interview with Seth Lloyd and Sean Carroll on Science Friday last month.

What Should We Be Worried About is one of the most depressing books I have read in a long time. As if I already didn’t lie awake thinking about global warming, financial collapse, human population-thinning disease, or stupidity, now I have about 170 other things to worry about it. Only read this book if your glass is half full or you are current on your selective serotonin reuptake inhibitor prescription. One vignette is slightly humorous. It discusses protecting young ears from the seven words the FCC won’t let on the air. However, the author suggests making something taboo makes it all the more interesting, and that’s the problem. Make the seven words everyday and no one will care.

The second book, This Idea Must Die, is based on the tenet of Planck that an existing paradigm will subside when the last proponent is dead. This is much more upbeat in the sense that the essays present solutions to problems as opposed to just listing problems as in the former book. The ideas that “must die” range far and wide: from the idea of the universe, as opposed to the multiverse, to races, anonymous peer review and bad statistics.


I just finished volumes one and two of the epic biography of Lyndon Johnson by Robert A. Caro. When I picked up these books I did not think this subject would hold my attention, but both The Path to Power and Means of Ascent did. The books are not just about Johnson, but provide a detailed look into life in the Texas Hill Country in the early 20th century, as well as Texas and US politics until 1948. I will start Master of the Senate this summer.

The Path to Power: The Years of Lyndon Johnson, Volume I, Robert A. Caro, Alfred A. Knopf, New York, 1990, 960 pages, ISBN: 978-0679729457

Means of Ascent: The Years of Lyndon Johnson, Volume II, Robert A. Caro, Alfred A. Knopf, New York, 1990, 562 pages, 978-0679733713

Joseph D. Ferrara, Ph.D.
Chief Science Officer

Rigaku


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