Rigaku

Protein Crystallography Newsletter
Volume 6, No. 11, November 2014
subscribe

In this issue:


Survey of the Month

11/2014 survey

survey



Science Video of the Month
A new Live Fourier Transform demonstration

video

The Live Fourier Transform demonstration can be used to explain the patterns we see in X-ray scattering and diffraction experiments. The live FT program can be downloaded and should work on any modern mac with Python 2.7 with the OpenCV library. For more information, read more >

video



Dr. Frank Allen FRSC 1944-2014

Dr. Frank Allen

Frank Allen passed away at the age of 70 on November 11th. He played a pivotal role in the foundation of the Cambridge Structural Database as a member of the Chemical Crystallography Group at the University of Cambridge in the 1970s. He later became the Scientific Director and then the Executive Director of the Cambridge Crystallographic Data Centre. He was always a positive influence on the BCA and will be missed by all.


Upcoming Events

Groupe de Recherche Axé sur la Structure des Protéines on Monday, November 24, 2014 in Montreal, QC, Canada.

Macromolecular training class at Rigaku, February 18-25, 2015 at The Woodlands, TX. Class outline and online registration form.


Last Month's Survey

Forget about fear. Don't think about politics. From a scientific perspective, should people who are traveling from a country with a large number of Ebola cases be quarantined when arriving in countries with a small number of infections?

results


 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

book1

book2

like tweet Share

Crystallography in the news

October 31, 2014. "X marks the structure" is an overview of X-ray diffraction in 2014. Author Elisabeth Jeffries discovers that, from single crystals to powders and even proteins, there's a diffractometer for every structure.

November 5, 2014. Researchers have used DESY's X-ray light source PETRA III to investigate a photosynthesis subsystem in a near-natural state. According to scientists led by Privatdozentin Dr. Athina Zouni from the Humboldt University (HU) Berlin, X-ray diffraction experiments on the so-called photosystem II revealed structures that were as-yet unknown.

November 6, 2014. The Canadian Macromolecular Crystallography Facility (CMCF) has announced the successful solution of 500 protein structures using the Canadian Light Source. Many of these structures have been critical to the publication of 286 peer-reviewed journal articles. The first protein structure from the CLS was obtained in 2006 on the first CMCF beamline. In 2011, a second beamline was commissioned.

November 6, 2014. For the first time, Polycomb Repressive Complex 1 (PRC1) was imaged as it interacted with cellular machinery. Crystallographic images of the cancer-related enzyme may give insight into how proteins regulate genetic activity in disease processes.

November 10, 2014. Photographs by London-based photographer Max Alexander shed light on X-ray crystallography by capturing amazing crystal structures in objects and revealing how they are created.

November 10, 2014. Researchers at the University of Manchester discovered that certain microscopic organisms use the common vitamin B12 to break down toxic organohalides. The study explains how they used X-ray crystallography to visualize that vitamin B12 was key to the process, as it contains a reactive cobalt atom that breaks the carbon-halogen bond.

November 11, 2014. A study conducted in part at the U.S. Dept. of Energy's SLAC National Accelerator Laboratory has revealed how a key human protein, called cIAP1, switches from a form that protects cells to a form that kills them—a property that scientists hope to exploit as a "kill switch" for cancer. The results showed that cIAP1 switches from "closed" to "open within only 300 ms, as determined using time-resolved small-angle X-ray scattering.

November 13, 2014. A team of researchers from the Department of Biochemistry at the University of Zurich, led by Professor Raimund Dutzler, unveiled the structure of a lipid scramblase from the TMEM16 family as determined by X-ray crystallography. The structure provides insight into the activation of the protein by calcium and the transport of lipids.

November 14, 2014. Thanks to research performed at RIKEN's SACLA X-ray free electron laser facility, the dream of analyzing the structure of large, hard-to-crystallize proteins and other bio-molecules has come one step closer to reality. Researchers used a newly developed grease to suspend small crystals of lysozyme, glucose isomerase, thaumatin and fatty acid-binding protein type-3, which they then analyzed using a method known as serial femtosecond crystallography.

November 14, 2014. Richard Cooper and Jerome Wicker at the University of Oxford, UK, have developed a machine-learning approach to predict whether a small organic molecule will be able to crystallize. Since crystallinity is vital both for determining structures and for the delivery of many drugs, this work could provide valuable information.

November 17, 2014. A planned macromolecular femtosecond X-ray crystallography experimental station at the Department of Energy's SLAC National Accelerator Laboratory will expand capabilities for atomic-scale explorations in human health, biology, energy and environmental science using one of the brightest X-ray sources on the planet.


Product spotlight: ASC 96 SAXS automatic sample changer

SAXS continues to be an important technique in structural biology and, in particular, is becoming a powerful QA/QC technique for the biotech industry. In order to match the high-throughput demands of large structural biology laboratories and industrial facilities, a 96-well sample changer has been developed.

The ASC 96 provides unattended sample mounting and data collection for those labs who want to take advantage of the higher throughput capabilities offered by the BioSAXS-2000. The ASC 96 supports samples supplied in 96-well plates or 0.2 mL PCR tube arrays, and seamlessly integrates with the hardware and SAXSLab software control package. Solution samples can be foil-sealed to ensure they won't evaporate prior to data collection. The ASC 96 also includes support for temperature controlled sample storage and for multiple cleaning solutions and cleaning protocols. ASC 96 SAXS
Visit Rigaku.com for more information on the BioSAXS-2000 and accessories such as the ASC 96.


Lab spotlight: Imperial College X-ray Crystallography Facility

Imperial College Centre for Structural Biology

Dr. Andreas Förster
Macromolecular Structure and Function Research Group (MSF)
Imperial College London
Sir Ernst Chain Building – Wolfson Laboratories
London SW7 2AZ

As part of the Centre for Structural Biology, the X-ray Crystallography Facility serves the macromolecular crystallography community at Imperial College London. About 75 users from twenty-five research groups come to the facility on a regular basis to crystallize the proteins they study, optimize obtained hits, test diffraction and cryo-conditions, and collect diffraction data. The projects cover bacterial pathogenesis, molecular plant biology, membrane biology, molecular mechanisms of disease, and the understanding of protein crystallization.

Dr. Andreas Förster The facility manager, Dr. Andreas Förster, is involved in intramural collaborations to understand bacterial type VI secretion and paramyxoviral assembly and budding. He frequently uses data collected on his Rigaku home instrument to solve protein crystal structures by S-SAD methods. Recently, he solved the structure of a viral matrix protein by sulfur-SAD using this system (MicroMax-007 HF generator, AFC11 goniometer and Saturn 944+ CCD detector). Besides leading to beautiful maps, the anomalous signal clearly showed the presence of a potassium ion with possible implications for stability.


Useful link: CCDC

The Cambridge Crystallographic Data Centre (CCDC) is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high quality information, software and services.

Structures deposited with CCDC are made publically available for download at the point of publication or at consent from the depositor. They are also scientifically enriched and included in the Cambridge Structural Database (CSD) which underpins a range of software solutions offered by CCDC. Targeted subsets of the CSD are also freely available to support teaching and other activities.


Selected recent crystallographic papers

Efficient cryoprotection of macromolecular crystals using vapor diffusion of volatile alcohols. Farley, Christopher; Juers, Douglas H. Journal of Structural Biology. Nov2014, Vol. 188 Issue 2, p102-106. 5p. DOI: 10.1016/j.jsb.2014.09.011.

Botulinum neurotoxins: new questions arising from structural biology. Kammerer, Richard A.; Benoit, Roger M. Trends in Biochemical Sciences. Nov2014, Vol. 39 Issue 11, p517-526. 10p. DOI: 10.1016/j.tibs.2014.08.009.

Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex. Jun Yong Ha; Pokrovskaya, Irina D.; Climer, Leslie K.; Shimamura, Gregory R.; Kudlyk, Tetyana; Jeffrey, Philip D.; Lupashin, Vladimir V.; Hughson, Frederick M. Proceedings of the National Academy of Sciences of the United States of America. 11/4/2014, Vol. 111 Issue 44, p15762-15767. 6p. DOI: 10.1073/pnas.1414829111.

Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM. Peng, Yun; Lu, Jun; Wong, Joyce J.W.; Edwards, Ross A.; Frost, Laura S.; Mark Glover, J.N. Journal of Molecular Biology. Nov2014, Vol. 426 Issue 22, p3783-3795. 13p. DOI: 10.1016/j.jmb.2014.09.018.

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins. Curtis, Joseph E.; Zhang, Hailiang; Nanda, Hirsh. Computer Physics Communications. Nov2014, Vol. 185 Issue 11, p3010-3015. 6p. DOI: 10.1016/j.cpc.2014.07.006.

Regulation of the catalytic activity of the human phosphatase PTPN4 by its PDZ domain. Maisonneuve, Pierre; Caillet-Saguy, Célia; Raynal, Bertrand; Gilquin, Bernard; Chaffotte, Alain; Pérez, Javier; Zinn-Justin, Sophie; Delepierre, Muriel; Buc, Henri; Cordier, Florence; Wolff, Nicolas. FEBS Journal. Nov2014, Vol. 281 Issue 21, p4852-4865. 14p. DOI: 10.1111/febs.13024.

Time-resolved crystallography using the Hadamard transform. Yorke, Briony A; Beddard, Godfrey S; Owen, Robin L; Pearson, Arwen R. Nature Methods. Nov2014, Vol. 11 Issue 11, p1131-1134. 4p. 3 Graphs. DOI: 10.1038/nmeth.3139.

Structure-specificity relationships in Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus T6. Lansky, Shifra; Salama, Rachel; Solomon, Hodaya V.; Feinberg, Hadar; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil. Acta Crystallographica: Section D. Nov2014, Vol. 70 Issue 11, p2994-3012. 19p. DOI: 10.1107/S139900471401863X.

Structural Basis of a Kv7.1 Potassium Channel Gating Module: Studies of the Intracellular C-Terminal Domain in Complex with Calmodulin. Sachyani, Dana; Dvir, Meidan; Strulovich, Roi; Tria, Giancarlo; Tobelaim, William; Peretz, Asher; Pongs, Olaf; Svergun, Dmitri; Attali, Bernard; Hirsch, Joel A. Structure. Nov2014, Vol. 22 Issue 11, p1582-1594. 13p. DOI: 10.1016/j.str.2014.07.016.

The Mre11/Rad50/Nbs1 complex: Recent insights into catalytic activities and ATP-driven conformational changes. Paull, Tanya T.; Deshpande, Rajashree A. Experimental Cell Research. Nov2014, Vol. 329 Issue 1, p139-147. 9p. DOI: 10.1016/j.yexcr.2014.07.007.

Ultra-high resolution crystal structure of recombinant caprine β-lactoglobulin. Crowther, Jennifer M.; Lassé, Moritz; Suzuki, Hironori; Kessans, Sarah A.; Loo, Trevor S.; Norris, Gillian E.; Hodgkinson, Alison J.; Jameson, Geoffrey B.; Dobson, Renwick C.J. Febs Letters. Nov2014, Vol. 588 Issue 21, p3816-3822. 7p. DOI: 10.1016/j.febslet.2014.09.010.

The X-ray Structure of NccX from Cupriavidus metallidurans 31A Illustrates Potential Dangers of Detergent Solubilization When Generating and Interpreting Crystal Structures of Membrane Proteins. Ziani, Widade; Maillard, Antoine P.; Petit-Härtlein, Isabelle; Garnier, Norbert; Crouzy, Serge; Girard, Eric; Covès, Jacques. Journal of Biological Chemistry. 11/7/2014, Vol. 289 Issue 45, p31160-31172. 13p. DOI: 10.1074/jbc.M114.586537.

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology. Shinoda, Akira; Tanaka, Yoshikazu; Yao, Min; Tanaka, Isao. Acta Crystallographica: Section D (International Union of Crystallography - IUCr). Nov2014, Vol. 70 Issue 11, p2794-2799. 6p. DOI: 10.1107/S139900471401476X.

Crystal structures of free and antagonist-bound states of human α9 nicotinic receptor extracellular domain. Zouridakis, Marios; Giastas, Petros; Zarkadas, Eleftherios; Chroni-Tzartou, Dafni; Bregestovski, Piotr; Tzartos, Socrates J. Nature Structural & Molecular Biology. Nov2014, Vol. 21 Issue 11, p976-980. 5p. DOI: 10.1038/nsmb.2900.

Structural Basis of the pH-Dependent Assembly of a Botulinum Neurotoxin Complex. Matsui, Tsutomu; Gu, Shenyan; Lam, Kwok-ho; Carter, Lester G.; Rummel, Andreas; Mathews, Irimpan I.; Jin, Rongsheng. Journal of Molecular Biology. Nov2014, Vol. 426 Issue 22, p3773-3782. 10p. DOI: 10.1016/j.jmb.2014.09.009.

Reptation-Induced Coalescence of Tunnels and Cavities in Escherichia Coli XylE Transporter Conformers Accounts for Facilitated Diffusion. Cunningham, Philip; Naftalin, Richard. Journal of Membrane Biology. Nov2014, Vol. 247 Issue 11, p1161-1179. 19p. DOI: 10.1007/s00232-014-9711-7.

Alliin is a suicide substrate of Citrobacter freundii methionine γ-lyase: structural bases of inactivation of the enzyme. Morozova, Elena A.; Revtovich, Svetlana V.; Anufrieva, Natalya V.; Kulikova, Vitalia V.; Nikulin, Alexey D.; Demidkina, Tatyana V. Acta Crystallographica: Section D (International Union of Crystallography - IUCr). Nov2014, Vol. 70 Issue 11, p3034-3042. 9p. DOI: 10.1107/S1399004714020938.

Covering complete proteomes with X-ray structures: a current snapshot. Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz. Acta Crystallographica: Section D. Nov2014, Vol. 70 Issue 11, p2781-2793. 13p. DOI: 10.1107/S1399004714019427.

Structural basis for the assembly of the Sxl-Unr translation regulatory complex. Hennig, Janosch; Militti, Cristina; Popowicz, Grzegorz M.; Wang, Iren; Sonntag, Miriam; Geerlof, Arie; Gabel, Frank; Gebauer, Fátima; Sattler, Michael. Nature. 11/13/2014, Vol. 515 Issue 7526, p287-290. 4p. 4 Diagrams, 3 Charts, 6 Graphs. DOI: 10.1038/nature13693.

Insights into the relationship between the haem-binding pocket and the redox potential of c6 cytochromes: four atomic resolution structures of c6 and c6-like proteins from Synechococcus sp. PCC 7002. Bialek, Wojciech; Krzywda, Szymon; Zatwarnicki, Pawel; Jaskolski, Mariusz; Kolesinski, Piotr; Szczepaniak, Andrzej. Acta Crystallographica: Section D. Nov2014, Vol. 70 Issue 11, p2823-2832. 10p. DOI: 10.1107/S1399004714013108.

Functional and Structural Analysis of HicA3-HicB3, a Novel Toxin-Antitoxin System of Yersinia pestis. Bibi-Triki, Sabrina; de la Sierra-Gallay, Inès Li; Lazar, Noureddine; Leroy, Arnaud; Van Tilbeurgh, Herman; Sebbane, Florent; Pradel, Elizabeth. Journal of Bacteriology. Nov2014, Vol. 196 Issue 21, p3712-3723. 12p. DOI: 10.1128/JB.01932-14.

Crystal Structure of the Bacillus subtilis Phosphodiesterase PhoD Reveals an Iron and Calcium-containing Active Site. Rodriguez, Fernanda; Lillington, James; Johnson, Steven; Timme, Christiane R.; Lea, Susan M.; Berks, Ben C. Journal of Biological Chemistry. 11/7/2014, Vol. 289 Issue 45, p30889-30899. 11p. DOI: 10.1074/jbc.M114.604892.

Implementation of interference in a confocal laser scanning microscope and its application for in situ observation of crystal growth processes. Grebenev, V.; Voloshin, A.; Lyasnikova, M.; Dyatlova, N. Crystallography Reports. Nov2014, Vol. 59 Issue 6, p923-927. 5p. DOI: 10.1134/S106377451406011X.

Structural and functional characterization of an arylamine N-acetyltransferase from the pathogen Mycobacterium abscessus: differences from other mycobacterial isoforms and implications for selective inhibition. Cocaign, Angélique; Kubiak, Xavier; Xu, Ximing; Garnier, Guillaume; Li de la Sierra-Gallay, Inès; Chi-Bui, Linh; Dairou, Julien; Busi, Florent; Abuhammad, Areej; Haouz, Ahmed; Dupret, Jean-Marie; Herrmann, Jean-Louis; Rodrigues-Lima, Fernando. Acta Crystallographica: Section D. Nov2014, Vol. 70 Issue 11, p3066-3079. 14p. DOI: 10.1107/S1399004714021282.

Crystal structure of the vitamin B₃ transporter PnuC, a full-length SWEET homolog. Jaehme, Michael; Guskov, Albert; Slotboom, Dirk Jan. Nature Structural & Molecular Biology. Nov2014, Vol. 21 Issue 11, p1013-1015. 3p. DOI: 10.1038/nsmb.2909.

Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias. Borko, Lubomír; Bauerová-Hlinková, Vladena; Hostinová, Eva; Gašperík, Juraj; Beck, Konrad; Lai, F. Anthony; Zahradníková, Alexandra; Ševc(ík, Jozef. Acta Crystallographica: Section D. Nov2014, Vol. 70 Issue 11, p2897-2912. 16p. DOI: 10.1107/S1399004714020343.


Book review: The Innovators: How a Group of Hackers, Geniuses, and Geeks Created the Digital Revolution

     by Walter Isaacson
     Simon and Schuster, New York, 2014, 560 pages, 978-1476708690

I thoroughly enjoyed the biographies of Ben Franklin and Steve Jobs by Isaacson, so when I heard about this book on ScienceFriday several months ago I preordered a copy. The cover painting of Ada Lovelace and photos of Steve Jobs, Bill Gates and Alan Turing do not do justice to the expansiveness of the topic and by no means represent the endpoint.

As I write this, I am on an Apple MAC running Windows (gasp) connected to the Internet in Australia. This book explains just how I arrived in this state. You could cheat and look at the timeline at the beginning of the book, but you would miss out completely on the rich history. For the major players, a short biography provides context for each step.

The author starts with Charles Babbage and Ada Lovelace nee Byron. While the former conceived of the difference and analytical engines, it was Ada Lovelace who conceived of the idea of a general purpose machine that could be used not just for computation but for enhancing all aspects of human existence – in the 1840s.

From here the book follows three major trajectories that are deeply intertwined: hardware, software and networking. The hardware path follows the concepts that led to the first general purpose computer, ENIAC, then the developments that made it possible to put a computer in your pocket: development of the transistor by AT&T, the integrated circuit by Fairchild and Texas Instruments, and the birth of Intel. Individual chips are one thing, but it was Apple who brought the computer home.

The software path starts with Ada Lovelace again, and with Grace Hopper, who wrote the first compiler, to Bill Gates and Paul Allen, and ultimately to Larry Page and Sergey Brin. It is interesting to note that women were relegated to software because it was thought the hardware was too much for them. Ironic, since women are a distinct minority of software developers today.

We learn that the Internet came about as a way to provide a nuclear-hardened communication system, because the phone system could not hold up to such a calamity. It is clear that Al Gore did not invent the Internet, but he is responsible for starting the declassification of the ARPAnet so we could all get on it.

Once all the pieces are together, we have the connected world in which we live via our smartphones. This is literally the Memex of Vannevar Bush, as described in his essay As We May Think, published July 1, 1945. I think he would be amazed how that vision came to fruition.

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

Rigaku


Rigaku Corporation
e-mail: info@rigaku.com
Tel: +[81] 3-3479-0618
FAX: +[81] 3-3479-6112

Rigaku China
e-mail: info@rigaku.com
Tel: +[86] 010-82800840
FAX: +[86] 010-82800864


Rigaku Americas
e-mail: info@Rigaku.com
Tel: (281) 362-2300
FAX: (281) 364-3628

Rigaku Europe
e-mail: info@Rigaku.com
Tel: +[44] 1732 763 367
FAX: +[44] 1732 763 757


Copyright © 2014 — Rigaku Corporation and its Global Subsidiaries. All Rights Reserved

Valid HTML 4.01 Transitional