Crystallography in the news

October 2, 2015. The origin and evolution of viruses may be hard to determine, but new research discovered evidence that they are alive and may have emerged ahead of the first modern cells. The analysis backs the hypothesis that viruses are living organisms that share a long evolutionary history with cells. The study traces viral evolution back to when both viruses and cells exist in their currently recognized forms. Gustavo Caetano-Anollés, professor at the University of Illinois and the Carl R. Woese Institute for Genomic Biology who led the analysis, said viruses have just been placed on the tree of life, on the senior-most position at the bottom of the tree and existing in their own unique group.

October 6, 2015. For chemists, the Cambridge Structural Database (CSD) is part of the furniture. It contains data for every small molecule crystal structure ever determined – over 750,000 of them – and is a mine of useful information for anyone researching or teaching chemistry. Structures are deposited from around the world, with the most rapid growth in India, China, Japan, Germany, France, the UK, Australia and the US.

October 6, 2015. A new study has shown that residual movements continue to animate proteins inside a crystal and that this movement "blurs" the structures obtained via crystallography. The study stresses that the more these residual movements are restricted, the better the crystalline order. That is why molecules consisting of the most compact crystals generally make it possible to obtain structures of better quality.

October 8, 2015. Thirty-eight years after the last member of the [n]radialene class of star-shaped hydrocarbons was first reported, chemists have made its missing member. To isolate cyclopentane-based radialene, the team led by Mick Sherburn at the Australian National University in Canberra had to overcome its tendency to polymerise extremely rapidly. Their success provides both a potentially powerful synthetic reagent and an important example of producing and characterising highly unstable compounds

October 13, 2015. At very low temperatures, atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation

October 13, 2015. Using a multidisciplinary approach, an international team of scientists has revealed in never-before-seen detail the 3D structure of biologically active DNA. The team, led by scientists at Baylor College of Medicine (BCM) in Houston, Texas, imaged various DNA shapes – including figure-8s – using electron cryo-tomography, and then examined them using supercomputer simulations.

October 15, 2015. Scientists from UCLA and UC Berkeley have produced structural images of telomerase in much higher resolution than ever before, giving them major new insights about the enzyme. Their findings could ultimately lead to new directions for treating cancer and preventing premature aging.

October 20, 2015. Researchers in UCD and Trinity have helped develop a new crystal-focused scientific technique for viewing the early stages of DNA 'oxidation', the precursor to DNA damage, mutations and cancer. They demonstrated the ability to follow the flow of electrons from an individual DNA base to a bound molecule whose exact position is known and this is an enormous advantage in the study of the early events that lead to oxidative DNA damage.

Product spotlight: EZ Aligner

Rigaku introduces the EZ Aligner tool that allows for safe and remote alignment for VariMax or OptiSAXS optics. As the name implies, the EZ Aligner makes optimization of beam intensities an easy task. Simply set up your pin diode and pinhole, then use the EZ Aligner remote to optimize the beam from a safe place outside the radiation enclosure. Each EZ Aligner remote produces a radio signal strong enough to penetrate enclosure material or from another room. The EZ Aligner kit includes a remote control that communicates to 4 motors attached to optic micrometers to adjust optic rotation and translation.

Ask for more information about the EZ Aligner tool.

Lab spotlight: The Taylor Structural Biology Group

Garry Lindsay Taylor, Professor
School of Biology
University of St Andrews
United Kingdom

The Taylor lab uses molecular, cellular and structural biology to understand the structure and function of proteins involved in pathogenesis with a view to developing new drugs against a range of disease caused by microorganisms. The sialidase (or neuraminidase) superfamily are virulence factors in influenza, parainfluenza, cholera and pneumonia. Their structural studies on the paramyxovirus hemagglutinin-neuraminidase (HN) has led to the structure-based development of a new drug that is a potential treatment for childhood parainfleunza. They are currently studying the sialidases from Streptococcus pneumoniae and Pseudomonas aeruginosa, and developing inhibitors against these enzymes that are key virulence factors in the respiratory diseases caused by these bacteria.

More recently, they have engineered multivalent forms of a couple of carbohydrate-binding modules specific for sialic acid, a key component of the receptor used by the influenza virus, parainfluenza virus, some coronaviruses and pneumococci. Experiments in mice using lethal viral challenges show that these multivalent biologics have great potential as a prophylactic for the prevention of certain respiratory diseases.

Useful link: ATSAS 2.7

ATSAS 2.7 has been released. Academic users can download ATSAS here:
http://www.embl-hamburg.de/biosaxs/download.html

New programs:

• sreflex: flexible refinement of high-resolution structures based on SAXS and normal mode analysis
• supalm: rapid superposition of high and low resolution models (including EM density maps) using spherical harmonics
• datshanum: quantitative assessment of useful angular data range
• datmow: molecular weight estimation
• SASpy: ATSAS plugin for PyMOL

In vacuo X-ray data collection from graphene-wrapped protein crystals. Warren, Anna J.; Crawshaw, Adam D.; Trincao, Jose; Aller, Pierre; Alcock, Simon; Nistea, Ioana; Salgado, Paula S.; Evans, Gwyndaf. Acta Crystallographica: Section D. Oct2015, Vol. 71 Issue 10, p2079-2088. 10p. DOI: 10.1107/S1399004715014194.

Vanadium haloperoxidases: From the discovery 30 years ago to X-ray crystallographic and V K-edge absorption spectroscopic studies. Leblanc, C.; Vilter, H.; Fournier, J.-B.; Delage, L.; Potin, P.; Rebuffet, E.; Michel, G.; Solari, P.L.; Feiters, M.C.; Czjzek, M. Coordination Chemistry Reviews. Oct2015, Vol. 301, p134-146. 13p. DOI: 10.1016/j.ccr.2015.02.013.

Molecular weight-gyration radius relation of globular proteins: a comparison of light scattering, small-angle X-ray scattering and structure-based data. Smilgies, Detlef-M.; Folta-Stogniew, Ewa. Journal of Applied Crystallography. Oct2015, Vol. 48 Issue 5, p1604-1606. 3p. DOI: 10.1107/S1600576715015551.

Conserved water molecules in bacterial serine hydroxymethyltransferases. Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano. PEDS: Protein Engineering, Design & Selection. Oct2015, Vol. 28 Issue 10, p415-426. 12p. DOI: 10.1093/protein/gzv026.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques. De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean; Stojanoff, Vivian; Siliqi, Dritan; Sánchez-Puig, Nuria; Moreno, Abel. Journal of Applied Crystallography. Oct2015, Vol. 48 Issue 5, p1551-1559. 9p. DOI: 10.1107/S1600576715016556.

Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein. Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan. Journal of Chemical Physics. 10/7/2015, Vol. 143 Issue 13, p1-7. 7p. DOI: 10.1063/1.4931922.

Crystallizing the 6S and 8S spliceosomal assembly intermediates: a complex project. Pelz, Jann-Patrick; Schindelin, Hermann; van Pee, Katharina; Kuper, Jochen; Kisker, Caroline; Diederichs, Kay; Fischer, Utz; Grimm, Clemens. Acta Crystallographica: Section D. Oct2015, Vol. 71 Issue 10, p2040-2053. 14p. DOI: 10.1107/S1399004715014832.

The αRep artificial repeat protein scaffold: a new tool for crystallization and live cell applications. Valerio-Lepiniec, Marie; Urvoas, Agathe; Chevrel, Anne; Guellouz, Asma; Ferrandez, Yann; Mesneau, Agnès; Li de la Sierra-Gallay, Ines; Aumont-Nicaise, Magali; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe. Biochemical Society Transactions. Oct2015, Vol. 43 Issue 5, p819-824. 6p. DOI: 10.1042/BST20150075.

Structure of the Human Atg13-Atg101 HORMA Heterodimer: an Interaction Hub within the ULK1 Complex. Qi, Shiqian; Kim, Do Jin; Stjepanovic, Goran; Hurley, James H. Structure. Oct2015, Vol. 23 Issue 10, p1848-1857. 10p. DOI: 10.1016/j.str.2015.07.011.

A historical overview of protein kinases and their targeted small molecule inhibitors. Roskoski, Robert. Pharmacological Research. Oct2015, Vol. 100, p1-23. 23p. DOI: 10.1016/j.phrs.2015.07.010.

Stabilization of Protein–Protein Interactions in chemical biology and drug discovery. Bier, David; Thiel, Philipp; Briels, Jeroen; Ottmann, Christian. Progress in Biophysics & Molecular Biology. Oct2015, Vol. 119 Issue 1, p10-19. 10p. DOI: 10.1016/j.pbiomolbio.2015.05.002.

Can template-based protein models guide the design of sequence fitness for enhanced thermal stability of single domain antibodies? Olson, Mark A.; Zabetakis, Dan; Legler, Patricia M.; Turner, Kendrick B.; Anderson, George P.; Goldman, Ellen R. PEDS: Protein Engineering, Design & Selection. Oct2015, Vol. 28 Issue 10, p395-402. 8p. DOI: 10.1093/protein/gzv047.

Crystal Structure of Xanthomonas AvrRxo1-ORF1, a Type III Effector with a Polynucleotide Kinase Domain, and Its Interactor AvrRxo1-ORF2. Han, Qian; Zhou, Changhe; Wu, Shuchi; Liu, Yi; Triplett, Lindsay; Miao, Jiamin; Tokuhisa, James; Deblais, Loïc; Robinson, Howard; Leach, Jan E.; Li, Jianyong; Zhao, Bingyu. Structure. Oct2015, Vol. 23 Issue 10, p1900-1909. 10p. DOI: 10.1016/j.str.2015.06.030.

Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor. Griese, Julia J.; Kositzki, Ramona; Schrapers, Peer; Branca, Rui M. M.; Nordström, Anders; Lehtiö, Janne; Haumann, Michael; Högbom, Martin. Journal of Biological Chemistry. 10/16/2015, Vol. 290 Issue 42, p25254-25272. 19p. DOI: 10.1074/jbc.M115.675223.

Structural glycobiology of human a1-acid glycoprotein and its implications for pharmacokinetics and inflammation. Fernandes, Cláudia L.; Ligabue-Braun, Rodrigo; Verli, Hugo. Glycobiology. Oct2015, Vol. 25 Issue 10, p1125-1133. 9p. DOI: 10.1093/glycob/cwv041.

Crystallographic and solution studies of NAD⁺- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps. Kamariah, Neelagandan; Manimekalai, Malathy Sony Subramanian; Nartey, Wilson; Eisenhaber, Frank; Eisenhaber, Birgit; Grüber, Gerhard. BBA - Bioenergetics. Oct2015, Vol. 1847 Issue 10, p1139-1152. 14p. DOI: 10.1016/j.bbabio.2015.06.011.

Crystallization of high-quality protein crystals using an external electric field. Koizumi, H.; Uda, S.; Fujiwara, K.; Tachibana, M.; Kojima, K.; Nozawa, J. Journal of Applied Crystallography. Oct2015, Vol. 48 Issue 5, p1507-1513. 7p. DOI: 10.1107/S1600576715015885.

Structural and functional studies of a metallo-β-lactamase unveil a new type of structurally encoded nickel-containing heterodinuclear site. Choi, Hwajung; Kim, Hee Jung; Matsuura, Atsushi; Mikami, Bunzo; Yoon, Hye-Jin; Lee, Hyung Ho. Acta Crystallographica: Section D. Oct2015, Vol. 71 Issue 10, p2054-2065. 12p. DOI: 10.1107/S1399004715014807.

Synthesis and Crystal Structure of A New Co(II) Coordination Polymer With a Rare Two-Fold bbg Topology. Yao, Peng. Synthesis & Reactivity in Inorganic, Metal-Organic, & Nano-Metal Chemistry. 2015, Vol. 45 Issue 10, p1470-1473. 4p. DOI: 10.1080/15533174.2013.862714.

Two novel organic–inorganic hybrid compounds with straight and zigzag chain alignments of Cu(II) centers: Synthesis, crystal structure, spectroscopy, thermal analysis and magnetism. Nenwa, Justin; Djomo, Edith D.; Nfor, Emmanuel N.; Djonwouo, Patrick L.; Mbarki, Mohammed; Fokwa, Boniface P.T. Polyhedron. Oct2015, Vol. 99, p26-33. 8p. DOI: 10.1016/j.poly.2015.06.023.

A 3D-diamond-like metal–organic framework: Crystal structure, nonlinear optical effect and high thermal stability. Wang, Lihua; Ye, Yingxiang; Zhang, Liuqin; Chen, Qianhuo; Ma, Xiuling; Zhang, Zhangjing; Xiang, Shengchang. Inorganic Chemistry Communications. Oct2015, Vol. 60, p19-22. 4p. DOI: 10.1016/j.inoche.2015.07.015.

Structural diversity of bimetallic rhodium and iridium half sandwich dithiolato complexes. Nejman, Phillip S.; Morton-Fernandez, Brian; Moulding, David J.; Athukorala Arachchige, Kasun S.; Cordes, David B.; Slawin, Alexandra M. Z.; Kilian, Petr; Woollins, J. Derek. Dalton Transactions: An International Journal of Inorganic Chemistry. 10/14/2015, Vol. 44 Issue 38, p16758-16766. 9p. DOI: 10.1039/c5dt02542g.

Streptococcus pneumoniae NanC: Structural Insights into the Specificity and Mechanism of a Sialidase that Produces a Sialidase Inhibitor. Owen CD, Lukacik P, Potter JA, Sleator O, et al. J Biol Chem. 2015. DOI: jbc.M115.673632.

Book review:

Alan Turing: The Enigma
By Andrew Hodges

Even though Andrew Hodges' Alan Turing: The Enigma is now thirty-two years old, it is still regarded as one of the best-researched biographies of Alan Turing. Its relevance prevails despite its age, and the book was the inspiration for the Academy Award-winning film, The Imitation Game (which, ironically enough, was heavily criticized for its manifold historical inaccuracies that in no way came from the book that supposedly inspired it). Despite The Imitation Game's particular failures, the film's impending release led to a re-release of Hodges' book. The new "movie-tie-in" edition's cover is a scene from the movie, showing Benedict Cumberbatch as Turing from behind, facing his famed Enigma decryption machine. That was about the extent to which the book tied in to the movie.

The film was well-received by audiences who were willing to ignore—or were perhaps unaware of—its historical inaccuracies. After seeing the film, I wanted to learn more, having heard Turing's name mentioned repeatedly in my brief undergraduate career as a programmer. Though I found the book a thrilling and fast-paced read (albeit a bit hefty at 736 pages), I was wildly disappointed that someone responsible for the making of The Imitation Game could have read the same book and come out with the screenplay for said film, particularly because the extreme care with which Hodges researched and wrote The Enigma is ever-present in his prose, which the film idly cast aside. Hodges sought to provide his audience with a detailed and accurate account of Alan Turing, a brilliant man whose work provided the foundation for modern computing as we know it.

Given the role Turing played in helping the Allies crack German codes during World War II, one might expect him to have been the subject of myriad biographies, with Hodges' only being one of the many. Yet the top-secret nature of Turing's work meant that for many years his contributions went unrecognized. His universal machine, something we today recognize as a fundamental concept of computing, was ahead of its time. Hodges' biography helped garner recognition both for Turing and for the importance of his research in broader cultural circles. And, as I mentioned previously, it provided inspiration for The Imitation Game, which despite its inaccuracies made Turing a household name in an age of technology that arguably would not exist without his contributions.

Whether you saw The Imitation Game and want to learn more or you just have an interest in the history of computing or codebreaking or World War II (or all of the above), Hodges' book is an excellent read, and one that I highly recommend.

Jeanette S. Ferrara
NYU School of Journalism