Protein Crystallography Newsletter Volume 3, No. 8, August 2011

Crystallography in the news In this issue: August 2, 2011. Dr. Kalle Gehring, a professor in McGill University's Department of Crystallography in the news Biochemistry, has been awarded a Pilot Project Grant by the Parkinson Society of Photo of the month Canada (PSC) for his ongoing work that looks at the molecular and cellular processes that underlie neurological diseases like Parkinson's Disease (PD). Call for nominations: Carl Brändén Award BioSAXS-1000 Kratky camera August 03, 2011 Mitegen LLC, a provider of innovative consumables for X-ray diffraction, crystallography and protein crystallization to academic, pharmaceutical, industrial and Spotlight: UTMB, Sealy Center government researchers around the world, announced that it has signed an agreement Useful links for crystallography with AP Innovations to distribute their first product, the Quick Puck Loader for the Professional education opportunities Rigaku ACTOR robot. Science video of the month August 8, 2011. Coupling laser-driven, two-dimensional fluorescence imaging and high- Funny video of the month performance computer modeling, a six-member team - led by University of Oregon chemist Andrew H. Marcus and Harvard University chemist Alan Aspuru-Guzik - solved Last month's survey results the conformation of self-assembled porphyrin molecules in a biological membrane. Survey question of the month August crystallographic papers August 10, 2011. The availability of a postdoctoral fellowship was announced for the laboratory of Dr Ian Taylor (MRC National Institute for Medical Research, London), to Book reviews study the structure and mechanism of the recently described retroviral restriction factor SAMHD1. The primary focus of the project will be to establish the relationship between the biochemical and enzymatic properties of SAMHD1 and the mechanism of virus Mark Your Calender restriction. Multi-Pole Approach to Structural Biology November 16-19, 2011 August 12, 2011. In a paper published online in advance in Science, a team led by INTERNATIONAL INSTITUTE OF MOLECULAR AND investigators at the National Institutes of Health Vaccine Research Center reported their CELL BIOLOGY IN WARSAW use of X-ray crystallography and 454 pyrosequencing to characterize VRC01-like Ks. Trojdena 4, Warsaw, Poland antibodies derived from HIV-1-infected individuals.

International conference discussing advances in August 17, 2011. One of the currently intriguing evaluations of a biotech firm is that of structural biology that have been promoted through Array Pharmaceuticals (ARRY). Its stock has been incapable of luring investors contributions of scientists with significant links to regardless of how large the number of its cancer products, how encouraging the news Poland. Open to participants from all countries. about clinical trial results, or how generous the upfront and promised milestone Official language is English. Abstract submission payments and royalties by the collaborating pharmaceutical companies. deadline: August 31st. Topics include: August 18, 2011. Imperial College London is seeking to appoint a Research Associate to Practical applications of structural biology investigate the roles of assembly factors involved in the assembly and repair of Biocrystallography Photosystem II using biochemical and structural biology techniques. The successful Structural bioinformatics applicant will be based within the Nixon group in the Department of Life Sciences at the Nucleic acids South Kensington Campus of Imperial College London. Multi-pole expansion to complex systems Panel discussion August 18, 2011. Laboratory of Bioinformatics and Protein Engineering (Warsaw, Poland) reported two medium-resolution, knowledge-based potentials for scoring protein-RNA Biophysical Society 56th Annual Meeting models obtained by docking: the quasichemical potential (QUASI-RNP) and the Decoys February 25-29 2012, San Diego, CA As the Reference State potential (DARS-RNP).

Di Xia of NCI/NIH and Bill Cramer of Purdue August 24, 2011. The research and career path of Brian Kobilka, M.D., Professor of University are organizing a half-day symposium for Molecular and Cellular Physiology and Medicine at Stanford University, was extensively next year's Biophysical Society annual meeting on profiled in Nature. "Structure-Function of Hetero-Oligomeric Membrane Protein Complexes." Confirmed speakers include: August 24, 2011. What's One Billion Times Brighter Than the Sun? In the rolling Berkeley hills, under a dome that once housed its Nobel-Winning predecessor, lies the Leonid Sazanov of MRC, UK on structure of Advanced Light Source: an X-Ray generating system one billion times brighter than the complex I of the bacterial respiratory chain sun. Petra Fromme of Arizona State University on photosystem I and the use of X-ray lasers August 26, 2011. The three-dimensional structure of a site on an influenza B virus Robert Stroud of UC San Francisco on the protein that suppresses human defenses to infection has been determined by structure of Sec translocon researchers at Rutgers University (Prof. Gaetano Montelione) and The University of Bryan Krantz of UC Berkley on the Texas at Austin (Prof. Robert Krug). Their discovery also helps explain how influenza B translocation mechanism of anthrax toxin is limited to humans, and why it cannot be as virulent as A strains that incorporate new Di Xia on the mechanism and function of cyt genes from influenza viruses that infect other species. bc1 complex August 26, 2011. U.S. Department of Energy Office of Science's (DOE-SC's) national laboratories, including the Advanced Photon Source at Argonne National Laboratory, have enabled the discovery of a groundbreaking new drug treatment for malignant Photo of the Month melanoma, the deadliest form of skin cancer. The drug, Zelboraf (vemurafenib), "Future Structural Biologist" by Paul Swepston received Food and Drug Administration (FDA) approval on Wednesday, August 17, 2011.

August 26, 2011. There are two vacancies for recent PhD graduates for NIH and American Cancer Society-funded postdoctoral positions in the Gaponenko laboratory in the Department of Bicohemistry and Molecular Genetics at the University of Illinois at Chicago.

Call for nominations: 2012 Carl Brändén Award

2012 Awards of The Protein Society - The Carl Brändén Award

We encourage submissions for "Photo of the Month." In the tradition of the late Carl Brändén, pioneer in structural biology, co-author of the Jpeg (250px wide) files should be sent to seminal text Introduction to Protein Structure and leader of the world-class synchrotron [email protected] along with a link to facility at Grenoble, the Carl Brändén Award - sponsored by Rigaku Corporation - is the high-res image (or we can host it). Entries must given to an outstanding protein scientist who has also made exceptional contributions in be original art (with specific permission for use) and the areas of education and/or service to the science. somehow connected to protein crystallography or structural biology. Submit a complete Award Nomination Package by September 1, 2011. Submission and questions should be addressed to: [email protected]

Macromolecular Crystallography Class October 26-28, 2011 The Woodlands, Texas Register Product spotlight: BioSAXS-1000 Kratky Camera This is tailored towards the needs of macro- molecular crystallographers and their staff. Course format will be a series of short lectures on theory Introducing the BioSAXS-1000, a new SAXS camera based on a patented two- followed by hands-on activities with detectors, X-ray dimensional Kratky geometry, which produces significantly higher flux at the sample generators, and software. This class will also feature a with no need for desmearing. Designed to fit on an open port of a rotating anode training session on processing data with HKL. generator, or as a standalone system with a micro-focus sealed tube X-ray port, the small size and high flux performance make it the perfect instrument for incorporating SAXS into the workflow of your lab.

Information derived from a SAXS experiment performed on a protein in solution has Rigaku BioSAXS-1000 been shown to be useful for predicting crystallizability, as well as in modeling after structure determination. And, in the absence of a successful crystallography experiment, the SAXS experiment can at a minimum provide information about the oligomeric state and shape of the molecule or complex.

Request more information on Rigaku BioSAXS-1000.

Lab spotlight: UTMB, Sealy Center

UTMB, Sealy Center for Structural Biology and Molecular Biophysics

The mission of the Sealy Center for Structural Biology and Molecular Biophysics (SCSB) is to elucidate the basic relationships between macromolecular sequence, structure and function, and to leverage this information into the understanding and treatment of disease. The center recently took delivery of the first Rigaku BioSAXS-1000 biological SAXS system, along with a FR-E+ Superbright X-ray source and an R-AXIS IV++ detector. Crystallographers associated with this center include Stanley J. Watowich, Kyung (Kay) H. Choi, Marc C. Morais, and Mark A. White (pictured in front of their new BioSAXS-100 system).

Useful links for crystallography

The Protein Data Bank in Europe (PDBe) has introduced PDBeXpress, an umbrella name for a set of easy-to-use yet powerful PDB analysis tools. PDBeXpress is a collection of tools that extract and present useful information and statistics from the PDB using PDBe services and resources such as PDBeMotif. These tools have a simple interface with minimal input.

UTMB Crystallography Selected recent crystallographic papers

Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95. Svetlana Fomina, Tina D Howard, Olivia K Sleator, Marina Golovanova, Liam O'Ryan, Mark L Leyland, J Günter Grossmann, Richard F Collins, Stephen M Prince. Biochim Biophys Acta. 2011 Jul 5;1808 (10):2374-2389. http://dx.doi.org/10.1016/j.bbamem.2011.06.021

Dynamic Interaction of Hsp90 with Its Client Protein p53. Park, Sung Jean; Kostic, Milka; Dyson, H. Jane. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 1, p158-173, 16p; http://dx.doi.org/10.1016/j.jmb.2011.05.030

UTMB crystallographers Prof. Mark White, Prof. Kay Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein-Protein Choi, Prof. Marc Morais, and Prof. Stanley Watowich. Interaction. Bonsor, Daniel A.; Postel, Sandra; Pierce, Brian G.; Wang, Ningyan; Zhu, Penny; Buonpane, Rebecca A.; Weng, Zhiping; Kranz, David M.; Sundberg, Eric J. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 2, p321-328, 8p; http://dx.doi.org/10.1016/j.jmb.2011.06.009 Science Video Freezing Protein Crystals Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data. Wang, Xu; Watson, Caroline; Sharp, Joshua S.; Handel, Tracy M.; Prestegard, James H. Structure, Aug2011, Vol. 19 Issue 8, p1138-1148, 11p; http://dx.doi.org/10.1016/j.str.2011.06.001

Protein dynamics and pressure: What can high pressure tell us about protein structural flexibility? Cioni, Patrizia; Gabellieri, Edi. BBA - Proteins & Proteomics, Aug2011, Vol. 1814 Issue 8, p934-941, 8p; http://dx.doi.org/10.1016/j.bbapap.2010.09.017

Investigating a macromolecular complex: The toolkit of methods. Perrakis, Anastassis; Musacchio, Andrea; Cusack, Stephen; Petosa, Carlo. Journal of Structural Biology, Aug2011, Vol. 175 Issue 2, p106-112, 7p; http://dx.doi.org/10.1016/j.jsb.2011.05.014

The Native Ensemble and Folding of a Protein Molten-Globule: Functional Consequence of Downhill Folding. Naganathan, Athi N.; Orozco, Modesto. Journal of the American Chemical Society, 8/10/2011, Vol. 133 Issue 31, p12154-12161, 8p; http://dx.doi.org/10.1021/ja204053n

Watch YouTube Three-Dimensional Structure of a-Crystallin Domain Dimers of Human Small Heat Shock Proteins HSPB1 and HSPB6. Baranova, E.V.; Weeks, S.D.; Beelen, S.; Bukach, O.V.; Gusev, N.B.; Strelkov, S.V. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 1, p110-122, 13p; http://dx.doi.org/10.1016/j.jmb.2011.05.024 Funny Science Video Uploaded by Sciencerapper: Intro and then a rap Strategies for the structural analysis of multi-protein complexes: Lessons from the 3D- about the laboratory practice of structural biology. Repertoire project. Collinet, B.; Friberg, A.; Brooks, M.A.; van den Elzen, T.; Henriot, V.; Four verses about recombinant protein expression, Dziembowski, A.; Graille, M.; Durand, D.; Leulliot, N.; Saint André, C.; Lazar, N.; Sattler, NMR spectroscopy, X-ray crystallography and cryo- M.; Séraphin, B.; van Tilbeurgh, H. Journal of Structural Biology, Aug2011, Vol. 175 electron microscopy. Issue 2, p147-158, 12p; http://dx.doi.org/10.1016/j.jsb.2011.03.018

The Crystal Structure of the Substrate-Binding Protein OpuBC from Bacillus subtilis in Complex with Choline. Pittelkow, Marco; Tschapek, Britta; Smits, Sander H.J.; Schmitt, Lutz; Bremer, Erhard. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 1, p53-67, 15p; http://dx.doi.org/10.1016/j.jmb.2011.05.037

Complexin arrests a neighbor. Weninger, Keith R. Nature Structural & Molecular Biology, Aug2011, Vol. 18 Issue 8, p861-863, 3p; http://dx.doi.org/10.1038/nsmb.2118

Crystallographic Snapshots of the Complete Catalytic Cycle of the Unregulated Aspartate Transcarbamoylase from Bacillus subtilis. Harris, Katharine M.; Cockrell, Gregory M.; Puleo, David E.; Kantrowitz, Evan R. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 1, p190-200, 11p; http://dx.doi.org/10.1016/j.jmb.2011.05.036

Cells under siege: Viral glycoprotein interactions at the cell surface. Bowden, Thomas A.; Jones, E. Yvonne; Stuart, David I. Journal of Structural Biology, Aug2011, Vol. 175 Issue 2, p120-126, 7p; http://dx.doi.org/10.1016/j.jsb.2011.03.016 Watch YouTube Bacterial, Fungal, and Algal Lectins: Combatants in Tug of War against HIV. Feizi, Ten; Liu, Yan; Palma, Angelina S. Structure, Aug2011, Vol. 19 Issue 8, p1035-1037, 3p; http://dx.doi.org/10.1016/j.str.2011.05.010 July Survey Results Dynamics May Significantly Influence the Estimation of Interatomic Distances in There are many outstanding biological SAXS Biomolecular X-ray Structures. Kuzmanic, Antonija; Kruschel, Daniela; van Gunsteren, beamlines at synchrotrons around the world. Which Wilfred F.; Pannu, Navraj S.; Zagrovic, Bojan. Journal of Molecular Biology, Aug2011, is your favorite facility to visit for measuring data Vol. 411 Issue 1, p286-297, 12p; http://dx.doi.org/10.1016/j.jmb.2011.05.033 (select one)? Structural insights into transcription complexes. Berger, Imre; Blanco, Alexandre G.; Boelens, Rolf; Cavarelli, Jean; Coll, Miquel; Folkers, Gert E.; Nie, Yan; Pogenberg, Vivian; Schultz, Patrick; Wilmanns, Matthias; Moras, Dino; Poterszman, Arnaud. Journal of Structural Biology, Aug2011, Vol. 175 Issue 2, p135-146, 12p; http://dx.doi.org/10.1016/j.jsb.2011.04.015

Crucial Points within the Pore as Determinants of K+ Channel Conductance and Gating. Shi, Ning; Zeng, Weizhong; Ye, Sheng; Li, Yang; Jiang, Youxing. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 1, p27-35, 9p; http://dx.doi.org/10.1016/j.jmb.2011.04.058

A Eukaryotic-Like Interaction of Soluble Cyanobacterial Sensory Rhodopsin Transducer with DNA. Wang, Shenlin; Kim, So Young; Jung, Kwang-Hwan; Ladizhansky, Vladimir; Brown, Leonid S. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 2, p449-462, 14p; http://dx.doi.org/10.1016/j.jmb.2011.06.002

Structural and Computational Investigations of VIM-7: Insights into the Substrate Specificity of VIM Metallo-ß-Lactamases. Borra, Pardha Saradhi; Leiros, Hanna-Kirsti S.; Ahmad, Rafi; Spencer, James; Leiros, Ingar; Walsh, Timothy R.; Sundsfjord, Arnfinn; Samuelsen, Ørjan. Journal of Molecular Biology, Aug2011, Vol. 411 Issue 1, p174-189, Survey Question of the Month 16p; http://dx.doi.org/10.1016/j.jmb.2011.05.035

ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization. Iwasaki, Toshio; Kappl, Reinhard; Bracic, Gerhard; Shimizu, Nobutaka; Ohmori, Daijiro; Kumasaka, Takashi. Journal of Biological Inorganic Chemistry, Aug2011, Vol. 16 Issue 6, p923-935, 13p; http://dx.doi.org/10.1007/s00775-011-0793-8

Inducing phase changes in crystals of macromolecules: Status and perspectives for controlled crystal dehydration. Russi, Silvia; Juers, Douglas H.; Sanchez-Weatherby, Juan; Pellegrini, Erika; Mossou, Estelle; Forsyth, V. Trevor; Huet, Julien; Gobbo, Alexandre; Felisaz, Franck; Moya, Raphael; McSweeney, Sean M.; Cusack, Stephen; Cipriani, Florent; Bowler, Matthew W. Journal of Structural Biology, Aug2011, Vol. 175 Issue 2, p236-243, 8p; http://dx.doi.org/10.1016/j.jsb.2011.03.002

Cloning, functional expression, biochemical characterization, and structural analysis of a haloalkane dehalogenase from Plesiocystis pacifica SIR-1. Hesseler, Martin; Bogdanovic', Xenia; Hidalgo, Aurelio; Berenguer, Jose; Palm, Gottfried J.; Hinrichs, Winfried; Bornscheuer, Uwe T. Applied Microbiology & Biotechnology, Aug2011, Vol. 91 Issue 4, p1049-1060, 12p; http://dx.doi.org/10.1007/s00253-011-3328-x

A second Ig-like domain identified in dystroglycan by molecular modelling and dynamics. De Rosa, Maria Cristina; Pirolli, Davide; Bozzi, Manuela; Sciandra, Francesca; Giardina, Bruno; Brancaccio, Andrea. Journal of Molecular Graphics & Modelling, Aug2011, Vol. 29 Issue 8, p1015-1024, 10p; http://dx.doi.org/10.1016/j.jmgm.2011.04.008 Take Survey or cut-and-paste Nucleotide docking: prediction of reactant state complexes for ribonuclease enzymes. http://www.surveymonkey.com/s/aug_survey into your browser. Elsässer, Brigitta; Fels, Gregor. Journal of Molecular Modeling, Aug2011, Vol. 17 Issue 8, p1953-1962, 10p; http://dx.doi.org/10.1007/s00894-010-0900-8

A tetrameric structure is not essential for activity in dihydrodipicolinate synthase (DHDPS) from Mycobacterium tuberculosis. Evans, Genevieve; Schuldt, Linda; Griffin, Michael D.W.; Devenish, Sean R.A.; Grant Pearce, F.; Perugini, Matthew A.; Dobson, Renwick C.J.; Jameson, Geoffrey B.; Weiss, Manfred S.; Gerrard, Juliet A. Archives of Biochemistry & Biophysics, Aug2011, Vol. 512 Issue 2, p154-159, 6p; http://dx.doi.org/10.1016/j.abb.2011.05.014

Structure of the Flagellar Motor Protein Complex PomAB: Implications for the Torque- Generating Conformation. Yonekura, Koji; Maki-Yonekura, Saori; Homma, Michio. Journal of Bacteriology, Aug2011, Vol. 193 Issue 15, p3863-3870, 1p; http://dx.doi.org/10.1128/JB.05021-11

Crystal structure of the human centromeric nucleosome containing CENP-A. Tachiwana, Hiroaki; Kagawa, Wataru; Shiga, Tatsuya; Osakabe, Akihisa; Miya, Yuta; Saito, Kengo; Hayashi-Takanaka, Yoko; Oda, Takashi; Sato, Mamoru; Park, Sam-Yong; Kimura, Hiroshi; Kurumizaka, Hitoshi. Nature, 8/11/2011, Vol. 476 Issue 7359, p232-235, 4p; http://dx.doi.org/10.1038/nature10258

Book review:

The Mathematics of Life by Ian Stewart, Basic Books, 2011 ISBN: 978-0-4650-2238-0

Ian Stewart suggests that there have been five revolutions in biology and that we are experiencing a sixth one now. He first lays out the five revolutions: invention of the microscope, the classification of life, the theory of evolution, the discovery of genetics, and the determination of the structure of DNA. The current revolution is then the mathematical interpretation of biological information. As the book follows the timeline of discovery, chapters elaborating on Stewart's position are interspersed with chapters describing the first five revolutions. Chapter 2 provides a brief history of the technology that led to the invention of the microscope by Leeuwenhoek and information that the microscope revealed - small creatures and cell structures - and how it impacted science. The next chapter explores Linnaeus' classification scheme.

Chapter 4 is the first chapter to look at the impact of mathematics on understanding biology. Here we see the use of the Fibonacci series to describe plant growth and an explanation of why it works. The next chapter is devoted to evolution and nicely summarizes the Wallace-Darwin theory. Chapter 6 introduces the reader to Mendelian genetics and chapter 7 reviews the determination of the structure of DNA.

The remaining chapters support the author's thesis that the sixth revolution is mathematics. A description of the Human Genome Project, and how it was realized and the results (not very useful yet), is followed by reclassification of life via heuristics and associated calculations to best define the tree of life. I found chapter 10 particularly interesting in the way that Stewart describes the packing of virus particles in 3 and 4 dimensions. The latter representation allows for a lattice representation of icosahedra. We only see the non-lattice representation in three dimensions.

Chapter 11 covers neural processing which includes a discussion about signal transmission, walking and image processing in the visual cortex. Stewart next looks at knots and folds, important for understanding DNA and proteins. In chapter 13, the author looks at stripes and spots and how we model their generation. Game theory and how it impacts evolution is described in chapter 14. Chapter 15 takes a look at networks while Chapter 16 reviews population dynamics. The next two chapters ask the questions "what is life?" and "are we alone?" These interrogatories are intimately related since we may not be alone and we might not recognize life unless it looks a lot like us. The last chapter summarizes the author's proposition regarding the sixth revolution of biology.

The book is well written and well referenced. The author has a grasp of the literature and uses it well. It is a book I would recommend for a good history of the integration of biology and mathematics targeting the average reader. The author does take a few jabs at American philosophy but I think readers of the book would understand.

Joseph D. Ferrara, Ph.D.

Ian Stewart

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