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Protein Crystallography Newsletter

Volume 4, No. 9, September 2012

In this issue:

Crystallography news summary

Continuing education

Lab spotlight: Prof. Jim Naismith

Useful link for structural biology

Product spotlight: Fluor-Score

Science video of the month

Survey of the month

Monthly crystallographic papers

Book reviews

Continuing Education Webinar Radiation Damage in Macromolecular

Crystallography: What is it and why do we care?

Presenter: Prof. Elspeth GarmanThursday, Oct 4, 2012 10:00am CDT (Chicago, GMT-05:00)4:00 pm GMT Summer (London, GMT+01:00)

Radiation damage inflicted during diffraction datacollection in macromolecular crystallography has re-emerged in the last decade as a major experimentaland computational challenge. Even for crystals held at100 K, such damage can result in severe data qualitydegradation and the appearance in solved structuresof artifacts that affect biological interpretations. Inthis Webinar, the observable symptoms and basicphysical processes involved in radiation damage aredescribed and the concept of absorbed dose as thebasic metric against which to monitor the experimen-

tally observed changes is outlined. Investigations intoradiation damage in macromolecular crystallographyare ongoing and the number of studies is rapidly

Crystallography in the news

September 1, 2012. Edward Yu's team at Iowa State University has taken anotherstep forward in our understanding of how bacterial resistance to antibiotics can emergeby using crystallography to reveal the structure of a protein regulator that controls theexpression of the multi-drug efflux pump in Mycobacterium tuberculosis.

September 6, 2012. A neutron detector developed for studies focused on life science,drug discovery, and materials technology has been licensed by PartTec Ltd. TheIndiana-based manufacturer of radiation detection technologies is moving thetechnology—developed at the U.S. Department of Energy (DOE)'s Oak Ridge NationalLaboratory (ORNL)—toward the commercial marketplace. The Neutron-Sensitive AngerCamera allows researchers to study a wider variety of crystalline structures, supportingstudies in biology, earth science, geology, materials science, and condensed matterphysics.

September 12, 2012. A team of researchers in Singapore has determined thestructure of a pair of proteins that may play an important role in tumor growth and theprogression of cancer. The proteins, Vestigial (Vg) and Scalloped (Sd), normally controlwing development in fruit flies, but the team found they show a remarkable structuraland functional similarity to the cancer-promoting proteins called YAP and TAZ.

September 20, 2012. University of Toledo, Los Alamos National Laboratory and OakRidge National Laboratory used neutron crystallography to locate hydrogen atoms inprotein structures. Research Professor Julian C.-H. Chen discussed how their techniqueleverages the scattering properties of deuterium.

September 20, 2012. As Prof. Rohit Pappu (Department of Biomedical Engineering atWashington University in St. Louis) and two colleagues explain in a perspective, a largeclass of proteins doesn't adhere to the structure-function paradigm. Called intrinsicallydisordered proteins, these proteins fail to fold either in whole or in part and yet theyare functional.

September 21, 2012. Astellas Pharma and The High Energy Accelerator ResearchOrganization (KEK) have announced a collaborative research agreement to discovernew drugs for neglected tropical diseases (NTDs). The collaboration will leveragesynchrotron X-ray crystallography to design the pharmaceuticals based on the three-dimensional structure of proteins. The research will primarily focus on infectiousdiseases caused by parasitic protozoans, namely leishmaniasis, Chagas disease andsleeping sickness.

September 24, 2012. Dr. Friedrich Förster from the Max Planck Institute ofBiochemistry relates that the main challenges the researchers faced to achieve the aimof automated single particle acquisition is to collect large amounts of high-qualityelectron micrographs. Acquiring the cryo-EM structure of the S. cerevisiae 26Sproteasome is discussed.

September 27, 2012. A collaboration between groups from France and the UK, led byresearchers from the Institut de Biologie et Chimie des Protéines, has just determinedthe three-dimensional structure of a key region of the procollagen molecule, theprecursor form of collagen, the most abundant protein in the body.

Product spotlight: Fluor-Score automatic drop scoring with UV

In protein crystallography, 90% of your time is spent inspecting clear drops. Rigakudesigned Fluor-Score so that, instead of going over endless numbers of clear drops,you can start your inspections by looking at the most promising images. Our UV

are ongoing and the number of studies is rapidlyincreasing. Our understanding is improving andvarious possible counter measures are summarized.

Register.

Rigaku Fluor-Score Software

Professor James H Naismith FRSE

Wza, a protein that exports the polysaccharide thatforms the capsule required for infection by pathogenic

bacteria. The protein weighs 340,000 amu andmeasures over 150 Å x 100 Å x 100 Å.

Science Video of the Month

you can start your inspections by looking at the most promising images. Our UVimagers are optimized to achieve the best possible resolution and image contrast. Thistechnology paved the way to building Fluor-Score, the first ever program that allowsyou to reliably answer the question, "Which drops do I really have to look at?" Fluor-Score calculations rely upon a combination of factors related to fluorescence signalstrength—clearly indicating whether or not your drop contains something of interest.

The unique advantage of Fluor-Score is that it is not focused on determining whethera drop contains a crystallization event, but rather on determining which drops do not.Flour-Score results can be used in various ways, e.g. by applying a threshold thatsuppresses clear drop images from more detailed visual inspections. Fluor-Score relies onhigh-resolution/high-contrast images, currently only available from Rigaku's Minstrel DTUV and HT UV imagers, and is an example of how a well-aligned combination ofhardware and software can be used to tackle exceedingly complex problems in proteincrystallization. Ask for more information.

Lab in the spotlight: Naismith Lab

Professor James H Naismith FRSEProfessor of Chemical BiologyUniversity of St Andrews

The focus of Jim Naismith's research group is the application of protein structuredetermination (by X-ray crystallography) coupled to molecular biology and biochemistryto probe biological mechanisms and to target specific disease pathways. They haveongoing research in (1) signal transduction (2) physical basis of protein carbohydrateinteractions (3) pathogenic bacteria glycan assembly [they have cloned and crystallizeda number of the enzymes involved in key steps of glycan synthesis in pathogenicbacteria] (4) viral replication [they are purifying and crystallizing a hetero dimer crucialto replication of viruses in vivo], and (5) the biosynthesis of unusual natural products.

Jim was the RSC Jeremy Knowles Award 2009 winner for his outstanding applicationsof protein crystallography in the study of enzyme reaction mechanisms. He has alsobeen awarded the RSC prizes Carbohydrate Medal, the RSC Corday-Morgan Medal, theBiochemical Society Colworth Medal, the Leverhulme Prize in Biological Science, aBBSRC career development fellowship and was elected to fellowship of The RoyalSociety of Edinburgh. This year he became a Fellow of the Academy of Medical Scienceand in 2009 he became a Member of EMBO.

Useful link for structural biology

MobiDB: a database of protein disorder and mobility annotations. Disordered proteinregions are key for the function of numerous processes within an organism, and thedetermination of the protein's biological role. The current most common sources forprotein disorder annotations, DisProt and the PDB, cover only a fraction of the availablesequences in the SwissProt database and up to now deal only with X-ray resolvedstructures. MobiDB's motivation is to build on the content provided by those sourcesand expand it, with the goal of providing a centralized source for data on disorderedregions in protein structures, featuring full coverage of the SwissProt database.

MobiDB: a comprehensive database of intrinsic protein disorder annotations. DiDomenico, Tomás; Walsh, Ian; Martin, Alberto J.M.; Tosatto, Silvio C.E. Bioinformatics.Aug2012, Vol. 28 Issue 15, p2080-2081. 2p.

http://dx.doi.org/10.1093/bioinformatics/bts327.

Selected recent crystallographic papers

Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plusvascular endothelial growth factor} protein complex by racemic crystallography. Mandal,Kalyaneswar; Uppalapati, Maruti; Ault-Riché, Dana; Kenney, John; Lowitz, Joshua;Sidhu, Sachdev S.; Kent, Stephen B. H. Proceedings of the National Academy ofSciences of the United States of America. 9/11/2012, Vol. 109 Issue 37, p14779-14784. 6p. http://dx.doi.org/10.1073/pnas.1210483109.

Science Video of the Month Structural Biology Approaches to HIV Vaccine

Research

http://www.y outube.com/watch?v =aMTm6qWoeIM

Tongqing Zhou, Ph.D., a staff scientist in the VaccineResearch Center at the National Institute of Allergyand Infectious Diseases, and Stephanie Moquin, apost-baccalaureate Intramural Research TrainingAwardee (IRTA), describe their research usingstructural biology approaches to developing a vaccinefor HIV.

Survey of the Month

14784. 6p. http://dx.doi.org/10.1073/pnas.1210483109.

Computational methods for prediction of protein–RNA interactions. Puton, Tomasz;Kozlowski, Lukasz; Tuszynska, Irina; Rother, Kristian; Bujnicki, Janusz M. Journal ofStructural Biology. Sep2012, Vol. 179 Issue 3, p261-268. 8p.http://dx.doi.org/10.1016/j.jsb.2011.10.001.

Crystal Structure of the Coat Protein of the Flexible Filamentous Papaya Mosaic Virus.Yang, Shaoqing; Wang, Tao; Bohon, Jen; Gagné, Marie-Ève Laliberté; Bolduc, Marilène;Leclerc, Denis; Li, Huilin. Journal of Molecular Biology. Sep2012, Vol. 422 Issue 2, p263-273. 11p. http://dx.doi.org/10.1016/j.jmb.2012.05.032.

High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determinationof the identity of the protein and its potential role in detoxification. Pietrzyk, AgnieszkaJ.; Panjikar, Santosh; Bujacz, Anna; Mueller-Dieckmann, Jochen; Lochynska, Malgorzata;Jaskolski, Mariusz; Bujacz, Grzegorz. Acta Crystallographica: Section D (InternationalUnion of Crystallography - IUCr). Sep2012, Vol. 68 Issue 9, p1140-1151. 12p.http://dx.doi.org/10.1107/S0907444912021555.

Contrast-Matched Small-Angle X-ray Scattering from a Heavy-Atom-Labeled Protein inStructure Determination: Application to a Lead-Substituted Calmodulin-PeptideComplex. Grishaev, Alexander; Anthis, Nicholas J.; Clore, G. Marius. Journal of theAmerican Chemical Society. 9/12/2012, Vol. 134 Issue 36, p14686-14689. 4p.http://dx.doi.org/10.1021/ja306359z.

Experimental phasing using zinc anomalous scattering. Cha, Sun-Shin; An, Young Jun;Jeong, Chang-Sook; Kim, Min-Kyu; Lee, Sung-Gyu; Lee, Kwang-Hoon; Oh, Byung-Ha.Acta Crystallographica: Section D. Sep2012, Vol. 68 Issue 9, p1253-1258. 6p.http://dx.doi.org/10.1107/S0907444912024420.

Structure and stability of a thermostable carboxylesterase from the thermoacidophilicarchaeon Sulfolobus tokodaii. Angkawidjaja, Clement; Koga, Yuichi; Takano, Kazufumi;Kanaya, Shigenori. FEBS Journal. Sep2012, Vol. 279 Issue 17, p3071-3084. 14p.http://dx.doi.org/10.1111/j.1742-4658.2012.08687.x.

Structural insights into Helicobacter pylori oncoprotein CagA interaction with β1integrin. Kaplan-Türköz, Burcu; Jiménez-Soto, Luisa F.; Dian, Cyril; Ertl, Claudia; Remaut,Han; Louche, Arthur; Tosi, Tommaso; Haas, Rainer; Terradot, Laurent. Proceedings ofthe National Academy of Sciences of the United States of America. 09/04/2012, Vol.109 Issue 36, p14640-14645. 6p. http://dx.doi.org/10.1073/pnas.1206098109.

Design and Characterization of Modular Scaffolds for Tubulin Assembly. Mignot, Ingrid;Pecqueur, Ludovic; Dorléans, Audrey; Karuppasamy, Manikandan; Ravelli, Raimond B.G.; Dreier, Birgit; Plückthun, Andreas; Knossow, Marcel; Gigant, Benoît. Journal ofBiological Chemistry. 9/7/2012, Vol. 287 Issue 37, p31085-31094. 10p.http://dx.doi.org/10.1074/jbc.M112.383869.

Spatial distribution of radiation damage to crystalline proteins at 25-300 K. Warkentin,Matthew; Badeau, Ryan; Hopkins, Jesse B.; Thorne, Robert E. Acta Crystallographica:Section D. Sep2012, Vol. 68 Issue 9, p1108-1117. 10p.http://dx.doi.org/10.1107/S0907444912021361.

X-ray Crystal Structure and Specificity of the Plasmodium falciparum MalariaAminopeptidase PfM18AAP. Sivaraman, Komagal Kannan; Oellig, Christine A.; Huynh,Kitmun; Atkinson, Sarah C.; Poreba, Marcin; Perugini, Matthew A.; Trenholme,Katharine R.; Gardiner, Donald L.; Salvesen, Guy; Drag, Marcin; Dalton, John P.;Whisstock, James C.; McGowan, Sheena. Journal of Molecular Biology. Sep2012, Vol.422 Issue 4, p495-507. 13p. http://dx.doi.org/10.1016/j.jmb.2012.06.006.

Structural analysis of trimeric phospholipase A2 neurotoxin from the Australian taipansnake venom. Cendron, Laura; Mičetić, Ivan; Polverino de Laureto, Patrizia; Paoli,Marco. FEBS Journal. Sep2012, Vol. 279 Issue 17, p3121-3135. 15p.http://dx.doi.org/10.1111/j.1742-4658.2012.08691.x.

Toward Rational Fragment-Based Lead Design without 3D Structures. MorkosA. Henen;

Nicolas Coudevylle; Leonhard Geist; Robert Konrat. Journal of Medicinal Chemistry.Sep2012, Vol. 55 Issue 17, p7909-7919. 11p. http://dx.doi.org/10.1021/jm301016m.

Structural features of the single-stranded DNA-binding protein MoSub1 fromMagnaporthe oryzae. Huang, Jinguang; Zhao, Yanxiang; Huang, Dan; Liu, Huaian;Justin, Neil; Zhao, Wensheng; Liu, Junfeng; Peng, Youliang. Acta Crystallographica:Section D. Sep2012, Vol. 68 Issue 9, p1071-1076. 6p.http://dx.doi.org/10.1107/S0907444912019932.

http://www.surveymonkey.com/s/rigaku

August Survey Results

Anyone who studies diffraction knows that optimizingsignal-to-noise is one of the most importantexperimental concepts for obtaining high quality data.But in practice, people often ignore the steps that canbe taken to improve signal-to-noise. Where do youstand on this subject?

http://dx.doi.org/10.1107/S0907444912019932.

Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcusaureus. Matsui, Takashi; Yamane, Junji; Mogi, Nobuyuki; Yamaguchi, Hiroto; Takemoto,Hiroshi; Yao, Min; Tanaka, Isao. Acta Crystallographica: Section D. Sep2012, Vol. 68Issue 9, p1175-1188. 14p. http://dx.doi.org/10.1107/S0907444912022640.

Corrigendum to "Common Structural Traits across Pathogenic Mutants of the HumanPrion Protein and Their Implications for Familial Prion Diseases". By: Rossetti, Giulia;Cong, Xiaojing; Caliandro, Rocco; Legname, Giuseppe; Carloni, Paolo. Journal ofMolecular Biology. Sep2012, Vol. 422 Issue 1, p157-157. 1p.http://dx.doi.org/10.1016/j.jmb.2011.06.008.

Book reviews:

In Pursuit of the Unknown: 17 Equations That Changed the World

by Ian Stewart Basic Books, 2012; ISBN: 0465029736, 9780465029730

Ian Stewart's latest book, In Pursuit of the Unknown: 17 Equations That Changed theWorld, offers a refreshing juxtaposition of theoretical and anecdotal materialconcerning, as the book's tit le implies, 17 equations that have fundamentally affectedthe various disciplines of math and science. These equations range from Pythagoras'Theorem (a sure throwback to any high school geometry class) to the Black-ScholesEquation (a financial market model that earned its namesakes the Nobel Prize in 1997)to Maxwell's Equations (another high school throwback- AP Physics) and the Navier-Stokes Equation (derived from the application of Newton's Second Law to fluidmotion). Stewart begins his discussion of each equation with an anecdote, thenprogresses into the historical context of the equation, concluding with insight into thetheoretical nature of the equation and how it will continue to maintain its relevance inits respective field. Each discussion maintains a balance between entertainment andenlightenment that can only be applauded in mathematic literature. The historicalbreadth and explanatory depth of Stewart's book is admirable. He transitions smoothlyfrom his discussions of older mathematical concepts, such as the controversialdevelopment of Calculus and Newton's Law of Gravity, to more recent ideas, includingEinstein's Theory of Relativity and Information Theory. Additionally, Stewart dispelsmany modern misconceptions concerning the applications of these equations, and notonly addresses appropriate situations for their use, but corrects inappropriate situationsin which they can be mistakenly applied.

All in all, In Pursuit of the Unknown is an engaging and enjoyable read, appropriate notonly for those interested in broadening their mathematical horizons, but really foranyone. It is humbling to realize just how essential mathematics is in the modern world.

Jeanette S. Ferrara, Princeton, Class of 2015

International Tables for Crystallography, Volume F Crystallography of Biological Macromolecules Editors: Eddy Arnold, Daniel M. Himmel and Michael G. Rossmann John Wiley & Sons, 2012; ISBN: 0470660783, 9780470660782

The first thing I have to say is that I did not read this encyclopedia of crystallographycover to cover. This is the first book I have reviewed for which I have not done this.Given its size and the fact this is a second edition, I think you will forgive me for this.However, I did look carefully at sections that were new or had received major updates.

This book attempts to collate the sum total of all knowledge in macromolecularcrystallography. The editors have done this by solicit ing experts on a particular topic tocodify their knowledge on it. The volume is very well indexed, so it is easy to find theanswers to a particular question. It is also well referenced, so the reader can go backto the original paper describing a particular topic. If you place the first edition and the

second together, you will notice that the second edition is a full centimeter thicker.This is because many sections of the book have been updated. Some sections havereceived little or no revision. Some of these are historical and are complete as originallywritten, while some sections should have received a refresher. Part 24 of the firstedition, which covered the software of crystallography, has been dispersed into thesections for which the particular package is relevant.

When the first edition came out in 2001, I bought two copies, one for myself and onefor my company. I can never find the company copy on the bookshelf because it is ona colleague's desk. I reference my copy frequently. The only books more worn on myshelf are my International Tables, Volume C, and my CRC Handbook of Chemistry and

shelf are my International Tables, Volume C, and my CRC Handbook of Chemistry andPhysics from graduate school.

Part 1 provides a historical perspective and prospective on crystallography from theeditors and three contributors. For the most part these sections were not updated,but this, along with Part 25, the story of the determination of the structure oflysozyme, is a must read for everyone. We often forget how easy crystallography istoday and these parts remind us it wasn't so easy not very long ago. Part 1 receivednew sections by Himmel, Spence and Sun. Part 2.2 by Einspahr and Weiss covers thequality indicators for crystallography from diffraction data, various structure solutionmethods and refinement. The most commonly used indicators are tabulated at theend of the section. Part 3.2 by Ernst, Yansura and Koth describes membrane proteincloning, expression and purification. Part 4 provides a current survey of crystallizationmethods for soluble proteins (Sauter, et al.), modification of proteins to aid incrystallization (Derewenda), and high throughput methods (Choi).

Part 8.1 by Helliwell covers the current state of synchrotron radiation sources. Datacollection is covered in Part 9. Part 9.1 by Dauter and Wilson, which covers the basicsof monochromatic data collection, has been updated. Section 9.2 by Earnest and Corkreviews automatic sample changing, while section 9.3 by Shapiro covers the new fieldof diffraction imaging. Section 10.3 by Garman provides the current state ofknowledge about radiation damage to crystals, an important topic not included in thefirst edition. Section 11.7 by Yeates and Tsai, on detecting merohedry, is completelynew and is complemented by Section 18.12, which covers structure determination inthe presence of twinning (Yeates and Sawaya). Section 13. 5, on the use of MOLREP(Vagin and Teplyakov), is also completely new.

Section 16.1 on ab initio phasing, by Sheldrick, et al., is an older section but hasreceived numerous updates in this edition and includes a discussion of the deceptivelysimple charge flipping method, while section 16.3, ab initio phasing or low resolutionFourier syntheses by Lunin, Urzhumtsev and Podjarny, is completely new. Section 17.1,macromolecular model building and validation with Coot, by Emsley, Lohkamp andCowtan, completely replaces the section on O from the first edition. Part 18,Refinement, has a number of new additions, including sections that came over fromthe software section (Section 24 in the first edition). The sections on atomicresolution refinement (Dauter et al.), ARP/wARP (Lamzin et al.), SHELX (Sheldrick),PrimeX (Bell et al.) are not new but have been updated, while a section on PHENIX(Adams et al.) is new. Part 19 covers other methods and includes several updatedsection related to cryoEM and single particle reconstruction. Part 21, StructureValidation, has new sections on KiNG (Chen et al.) and MolProbity (Chen et al.). Part22 covers Molecular Geometry and Features. Section 22.3, Hydrogen Bonding inBiological Macromolecules (Baker), has been updated. Part 23, Structural Analysis andClassifications, has been refreshed with a new version of Protein-Fold Classification byOrenco and Thornton, as well as a new section on the interaction of halides withprotein crystals by Vallelios et al, (23.6).

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

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