volume 5, no. 2, february 2013 crystallography in the news
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Protein Crystallography Newsletter
Volume 5, No. 2, February 2013
In this issue:
Crystallography in the news
Science video of the month
Product spotlight: BioSAXS-1000 AUTO
Lab spotlight: Membrane Protein Laboratory
Useful links for crystallography
Crystallographers in the news
Survey of the month
Monthly crystallographic papers
Book review
Science Video of the Month Animation of amyloid fibril formation
in Alzheimer's disease
http://www.youtube.com/watch?v=OGxpp0KbrzU
This is a snapshot of an animation on Small Angle X-
ray Scattering for the WeNMR project, using anexample from amyloid fibril formation in Alzheimer's
disease. Produced by Spronk | 3D.
Product Video of the Month Rigaku BioSAXS-1000 AUTO
www.youtube.com/watch?v=ZbzAYNw1awM
Crystallography in the news
January 30, 2013. Using the Canadian Light Source (CLS) synchrotron, researchershave determined the structure of a key protein that stops viruses from spreading, animportant step towards developing new ways of fighting viral diseases. Researchersfrom McGill University and the Austrian Research Center for Molecular Medicine (CeMM)discovered the molecular blueprint behind the IFIT protein.
February 5, 2013. Led by Dr. Walter Chazin of Vanderbilt University, scientists at OakRidge National Laboratory in Oak Ridge, Tenn., in conjunction with the LawrenceBerkeley National Laboratory in Berkeley, Calif., are currently conducting research onRPA, a replication protein that prevents a single strand of DNA (ssDNA) from gettingdamaged when being unwound from the DNA double helix.
February 14, 2013. Researchers from the Laboratoire biotechnologie et signalisationcellulaire at the Strasbourg-based Ecole supérieure de biotechnologie (CNRS/Universitéde Strasbourg) and Institut de génétique et de biologie moléculaire et cellulaire(CNRS/Université de Strasbourg/Inserm) have solved the three-dimensional structure ofan important oncoprotein involved in cell proliferation and in the development of thehuman papilloma virus (HPV).
February 15, 2013. Streptomyces bacteria are among few microorganisms known todegrade and consume lignin. Now a group of researchers at Brown University hasunlocked the genetic and molecular mechanisms behind a key part of that process.Jason Sello, Professor of Chemistry, and Rebecca Page, Professor in Biology in theDepartment of Molecular Biology, Cell Biology, and Biochemistry, directed the researchwith graduate students Jennifer Davis and Breann Brown.
February 21, 2013. Structural biologists use the ultra-intense pulses from the LinacCoherent Light Source (X-ray free-electron laser) at the SLAC National AcceleratorLaboratory to overcome the problem of radiation damage in crystallography, removingthe need for large, well-diffracting crystals.
February 22, 2013. UCB, a global biopharmaceutical company, has sealed a researchagreement with ConfometRx to enable the discovery of novel medicines addressingunmet medical needs in Neuroscience. Under this two-year multi-target agreement,UCB and ConfometRx will leverage structural biology to gain insight into G-proteincoupled receptor (GPCR) modulation towards the design of differentiated drugs.
BioSAXS-1000 AUTO
Rigaku's BioSAXS-1000 AUTO combines Rigaku's proven BioSAXS-1000 system withautomatic sample handling, automatic data collection and automatic dataanalysis for biological solution scattering experiments. Integral to the BioSAXS-1000AUTO is a state-of-the-art SAXS analysis pipeline, called AAP, that utilizes automatedmodules from the world's most popular and comprehensive ATSAS program suite.Resulting from collaboration between Rigaku and EMBL scientists in Hamburg, Germany,the automatic ATSAS-based pipeline inherent to AAP automates data processing stepssuch as profile averaging and buffer subtraction, as well as data analysis steps such asGuinier and Porod analyses, P(r) calculation, ab initio shape determination and evalua-tion. The end result of AAP is a summary of results for several concentrations of yourprotein solution, presented in an easy-to-review format with hyperlinks to visualize thedata and models. With the BioSAXS-1000 and AAP, Rigaku gives you all the tools you
need to perform successful SAXS experiments in the home lab and to make theinformation obtained from SAXS an integral part of your research flow.
ATSAS Pipeline
Imperial's Membrane Protein Laboratory team: Backrow: Yilmaz Alguel, Mutsuko Grant, Indran Mathavan,James Birch, Nienjen Hu, Matthew Jennions, James
Foadi. Front row: Tian Geng, Isabel Moraes, SoIwata, Alex Cameron, Momi Iwata.
Survey of the Month
Watch a video that illustrates how the BioSAXS-1000 works, including the new samplechanger and the Automatic Analysis Pipeline.
Ask for more information.
Lab in the spotlight: Membrane Protein Laboratory
The Membrane Protein Laboratory (MPL) is a facility forresearch, training and methods development in the area ofmembrane protein structural biology. The MPL is based atDiamond Light Source, the synchrotron in Oxfordshire, UK.The MPL is a collaboration between Prof. So Iwata atImperial College London and Diamond, funded by theWellcome Trust. A Mhp1 transporter protein structure isshown at right.
Useful links: Databases for membrane structural work
Orientations of Proteins in Membranes (OPM) databaseMembrane Proteins of Known StructureMembrane Protein DatabankPDBTM: Protein Data Bank of Transmembrane Proteins
Selected recent crystallographic papers
A proteomic Ramachandran plot (PRplot). Carugo, Oliviero; Djinović-Carugo, Kristina.Amino Acids. Feb2013, Vol. 44 Issue 2, p781-790. 10p.http://dx.doi.org/10.1007/s00726-012-1402-z.
Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. EdwardsJS, Betts L, Frazier ML, Pollet RM, Kwong SM, Walton WG, Ballentine WK 3rd, HuangJJ, Habibi S, Del Campo M, Meier JL, Dervan PB, Firth N, Redinbo MR. Proc Natl Acad SciUSA. 2013 Feb 19;110(8):2804-9. http://dx.doi.org/10.1073/pnas.1219701110.
The crystal structure of the cysteine protease Xylellain from Xylella fastidiosa reveals anintriguing activation mechanism. Leite, Ney Ribeiro; Faro, Aline Regis; Dotta, MariaAmélia Oliva; Faim, Livia Maria; Gianotti, Andreia; Silva, Flavio Henrique; Oliva, Glaucius;Thiemann, Otavio Henrique. Febs Letters. Feb2013, Vol. 587 Issue 4, p339-344. 6p.http://dx.doi.org/10.1016/j.febslet.2013.01.009.
http://www.surveymonkey.com/s/rigaku
Last Month's Survey Results
What is your SECOND FAVORITE instrumentaltechnique for structural biology?
Crystallographers in the News
Structural Biology Lab Surfs for a Cure
http://dx.doi.org/10.1016/j.febslet.2013.01.009.
X-ray crystallography and NMR studies of domain-swapped canecystatin-1. Valadares,Napoleão F.; Oliveira-Silva, Rodrigo; Cavini, Italo A.; Almeida Marques, Ivo; D'MunizPereira, Humberto; Soares-Costa, Andrea; Henrique-Silva, Flavio; Kalbitzer, Hans R.;Munte, Claudia E.; Garratt, Richard C. FEBS Journal. Feb2013, Vol. 280 Issue 4, p1028-1038. 11p. http://dx.doi.org/10.1111/febs.12095.
In-house UV radiation-damage-induced phasing of selenomethionine-labeled proteinstructures. Pereira, Pedro José Barbosa; Royant, Antoine; Panjikar, Santosh; de Sanctis,Daniele. Journal of Structural Biology. Feb2013, Vol. 181 Issue 2, p89-94. 6p.http://dx.doi.org/10.1016/j.jsb.2012.11.003.
X-ray crystallography and QM/MM investigation on the oligosaccharide synthesismechanism of rice BGlu1 glycosynthases. Wang, Jinhu; Pengthaisong, Salila; Cairns,James R. Ketudat; Liu, Yongjun. BBA - Proteins & Proteomics. Feb2013, Vol. 1834Issue 2, p536-545. 10p. http://dx.doi.org/10.1016/j.bbapap.2012.11.003.
Structure-Function of the G Protein-Coupled Receptor Superfamily. Katritch, Vsevolod;Cherezov, Vadim; Stevens, Raymond C. Annual Review of Pharmacology & Toxicology.2013, Vol. 53 Issue 1, p531-556. 6p. http://dx.doi.org/10.1146/annurev-pharmtox-032112-135923.
Expression, purification, crystallization and preliminary X-ray crystallographic studies ofhepatitis B virus core fusion protein corresponding to octahedral particles. Kikuchi,Masaki; Iwabuchi, Shinichiro; Kikkou, Tatsuhiko; Noguchi, Keiichi; Odaka, Masafumi;Yohda, Masafumi; Kawata, Masaaki; Sato, Chikara; Matsumoto, Osamu. ActaCrystallographica: Section F. Feb2013, Vol. 69 Issue 2, p165-169. 5p.http://dx.doi.org/10.1107/S1744309112052074.
Investigations on the Use of Graphite Electrodes Usinga Hull-Type Growth Cell forElectrochemically Assisted Protein Crystallization. Espinoza-Montero, Patricio J.; Moreno-Narváez, María Esther; Frontana-Uribe, Bernardo A.; Stojanoff, Vivian; Moreno, Abel.Crystal Growth & Design. Feb2013, Vol. 13 Issue 2, p590-598. 9p.http://dx.doi.org/10.1021/cg301250c.
Evaluation of cell-free protein synthesis for the crystallization of membrane proteins – acase study on a member of the glutamate transporter family from Staphylothermusmarinus. Jaehme, Michael; Michel, Hartmut. FEBS Journal. Feb2013, Vol. 280 Issue 4,p1112-1125. 14p. http://dx.doi.org/10.1111/febs.12105.
Crystallization, characterization and preliminary X-ray crystallographic analysis of GK2848,a putative carbonic anhydrase of Geobacillus kaustophilus. Ragunathan, Preethi;Raghunath, Gokul; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kumarevel, Thirumananseri;Ponnuraj, Karthe. Acta Crystallographica: Section F. Feb2013, Vol. 69 Issue 2, p162-164. 3p. http://dx.doi.org/10.1107/S1744309112051913.
Improvement of crystal quality for tetragonal hen egg white lysozyme crystals underapplication of an external alternating current electric field. Koizumi, H.; Uda, S.;Fujiwara, K.; Tachibana, M.; Kojima, K.; Nozawa, J. Journal of Applied Crystallography.Feb2013, Vol. 46 Issue 1, p25-29. 5p.http://dx.doi.org/10.1107/S0021889812048716.
A high-pressure cryocooling method for protein crystals and biological samples withreduced background X-ray scatter. Kim, Chae Un; Wierman, Jennifer L.; Gillilan, Richard;Lima, Enju; Gruner, Sol M. Journal of Applied Crystallography. Feb2013, Vol. 46 Issue 1,p234-241. 8p. http://dx.doi.org/10.1107/S0021889812045013.
Some practical guidelines for UV imaging in the protein crystallization laboratory.Desbois, Sebastien; Seabrook, Shane A.; Newman, Janet. Acta Crystallographica:Section F. Feb2013, Vol. 69 Issue 2, p201-208. 8p.http://dx.doi.org/10.1107/S1744309112048634.
RRM–RNA recognition: NMR or crystallography…and new findings. Daubner, Gerrit M;Cléry, Antoine; Allain, Frédéric H-T. Current Opinion in Structural Biology. Feb2013, Vol.
23 Issue 1, p100-108. 9p. http://dx.doi.org/10.1016/j.sbi.2012.11.006.
Utilization of protein intrinsic disorder knowledge in structural proteomics. Oldfield,Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A.Keith; Uversky, Vladimir N. BBA - Proteins & Proteomics. Feb2013, Vol. 1834 Issue 2,p487-498. 12p. http://dx.doi.org/10.1016/j.bbapap.2012.12.003.
Preparation of purified GPCRs for structural studies. Cooke, Robert M.; Koglin, Markus;Errey, James C.; Marshall, Fiona H. Biochemical Society Transactions. Feb2013, Vol. 41
Structural Biology researcher Dr. Josep "Pep" Fontrecently competed in one of the world's most gruelingironman races — The Coolangatta Gold. In October,Dr Font raised funds for the Structural Biology lab inwhich he works at Centenary Institute, an indepen-dent medical research institute in Sydney, Australia.The men's race begins with a 23 km surf-ski leg, a650 m beach run, a 3.5 km surf swim, another 4 kmbeach run, and a 5.5 km board paddle – all before thefinal torturous 10 km beach run to the finish line. Notonly did Dr. Font rise to the occasion by finishing therace, he did so in 4 hours and 30 minutes and raisedover $2,500 for his work into helping find cures for
degenerative diseases like cancer. Moreinformation.
2013 Protein Society Awards Announced
The 2013 Carl Brändén Award Sponsored by Rigaku Corporation
Sheena Radford, University of Leeds
Errey, James C.; Marshall, Fiona H. Biochemical Society Transactions. Feb2013, Vol. 41Issue 1, p185-190. 6p. http://dx.doi.org/10.1042/BST20120240.
Book review:
Foundations of Crystallography with Computer Applications By Maureen M. Julian Taylor and Francis, LLC, 2008, ISBN 978-1-4200-6075-1
I came across this book after I lectured in Tokyo last month and decided to keep thetheme of teaching crystallography going. Although the book appeared to be gearedtoward small molecule crystallography, I thought it would a good read.
This book is the first I have seen since Prince's Mathematical Techniques inCrystallography and Materials Science that actually provides computer code to teachcrystallography. The code is specific to MatLab, so I could not test it myself, but Iunderstand that MatLab is a common teaching tool on many campuses so that shouldnot be a real hindrance. The code teaches students rudimentary programming,something all of us older crystallographers had to do and to which many youngercrystallographers should be exposed.
The first chapter covers the basics of lattices in two and three dimensions, usinghexamethylbenzene (HMB) and anhydrous alum as examples. The author was apostdoc of Kathleen Lonsdale's, hence the use of HMB as an example throughout thebook. HMB is also triclinic (P1), providing a simple general case. The second chaptercovers important concepts like fractional coordinates, placing atoms in the unit cell,calculating bond distances and angles, and crystallographic transformations. The bookdoes not cover least squares or maximum likelihood refinement, so the calculation oferrors is not described.
Chapter 3 provides a detailed description of two- and three-dimensional point groups,starting with the basic symmetry elements. Chapter 4 adds the lattice and translationsto the concept of the point group, developing space groups in two and threedimensions. All seventeen 2D space groups and a number of 3D space groups arereviewed in detail. Further, a flowchart for dissecting space groups and how to readthe International Tables for Crystallography, Volume A is given. Chapter 5 covers theconcept of the reciprocal lattice, along with the topics of making transformationsbetween the direct and reciprocal lattice and the significance of vectors and planes inboth types.
Chapter 6 introduces X-rays and how they interact with matter. Bragg's Law is derived.The final chapter derives the structure factor and electron density, as well as thescattering factor of an atom. The author discusses the effect of atom position on theamplitude and phase of a reflection. The concept of the Fourier relationship betweenelectron density and structure factors would have been benefited from a codeexample. However, this chapter does provide example calculations of the structurefactors for a number of simple structures (P, C, I and F) and of how systematicabsences arise. The absences arising from glide planes and screw axes are described aswell. Friedel's law is covered but not its breakdown.
Each chapter is bracketed by section objectives and an introduction at the beginningand definitions, exercises and a starter program (except in one case) at the end. Thisis not a complete book for a crystallography course, but it does provide an excellenttool for teaching the concepts of lattices and symmetry.
Joseph D. Ferrara, Ph.D. Chief Science Officer
P.S. I finished the Meacham biography of Thomas Jefferson and am half way throughTeam of Rivals: The Polit ical Genius of Abraham Lincoln. The Jefferson biography isactually the first I have read. All of my prior knowledge about Jefferson has beenderived from contemporaneous biographies or from what I learned in grade school.Jefferson was a very complex man and, despite his failings, we owe much to hisenlightened reasoning.
The 2013 Christian B. Anfinsen AwardTom Alber, U.C. Berkeley
The 2013 Dorothy Crowfoot Hodgkin AwardSponsored by Genentech
Christopher Hill, Univ. of Utah
The 2013 Dorothy Crowfoot Hodgkin AwardSponsored by Genentech
Cynthia Wolberger, Johns Hopkins Univ.
The 2013 Stein & Moore AwardRobert Sauer, MIT
The 2013 Emil Thomas Kaiser AwardWilfred van der Donk, Univ. of Illinois
The 2013 Hans Neurath AwardSponsored by the Hans Neurath Foundation
Jennifer Doudna, U.C. Berkeleyand
Chuck Sanders, Vanderbilt Univ. Medical Center
The 2013 Protein Society Young Investigator AwardFeng Shao, Nat. Inst. of Bio. Sciences, Beijing
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