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Protein Crystallography NewsletterVolume 4, No. 10, October 2012
In this issue:
Crystallography news summary
Lab spotlight: Prof. Jenny Martin
Useful link for structural biology
Product spotlight: ScreenMachine
Science video of the month
Survey of the month
Monthly crystallographic papers
Book review
Science Video of the Month Science Nation - 3D Proteins, the Big Picture
http://www.y outube.com/watch?v =Q jMkqiBuixk
Proteins are the workhorses of cells. With supportfrom the National Science Foundation, University ofArkansas biochemist James Hinton has beenresearching their structure and function for decades.In the 1990s, he had a vision to study these hugeprotein structures in 3D and now, in cooperation witha company called Virtalis, his vision has become areality. The new system allows researchers to enlargethe visual of a protein to room-size, so they canexamine it from all angles, to better understand itsstructure and function. The new 3D visuals are alsohelping Hinton realize his other vision: to betterengage students in his discoveries and science ingeneral.
Crystallography in the news
Oct 5, 2012. Columbia University researchers have developed an algorithm – namedPrePPI – for predicting protein-protein interactions based on a combination of three-dimensional structural information and functional data.
Oct 9, 2012. Researchers at Los Alamos National Laboratory have used neutroncrystallography for the first time to determine the structure of a clinical drug in complexwith its human target enzyme. Seeing the detailed structure of the bondedcomponents provides insights into developing more effective drugs with fewer sideeffects for patients.
Oct 10, 2012. Brian Kobilka (Stanford) and Robert Lefkowitz (Duke) have won the2012 Nobel Prize in Chemistry for their work on one of the most important classes ofproteins in living organisms, the G Protein Coupled Receptors (GPCRs).
Oct 11, 2012. Researchers have published the first highly detailed description of howneurotensin, a neuropeptide hormone that modulates nerve cell activity in the brain,interacts with its receptor. Their results suggest that neuropeptide hormones use anovel binding mechanism to activate a class of receptors called G-protein coupledreceptors (GPCRs).
Oct 24, 2012. A team of Stanford University researchers used the StanfordSynchrotron Radiation Lightsource (SSRL) to gain a deeper understanding of a vitalfamily of signaling proteins (Wnt) responsible for regulating an organism's developmentand growth, as well as tissue regeneration and wound healing.
Oct 26, 2012. Researchers at Johns Hopkins have figured out the three-dimensionalshape of the protein responsible for creating unique bonds within the cell wall of thebacteria that cause tuberculosis. The bonds make the bacteria resistant to currentlyavailable drug therapies.
Oct 30, 2012. The global proteomics market is estimated to grow at a CAGR of 14.2%to reach $17.2 billion by 2017. The market is comprised of: Protein Microarray, MassSpectrometry, NMR Spectroscopy, Chromatography, Electrophoresis, Surface PlasmonResonance, Protein Fractionation, X-ray Crystallography, Immunoassay) - Instruments,Reagents and Services.
Oct 30, 2012. A tiny device invented at SLAC National Accelerator Laboratory will makeit much easier for scientists to determine the structures of important, delicate proteinsby greatly reducing the amount of protein needed for study. Called a microjet, thedevice injects a thin stream of liquid containing crystallized proteins into the path of anX-ray laser.
ScreenMachine™ - Easily and simply screen crystals
As synchrotron beamlines have become more prevalent for research in structuralbiology, many home lab X-ray systems are used mainly for screening crystals in advance
of synchrotron data collection. To meet the needs of this type of work flow, Rigakuhas developed the ScreenMachine, a self contained unit that is optimized for safecrystal mounting and recovery, optimized for evaluating small crystals, designed forminimal maintenance, and, best of all, collects amazingly high quality data.
Built around the time-tested design of an inverted φ-axis, the ScreenMachine offersthe best possible geometry for safe crystal mounting and recovery. Utilizing the mostpopular processing software in use today, researchers can quickly and efficientlyevaluate the diffraction quality of a mounted sample. Ask for more information.
ScreenMachine - Easily and simply screen crystals
One of Professor Martin's most recent publications is
"Membrane-curvature protein exhibitsinterdomain flexibility and binds a small
GTPase", published in the Journal of BiologicalChemistry.
Survey of the Month
Lab in the spotlight: Martin Lab
Professor Jenny MartinInstitute for Molecular BioscienceThe University of Queensland, Brisbane, Australia
The Institute for Molecular Bioscience (IMB) undertakes globally competitive researchto decipher the information contained in the genes and proteins of plants, animals andhumans.
The goal of the Martin group is to better understand the role of proteins in diseaseand to develop novel drugs targeting disease-causing proteins. They use a range ofbiochemical and biophysical techniques to investigate the structure, function andinteractions of proteins, with a particular emphasis on high-throughput proteincrystallography and structure-based approaches for inhibitor design.
Useful link for structural biology
Viruses: from Structure to Biology. This is a very interesting website that contains agood deal of information concerning virus structures and function. The website wascreated by Sondra and Milton Schlesinger of Washington University, St. Louis.
Selected recent crystallographic papers
High-throughput counter-diffusion capillary crystallization and in situ diffraction usinghigh-pressure freezing in protein crystallography. Kurz, Mareike; Blattmann, Beat;Kaech, Andres; Briand, Christophe; Reardon, Paul; Ziegler, Urs; Gruetter, Markus G.Journal of Applied Crystallography. Oct2012, Vol. 45 Issue Part 5, p999-1008. 10p.http://dx.doi.org/10.1107/S0021889812034061.
Contamination from an affinity column: an encounter with a new villain in the world ofmembrane-protein crystallization. Panwar, Pankaj; Deniaud, Aurélien; Pebay-Peyroula,Eva. Acta Crystallographica: Section D. Oct2012, Vol. 68 Issue 10, p1272-1277. 6p.http://dx.doi.org/10.1107/S090744491202639X.
Hans Charles Freeman (1929–2008): A scientific journey from dipole moments toprotein crystallography. Guss, J. Mitchell. Journal of Inorganic Biochemistry. Oct2012,Vol. 115, p114-118. 5p. http://dx.doi.org/10.1016/j.jinorgbio.2012.02.036.
Cloning, purification, crystallization and preliminary X-ray analysis of two low-molecular-weight protein tyrosine phosphatases from Vibrio cholerae. By: Nath, Seema; Banerjee,Ramanuj; Khamrui, Susmita; Sen, Udayaditya. Acta Crystallographica: Section F.Oct2012, Vol. 68 Issue 10, p1204-1208. 5p.http://dx.doi.org/10.1107/S174430911203518X.
Unique water distribution of Langmuir–Blodgett versus classical crystals. Pechkova,Eugenia; Sivozhelezov, Victor; Belmonte, Luca; Nicolini, Claudio. Journal of StructuralBiology. Oct2012, Vol. 180 Issue 1, p57-64. 8p.http://dx.doi.org/10.1016/j.jsb.2012.05.021.
Metalloprotein active site structure determination: Synergy between X-ray absorptionspectroscopy and X-ray crystallography. Cotelesage, Julien J.H.; Pushie, M. Jake;Grochulski, Pawel; Pickering, Ingrid J.; George, Graham N. Journal of InorganicBiochemistry. Oct2012, Vol. 115, p127-137. 11p.http://dx.doi.org/10.1016/j.jinorgbio.2012.06.019.
How many packing contacts are observed in protein crystals? Carugo, Oliviero; Djinović-Carugo, Kristina. Journal of Structural Biology. Oct2012, Vol. 180 Issue 1, p96-100. 5p.http://dx.doi.org/10.1016/j.jsb.2012.05.009.
Structural determination of the phosphorylation domain of the ryanodine receptor.Sharma, Parveen; Ishiyama, Noboru; Nair, Usha; Li, Wenping; Dong, Aiping; Miyake,Tetsuaki; Wilson, Aaron; Ryan, Tim; MacLennan, David H.; Kislinger, Thomas; Ikura,Mitsuhiko; Dhe-Paganon, Sirano; Gramolini, Anthony O. FEBS Journal. Oct2012, Vol.
http://www.surveymonkey.com/s/rigaku
September Survey Results
A famous crystallographer was captured last monthon a cell phone camera singing karaoke. This month’ssurvey gives you the chance to guess which song hewas singing. "Madness - Our House" was the rightanswer.
Mitsuhiko; Dhe-Paganon, Sirano; Gramolini, Anthony O. FEBS Journal. Oct2012, Vol.279 Issue 20, p3952-3964. 13p.http://dx.doi.org/10.1111/j.1742-4658.2012.08755.x.
Superstructure of the centromeric complex of TubZRC plasmid partitioning systems.Aylett, Christopher H. S.; Löwe, Jan. Proceedings of the National Academy of Sciencesof the United States of America. 10/9/2012, Vol. 109 Issue 41, p16522-16527. 6p.http://dx.doi.org/10.1073/pnas.1210899109.
Structures of Hepatitis B Virus Cores Presenting a Model Epitope and Their Complexeswith Antibodies. Roseman, A.M.; Borschukova, O.; Berriman, J.A.; Wynne, S.A.;Pumpens, P.; Crowther, R.A. Journal of Molecular Biology. Oct2012, Vol. 423 Issue 1,p63-78. 16p. http://dx.doi.org/10.1016/j.jmb.2012.06.032.
Crystal Structure of a Preacylation Complex of the β-Lactamase Inhibitor SulbactamBound to a Sulfenamide Bond-Containing Thiol-β-lactamase. Rodkey, Elizabeth A.;Drawz, Sarah M.; Sampson, Jared M.; Bethel, Christopher R.; Bonomo, Robert A.; vanden Akker, Focco. Journal of the American Chemical Society. 10/10/2012, Vol. 134Issue 40, p16798-16804. 7p. http://dx.doi.org/10.1021/ja3073676.
Fragment and Conquer: From Structure to Complexes to Function. Guichou, Jean-François; Labesse, Gilles. Structure. Oct2012, Vol. 20 Issue 10, p1617-1619. 3p.http://dx.doi.org/10.1016/j.str.2012.07.016.
Digital topography with an X-ray CCD camera for characterizing perfection in proteincrystals. Wako, Kei; Kimura, Kunio; Yamamoto, Yu; Sawaura, Takuya; Shen, Mengyuan;Tachibana, Masaru; Kojima, Kenichi. Journal of Applied Crystallography. Oct2012, Vol.45 Issue Part 5, p1009-1014. 6p. http://dx.doi.org/10.1107/S0021889812032049.
Structure of the primed paramyxovirus fusion protein. Steinhauer, David A.; Plemper,Richard Karl. Proceedings of the National Academy of Sciences of the United States ofAmerica. 10/9/2012, Vol. 109 Issue 41, p16404-16405. 2p.http://dx.doi.org/10.1073/pnas.1214903109.
High-pressure macromolecular crystallography and NMR: status, achievements andprospects. Fourme, Roger; Girard, Eric; Akasaka, Kazuyuki. Current Opinion in StructuralBiology. Oct2012, Vol. 22 Issue 5, p636-642. 7p.http://dx.doi.org/10.1016/j.sbi.2012.07.007.
Probing the diverse landscape of protein flexibility and binding. Marsh, Joseph A;Teichmann, Sarah A; Forman-Kay, Julie D. Current Opinion in Structural Biology.Oct2012, Vol. 22 Issue 5, p643-650. 8p. http://dx.doi.org/10.1016/j.sbi.2012.08.008.
Ab Initio Quantum Chemistry for Protein Structures. Heather J. Kulik; Nathan Luehr;Ivan S. Ufimtsev; Todd J. Martinez. Journal of Physical Chemistry B. Oct2012, Vol. 116Issue 41, p12501-12509. 9p. http://dx.doi.org/10.1021/jp307741u
Emerging opportunities in structural biology with X-ray free-electron lasers. Schlichting,Ilme; Miao, Jianwei. Current Opinion in Structural Biology. Oct2012, Vol. 22 Issue 5,p613-626. 14p. http://dx.doi.org/10.1016/j.sbi.2012.07.015.
The 1.2 Å resolution crystal structure of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera-toxin production. Walden, Patricia M.;Heras, Begoña; Chen, Kai-En; Halili, Maria A.; Rimmer, Kieran; Sharma, Pooja; Scanlon,Martin J.; Martin, Jennifer L. Acta Crystallographica: Section D. Oct2012, Vol. 68 Issue10, p1290-1302. 13p. http://dx.doi.org/10.1107/S0907444912026388.
Book review:
The Violinist's Thumb and Other Lost Tales of Love, War and Genius, as Written by Our Genetic Code By Sam Kean Little Brown Books, 2012, ISBN: 978-0-316-18231-7
I heard about this book while listening to an interview with the author on ScienceFriday. I read and thoroughly enjoyed Kean's earlier book, The Disappearing Spoon,and so bought a copy of The Violinist's Thumb immediately. Many of the topicsdescribed in TVT are well known to this community, but Kean's treatment of thesubject is refreshing. More importantly, I learned some new and interesting tidbitsabout DNA.
The book is divided into four major parts. The first part tit led, A, G, C, T and You,covers our understanding of what genes and DNA are and how we came to that
covers our understanding of what genes and DNA are and how we came to thatunderstanding. The works of Mendel (peas), Meischer (pus) and Morgan (fruit flies)that gave us the basic understanding of the genetic code are described. Of course,Watson, Crick and Franklin are mentioned here as well.
The next part, Our Animal Past, covers the work of McClintock, who elucidated themolecular basis of evolution. We also learn how the entire history of life on earth isencoded in our genes, how packed our genes are with foreign DNA, and when andhow humans with 46 chromosomes diverged from other primates with 48 chromo-somes. This latter story is backed by the discovery of a healthy man in China with 44chromosomes.
Part III, Genes and Geniuses, looks at how the genetic record shows we've gonethrough several evolutionary bottlenecks and how lucky we are to be here. Theauthor looks at how genes and brain size interact, as well as how we might use art inthe mating process. The last major section, The Oracle of DNA, looks at forensicanalysis of DNA of famous people, for example Tutankhamen, who died at the age of19, probably because of too much inbreeding. A litt le bit of modern history comes outin the battle between Venter and Watson—and then Venter and Collins—to sequencethe human genome, with the result that neither group would have been successfulwithout the other. In this section the author also reviews cloning and epigenetics.
In the epilogue, the author describes his experience with having his genomesequenced and the trepidation associated with finding out whether one has the genesfor a specific familial disease. The only flaw I could find was the lumping of the greatapes and monkeys into a group called monkeys, as opposed to primates. It is not a bigmistake, but means one has to be careful about other statements.
Joseph D. Ferrara, Ph.D. Chief Science Officer
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