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Protein Crystallography Newsletter
Volume 5, No. 3, March 2013
In this issue:
Crystallography in the news
Science video of the month
Product spotlight: UV+ Low Profile Microplate
Lab spotlight: Ke Lab @ Cornell
Installation spotlight: Dart NeuroScience LLC
Useful links for crystallography
Crystallographers in the news
Survey of the month
Monthly crystallographic papers
Book review
Science Video of the Month The Ada Yonath Story
http://www.youtube.com/watch?v=s0WBK0R3QQA
Prof. Ada Yonath of the Weizmann Institute ofScience received
the 2009 Nobel Prize in Chemistry.Prof. Yonath is the Martin S. and
Helen KimmelProfessor of Structural Biology. She is best known
forher pioneering work on the structure of the ribosome.
Product in the Spotlight
Installation of the Month
Crystallography in the news
March 5, 2013. Crystallographer Suzanne Fortier, President of
the Natural Sciences andEngineering Research Council of Canada
(NSERC) in Ottawa and a McGill alumna, wasthe unanimous choice of
the Board of Governors to succeed Heather Munroe-Blum andbecome
McGill University’s 17th Principal and Vice-Chancellor.
March 11, 2013. Biopharmaceutical company Receptos has
successfully determined anovel protein crystal structure of an
undisclosed proprietary GPCR drug discovery targetfor Ono
Pharmaceuticals. The structure determination represents the third
significantmilestone met under the terms of the collaboration, all
of which have been achievedahead of originally anticipated
timelines.
March 13, 2013. An international team of researchers, including
Lawrence LivermoreNational Laboratory (LLNL) physicist Matthias
Frank and postdoctoral researcher MarkHunter, have for the first
time used an ultra-intense X-ray laser to determine thepreviously
unknown atomic-scale structure of a protein.
March 18, 2013. A research group has developed the necessary
infrastructure at theBioCARS 14-ID-B beamline at the U.S.
Department of Energy Office of Science’sAdvanced Photon Source to
watch proteins function in real-time on the picosecondtime scale.
Researchers from the National Institutes of Health, the Nara
Institute ofScience and Technology (Japan), the University of
Chicago, and the EuropeanSynchrotron Radiation Facility (France)
developed a time-resolved, 150-ps Lauecrystallography technique to
study structural changes in the photocycle of a proteinfirst
discovered in the photosynthetic bacterium Halorhodospira
halophila.
March 25, 2013. Emerald BioSystems Inc. is part of team of
researchers using the low-gravity atmosphere of the International
Space Station to develop a more completeunderstanding of the
intricate structure of proteins, which in turn would give
drugmakers more insight into treating diseases.
March 25, 2013. Michael E. Salvucci, an Agricultural Research
Service plant physiologistwith the U.S. Arid-Land Agricultural
Research Center, has teamed with researchassociate Nathan Henderson
and Arizona State University professor Rebekka Wachter,both
structural biochemists, to determine the three-dimensional view
(via X-raycrystallography) of rubisco activase from creosote
bush.
March 26, 2013. A team including scientists from The Scripps
Research Institute(TSRI), the University of North Carolina at
Chapel Hill and the Chinese Academy ofSciences has determined and
analysed the high-resolution atomic structures of twokinds of human
serotonin receptor.
UV+ Low Profile Microplate
Rigaku has partnered with SWISSCI to provide researchers in
structural biology a lowprofile plate with excellent visible and UV
imaging characteristics. Designed to supporthigh-throughput
research utilizing a low background fluorescence material,
researcherswill obtain significantly increased quality UV images
with Rigaku's UV+ Low ProfileMicroplate. The Rigaku UV+ plate is
designed to support high-throughput research byfocusing on the
following features:
Low Background Fluorescence Material: for increased quality of
UV images
L-Shaped 3-Well Layout: for increased throughput, multiple
samples and co-
http://www.rigakucrystallographytimes.com/mailto:[email protected]?subject=Subscribe%20to%20newsletter&body=Please%20type%20your%20email%20address%20and%20click%20send.file:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#newsfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#videofile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#vertorialfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#spotlightfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#installfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#linksfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#currentfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#surveyfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#papersfile:///C:/Users/bev.vincent/Downloads/Crystallography_eNewsMar13-Rev3.html#reviewhttp://www.youtube.com/watch?v=s0WBK0R3QQAhttp://www.youtube.com/watch?v=s0WBK0R3QQAhttp://www.rigakuautomation.com/microplatehttp://www.facebook.com/plugins/like.phphttp://twitter.com/share?url=http://www.rigakucrystallographytimes.com&via=Crystallography_Timeshttp://publications.mcgill.ca/reporter/2013/03/dr-suzanne-fortier-to-be-mcgill%E2%80%99s-17th-principal/http://www.pharmabiz.com/NewsDetails.aspx?aid=74219&sid=2http://www.rdmag.com/news/2013/03/first-ever-determination-protein-structure-x-ray-laserhttp://www.laboratoryequipment.com/news/2013/03/watching-protein-it-functionshttp://bostonglobe.com/business/2013/03/24/space-final-frontier-for-drug-makers/xyUzCQSbRjkropEjCD9tEI/story.htmlhttp://phys.org/news/2013-03-long-sought-goal-crystallizing-elusive-protein.htmlhttp://www.domain-b.com/technology/Health_Medicine/20130326_drug_effects.htmlhttp://www.rigakuautomation.com/microplate
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Dart NeuroScience LLC, a San Diego based company,
has acquired Rigaku Automation's CrystalMation™system, a fully
integrated and automated crystalliza-tion platform, to assist in
their drug discoveryprojects. Rigaku's CrystalMation system
providesseamless integration of high-throughput proteindispense,
screen preparation, crystallization platestoring and imaging.
Dr. Kathleen Aertgeerts, Director of Structural Biologyat DNS,
stated, "Dart NeuroScience (DNS) is verypleased to apply Rigaku's
CrystalMation system to ourhigh-throughput crystallography-based
drugdiscovery platform, which will aid in achieving thecompany's
mission to discover and develop newtherapies that help maintain
cognitive vitalitythroughout life."
Dr. Michael Willis, President of Rigaku Automation,further
commented, "Rigaku is very pleased to haveestablished this
relationship with Dart NeuroScienceand looks forward to their
future success."
Crystal structure of the tetrameric pRNA ring.
L-Shaped 3-Well Layout: for increased throughput, multiple
samples and co-
crystallization experiments
Shallow Wells: for easy harvesting and excellent visible and UV
imaging
Concave Wells: for precise drop-on-drop dispensing of
crystallization drops
Wide Separation Between Wells: for reliable tape sealing
Ask for more information.
Lab in the spotlight: Ke Lab @ Cornell
Associate Professor Ailong KeCornell UniversityDepartment of
Molecular Biology and Genetics
Research in the Ke lab centers around the biology of RNA.
Ineukaryotic cells, stable RNAs are transcribed with a 3'extension
that is subsequently trimmed from 3'-to-5', whereasaberrantly
processed RNAs are subject to rapid degradation. Aconserved 300 -
400 kDa exoribonuclease protein complex,the exosome, plays crucial
roles in both the RNA 3'-endformation and turnover processes. The
nuclear exosome isrequired for the 3' end formation of 5.8S rRNA,
small nuclear and nucleolar RNAs; andinvolved in the degradation of
inefficiently spliced and hyper- or hypo-adenylated pre-mRNAs. The
cytoplasmic exosome is required for the degradation of normal mRNAs
aswell as those containing premature termination codons, lacking
termination codons, orbearing AU-rich elements near the 3'
untranslated region. Using X-ray crystallographyand biochemical
tools, they aim to understand the architecture, working
mechanism,and the regulation of this multi-subunit machinery.
RNA-protein (ribonucleoprotein) complexes, such as the ribosome,
signal recognitionparticle (SRP), spliceosome, and telomerase,
carry out essential functions inside cells.They are currently
investigating the structural mechanism of SRP-mediated
co-translational translocation of proteins across or into cell
membranes. In this vital cellularprocess, SRP recognizes the
hydrophobic signal sequence of the nascent polypeptideemerging from
the ribosome, resulting in transient elongation arrest in
eukaryotes, andtargets the ribosome to the membrane via a
GTP-dependent interaction with the SRPreceptor (SR).
Useful link: Phyre Alarm
The latest version of the Phyre server, Phyre2, is designed
around the idea that youhave a protein sequence/gene and want to
predict its three-dimensional (3D)structure. Whereas Phyre used a
profile-profile alignment algorithm, Phyre2 uses thealignment of
hidden Markov models via HHsearch to significantly improve accuracy
ofalignment and detection rate.
Sometime Phyre2 can't detect any confident matches to known
structures. However,the fold library database increases by about
40-100 new structures each week. Soeven though there might be no
decent templates this week, there may well be in thecoming weeks.
Phyre Alarm allows you to submit a protein sequence to be
automa-tically scanned against new entries added to their fold
library every week. If aconfident hit is detected, you are notified
by email together with the results of thePhyre search.
Protein structure prediction on the web: a case study using the
Phyre server. Kelley LAand Sternberg MJE. Nature Protocols 4, 363 -
371 (2009). (PDF)
Selected recent crystallographic papers
Breaking the barriers in membrane protein crystallography. Kang,
Hae Joo; Lee, Chiara;Drew, David. International Journal of
Biochemistry & Cell Biology. Mar2013, Vol. 45Issue 3, p636-644.
9p. http://dx.doi.org/10.1016/j.biocel.2012.12.018.
http://www.rigaku.com/products/automation/crystalmationhttp://mbg.cornell.edu/faculty-staff/faculty/ke.cfmmailto:[email protected]?subject=information%20request&Body=Please%20email%20me%20information%20on%20UV+%20Microplate.http://mbg.cornell.edu/faculty-staff/faculty/ke.cfmhttp://www.sbg.bio.ic.ac.uk/phyre2/html/help.cgi?id=help/phyrealarmhttp://www.sbg.bio.ic.ac.uk/~phyre/html/nprot.2009.2.pdfhttp://dx.doi.org/10.1016/j.biocel.2012.12.018
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Ke Lab at Cornell.
Survey of the Month
http://www.surveymonkey.com/s/rigaku
Last Month's Survey Results
How much additional funding (USD) wouldyour group need to
operate at peakefficiency?
Issue 3, p636-644. 9p.
http://dx.doi.org/10.1016/j.biocel.2012.12.018.
Sagittal focusing of synchrotron radiation X-rays using a winged
crystal. Nisawa, A.;Yoneda, Y.; Ueno, G.; Murakami, H.; Okajima,
Y.; Yamamoto, K.; Senba, Y.; Uesugi,K.; Tanaka, Y.; Yamamoto, M.;
Goto, S.; Ishikawa, T. Journal of Synchrotron Radiation.Mar2013,
Vol. 20 Issue 2, p219-225.
7p.http://dx.doi.org/10.1107/S0909049512049813.
Structural and functional aspects of PR-10 proteins. Fernandes,
Humberto; Michalska,Karolina; Sikorski, Michal; Jaskolski, Mariusz.
FEBS Journal. Mar2013, Vol. 280 Issue 5,p1169-1199. 31p.
http://dx.doi.org/10.1111/febs.12114.
A new high-performance thin layer chromatography-based assay of
detergents andsurfactants commonly used in membrane protein
studies. Barret, Laurie-Anne; Polidori,Ange; Bonneté, Françoise;
Bernard-Savary, Pierre; Jungas, Colette. Journal ofChromatography
A. Mar2013, Vol. 1281, p135-141.
7p.http://dx.doi.org/10.1016/j.chroma.2013.01.061.
Structural constraints on the three-dimensional geometry of
simple viruses: case studiesof a new predictive tool. Keef, Thomas;
Wardman, Jessica P.; Ranson, Neil A.;Stockley, Peter G.; Twarock,
Reidun. Acta Crystallographica: Section A. Mar2013, Vol.69 Issue 2,
p140-150. 11p. http://dx.doi.org/10.1107/S0108767312047150.
Breaking the barriers in membrane protein crystallography. Kang,
Hae Joo; Lee, Chiara;Drew, David. International Journal of
Biochemistry & Cell Biology. Mar2013, Vol. 45Issue 3, p636-644.
9p. http://dx.doi.org/10.1016/j.biocel.2012.12.018.
Molecular tweezers modulate 14-3-3 protein-protein interactions.
Bier, David; Rose,Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria;
Ramirez-Anguita, Juan Manuel; Dutt, Som;Wilch, Constanze; Klärner,
Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas;Ottmann,
Christian. Nature Chemistry. Mar2013, Vol. 5 Issue 3, p234-239.
6p.http://dx.doi.org/10.1038/nchem.1570.
Volume-conserving trans-cis isomerization pathways in
photoactive yellow proteinvisualized by picosecond X-ray
crystallography. Jung, Yang Ouk; Lee, Jae Hyuk; Kim,Joonghan;
Schmidt, Marius; Moffat, Keith; Šrajer, Vukica; Ihee, Hyotcherl.
NatureChemistry. Mar2013, Vol. 5 Issue 3, p212-220.
9p.http://dx.doi.org/10.1038/nchem.1565.
High-resolution NMR studies of structure and dynamics of human
ERp27 indicateextensive interdomain flexibility. Amin, Nader T.;
Katrine Wallis, A.; Wells, Stephen A.;Rowe, Michelle L.;
Williamson, Richard A.; Howard, Mark J.; Freedman, Robert
B.Biochemical Journal. 3/1/2013, Vol. 450 Issue 2, p321-332.
12p.http://dx.doi.org/10.1042/BJ20121635.
Competition for space between a protein and lipid monolayers.
Fragneto, Giovanna;Alexandre, Stéphane; Valleton, Jean-Marc;
Rondelez, Francis. Colloids & Surfaces B:Biointerfaces.
Mar2013, Vol. 103, p416-421.
6p.http://dx.doi.org/10.1016/j.colsurfb.2012.10.057.
Discovery of a chemical probe for the L3MBTL3 methyllysine
reader domain. James,Lindsey I; Barsyte-Lovejoy, Dalia; Zhong, Nan;
Krichevsky, Liubov; Korboukh, Victoria K;Herold, J Martin;
MacNevin, Christopher J; Norris, Jacqueline L; Sagum, Cari A;
Tempel,Wolfram; Marcon, Edyta; Guo, Hongbo; Gao, Cen; Huang,
Xi-Ping; Duan, Shili; Emili,Andrew; Greenblatt, Jack F; Kireev,
Dmitri B; Jin, Jian; Janzen, William P. NatureChemical Biology.
Mar2013, Vol. 9 Issue 3, p184-191.
8p.http://dx.doi.org/10.1038/nchembio.1157.
PUMA binding induces partial unfolding within BCL-xL to disrupt
p53 binding andpromote apoptosis. Follis, Ariele Viacava; Chipuk,
Jerry E; Fisher, John C; Yun, Mi-Kyung;Grace, Christy R; Nourse,
Amanda; Baran, Katherine; Ou, Li; Min, Lie; White, StephenW; Green,
Douglas R; Kriwacki, Richard W. Nature Chemical Biology. Mar2013,
Vol. 9Issue 3, p163-168. 6p.
http://dx.doi.org/10.1038/nchembio.1166.
PIM: Phase Integrated Method for Normal Mode Analysis of
Biomolecules in a CrystallineEnvironment. Lu, Mingyang; Ma,
Jianpeng. Journal of Molecular Biology. Mar2013, Vol.
425 Issue 6, p1082-1098. 17p.
http://dx.doi.org/10.1016/j.jmb.2012.12.026.
ViewMotions Rainbow: A new method to illustrate molecular
motions in proteins.Cockrell, Gregory M.; Kantrowitz, Evan R.
Journal of Molecular Graphics & Modelling.Mar2013, Vol. 40,
p48-53. 6p. http://dx.doi.org/10.1016/j.jmgm.2012.12.012.
Ligand action on sodium, potassium, and calcium channels: role
of permeant ions.Zhorov, Boris S.; Tikhonov, Denis B. Trends in
Pharmacological Sciences. Mar2013, Vol.
http://mbg.cornell.edu/faculty-staff/faculty/ke.cfmhttp://www.surveymonkey.com/s/rigakuhttp://www.surveymonkey.com/s/rigakuhttp://dx.doi.org/10.1016/j.biocel.2012.12.018http://dx.doi.org/10.1107/S0909049512049813http://dx.doi.org/10.1111/febs.12114http://dx.doi.org/10.1016/j.chroma.2013.01.061http://dx.doi.org/10.1107/S0108767312047150http://dx.doi.org/10.1016/j.biocel.2012.12.018http://dx.doi.org/10.1038/nchem.1570http://dx.doi.org/10.1038/nchem.1565http://dx.doi.org/10.1042/BJ20121635http://dx.doi.org/10.1016/j.colsurfb.2012.10.057http://dx.doi.org/10.1038/nchembio.1157http://dx.doi.org/10.1038/nchembio.1166http://dx.doi.org/10.1016/j.jmb.2012.12.026http://dx.doi.org/10.1016/j.jmgm.2012.12.012
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Crystallographers in the News
Oliver Einsle receives SBIC Early Career Award 2013
The Society of Biological Inorganic Chemistry (SBIC)has awarded
Prof. Dr. Oliver Einsle of the University
of Freiburg with the 2013 Early Career Award. Thisaward is given
annually to an early career scientist(no more than 15 years post
Ph.D.) who has alreadyaccomplished distinguished research in
biologicalinorganic chemistry.
The Award will be handed over during the 16thInternational
Conference on Bio-Inorganic Chemistry
(ICBIC 16) in Grenoble, where the awardees of thetwo previous
years will deliver plenary lectures.
Zhorov, Boris S.; Tikhonov, Denis B. Trends in Pharmacological
Sciences. Mar2013, Vol.34 Issue 3, p154-161. 8p.
http://dx.doi.org/10.1016/j.tips.2013.01.002.
Structural and biochemical characterization of an atypical
short-chain dehydrogenase/reductase reveals an unusual cofactor
preference. Buysschaert, Géraldine; Verstraete,Kenneth; Savvides,
Savvas N.; Vergauwen, Bjorn. FEBS Journal. Mar2013, Vol. 280Issue
5, p1358-1370. 13p. http://dx.doi.org/10.1111/febs.12128.
Observation of the orientation of membrane protein crystals
grown in high magneticforce fields. Numoto, Nobutaka; Shimizu,
Ken-ichi; Matsumoto, Kazuya; Miki, Kunio; Kita,Akiko. Journal of
Crystal Growth. Mar2013, Vol. 367, p53-56.
4p.http://dx.doi.org/10.1016/j.jcrysgro.2013.01.003.
Structural basis for potent inhibitory activity of the
antibiotic tiqecycline during proteinsynthesis. Jenner, Lasse;
Starosta, Agata L.; Terry, Daniel S.; Mikolajka,
Aleksandra;FiIonava, Liudmila; Yusupov, Marat; Blanchard, Scott C.;
Wilson, Daniel N.; Yusupova,Gulnara. Proceedings of the National
Academy of Sciences of the United States ofAmerica. 3/5/2013, Vol.
110 Issue 10, p3812-3816.
5p.http://dx.doi.org/10.1073/pnas.1216691110.
Book review:
On A Farther Shore By William Souder Crown Publishing Group,
2012, ISBN-13: 9780307462206
William Souder's new biography of Rachel Carson, On a Farther
Shore, which wasreleased in honor of the 50th anniversary of
Carson's revolutionary polemic, SilentSpring, seeks to add a
humanizing dimension to Carson's public profile as an
environ-mental crusader. Souder explores Carson's early life, her
relationship with her mother,her education, her close friendships,
and her earlier works before delving into the storybehind Silent
Spring, which is refreshing.
Carson was already famous by the time Silent Spring was
published in 1962. She hadwritten three books about the ocean:
Under the Sea-Wind, The Sea Around Us, andThe Edge of the Sea. All
three were hits, as evidenced by their presence near the topof the
respective year's New York Times' Bestseller Lists. Unbeknownst to
her manyfans (and critics), Carson had been battling cancer for
quite some time when SilentSpring was released, and thus she was
not able to celebrate the extent of theadditional fame it brought
her. In fact, her publishers sought to keep word of hercondition
from reaching the public because they felt it would taint her
argumentregarding the carcinogenic properties of pesticides and
other agricultural chemicals.Carson died in 1964 from complications
due to the spread of her cancer. Her fifthbook, The Sense of
Wonder, was published posthumously.
Souder dedicates a large part of his narrative to Carson's
relationship with DorothyFreeman, a woman Carson met during her
summer vacations in Boothbay Harbor,Maine. Carson befriended
Freeman and her husband, Stan, during one day of
outdoorexploration. This single six-hour excursion resulted in an
intense relationship mainlyconsisting of written correspondence
between Carson and Dorothy that lasted overeleven years. Dorothy
and Carson remained close until Carson's death, and Carsonnamed
Dorothy as a guardian for her orphaned grandnephew, who she had
raised untilthe time of her own death. Whether or not Carson and
Dorothy's relationship wasromantic is a matter of speculation, but
both women shared a deep passion for nature,particularly for the
ecology of the oceans. Carson was deeply dedicated to her work,and
Dorothy was one of the few people with whom she felt comfortable
discussingher professional interests on a personal level.
Carson had a degree in biology from Pennsylvania College for
Women, but she was first
and foremost a writer. She had originally intended to major in
English, and alwaysintended to pursue a writing career. She told
friends and family that her interest inbiology gave her writing
direction—she knew what she wanted to write about. Carsonwas deeply
concerned with the aftereffects of the so-called "Green Revolution"
onglobal ecosystems. The deceptively named "Green Revolution" was
an agriculturalrevolution that resulted in a boom in food
production as a result of increased use ofpesticides and
herbicides. It was by no means "Green" in the sense of the word
today,where it is applied to environmentally conscious practices. A
number of farmers andagricultural workers across America (including
children) died after exposure to thesetoxic chemicals that were
also in the food Americans were consuming. Though manyviewed Silent
Spring as pessimistic, Carson sought to offer a realistic vision of
the
http://www.sbichem.org/http://www.sbichem.org/awards.phphttp://icbic16.com/http://books.google.com/books?id=eUEs6Gr7kmcC&printsec=frontcover#v=onepage&q&f=falsehttp://dx.doi.org/10.1016/j.tips.2013.01.002http://dx.doi.org/10.1111/febs.12128http://dx.doi.org/10.1016/j.jcrysgro.2013.01.003http://dx.doi.org/10.1073/pnas.1216691110http://books.google.com/books?id=eUEs6Gr7kmcC&printsec=frontcover#v=onepage&q&f=false
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viewed Silent Spring as pessimistic, Carson sought to offer a
realistic vision of theenvironmental future of America, and that of
other countries who would follow theseagricultural practices. As
many know, her work in Silent Spring contributed to theprohibition
of DDT in agricultural practices. However, as late as 2006, DDT was
stillbeing used in third world countries to fight diseases such as
malaria by killing the insectcarriers of these diseases. Carson's
work was an impetus for change, but that change isnot complete.
Souder provides an inclusive portrait of one of America's most
famous writers, yet thebook is a quick and enjoyable read.
Jeanette S. Ferrara
Rigaku Corporatione-mail:
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