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Protein Crystallography Newsletter
Volume 6, No. 9, September 2014
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In this issue:


Science Video
Gregory Petsko: The coming neurological epidemic

video

Biochemist Gregory Petsko makes a convincing argument that, in the next 50 years, we'll see an epidemic of neurological diseases, such as Alzheimer's, as the world population ages. His solution: more research into the brain and its functions.

video


Structural Biologists in the News

IUCr prise

Rigaku awarded a prize at the Montreal IUCr meeting for the best poster from a graduate student or post-doc describing applications of macromolecular small angle X-ray scattering. The winner of the award was Monica Pillon from McMaster Univ (Dept of Bio­chemistry and Biomedical Sciences). Monica is a graduate student in Alba Guarne's lab. Monica's poster, titled "Structural characterization of transient interactions in DNA mismatch repair", featured SAXS data that was collected in part on the BioSAXS-1000 system that was installed in December, 2012. The photo (courtesy of Daniel Wilson) shows Prof. Desiraju (President of the IUCr) presenting the award to Monica.


Educational Video
The Braggs Legacy
from Diamond Light Source


video

video



Upcoming Events

SCIX 2014 from Sep. 28, 2014 to Oct. 3, 2014 in Reno, NV.

GTBio/AFC (Assoc of French Crystallography) 2014 from Oct. 7, 2014 to Oct. 10, 2014 in Grenoble, France.

International Symposium on Crystallography from Sunday, October 12, 2014 to Wednesday, October 15, 2014 in Fortaleza/CE, Brazil.

X Reunión Anual de la Asociación Argentina de Cristalografía AACr from Tuesday, October 28, 2014 to Friday, October 31, 2014 in Mar del Plata, Argentina.

BHT Crystallographic meeting on Friday, November 7, 2014 in Hamilton, ON, Canada.

Groupe de Recherche Axé sur la Structure des Protéines on Monday, November 24, 2014 in Montreal, QC, Canada.



Survey of the Month

9/2014 survey

survey



Last Month's Survey

The importance of collaborative structural biology in attacking a threat like the Ebola virus is evident in (last) month's video. How do you feel about collaborative research in targeting diseases?

results



 

 
 

 

 

 

 

 

 

 

 

 

 

 

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Crystallography in the news

September 2, 2014. An X-ray crystal structure (nitroprusside) determined by a University at Buffalo chemist has been chosen as one of the world's top 10 molecular structures ever solved. The list was compiled by Chemical & Engineering News, the science and technology magazine of the American Chemical Society, to celebrate the 100th anniversary of X-ray crystallography. The editors chose the work of Philip Coppens, SUNY Distinguished Professor in the Department of Chemistry, from the 1990s because it ushered in a new era of X-ray crystallographic research, allowing chemists to study short-lived, excited-state molecules.

September 8, 2014. Without crystallography we wouldn't have solar panels, mobile phones, computers or HIV medication. Now a small group of scientists is celebrating the International Year of Crystallography by building huge outdoor sculptures of crystals. Called "Crystals in the City," the project spans a number of Australian cities.

September 11, 2014. William Weis, Ph.D., the William M. Hume Professor in the School of Medicine, has been appointed chair of Stanford University's Department of Structural Biology. He replaces Joseph "Jody" Puglisi, Ph.D., professor of structural biology, who stepped down Sept. 1 after leading the department for 10 years. Weis holds professorships in structural biology and molecular and cellular physiology. He is also professor and chair of photon science at the SLAC National Accelerator Laboratory.

September 19, 2014. Gunnar Schröder of the Institute of Complex Systems at the Forschungszentrum Jülich and the University of Düsseldorf, Germany and colleagues at Stanford University School of Medicine have reviewed their earlier refinement technique known as Deformable Elastic Network (DEN) and found ways to optimize it successfully for the investigation of several particularly problematic protein structures, including soluble proteins and membrane proteins up to a resolution limit ranging from 3 to 7Å.

September 21, 2014. A team of Stanford researchers has developed a protein therapy that disrupts the process that causes cancer cells to break away from original tumor sites, travel through the blood stream and start aggressive new growths elsewhere in the body. The Stanford team seeks to stop metastasis, without side effects, by preventing two proteins - Axl and Gas6 - from interacting to initiate the spread of cancer.

September 23, 2014. Despite the fundamental importance of ion channels to larger-scale activities in the body, scientists do not have a full understanding of how these channels work. A research group from Thomas Jefferson University in Philadelphia has recently taken a step in this direction by investigating a variety of potassium-ion (K⁺) channel that is activated by calcium ions (Ca²⁺).

September 23, 2014. Dr. Derek Lowe muses on fragment based drug discovery, "Fragment-based methods have clearly made a big impression across drug discovery - academia finds it a low-barrier way to get into compound screening, and the industrial groups clearly find it useful as well."

September 24, 2014. An interwoven molecular knot, shaped like the Star of David has been synthesized by David Leigh and colleagues at Manchester University, UK. To make a microscopic version of the star, two molecular links, or catenanes, were woven together and each joined up in three places. In total, the star consists of six tris(bipyridine) ligands around six octahedral iron (III) centers.

September 24, 2014. Case Western Reserve University's synchrotron facility at Brookhaven National Laboratory is on its way to becoming the No. 1 beamline facility for biology in the world by early 2016, thanks to a jumpstart grant of $4.6 million from the National Institute of Biomedical Imaging and Bioengineering (NIBIB), a component of the National Institutes of Health (NIH).


New product spotlight: XtalDetectR and Gallery DTX

xtaldetectrThe XtalDetectR and XtalDetectR UV imagers are designed to simplify the inspection and management of experimental plates during a protein crystallization experiment. Designed to fit on a lab bench, the XtalDetectR and XtalDetectR UV are fully modular and expandable protein crystal imaging and analysis systems. They are the perfect systems for labs that are working on difficult conditions, such as membrane proteins, where the crystal may be invisible in LCP with visible light.

Ultra high resolution optics and superior UV Imaging

   · Best drop illumination
        – with patented programmable LED light source for visible imaging
   · SBS and Linbro footprints supported
   · Ability to detect crystals as small as 2 μm
   · Automatic drop locate, auto focus and auto combine features

Gallery DTX offers flexibility in capacity

The capabilities of the XtalDetectR UV may be expanded by adding the Gallery™ DTX plate hotel. With capacity for up to 259 low profile SBS plates, 189 standard SBS plates, 147 Linbro plates, or combination thereof, the Gallery DTX is a specially designed vibration minimizing robotic and plate transfer system that protects fragile protein crystals.

Ask for more information.



Lab spotlight: Newcastle Structural Biology Lab  

NSBL The Newcastle Structural Biology Laboratory is part of the Institute for Cell and Molecular Bioscience (ICaMB), University of Newcastle. The NSBL was founded in 2003, but in the last ~18 months they have undergone some expansion and there are now 4 research groups in ICaMB and another group based in the Northern Institute for Cancer Research. Rick Lewis, Paula Salgado and Bert van den Berg concentrate their research activities on important questions in microbial lifestyle:

NSBL    · How do bacteria build the protective wall that
     protects the cell?
   · How do bacteria co-ordinate cell division and cell growth?
   · How do bacteria protect themselves from the host immune
     system during infection?
   · How do bacteria traffic molecules into and out of the cell?

NSBL The fourth group in ICaMB, Owen Davies, is interested in meiosis, and in particular the synaptonemal complex that holds together homologous chromosomes to co-ordinate the recombination steps that are necessary to complete meiosis. Martin Noble and Jane Endicott in NICR are interested in understanding the progression through the eukaryotic cell cycle at the molecular level, and in exploiting that knowledge to produce new chemical probes and potential leads for drug discovery.



Useful link: RADDOSE-3D

Image
Prof. Elspeth Garman
Developed by the Garman Lab, University of Oxford, RADDOSE-3D is a software program that allows the macroscopic modeling of an X-ray diffraction experiment for the purpose of better predicting radiation-damage progression. A spatially and temporally resolved distribution of dose is calculated and output by the program. RADDOSE-3D is completely open source.

RADDOSE-3D: time- and space-resolved modeling of dose in macromolecular crystallography. Zeldin, Gerstel, Garman. (2013). J. Appl. Cryst. 46, 1225-1230.


Selected recent crystallographic papers

Structural biology: 'seeing' crystals the XFEL way. Marx, Vivien. Nature Methods. Sep2014, Vol. 11 Issue 9, p903-908. 6p. DOI: 10.1038/nmeth.3070.

Quasi-elastic light scattering and small-angle X-ray scattering study of a mixture of a biopolymer with microemulsion. Sharifi, Soheil. Physics & Chemistry of Liquids. Sep2014, Vol. 52 Issue 5, p618-626. 9p. DOI: 10.1080/00319104.2014.890897.

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Arnlund, David; Johansson, Linda C; Wickstrand, Cecilia; Barty, Anton; Williams, Garth J; Malmerberg, Erik; Davidsson, Jan; Milathianaki, Despina; DePonte, Daniel P; Shoeman, Robert L; Wang, Dingjie; James, Daniel; Katona, Gergely; Westenhoff, Sebastian; White, Thomas A; Aquila, Andrew; Bari, Sadia; Berntsen, Peter; Bogan, Mike; van Driel, Tim Brandt, et al. Nature Methods. Sep2014, Vol. 11 Issue 9, p923-926. 4p. DOI: 10.1038/nmeth.3067.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures. McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus. Acta Crystallographica: Section D. Sep2014, Vol. 70 Issue 9, p2344-2355. 12p. DOI: 10.1107/S1399004714013856.

Deformable elastic network refinement for low-resolution macromolecular crystallography. Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T. Acta Crystallographica: Section D. Sep2014, Vol. 70 Issue 9, p2241-2255. 15p. DOI: 10.1107/S1399004714016496.

Low resolution X-ray structure of γ-glutamyltranspeptidase from Bacillus licheniformis: Opened active site cleft and a cluster of acid residues potentially involved in the recognition of a metal ion. Long-Liu Lin; Yi-Yu Chen; Meng-Chun Chi; Merlino, Antonello. BBA - Proteins & Proteomics. Sep2014, Vol. 1844 Issue 9, p1523-1529. 7p. DOI: 10.1016/j.bbapap.2014.04.016.

Crystallization and preliminary X-ray analysis of two variants of the Escherichia coli O157 ParE2-PaaA2 toxin-antitoxin complex. Sterckx, Yann G. J.; Haesaerts, Sarah; Van Melderen, Laurence; Loris, Remy. Acta Crystallographica: Section F, Structural Biology Communications. Sep2014, Vol. 70 Issue 9, p1284-1291. 8p. DOI: 10.1107/S2053230X1401749X.

Crystalline guanine adducts of natural and synthetic trioxacarcins suggest a common biological mechanism and reveal a basis for the instability of trioxacarcin A. Pröpper, Kevin; Dittrich, Birger; Smaltz, Daniel J.; Magauer, Thomas; Myers, Andrew G. Bioorganic & Medicinal Chemistry Letters. Sep2014, Vol. 24 Issue 18, p4410-4413. 4p. DOI: 10.1016/j.bmcl.2014.08.016.

Structure of the Entire Stalk Region of the Dynein Motor Domain. Nishikawa, Yosuke; Oyama, Takuji; Kamiya, Narutoshi; Kon, Takahide; Toyoshima, Yoko Y.; Nakamura, Haruki; Kurisu, Genji. Journal of Molecular Biology. Sep2014, Vol. 426 Issue 19, p3232-3245. 14p. DOI: 10.1016/j.jmb.2014.06.023.

Structure of Rot, a global regulator of virulence genes in Staphylococcus aureus. Zhu, Yuwei; Fan, Xiaojiao; Zhang, Xu; Jiang, Xuguang; Niu, Liwen; Teng, Maikun; Li, Xu. Acta Crystallographica: Section D. Sep2014, Vol. 70 Issue 9, p2467-2476. 10p. DOI: 10.1107/S1399004714015326.

Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination. Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung. Acta Crystallographica: Section D. Sep2014, Vol. 70 Issue 9, p2331-2343. 13p. DOI: 10.1107/S1399004714013868.

X-ray Scattering from Immunostimulatory Tetrapod-Shaped DNA in Aqueous Solution To Explore Its Biological Activity-Conformation Relationship. Yusuke Sanada; Shunsuke Sakamoto; Tomoki Shiomi; Tadashi Okobira; Efstratios Mylonas; Noboru Ohta; Naoto Yagi; Makiya Nishikawa; Isamu Akiba; Yoshinobu Takakura; Kazuo Sakurai. Journal of Physical Chemistry B. Sep2014, Vol. 118 Issue 35, p10373-10379. 7p. DOI: 10.1021/jp505556r.

Recent progress in the study of the Rheb family GTPases. Heard, Jeffrey J.; Fong, Valerie; Zahra Bathaie, S.; Fuyuhiko Tamanoi. Cellular Signalling. Sep2014, Vol. 26 Issue 9, p1950-1957. 8p. DOI: 10.1016/j.cellsig.2014.05.011.

Three novel degraded steroids from cultures of the basidiomycete Antrodiella albocinnamomea. Zi-Ming Chen; Xiao-Yan Yang; Qiong-Ying Fan; Zheng-Hui Li; Kun Wei; He-Ping Chen; Tao Feng; Ji-Kai Liu. Steroids. Sep2014, Vol. 87, p21-25. 5p. DOI: 10.1016/j.steroids.2014.05.008.

Structural Characterization of Anti-Inflammatory Immunoglobulin G Fc Proteins. Ahmed, Alysia A.; Giddens, John; Pincetic, Andrew; Lomino, Joseph V.; Ravetch, Jeffrey V.; Wang, Lai-Xi; Bjorkman, Pamela J. Journal of Molecular Biology. Sep2014, Vol. 426 Issue 18, p3166-3179. 14p. DOI: 10.1016/j.jmb.2014.07.006.

Use of cysteine-reactive cross-linkers to probe conformational flexibility of human DJ-1 demonstrates that Glu18 mutations are dimers. Prahlad, Janani; Hauser, David N.; Milkovic, Nicole M.; Cookson, Mark R.; Wilson, Mark A. Journal of Neurochemistry. Sep2014, Vol. 130 Issue 6, p839-853. 15p. DOI: 10.1111/jnc.12763.

Disordered Cold Regulated15 Proteins Protect Chloroplast Membranes during Freezing through Binding and Folding, But Do Not Stabilize Chloroplast Enzymes in Vivo. Thalhammer, Anja; Bryant, Gary; Sulpice, Ronan; Hincha, Dirk K. Plant Physiology. Sep2014, Vol. 166 Issue 1, p190-201. 12p. 
DOI: 10.1104/pp.114.245399
.

Neuronal porosome - The secretory portal at the nerve terminal: Its structure-function, composition, and reconstitution. Jena, Bhanu P. Journal of Molecular Structure. Sep2014, Vol. 1073, p187-195. 9p. DOI: 10.1016/j.molstruc.2014.04.055.

L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Langan, Paul; Sangha, Amandeep K.; Wymore, Troy; Parks, Jerry M.; Yang, Zamin Koo; Hanson, B. Leif; Fisher, Zoe; Mason, Sax A.; Blakeley, Matthew P.; Forsyth, V. Trevor; Glusker, Jenny P.; Carrell, Horace L.; Smith, Jeremy C.; Keen, David A.; Graham, David E.; Kovalevsky, Andrey. Structure. Sep2014, Vol. 22 Issue 9, p1287-1300. 14p. DOI: 10.1016/j.str.2014.07.002.



Book review: The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid

     by Michael Alley
     Springer Science & Business Media, New York, ISBN 978-1-4419-8278-0

I found this book while perusing the racks at the Springer booth at a trade show and was intrigued by the title. I found it to be very easy to read and full of useful information. The subtitle could easily be "stop the bullets." I am guilty of using too many bullets myself, so let's start there. On numerous occasions, the author claims that bullet points do not demonstrate that the presenter prepared the content of the presentation for the audience in a thoughtful manner. In fact, Alley suggests that bullet points only give the presenter the sense that they have prepared well. The author also states that bullet points do not provide information in a format that is actually useful to most readers.

The author also stresses the need to use the assertion-evidence method in slide design, as opposed the bullet point list. In this method, the slide title is an assertion that can be as long as two lines, and the body provides the evidence proving the assertion. The author suggests using pictures and graphs, and as few words as possible to prove the assertion. He stresses the need for practice and to account for the audience and the environment. In addition to the assertion-evidence approach, the author describes the TED slide structure, as well as methods for presenting slides: PechaKucha, the Lessig Method and Prezi.

Alley spends some time on the specifics of slide design, at least those best suited for Western audiences. A few tips include using only sans serif fonts, which are quicker to read, putting the slide title (assertion) in the upper left hand corner, not wasting space with fancy backgrounds, and keeping colors simple and high contrast.

One of the more interesting examples of a poor presentation that Alley gives is a review of the slides presented by Morton Thiokol to NASA on January 27, 1986. The author suggests that the slides did not get the point across due to poor design, which resulted in key pieces of information not being understood. Alley suggests some changes to the slides that would have stressed the importance of temperature to the performance of the O-rings that ultimately failed and caused the Challenger disaster.

The author describes in detail thirteen critical errors. This list is self-explanatory but you should read the book to gain a full understanding of each of these important points and how to avoid them: Giving the Wrong Speech, Boring Your Audience, Trying to Cover Too Much, Losing the Audience on the Trail, Not Anticipating the Audience's Bias, Following the Defaults of PowerPoint, Following the Common Practices of PowerPoint Talks, Not Accounting for Murphy's Law, Not Preparing Enough, Drawing Words from the Wrong Well, Not Paying Attention and Losing Composure.

On the lighter side, these next two books are laugh-out-loud funny:

Dear Committee Members, Julie Schumacher, Doubleday, New York, 2014, 192 pages, 978-0385538138. This a story told through a series of letters of recommendation, with a random selection of non-related letters to various people in the protagonist's existence including a dean who happens to be his ex-wife. Some of the letters are just hilarious and the story is poignant. A quick, fun read.

Mark Twain's Helpful Hints for Good Living, edited by Lin Salamo, Victor Fischer, and Michael B Frank, University of California Press, Berkeley, 2014, 221 pages, ISBN: 978-0520242456. I did not include the subtitle because most spam filters would probably prevent this newsletter from getting through, and that should give you a hint about the content - nothing beyond PG-13 but risqué for 100+ years ago.

And, lastly.

Bruce by Peter Ames Carlin, Touchstone, New York, 2012, 512 pages, ISBN: 978-1439191828. This is the first biography of "the Boss" written with help from Springsteen himself. It covers his entire life, with a lot of emphasis on the early years. I recommend listening to the albums as you read the story of their creation.

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

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