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Protein Crystallography Newsletter
Volume 6, No. 12, December 2014
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In this issue:


Funny Science Video
The Lab Song

video

video


Crystallographers in the News

Edward Snell

Hauptman-Woodward Medical Research Institute has tapped an internal candidate as its fourth CEO. Edward Snell will take over the nonprofit research organization effective Dec. 1, following eight years at HWI as a senior research scientist. Snell has a long history as a principal investigator on several major projects, including ongoing research with NASA and past experience with the British government in defense and security research and development.


Educational Video
How to correctly pronounce "pH"

video

You might think that you understand the concept of pH, but do you really know how to pronounce it?

video



Upcoming Events

Macromolecular training class at Rigaku, February 18-25, 2015 at The Woodlands, TX. Class outline and online registration form.

Second International BioXFEL Conference, Jan 14-16, 2015, in Ponce, PR.

The New York Structural Biology Discussion Group 10th Winter Meeting, Jan 21, 2015, in New York, NY.

59th Biophysical Society Meeting, Feb 7-11, 2015, in Baltimore, MD.

40th Lorne Conf. on Protein Structure & Function, Feb 8-12, 2015 in Mantra Lorne, Victoria, Australia.

5th Winter School of Soft X-rays in Macromolecular Crystallography, Feb 28 - Mar 3, 2015 in Athens, GA.

Hybrid Methods in Structural Biology - Keystone Symposium, Mar 4-8 2015, in Tahoe City, CA.



Survey of the Month

12/2014 survey

survey



Last Month's Survey

Historically, structural biology has focused on generating three-dimensional (3D) descriptions of individual proteins, mainly through crystallography, and the PDB was created to archive these results. But as research has shifted to larger complexes, modeling has become more complicated as models can be based on numerous approaches. How should the PDB react to these changes?

results



Crystallographic Portraits

Tom Blundell

To celebrate the International Year of Crystallography, Illuminating Atoms presents a selection of photo­graphs by Max Alexander portraying the inspirational work of crystallographers. Through portrait and documentary photography, Max shows us the life of scientists at the cutting edge of discovery, including some of the world-class facilities they use. This is Max Alexander's second exhibition at the Royal Albert Hall, the first being Explorers of the Universe in 2009.

Science and Technology Facilities Council is proud to sponsor the Illuminating Atoms exhibit along with co-sponsors The Diamond Light Source Ltd, the Wellcome Trust, GlaxoSmithKline (GSK), Astra Zeneca and Pharmorphix.


book1

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Crystallography in the news

December 5, 2014. An international team, including scientists from Arizona State University, the University of Milwaukee-Madison (UMW), and Germany's Deutsches Elektronen-Synchrotron (DESY), has caught a light-sensitive biomolecule at work using an X-ray laser. Their new study proves that high speed X-ray lasers can capture the fast dynamics of biomolecules in ultra slow-motion, revealing subtle processes with unprecedented clarity.

December 10, 2014. Which chemistry stories got us talking in 2014? With the help of an expert panel of journal editors, Chemistry World looks back at some highlights from last year's groundbreaking chemical sciences research.

December 17, 2014. Mathematics is helping to drive a revolution in structural biology. Once dominated by X-ray crystallography, the field is now in the thrall of a technique called cryo-electron microscopy, or cryo-EM. Calculations by Sjors Scheres of the Laboratory for Molecular Biology have led to software that transforms grainy cryo-EM images into exquisitely detailed pictures, allowing biologists to visualize molecular machines more easily and accurately than ever before.

December 23, 2014. Scientists at The Scripps Research Institute (TSRI) have found that resveratrol powerfully activates an evolutionarily ancient stress response in human cells. The finding should dispel much of the mystery and controversy about how resveratrol really works.

December 23, 2014. US research agencies finally learn their fate. National Institutes of Health (NIH) receives $30.3 billion, which represents an increase of $150 million or 0.5% from FY2014 levels. NSF received $7.3 billion for FY2015, a 2.4% increase.


Technique spotlight: Combined SEC/DLS

W130iThe W130i dynamic light scattering (DLS) system from Avid Nano is a dual purpose detector used to directly measure molecular size, distribution and aggregation state in batch mode, as well as being a sensitive online size detector when fitted with a low volume flow cell and connected to any size exclusion chromatography (SEC) system.

W130iIn "flow mode," the W130i directly measures the hydrodynamic size (Rh) of each species as they elute from the SEC column without calibration and in real time, confirming the results found by traditional UV detection, calibrated with standards. In addition to absolute size and scattering intensity, the molecular weights of globular species may be reliably and quickly estimated using the customizable algorithms built into Avid Nano's latest, i-Size 3.0 software.

Request more information.



Lab spotlight: Pearson Lab / CUI  

CUI Prof. Dr. Arwen Pearson
Hamburg Centre for Ultrafast Imaging (CUI)

CUI's great scientific objective is to watch atoms and molecules move in real time, including the explanation of protein structures all the way to order formation in water.

Pearson's group is focused on understanding how macromolecular structure leads to function. Biological macromolecules are not static and therefore to understand how they work they must be visualized at high resolution in both space and time. CUITo address this challenge, the Pearson group is developing a suite of methodologies for time-resolved structure determination. Current major projects include:

  • Development of time-resolved X-ray crystallography and SAXS
  • Mechanistic enzymology
  • ssRNA virus capsid structure, assembly and disassembly
  • Using single crystal UV/Vis, Raman and THz spectroscopy to study protein dynamics and function


Useful link: Viruses - From structure to biology

Viruses: From structure to biology. This remarkable website explores the historical developments that led to the determination of the structure and biological functions of viruses and their macromolecular components. It investigates the history of how knowledge of the structure of viruses at atomic resolution has impinged on the more biological studies of viruses. It contains contributions to this history from two overlapping groups of scientists: those who were responsible for determining the structures, and those whose work was directly influenced by that information.

Just pick one of your favorite virus researchers (Michael Rossmann or Ian Wilson or Steve Harrison or ...) and be treated to a wonderful oral history of their early involvement in structural virus work. Very hard to stop reading.

This website was created by Sondra and Milton Schlesinger (Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO), who are responsible for its content.



Selected recent crystallographic papers

Structural biology: Using evolution to predict structure. Doerr, Allison. Nature Methods. Dec2014, Vol. 11 Issue 12, p1192-1193. 2p. http://dx.doi.org/10.1038/nmeth.3198.

De novo design of a transmembrane Zn2+-transporting four-helix bundle. Joh, Nathan H.; Tuo Wang; Bhate, Manasi P.; Acharya, Rudresh; Yibing Wu; Grabe, Michael; Mei Hong; Grigoryan, Gevorg; DeGrado, William F. Science. 12/19/2014, Vol. 346 Issue 6216, p1520-1524. 5p. http://dx.doi.org/10.1126/science.1261172.

Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities. Neumann, Piotr; Tittmann, Kai. Current Opinion in Structural Biology. Dec2014, Vol. 29, p122-133. 12p. http://dx.doi.org/10.1016/j.sbi.2014.11.001.

Overexpression of Pseudomonas aeruginosa LpxC with its inhibitors in an acrB-deficient Escherichia coli strain. Gao, Ning; McLeod, Sarah M.; Hajec, Laurel; Olivier, Nelson B.; Lahiri, Sushmita D.; Bryan Prince, D.; Thresher, Jason; Ross, Philip L.; Whiteaker, James D.; Doig, Peter; Li, Amanda Haixi; Hill, Pamela J.; Cornebise, Mark; Reck, Folkert; Hale, Michael R. Protein Expression & Purification. Dec2014, Vol. 104, p57-64. 8p. http://dx.doi.org/10.1016/j.pep.2014.09.006.

Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase. Balogun, Emmanuel Oluwadare; Inaoka, Daniel Ken; Shiba, Tomoo; Kido, Yasutoshi; Tsuge, Chiaki; Nara, Takeshi; Aoki, Takashi; Honma, Teruki; Tanaka, Akiko; Inoue, Masayuki; Matsuoka, Shigeru; Michels, Paul A. M.; Kita, Kiyoshi; Harada, Shigeharu. Molecular Microbiology. Dec2014, Vol. 94 Issue 6, p1315-1329. 16p. http://dx.doi.org/10.1111/mmi.12831.

Structural and biochemical characterizations of an intramolecular tandem coiled coil protein. Shin, Donghyuk; Kim, Gwanho; Kim, Gyuhee; Zheng, Xu; Kim, Yang-Gyun; Lee, Sangho. Biochemical & Biophysical Research Communications. Dec2014, Vol. 455 Issue 3/4, p339-346. 8p. http://dx.doi.org/10.1016/j.bbrc.2014.11.013.

Structural Characterization of a Flexible Two-Domain Protein in Solution Using Small Angle X-Ray Scattering and NMR Data. Lemak, Alexander; Wu, Bin; Yee, Adelinda; Houliston, Scott; Lee, Hsiau-Wei; Gutmanas, Aleksandras; Fang, Xianyang; Garcia, Maite; Semesi, Anthony; Wang, Yun-Xing; Prestegard, James H.; Arrowsmith, Cheryl H. Structure. Dec2014, Vol. 22 Issue 12, p1862-1874. 13p. http://dx.doi.org/10.1016/j.str.2014.09.013.

A model-free method for extracting interaction potential between protein molecules using small-angle X-ray scattering. Sumi, Tomonari; Imamura, Hiroshi; Morita, Takeshi; Nishikawa, Keiko. Journal of Molecular Liquids. Dec2014 Part A, Vol. 200, p42-46. 5p. http://dx.doi.org/10.1016/j.molliq.2014.03.014.

Intermolecular interactions and molecular dynamics in bovine serum albumin solutions studied by small angle X-ray scattering and dielectric relaxation spectroscopy. Yanase, Keiichi; Arai, Ryoichi; Sato, Takaaki. Journal of Molecular Liquids. Dec2014 Part A, Vol. 200, p59-66. 8p. http://dx.doi.org/10.1016/j.molliq.2014.05.021.

Structural stability of E. coli trigger factor studied by synchrotron small-angle X-ray scattering. Shi, Yi; Shinjo, Masaji; Zhou, Jun-Mei; Kihara, Hiroshi. Biophysical Chemistry. Dec2014, Vol. 195, p1-7. 7p. http://dx.doi.org/10.1016/j.bpc.2014.07.002.

Crystallization and preliminary X-ray diffraction analysis of eukaryotic α₂-macroglobulin family members modified by methylamine, proteases and glycosidases. Goulas, T.; Garcia-Ferrer, I.; García-Piqué, S.; Sottrup-Jensen, L.; Gomis-Rüth, F.X. Molecular Oral Microbiology. Dec2014, Vol. 29 Issue 6, p354-364. 11p. 1 Color Photograph, 2 Charts, 2 Graphs. http://dx.doi.org/10.1111/omi.12069.

The times they are a-changin' - news from Acta Crystallographica Section F. Hunter, W. N.; Weiss, Manfred S. Acta Crystallographica: Section F, Structural Biology Communications. Dec2014, Vol. 70 Issue 12, p1575-1575. 1p. http://dx.doi.org/10.1107/S2053230X14024789.

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Tenboer, Jason; Basu, Shibom; Zatsepin, Nadia; Pande, Kanupriya; Milathianaki, Despina; Frank, Matthias; Hunter, Mark; Boutet, Sébastien; Williams, Garth J.; Koglin, Jason E.; Oberthuer, Dominik; Heymann, Michael; Kupitz, Christopher; Conrad, Chelsie; Coe, Jesse; Roy-Chowdhury, Shatabdi; Weierstall, Uwe; James, Daniel; Wang, Dingjie; Grant, Thomas. Science. 12/5/2014, Vol. 346 Issue 6214, p1242-1246. 5p. http://dx.doi.org/10.1126/science.1259357.

Structure and stability of an unusual zinc-binding protein from Bacteroides thetaiotaomicron. Knaus, Tanja; Uhl, Michael K.; Monschein, Stefanie; Moratti, Sabrina; Gruber, Karl; Macheroux, Peter. BBA - Proteins & Proteomics. Dec2014, Vol. 1844 Issue 12, p2298-2305. 8p. http://dx.doi.org/10.1016/j.bbapap.2014.08.008.

Aromatic Anchor at an Invariant Hormone-Receptor Interface. Pandyarajan, Vijay; Smith, Brian J.; Phillips, Nelson B.; Whittaker, Linda; Cox, Gabriella P.; Wickramasinghe, Nalinda; Menting, John G.; Zhu-li Wan; Whittaker, Jonathan; Ismail-Beigi, Faramarz; Lawrence, Michael C.; Weiss, Michael A. Journal of Biological Chemistry. 12/12/2014, Vol. 289 Issue 50, p34709-34727. 19p. http://dx.doi.org/10.1074/jbc.M114.608562.

Atlas of coronavirus replicase structure. Neuman, Benjamin W.; Chamberlain, Peter; Bowden, Fern; Joseph, Jeremiah. Virus Research. Dec2014, Vol. 194, p49-66. 18p. http://dx.doi.org/10.1016/j.virusres.2013.12.004.

Membrane proteins, detergents and crystals: what is the state of the art? Loll, Patrick J. Acta Crystallographica: Section F, Structural Biology Communications. Dec2014, Vol. 70 Issue 12, p1576-1583. 8p. http://dx.doi.org/10.1107/S2053230X14025035.

The structure of vanin 1: a key enzyme linking metabolic disease and inflammation. Boersma, Ykelien L.; Newman, Janet; Adams, Timothy E.; Cowieson, Nathan; Krippner, Guy; Bozaoglu, Kiymet; Peat, Thomas S. Acta Crystallographica: Section D. Dec2014, Vol. 70 Issue 12, p3320-3329. 10p. http://dx.doi.org/10.1107/S1399004714022767.

The iron-sulfur core in Rieske proteins is not symmetric. Ali, Md.; Nair, Nisanth; Retegan, Marius; Neese, Frank; Staemmler, Volker; Marx, Dominik. Journal of Biological Inorganic Chemistry. Dec2014, Vol. 19 Issue 8, p1287-1293. 7p. http://dx.doi.org/10.1007/s00775-014-1185-7.

Crystal structure of HlyU, the hemolysin gene transcription activator, from Vibrio cholerae N16961 and functional implications. Mukherjee, Debadrita; Datta, Ajit Bikram; Chakrabarti, Pinak. BBA - Proteins & Proteomics. Dec2014, Vol. 1844 Issue 12, p2346-2354. 9p. http://dx.doi.org/10.1016/j.bbapap.2014.09.020.

Crystal structure of the VapBC-15 complex from Mycobacterium tuberculosis reveals a two-metal ion dependent PIN-domain ribonuclease and a variable mode of toxin-antitoxin assembly. Das, Uddipan; Pogenberg, Vivian; Subhramanyam, Udaya Kumar Tiruttani; Wilmanns, Matthias; Gourinath, Samudrala; Srinivasan, Alagiri. Journal of Structural Biology. Dec2014, Vol. 188 Issue 3, p249-258. 10p. http://dx.doi.org/10.1016/j.jsb.2014.10.002.

Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression. Bailey-Elkin, Ben A.; Knaap, Robert C. M.; Johnson, Garrett G.; Dalebout, Tim J.; Ninaber, Dennis K.; van Kasteren, Puck B.; Bredenbeek, Peter J.; Snijder, Eric J.; Kikkert, Marjolein; Mark, Brian L. Journal of Biological Chemistry. 12/12/2014, Vol. 289 Issue 50, p34667-34682. 16p. http://dx.doi.org/10.1074/jbc.M114.609644.



Book review: Undeniable: Evolution and the Science of Creation

     by Bill Nye
     St. Martin's Press, New York, 2014, 320 pages, 978-1250007131

Bill Nye's new book, Undeniable: Evolution and the Science of Creation, offers a fun, fresh approach to evolution and a number of other popular science hot topics, such as GMOs, cloning, and antibiotics. That said, the focus of the book is the science of evolution, and Nye sets out to debunk popular misconceptions about it.

Rather than simply say Creationism is wrong and evolution is right, Nye builds a logical argument through a series of short, well-constructed chapters. Each one tackles a self-contained subtopic, such as biodiversity or mass extinction, and by the end of the chapter, Nye has seamlessly incorporated the subtopic into the arch of his overall argument. He does an excellent job explaining how pervasive evolution and its effects are in everyday human lives.

One of the most interesting (and a bit gross) chapters, titled "Mosquitos in the Tube," is about the mosquito population living in the London Underground. This population has become isolated from the aboveground population, excellent conditions for the evolution of a new species. Although these underground mosquitoes are not yet a separate species from those aboveground, they are definitely on their way to becoming one. Laboratory experiments have shown that a significant portion of each population is unable to mate with members of the other, although some still can.

Similarly to the evolutionary divergence of these two mosquito populations, the populations of the Neanderthals and our human ancestors diverged approximately half a million years ago. For a long time, scientists believed that these two populations did not interact. However, current evidence shows that they intermingled until as recently as thirty thousand years ago, when natural selection took over and Neanderthals became extinct.

This instance, in which Nye takes an example of evolution as it is occurring today and applies it to a historical context, is quite representative of the work as a whole. Evolution is not just a thing of the past or a vision of the future; it is very much rooted in the present.

Undeniable was an excellent and fast-paced read. I'd highly recommend it to anyone, especially those who have concerns or questions about what exactly evolution is and what natural selection really means.

Jeanette S. Ferrara    
Princeton University, Class of 2015    

Rigaku


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