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Crystallography
in the news
February 28, 2014. An essential weapon in the body's fight against infection has come into sharper view. Researchers at Princeton University have discovered the 3D structure of an enzyme, known as RNase L, that cuts to ribbons the genetic material of viruses and helps defend against bacteria. The discovery of the structure of this enzyme, a first-responder in the body's "innate immune system," could enable new strategies for fighting infectious agents and possibly prostate cancer and obesity.
March 4, 2014. The enzyme PP1 has a key role in many of the body's healthy functions and diseases. It's so generally important that drug developers dare not target it. In a new study, Brown University scientists, led by Professor Rebecca Page,
report a big leap in understanding how PP1 interacts with other proteins to behave specifically in distinct situations. That could lead to medicines that target it for precise benefits.
March 5, 2014. Viva Biotech Ltd., a leading company in structure-based and fragment-based drug discovery
services based in Shanghai, China, and HQL Pharmaceuticals Ltd., a drug discovery company utilizing its proprietary ChemSpace Scanner (CSS™) computational
technology based in Rehovot, Israel, today announced that they have entered into a strategic alliance to jointly provide a
fully integrated drug discovery services, focused on leads generation based on fragment screening.
March 13, 2014. Non-steroidal anti-inflammatory drugs (NSAIDs) act on bacteria in a way that is fundamentally different from current antibiotics and stop bacterial DNA from replicating, according to research led by Professor Aaron Oakley of the University of Wollongong. This serendipitous find highlights the importance of a protein called the
"sliding clamp" as a possible target for a whole new class of antibiotics.
March 17, 2014. A new tool for analyzing mountains of data from SLAC National Accelerator Laboratory's Linac Coherent Lightsource (LCLS)
X-ray laser can produce high-quality images of important proteins using fewer samples. The software package, known as the Computational Crystallography Toolbox for X-ray Free-electron Lasers or cctbx.xfel, was developed as a part of an international project to study proteins involved in oxygen-producing stages in photosynthesis, but can be applied to other protein studies as well.
March 18, 2014. One mystery that remains is how HIV-1 recognizes and fishes out its own RNA from among all the other RNAs in the nucleus, an essential step in viral replication. The structural basis for this recognition has been defined in a small-angle
X-ray scattering (SAXS) study by researchers from the National Cancer Institute, National Institutes of
Health, and Argonne National Laboratory conducted at the X-ray Science Division 12-ID-B and -C beamlines at the U.S. Department of Energy Office of Science's Advanced Photon Source.
March 20, 2014. Scientists from the Division of Structural Biology at The Institute of Cancer Research, London, alongside colleagues from the University of Bristol, carried out a series of experiments to study proteins involved at a crucial stage in a process called homologous recombination, which is used by cells to repair breaks in DNA.
March 21, 2014. The initiation of protein synthesis within a cell is the process that is the most regulated and most critical, but it is still the least understood. Research by Ivan Lomakin and Thomas Steitz of Yale University has unlocked the genetic scanning mechanism that begins this crucial piece of cell machinery.
March 24, 2014. Comedienne Mel Giedroyc has narrated an animated video for Oxford University about using
X-rays to work out the shapes of proteins. The Great British Bake-Off presenter lent her voice to A Case of Crystal Clarity, available online at oxfordsparks.net.
Product spotlight: The Compact HomeLab
 Rigaku's Compact HomeLab was designed for researchers who want a low-maintenance X-ray system with the ultimate in experimental flexibility.
X-ray beam optimized for small crystals
The foundation of this system is the third generation Rigaku MicroMax™-003, an integrated microfocus sealed tube generator, and specialized confocal optic. The optic has been designed for the small crystals that are most frequently seen in today's structural biology labs. The beam size at the crystal is less than 100 μm in diameter, giving superior flux density for crystals smaller than 100 μm in size.
The X-ray tube includes a 3-year warranty, which ensures that your time will be spent measuring samples instead of maintaining your X-ray source. The MicroMax-003 utilizes a 30 μm focal spot running at 30 watts of power. Superior beam stability is maintained by a supplied cooling system.
Detector selected for performance
The standard detector in the Compact HomeLab is the Dectris® PILATUS™ 200K. This Hybrid Pixel Array Detector (HPAD) is a true photon counting detector that features: the highest sensitivity, the lowest readout noise, the highest dynamic range, the sharpest point spread function and the ability to collect data continuously, in "shutterless" mode. These combined detector characteristics make PILATUS detectors the best among today's commercially available detectors for crystallography.
Ask for more information.
Lab spotlight:
Professor P. Shing Ho
Professor P. Shing Ho, Chairman
Department of Biochemistry and Molecular Biology
Colorado State University
Fort Collins, CO USA
Nucleic acid structure and function; Biomolecular halogen bonds
The research interests in Shing Ho's laboratory focus on the structures and structural gymnastics of nucleic acids. More recently,
they have been developing both nucleic acid and protein model systems to characterize a set of interactions called halogen bonds,
which contribute significantly to the specificity and affinity of large classes of halogenated ligands used as inhibitors and as
drugs. They apply crystallographic, molecular modeling, and physical biochemical approaches to study these problems.
Useful link: Tango
Tango: A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains. Recent research in the field of amyloidosis suggests the soluble precursor aggregates and not the fibers themselves are the pathogenic species in amyloid diseases. Given the ubiquity of protein aggregation over amyloidosis under physiological conditions this stresses the importance of understanding the determinants modulating protein aggregation. Tango is a computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.
Selected
recent crystallographic papers
Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity. Nazmi, Ali Reza; Schofield, Linley R.; Dobson, Renwick C.J.; Jameson, Geoffrey B.; Parker, Emily J. Journal of Molecular Biology. Feb2014, Vol. 426 Issue 3, p656-673. 18p. http://dx.doi.org/10.1016/j.jmb.2013.11.008.
Long range correlations and folding angle with applications to α-helical proteins. Krokhotin, Andrey; Nicolis, Stam; Niemi, Antti J. Journal of Chemical Physics. 3/2/2014, Vol. 140 Issue 9, p095103-1-095103-6. 6p. http://dx.doi.org/10.1063/1.4865933.
Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis. Ni, Dongchun; Yang, Kun; Huang, Yihua. Acta Crystallographica: Section F, Structural Biology Communications. Mar2014, Vol. 70 Issue 3, p362-365. 4p. http://dx.doi.org/10.1107/S2053230X14003008.
Structural Insights into Membrane Interaction and Caveolar Targeting of Dynamin-like EHD2. Shah, Claudio; Hegde, Balachandra G.; Morén, Björn; Behrmann, Elmar; Mielke, Thorsten; Moenke, Gregor; Spahn, Christian M.T.; Lundmark, Richard; Daumke, Oliver; Langen, Ralf. Structure. Mar2014, Vol. 22 Issue 3, p409-420. 12p. http://dx.doi.org/10.1016/j.str.2013.12.015.
Nucleation precursors in protein crystallization. Vekilov, Peter G.; Vorontsova, Maria A. Acta Crystallographica: Section F, Structural Biology Communications. Mar2014, Vol. 70 Issue 3, p271-282. 12p. http://dx.doi.org/10.1107/S2053230X14002386.
Single particle 3D reconstruction for 2D crystal images of membrane proteins. Scherer, Sebastian; Arheit, Marcel; Kowal, Julia; Zeng, Xiangyan; Stahlberg, Henning. Journal of Structural Biology. Mar2014, Vol. 185 Issue 3, p267-277. 11p. http://dx.doi.org/10.1016/j.jsb.2013.12.011.
Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion. Wu, Hsin-Yi; Cheng, Yi-Sheng. Acta Crystallographica: Section F, Structural Biology Communications. Mar2014, Vol. 70 Issue 3, p378-383. 6p. http://dx.doi.org/10.1107/S2053230X14001897.
The Mitochondrial Fission Receptor MiD51 Requires ADP as a Cofactor. Losón, Oliver C.; Liu, Raymond; Rome, Michael E.; Meng, Shuxia; Kaiser, Jens T.; Shan, Shu-ou; Chan, David C. Structure. Mar2014, Vol. 22 Issue 3, p367-377. 11p. http://dx.doi.org/10.1016/j.str.2014.01.001.
Molecular structure and dynamics of the dimeric human small heat shock protein HSPB6. Weeks, Stephen D.; Baranova, Ekaterina V.; Heirbaut, Michelle; Beelen, Steven; Shkumatov, Alexander V.; Gusev, Nikolai B.; Strelkov, Sergei V. Journal of Structural Biology. Mar2014, Vol. 185 Issue 3, p342-354. 13p. http://dx.doi.org/10.1016/j.jsb.2013.12.009.
Structure of the Hemoglobin-IsdH Complex Reveals the Molecular Basis of Iron Capture by Staphylococcus aureus. Dickson, Claire F.; Kaavya Krishna Kumar; Jacques, David A.; Reza Malmirchegini, G.; Spirig, Thomas; Mackay, Joel P.; Clubb, Robert T.; Guss, J. Mitchell; Gell, David A. Journal of Biological Chemistry. 3/7/2014, Vol. 289 Issue 10, p6728-6738. 11p. http://dx.doi.org/10.1074/jbc.M113.545566.
pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state. Johal, Asha R; Blackler, Ryan J; Alfaro, Javier A; Schuman, Brock; Borisova, Svetlana; Evans, Stephen V. Glycobiology. Mar2014, Vol. 24 Issue 3, p237-246. 10p.
http://dx.doi.org/10.1093/glycob/cwt098.
Natural single amino acid polymorphism (F19Y) in human galectin-8: detection of structural alterations and increased growth-regulatory activity on tumor cells. Ruiz, Federico M.; Scholz, Barbara A.; Buzamet, Eliza; Kopitz, Jürgen; André, Sabine; Menéndez, Margarita; Romero, Antonio; Solís, Dolores; Gabius, Hans-Joachim. FEBS Journal. Mar2014, Vol. 281 Issue 5, p1446-1464. 19p. http://dx.doi.org/10.1111/febs.12716.
Structural basis for adaptation of lactobacilli to gastrointestinal mucus. Etzold, Sabrina; Kober, Olivia I.; MacKenzie, Donald A.; Tailford, Louise E.; Gunning, A. Patrick; Walshaw, John; Hemmings, Andrew M.; Juge, Nathalie. Environmental Microbiology. Mar2014, Vol. 16 Issue 3, p888-903. 16p. http://dx.doi.org/10.1111/1462-2920.12377.
Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics. Chen, Joe P. J.; Spence, John C. H.; Millane, Rick P. Acta Crystallographica. Section A, Foundations & Advances. Mar2014, Vol. 70 Issue 2, p143-153. 11p. http://dx.doi.org/10.1107/S2053273313032038.
Direct phasing in femtosecond nanocrystallography. II. Phase retrieval. Chen, Joe P. J.; Spence, John C. H.; Millane, Rick P. Acta Crystallographica. Section A, Foundations & Advances. Mar2014, Vol. 70 Issue 2, p154-161. 8p. http://dx.doi.org/10.1107/S2053273313032725.
Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Singh, Harkewal; Arentson, Benjamin W.; Becker, Donald F.; Tanner, John J. Proceedings of the National Academy of Sciences of the United States of America. 3/4/2014, Vol. 111 Issue 9, p3389-3394. 6p. http://dx.doi.org/10.1073/pnas.1321621111.
Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition. Kattner, Christof; Toussi, Deana N.; Zaucha, Jan; Wetzler, Lee M.; Rüppel, Nadine; Zachariae, Ulrich; Massari, Paola; Tanabe, Mikio. Journal of Structural Biology. Mar2014, Vol. 185 Issue 3, p440-447. 8p. http://dx.doi.org/10.1016/j.jsb.2013.12.006.
Crystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae, provides hints into its interaction with fibronectin. Beulin, D.S. Jemima; Yamaguchi, Masaya; Kawabata, Shigetada; Ponnuraj, Karthe. International Journal of Biological Macromolecules. Mar2014, Vol. 64, p168-173. 6p. http://dx.doi.org/10.1016/j.ijbiomac.2013.11.035.
The Perfect Theory. A Century of Geniuses and the Battle over General
Relativity. by Pedro G. Ferreira. Hardcover: Houghton Mifflin Harcourt 2014.
ISBN 978-0-547-55489-1 $28.00.
The Perfect Theory is described by the author as a "biography" of
Einstein's theory of general relativity. The book is as delightful and
entertaining to read as a great mystery novel, the kind that keeps you up until
the wee hours or that you have to read twice. The author wants us to intuitively
understand why Einstein's theory was and continues to be a revolution in the
understanding of gravity and the cosmos. Dr. Ferreira also clearly transmits his
great passion for and mastery of science communication in this book.
The Perfect Theory is a chronological tale, beginning in the early twentieth
century with a description of Albert Einstein's life and the personal and
scientific influences on his formulation of general relativity. The story
details Arthur Eddington's measurement, during a total eclipse, of the bending
of light from distant stars by the sun's gravity. That measurement proved one of
the predictions of Einstein's theory and made spacetime a reality. Subsequent
chapters interweave general relativity with major theoretical developments and
experimental measurements in gravity and cosmology of the last and current
century. Neutron stars, white dwarfs, black holes, quasars, pulsars,
singularities, event horizons, and wormholes; all these are characters in the
book. The many great geniuses of quantum physics, astrophysics, and cosmology
that predicted or measured those phenomena are characterized. Like a good
mystery, every chapter ends with a cliffhanger about how a new great discovery
in astronomy, cosmology or astrophysics gave credence to or was inconsistent
with general relativity. The Perfect Theory made this reader excited to learn
about attempts at unification of gravity with other forces and the quantum. On
the human side, the author makes clear how the terrible wars and some of the
political conflicts of the twentieth century influenced the lives of physicists
working on relativity and cosmology.
Time magazine designated Albert Einstein as the "person of the
century," the twentieth that is. The Perfect Theory will give anyone with a
deep curiosity about nature that has heard all the buzzwords like black holes,
string theory, M-theory, loop quantum gravity, dark matter and energy, and
inflation, an appreciation for the interrelationship of general relativity to
all of those. The last few chapters are about the limitations of the theory at
extremes of gravity. The book ends on a hopeful note that new technologies and
instruments may provide actual experiments that lead to an even more
perfect theory of everything.
Laurie Betts, Innatrix, Inc.
Carolina KickStart Labs, UNC Chapel Hill NC 27599
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