Crystallography in the news

June 2, 2014. Scientists from the Friedrich Miescher Institute for Biomedical Research have discovered how microRNAs repress translation of mRNAs. In a structure-function study, they report different modes of recruitment of the CCR4-NOT complex to mRNAs targeted by microRNAs. They also demonstrate that CCR4-NOT recruits and activates the ATPase DDX6, an important translational inhibitor. Activation of DDX6 by CCR4-NOT plays a key role in miRNA repression.

June 6, 2014. A team led by researchers at The Scripps Research Institute (TSRI) has used advanced electron microscopy techniques to determine the first accurate structural map of Mediator, one of the largest and most complex "molecular machines" in cells.

June 9, 2014. Unless you have resolution down below 1Å, then your X-ray structures are not quite "structures"; they're models. About ten years ago, Dr. Derek Lowe published a paper which suggested that many ligand-bound structures seemed to have strain energy in them that wouldn't have been predicted. One interpretation is that there's more to ligand (and binding site) reorganization than people tend to realize, and that ligands don't always bind in their lowest-energy conformations.

June 9, 2014. The New York Consortium on Membrane Protein Structure (NYCOMPS) used X-rays at Brookhaven Lab's National Synchrotron Light Source (NSLS) to decipher the atomic level structure of a protein that regulates the level of calcium in cells. The accumulation of calcium is a key signaling agent that can trigger programmed cell death. The research showed how this protein, embedded in a cellular membrane structure called the endoplasmic reticulum, serves as a molecular safety valve for keeping calcium levels steady.

June 9, 2014. Staph infections that become resistant to multiple antibiotics don't happen because the bacteria themselves adapt to the drugs, but because of a kind of genetic parasite they carry called a plasmid that helps its host survive the antibiotics. A team from Duke and the University of Sydney in Australia has solved the structure of a key protein that drives DNA copying in the plasmids that make staphylococcus bacteria antibiotic-resistant. Knowing how this protein works may now help researchers devise new ways to stop the plasmids from spreading antibiotic resistance in staph by preventing the plasmids from copying themselves.

June 10, 2014. Researchers are a step closer to establishing the link between a protein with a split personality and type 1 diabetes. New research shows how a protein, called GAD65, changes its shape when it turns itself on and off. The new research, led by Monash University, investigated how GAD65 regulates the production of neuro­transmitters by changing its shape.

June 13, 2014. A research team at the Institute for Biochemistry and Molecular Biology of the Faculty of Medicine and the Centre for Biological Signalling Studies BIOSS at the University of Freiburg, Germany, led by Prof. Dr. Carola Hunte, has succeeded in describing how the antimalarial drug atovaquone binds to its target protein. The scientists used X-ray crystallography to determine the three-dimensional structure of the protein with the active substance bound.

June 15, 2014. Multi-disciplinary research, spanning six years and undertaken by three departments at the Indian Institute of Science, has yielded promising results relative to multiple drug resistant TB bacteria. Their research shows that targeting a particular Histone-like protein in the mycobacterium tuberculosis (MTb) - a common bacteria found in most TB cases - hinders its growth, thus making the disease curable.

June 16, 2014. Scientists at the National Institutes of Health took a molecular-level journey into microtubules, the hollow cylinders inside brain cells that act as skeletons and internal highways. Dr. Roll-Mecak's team investigated this idea using X-ray crystallography to look at how atoms on tubulin acetyltransferase (TAT) molecules interact with acetylation sites on tubulin molecules. Their results suggested that TAT fit poorly around the sites.

June 16, 2014. A UNSW Australia-led team of researchers has discovered how algae that survive in very low levels of light are able to switch on and off, a weird quantum phenomenon that occurs during photosynthesis. In the new study, the team used X-ray crystallography to work out the crystal structure of the light-harvesting complexes from three different species of cryptophytes.

Product spotlight: Pflipper

Mounting and dismounting a sample using tongs is an art for the steady of hand. The Rigaku Pflipper (patent pending) is a tool designed to easily mount or dismount a crystal from a vial while maintaining the crystal at cryogenic temperatures. With the Pflipper you can be assured that your crystal will remain at near liquid nitrogen temperatures during these manipulations.

This video demonstrates the mounting and dismounting procedures while showing that the temperature does not rise above -160°C.

The Pfipper works with any low temperature system and any Rigaku multiple-axis goniometer.

Ask for more information.     View a product video.

Celia W. Goulding, Ph.D.
Associate Professor, Molecular Biology and Biochemistry
Associate Professor, Pharmaceutical Sciences
University of California, Irvine

The principal focus of Prof. Goulding's lab is to utilize proteomic and crystallographic techniques to elucidate and characterize new systems of protein complexes in Mycobacterium tuberculosis. Their overall goal is to create a systems approach to shift the focus of structural biology from a single protein to molecular assemblies. The systems of immediate interest contain potential anti-TB protein drug targets and protein membrane components. They also are studying contact-dependent growth inhibition in gram-negative bacteria.

Interactive Crystallography Timeline from the Royal Institution. The Royal Institution (Ri) was founded in March 1799 in the UK with the aim of introducing new technologies and teaching science to the general public. They are at the forefront of public engagement with science. Their charitable purpose has always been to encourage people to think more deeply about the wonders and applications of science.

A bittersweet celebration of crystallography. Nature Methods. Jun2014, Vol. 11 Issue 6, p593-593. 1p. http://dx.doi.org/10.1038/nmeth.2995.

Small-Angle X-ray Scattering Screening Complements Conventional Biophysical Analysis: Comparative Structural and Biophysical Analysis of Monoclonal Antibodies Ig G1, Ig G2, and Ig G4. Tian, Xinsheng; Langkilde, Annette E.; Thorolfsson, Matthias; Rasmussen, Hanne B.; Vestergaard, Bente. Journal of Pharmaceutical Sciences. Jun2014, Vol. 103 Issue 6, p1701-1710. 10p. http://dx.doi.org/10.1002/jps.23964.

Preliminary Crystallographic Analysis of a Cruciferin Protein from Seeds of Moringa oleifera. Akrem, Ahmed; Yousef, Nasser; Begum, Afshan; Negm, Amr; Meyer, Arne; Perbandt, Markus; Buck, Friedrich; Betzel, Christian. Protein Journal. Jun2014, Vol. 33 Issue 3, p253-257. 5p. http://dx.doi.org/10.1007/s10930-014-9558-x.

Interactions of ataxin-3 with its molecular partners in the protein machinery that sorts protein aggregates to the aggresome. Bonanomi, Marcella; Mazzucchelli, Serena; D'Urzo, Annalisa; Nardini, Marco; Konarev, Petr V.; Invernizzi, Gaetano; Svergun, Dmitri I.; Vanoni, Marco; Regonesi, Maria Elena; Tortora, Paolo. International Journal of Biochemistry & Cell Biology. Jun2014, Vol. 51, p58-64. 7p. http://dx.doi.org/10.1016/j.biocel.2014.03.015.

Chromatin as dynamic 10-nm fibers. Maeshima, Kazuhiro; Imai, Ryosuke; Tamura, Sachiko; Nozaki, Tadasu. Chromosoma. Jun2014, Vol. 123 Issue 3, p225-237. 13p. http://dx.doi.org/10.1007/s00412-014-0460-2.

Co-Crystallization with Conformation-Specific Designed Ankyrin Repeat Proteins Explains the Conformational Flexibility of BCL-W. Schilling, Johannes; Schöppe, Jendrik; Sauer, Evelyn; Plückthun, Andreas. Journal of Molecular Biology. Jun2014, Vol. 426 Issue 12, p2346-2362. 17p. http://dx.doi.org/10.1016/j.jmb.2014.04.010.

A Ctf4 trimer couples the CMG helicase to DNA polymerase α in the eukaryotic replisome. Simon, Aline C.; Zhou, Jin C.; Perera, Rajika L.; van Deursen, Frederick; Evrin, Cecile; Ivanova, Marina E.; Kilkenny, Mairi L.; Renault, Ludovic; Kjaer, Svend; Matak-Vinković, Dijana; Labib, Karim; Costa, Alessandro; Pellegrini, Luca. Nature. 6/12/2014, Vol. 510 Issue 7504, p293-297. 5p. http://dx.doi.org/10.1038/nature13234.

Nitrate as a probe of cytochrome c surface: Crystallographic identification of crucial "hot spots" for protein-protein recognition. De March, Matteo; Demitri, Nicola; De Zorzi, Rita; Casini, Angela; Gabbiani, Chiara; Guerri, Annalisa; Messori, Luigi; Geremia, Silvano. Journal of Inorganic Biochemistry. Jun2014, Vol. 135, p58-67. 10p. http://dx.doi.org/10.1016/j.jinorgbio.2014.02.015.

Non-covalent binding of membrane lipids to membrane proteins. Yeagle, Philip L. BBA - Biomembranes. Jun2014, Vol. 1838 Issue 6, p1548-1559. 12p. http://dx.doi.org/10.1016/j.bbamem.2013.11.009.

Your personalized protein structure: Andrei N. Lupas fused to GCN4 adaptors. Deiss, Silvia; Hernandez Alvarez, Birte; Bär, Kerstin; Ewers, Carolin P.; Coles, Murray; Albrecht, Reinhard; Hartmann, Marcus D. Journal of Structural Biology. Jun2014, Vol. 186 Issue 3, p380-385. 6p. http://dx.doi.org/10.1016/j.jsb.2014.01.013.

Structure-guided discovery of 1,3,5 tri-substituted benzenes as potent and selective matriptase inhibitors exhibiting in vivo antitumor efficacy. Goswami, Rajeev; Mukherjee, Subhendu; Ghadiyaram, Chakshusmathi; Wohlfahrt, Gerd; Sistla, Ramesh K.; Nagaraj, Jwala; Satyam, Leena K.; Subbarao, Krishnaprasad; Palakurthy, Rajendra K.; Gopinath, Sreevalsam; Krishnamurthy, Narasimha R.; Ikonen, Tarja; Moilanen, Anu; Subramanya, Hosahalli S.; Kallio, Pekka; Ramachandra, Murali. Bioorganic & Medicinal Chemistry. Jun2014, Vol. 22 Issue 12, p3187-3203. 17p. http://dx.doi.org/10.1016/j.bmc.2014.04.013.

Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N, N'-diacetylchitobiose deacetylase. Mine, Shouhei; Niiyama, Mayumi; Hashimoto, Wakana; Ikegami, Takahisa; Koma, Daisuke; Ohmoto, Takashi; Fukuda, Yohta; Inoue, Tsuyoshi; Abe, Yoshito; Ueda, Tadashi; Morita, Junji; Uegaki, Koichi; Nakamura, Tsutomu. FEBS Journal. Jun2014, Vol. 281 Issue 11, p2584-2596. 13p. http://dx.doi.org/10.1111/febs.12805.

Crystal structure studies of NADP+ dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain. Kumar, S.M.; Pampa, K.J.; Manjula, M.; Abdoh, M.M.M.; Kunishima, Naoki; Lokanath, N.K. Biochemical & Biophysical Research Communications. Jun2014, Vol. 449 Issue 1, p107-113. 7p. http://dx.doi.org/10.1016/j.bbrc.2014.04.164.

Fifty years of fibrous protein research: A personal retrospective. Parry, David A.D. Journal of Structural Biology. Jun2014, Vol. 186 Issue 3, p320-334. 15p. http://dx.doi.org/10.1016/j.jsb.2013.10.010.

Protein expression, characterization, crystallization and preliminary X-ray crystallographic analysis of a Fic protein from Clostridium difficile. Welner, Ditte; Dedic, Emil; van Leeuwen, Hans C.; Kuijper, Ed; Bjerrum, Morten Jannik; Østergaard, Ole; Jørgensen, René. Acta Crystallographica: Section F, Structural Biology Communications. Jun2014, Vol. 70 Issue 6, p827-831. 5p. http://dx.doi.org/10.1107/S2053230X1400987X.

Automation in biological crystallization. Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen. Acta Crystallographica: Section F, Structural Biology Communications. Jun2014, Vol. 70 Issue 6, p686-696. 11p. http://dx.doi.org/10.1107/S2053230X14011601.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6. Morita, Junko; Kato, Kazuki; Mihara, Emiko; Ishitani, Ryuichiro; Takagi, Junichi; Nishimasu, Hiroshi; Aoki, Junken; Nureki, Osamu. Acta Crystallographica: Section F, Structural Biology Communications. Jun2014, Vol. 70 Issue 6, p794-799. 6p. http://dx.doi.org/10.1107/S2053230X14008929.

Crystallization and preliminary X-ray diffraction analysis of the peripheral light-harvesting complex LH2 from Marichromatium purpuratum. Cranston, Laura J.; Roszak, Aleksander W.; Cogdell, Richard J. Acta Crystallographica: Section F, Structural Biology Communications. Jun2014, Vol. 70 Issue 6, p808-813. 6p. http://dx.doi.org/10.1107/S2053230X14009303.

Characterization, crystallization and preliminary X-ray crystallographic analysis of the Uba5 fragment necessary for high-efficiency activation of Ufm1. Xie, Shutao. Acta Crystallographica: Section F, Structural Biology Communications. Jun2014, Vol. 70 Issue 6, p765-768. 4p. http://dx.doi.org/10.1107/S2053230X14008826.

Book review: Neanderthal Man: In Search of Lost Genomes

     by Svante Pääbo
     Basic Books 2014. ISBN 978-0-465-02083-6.

Neanderthal Man recounts Svante Pääbo's scientific and personal journeys studying the genetic makeup of ancient and extinct animals and humans that culminated in 2010 with the publication of the full genomic sequence of a Neanderthal. Dr. Pääbo is the director of Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. One of the remarkable outcomes of the work described in the book was the discovery that modern humans and Neanderthals must have interbred while they both inhabited our planet.

Neanderthal Man tells the story of the author's long and painstaking development of methods required to sequence the ancient Neanderthal genome. It took years to develop techniques for extracting ancient DNA from tiny samples of bone or other tissues of animal or Neanderthal remains. The detection and prevention of contamination from modern DNA entails a significant part of Pääbo's body of work, and there are some technical descriptions in the book that may not appeal to non-molecular biologists. Technological and instrumental breakthroughs in DNA sequencing that arose out of the human genome projects were critical to the final result. Once the Neanderthal genome was sequenced, Pääbo described the major analysis and statistical undertaking required to interpret what the sequence actually told him about our relationship to Neanderthal man. Besides the interpretation that humans probably interbred with Neanderthals, there are implications about how and when human and other hominids originated and dispersed across the continents. That is a fascinating aspect, especially when one thinks about the enormous time scales over which this all occurred compared to a single human lifetime.

In his book, Dr. Pääbo describes the triumphs and the heartbreaks of a hard-driving and extremely ambitious career as a successful researcher. The author tries to share his decision-making processes, his quests for funding, his need for collaborations, his management style, and the importance of attending scientific conferences to hear about other people's work-and how it stimulated creative thinking about his own work. Most of us do not make the magnitude of discovery that this book describes, but we all share the happiness of seeing a scientific result before anyone else in the world until it is published. Also, Dr. Pääbo is very matter-of-fact about aspects of his personal life that were intertwined with his scientific life. For example, we are all somewhat driven by a competitive nature to be the first person to make a singular discovery, and he does not minimize that aspect of his story.

Reading Neanderthal Man re-invigorated my curiosity and wonder about evolution and human origins, and engendered a respect for someone whose own curiosity (and sheer persistence) uncovered the ghost of Neanderthal in ourselves.