Crystallography in the news

February 6, 2015. A device for precisely positioning small objects using acoustic waves has now been used to position fragile protein crystals a few micrometers or less in size in the path of a crystallography X-ray beam. This technique will make it possible to collect data on previously intractable samples and will expand the scope of what is now possible with X-ray crystallography.

February 6, 2015. A more accurate view of the structure of the oxygen-evolving complex that splits water during photosynthesis is now in hand thanks to a study involving researchers from the RIKEN SPring-8 Center, Okayama Univ. and the Japan Science and Technology Agency. The new model of natural photosynthesis provides a blueprint for synthesizing water-splitting catalysts that mimic this natural process.

February 7, 2015. A new technique being developed by researchers at MIT and elsewhere shows great promise for producing highly detailed images of individual proteins, no matter how complicated their structure, without the need for crystallization. The findings are described in the journal Physical Review X by MIT graduate student Ashok Ajoy, postdoc Ulf Bissbort, associate professor of nuclear science and engineering Paola Cappellaro, and others at MIT, the Singapore University of Technology and Design, and Harvard University.

February 8, 2015. Merck has joined Novartis, Pfizer and a host of other big pharma companies in the Structural Genomics Consortium (SGC), a transatlantic public-private collaboration focused on the 3-D structures of proteins.

February 10, 2015. In order to find the weak points of growth and transmission of the influenza virus, researchers at University of Oxford have created a highly accurate computer simulation of the outer shell of the influenza A virion derived using different imaging modalities.

February 11, 2015. Caroline Ajo-Franklin, a chemist and synthetic biologist at Berkeley Lab's Molecular Foundry, led a study in which high-throughput light scattering measurements and small angle X-ray scattering (SAXS) were used to investigate the self-assembly of 2D nanosheets from a common bacterial surface layer (S-layer) protein. This protein, called "SbpA," forms the protective armour for Lysinibacillus sphaericus, a soil bacterium used as a toxin to control mosquitoes.

February 13, 2015. A team of chemists, biochemists and mathematicians at the University of Bristol has published a paper in Nature Chemical Biology that explores how protein structures are stabilized. The research determined that we do not need to use the macrodipole concept anymore to explain the vast majority of phenomena that have been attributed to it in the past, including in textbooks.

Feb 17, 2015. Axel Becke, professor and Killam Chair in Computational Science at Dalhousie University, who helped make it practical to predict and explore the chemistry of complex molecules such as proteins using computers has won Canada's top science prize - a medal and $1 million.

Product spotlight: MicroMax™-007 HF

The MicroMax-007 HF is the most widely used home lab X-ray source for protein crystallography and nobody has yet been able to match the usability of the beam for structural biology research. The original MicroMax-007 introduced the world to the concept of a sub-100 micron focal spot size along the increased brilliance that can be more effectively used to illuminate small crystals. The current HF version increases the power loading by 50% over the original model providing an X-ray source that rivals second generation synchrotron sources,  but with better beam stability and, of course, easy access.

The MicroMax-007 HF is the perfect system for anyone who is planning to upgrade an old RU style generator, or for someone who is setting up a new lab and wants an X-ray source that will be easy to maintain and will provide an X-ray beam that will help you screen the smallest of crystals.

Learn more

Prof. Dr. Ralf Ficner
Institute for Microbiology and Genetics
Dept. of Molecular Structural Biology
University of Göttingen
Göttingen, Germany

To understand the relationship between the three-dimensional structure and the cellular function of biological macromolecules, Ralf's group determines the structures of proteins and protein-RNA complexes by means of X-ray crystallography. Their current projects concern proteins involved in the splicing and modification of RNA and, as well, proteins required for the nucleocytoplasmic transport, and enzymes of the polysialic acid metabolism.

BioSync is a structural bioligist's guide to high energy data collection facilities. It provides up-to-date information on over 130 beamlines at worldwide synchrotron radiation facilities where biological macromolecules are studied. The National Institutes of Health and the National Institute of General Medical Sciences fund BioSync.

Trapping a transition state in a computationally designed protein bottle. Pearson, Aaron D.; Mills, Jeremy H.; Song, Yifan; Nasertorabi, Fariborz; Gye Won Han; Baker, David; Stevens, Raymond C.; Schultz, Peter G. Science. 2/20/2015, Vol. 327 Issue 6224, p863-867. 5p. DOI: 10.1126/science.aaa2424.

Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression. Shevtsov, M. B.; Streeter, S. D.; Thresh, S.-J.; Swiderska, A.; McGeehan, J. E.; Kneale, G. G. Acta Crystallographica: Section D. Feb2015, Vol. 71 Issue 2, p398-407. 10p. DOI: 10.1107/S139900471402690X.

Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and ONX 0914. Huber, Eva M.; Heinemeyer, Wolfgang; Groll, Michael. Structure. Feb2015, Vol. 23 Issue 2, p407-417. 11p. DOI: 10.1016/j.str.2014.11.019.

Assembly States of FliM and FliG within the Flagellar Switch Complex. Sircar, Ria; Borbat, Peter P.; Lynch, Michael J.; Bhatnagar, Jaya; Beyersdorf, Matthew S.; Halkides, Christopher J.; Freed, Jack H.; Crane, Brian R. Journal of Molecular Biology. Feb2015, Vol. 427 Issue 4, p867-886. 20p. DOI: 10.1016/j.jmb.2014.12.009.

Molecular dynamics in drug design. Zhao, Hongtao; Caflisch, Amedeo. European Journal of Medicinal Chemistry. Feb2015, Vol. 91, p4-14. 11p. DOI: 10.1016/j.ejmech.2014.08.004.

Structural biology: XFELs probe protein dynamics. Strack, Rita. Nature Methods. Feb2015, Vol. 12 Issue 2, p109-109. 1p. DOI: 10.1038/nmeth.3277.

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08Å resolution: comparison with the Azotobacter vinelandii MoFe protein. Zhang, Li-Mei; Morrison, Christine N.; Kaiser, Jens T.; Rees, Douglas C. Acta Crystallographica: Section D. Feb2015, Vol. 71 Issue 2, p274-282. 9p. DOI: 10.1107/S1399004714025243.

Fast native-SAD phasing for routine macromolecular structure determination. Weinert, Tobias; Olieric, Vincent; Waltersperger, Sandro; Panepucci, Ezequiel; Chen, Lirong; Zhang, Hua; Zhou, Dayong; Rose, John; Ebihara, Akio; Kuramitsu, Seiki; Li, Dianfan; Howe, Nicole; Schnapp, Gisela; Pautsch, Alexander; Bargsten, Katja; Prota, Andrea E; Surana, Parag; Kottur, Jithesh; Nair, Deepak T; Basilico, Federica. Nature Methods. Feb2015, Vol. 12 Issue 2, p131-133. 3p. DOI: 10.1038/nmeth.3211.

CtIP tetramer assembly is required for DNA-end resection and repair. Davies, Owen R; Forment, Josep V; Sun, Meidai; Belotserkovskaya, Rimma; Coates, Julia; Galanty, Yaron; Demir, Mukerrem; Morton, Christopher R; Rzechorzek, Neil J; Jackson, Stephen P; Pellegrini, Luca. Nature Structural & Molecular Biology. Feb2015, Vol. 22 Issue 2, p150-157. 8p. DOI: 10.1038/nsmb.2937.

Emerging Structural Insights into Glycoprotein Quality Control Coupled with N-Glycan Processing in the Endoplasmic Reticulum. Tadashi Satoh; Takumi Yamaguchi; Koichi Kato. Molecules. 2015, Vol. 20 Issue 2, p2475-2491. 17p. DOI: 10.3390/molecules20022475.

The Crystal Structure of the Human Titin:Obscurin Complex Reveals a Conserved yet Specific Muscle M-Band Zipper Module. Pernigo, Stefano; Fukuzawa, Atsushi; Pandini, Alessandro; Holt, Mark; Kleinjung, Jens; Gautel, Mathias; Steiner, Roberto A. Journal of Molecular Biology. Feb2015, Vol. 427 Issue 4, p718-736. 19p. DOI: 10.1016/j.jmb.2014.11.019.

Structural and Functional Divergence of the Aldolase Fold in Toxoplasma gondii. Tonkin, Michelle L.; Halavaty, Andrei S.; Ramaswamy, Raghavendran; Ruan, Jiapeng; Igarashi, Makoto; Ngô, Huân M.; Boulanger, Martin J. Journal of Molecular Biology. Feb2015, Vol. 427 Issue 4, p840-852. 13p. DOI: 10.1016/j.jmb.2014.09.019.

The solution structure of the transducin-a-uncoordinated 119 protein complex suggests occlusion of the Gβ₁γ₁-binding sites. Cheguru, Pallavi; Majumder, Anurima; Yadav, Ravi; Gopalakrishna, Kota N.; Gakhar, Lokesh; Artemyev, Nikolai O. FEBS Journal. Feb2015, Vol. 282 Issue 3, p550-561. 12p. DOI: 10.1111/febs.13161.

Control of repeat-protein curvature by computational protein design. Park, Keunwan; Shen, Betty W; Parmeggiani, Fabio; Huang, Po-Ssu; Stoddard, Barry L; Baker, David. Nature Structural & Molecular Biology. Feb2015, Vol. 22 Issue 2, p167-174. 8p. DOI: 10.1038/nsmb.2938.

Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis. Wauer, Tobias; Swatek, Kirby N; Wagstaff, Jane L; Gladkova, Christina; Pruneda, Jonathan N; Michel, Martin A; Gersch, Malte; Johnson, Christopher M; Freund, Stefan MV; Komander, David. EMBO Journal. Feb2015, Vol. 34 Issue 3, p307-325. 19p. DOI: 10.15252/embj.201489847.

Structure-based design of low-nanomolar PIM kinase inhibitors. Ishchenko, Alexey; Zhang, Lin; Le Brazidec, Jean-Yves; Fan, Junhua; Chong, Jer Hong; Hingway, Aparna; Raditsis, Annie; Singh, Latika; Elenbaas, Brian; Hong, Victor Sukbong; Marcotte, Doug; Silvian, Laura; Enyedy, Istvan; Chao, Jianhua. Bioorganic & Medicinal Chemistry Letters. Feb2015, Vol. 25 Issue 3, p474-480. 7p. DOI: 10.1016/j.bmcl.2014.12.041.

The design and structural characterization of a synthetic pentatricopeptide repeat protein. Gully, Benjamin S.; Shah, Kunal R.; Lee, Mihwa; Shearston, Kate; Smith, Nicole M.; Sadowska, Agata; Blythe, Amanda J.; Bernath-Levin, Kalia; Stanley, Will A.; Small, Ian D.; Bond, Charles S. Acta Crystallographica: Section D. Feb2015, Vol. 71 Issue 2, p196-208. 13p. DOI: 10.1107/S1399004714024869.

Carbonyl reductase of Candida parapsilosis - Stability analysis and stabilization strategy. Grosch, Jan-Hendrik; Loderer, Christoph; Jestel, Tim; Ansorge-Schumacher, Marion; Spieß, Antje C. Journal of Molecular Catalysis B: Enzymatic. Feb2015, Vol. 112, p45-53. 9p. DOI: 10.1016/j.molcatb.2014.12.001.

Book review: Introduction to Nanoscience

     by S. M. Lindsay
     Oxford University Press, New York, 2009, 472 pages, ISBN: 978-0199544219

I received this book a couple of years ago and it has been sitting on my shelf waiting for me to read and review it since. As the title suggests, this is a book about the fundamentals of nanoscience. It is a textbook and, as such, covers just about every topic I studied as an undergraduate student in chemistry: organic and physical chemistry, quantum mechanics, solid state physics, instrumentation thermodynamics, statistical mechanics and so on, albeit in an order much different than I learned them in school. It was published in late 2009 and, while current then, is missing some of the new materials developed since. Keep in mind this is an introduction, so the basics are timeless.

I would suggest the reader start with Appendix B, a transcript of the 1959 lecture by Richard Feynman to the AIP meeting titled "There's Plenty of Room at the Bottom". This lecture may be considered the point of inception of nanoscience, even though many of tools and techniques were already coming into existence by the time of the lecture.

Chapter 1 covers the basics of nanoscience, including an analysis of the aforementioned Feynman lecture and how many of the predictions he got right (and not quite right). Part 1 consists of Chapters 2 and 3, and exposes the reader to the tools needed to understand the topics discussed in Part 2. Chapter 2 covers the basics of quantum mechanics. Chapter 3 follows with a discussion about statistical mechanics and thermodynamics. Part 2 looks at the tools needed to explore the nanoworld.

Chapter 4 reviews instrumentation, covering scanning tunneling, atomic force and electron microscopy, fluorescence techniques, and tools for physical manipulation of tiny objects. Chapter 5 reviews the processes of top-down construction of materials as is done in the semiconductor industry. Chapter 6 covers the bottom-up production of materials, starting with organic chemistry and biochemistry and ending with a discussion about DNA manipulation.

Part 3 consists of four chapters that look at the applications of nanoscience. This section includes chapters on electrons in nanostructures, molecular electronics, and properties of nanostructures, and ends with a chapter on molecular biology.

There is a plethora of appendices covering minute (pun intended) details on topics covered in the main text. The book also came with a CD containing movies and animated GIFs that demonstrate things like Brownian motion, DNA tethering, etc. One of the movies has a typo that I found somewhat humorous. When I was a student, my advisor taught me that "anyone who spells asymmetric with two esses is an a??." I leave it you to find the misspelling.