Crystallography in the news

September 1, 2016. Scientists at Oregon State University have made the first-ever detailed, atomic-level images of a peroxiredoxin, which has revealed a peculiar characteristic of this protein and might form the foundation for a new approach to antibiotics.

Researchers from Harvard Medical School and Boston Children's Hospital, together with colleagues at Kyoto University, are among the first to trace poison ivy's molecular path, following the effect from leaf to burning itch and pointing a potentially soothing way forward.

September 6, 2016. Using simulations of the distance distribution function (DDF) derived from small angle X-ray scattering (SAXS) theoretical data of a dense monodisperse system, Chinese researchers found a quantitative mathematical correlation between the apparent size of a spherically symmetric (or nearly spherically symmetric) homogenous particle and the concentration of the solution.

September 6, 2016. Neutron crystallography is an important complementary technique to X-ray crystallography, since it provides details of the hydrogen positions in biological molecules.

September 12, 2016. Researchers at the U.S. Department of Energy's (DOE's) Argonne National Laboratory have mapped out two very different types of protein. One helps soil bacteria digest carbon compounds; the other protects cells from the effects of harmful molecules.

September 12, 2016. Using the Diamond Light Source, researchers from the University of Oxford solved the structure of the Ebola virus in its native state, and also when bound with the anticancer drug toremifene and with ibuprofen.

September 12, 2016. Associate Professor Brian Abbey at La Trobe, in collaboration with Associate Professor Harry Quiney at the University of Melbourne, has discovered that buckyballs irradiated with hard X-ray free electron laser (XFEL) light change their shape to that of an AFL football.

September 14, 2016. Researchers develop methods to design small, targeted proteins with shapes not found in nature. A team led by scientists at the University of Washington has designed constrained peptides that have chemical properties that would make them ideal starting points for new drugs.

September 21, 2016. A team of researchers from Tokai University in Japan, using X-ray tomography, recently produced the first 3D model of a fruit fly's neuronal network.

September 21, 2016. Structural chemist and chemical crystallographer Dr Alison Edwards has contributed to the characterisation of two large, complex silver nanoclusters of 136 and 374 atoms as part of an international collaboration led by researchers from Xiamen University in China.

Product spotlight: XtaLAB mini™ II

Benchtop small molecule structure determination for teaching and research
The Rigaku XtaLAB mini II benchtop X-ray crystallography system is a compact single crystal X-ray diffractometer designed to produce publication-quality 3D structures. The perfect addition to any synthetic chemistry laboratory, the XtaLAB mini II will enhance research productivity by offering affordable structure analysis capability without the necessity of relying on a departmental facility. With the XtaLAB mini II, you no longer have to wait in line to determine your structures. Instead your research group can rapidly analyze new compounds as they are synthesized in the lab.

At a time where the teaching of crystallography in chemistry departments is gaining momentum, the XtaLAB mini II is the perfect instrument to perform this task, as the minimal design makes it essentially student-proof.

The XtaLAB mini II has several advances over its predecessor, including a new Hybrid Photon Counting detector for noise-free shutterless data collection and software control by the powerful CrysAlis^Pro software package. For more >

Rigaku's XtaLAB mini II for small molecule 3D molecular structure determination

Lab in the spotlight

Center for Biocrystallographic Research, Poznan
Head: Professor Mariusz Jaskolski , Ph.D.

The Center for Biocrystallographic Research in Poznan, which is affiliated with the Institute of Bioorganic Chemistry, Polish Academy of Sciences, was opened in June 1994. It is the first protein crystallography laboratory in Poland and the second in central-Eastern Europe. It was created through a joint initiative of the Institute of Bioorganic Chemistry (the "bio" part) and the Department of Crystallography, A. Mickiewicz University, Poznan (the "crystallography" part) and was funded by the Foundation for Polish Science.

The center is fully equipped with modern facilities for crystallization, X-ray data collection and processing, and has excellent computer facilities networked to Poznan Metropolitan Supercomputer Center. Their mission is to be a center of integration for the Polish and central-European structural biology community.

Prof. Jaskolski's research interest in structural biology covers a broad range, including structural mechanisms of amyloidogenesis, structural biology of retroviral enzymes, structural chemistry and biology of hydrolytic enzymes, plant hormone-binding proteins and macromolecular crystallography at ultimate resolution.

Useful link: ContaMiner

The StruBE group
Computational Bioscience Research Center
King Abdullah University of Science and Technology

ContaMiner is a rapid automated large-scale detection of contaminant crystals.

Protein contaminants, from the expression host, purification buffers or from the affinity tags used, may crystallise instead of a protein of interest. Unfortunately, this only becomes clear once the crystal structure has been determined…

ContaMiner allows rapid screening of X-ray diffraction data against the most likely proteins contaminants.

Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein. Altegoer, Florian; Rensing, Stefan A.; Bange, Gert. Proceedings of the National Academy of Sciences of the United States of America. 9/6/2016, Vol. 113 Issue 36, p10168-10173. 6p. DOI: 10.1073/pnas.1602425113.

Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry. Shah, Manish B.; Jang, Hyun-Hee; Wilderman, P. Ross; Lee, David; Li, Sheng; Zhang, Qinghai; Stout, C. David; Halpert, James R. Biophysical Chemistry. Sep2016, Vol. 216, p1-8. 8p. DOI: 10.1016/j.bpc.2016.05.007.

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm. He, Hongxing; Fang, Hengrui; Miller, Mitchell D.; Phillips, George N.; Su, Wu-Pei. Acta Crystallographica. Section A, Foundations & Advances. Sep2016, Vol. 72 Issue 5, p539-547. 8p. DOI: 10.1107/S2053273316010731.

Engineering, Structure and Immunogenicity of the Human Metapneumovirus F Protein in the Postfusion Conformation. Más, Vicente; Rodriguez, Laura; Olmedillas, Eduardo; Cano, Olga; Palomo, Concepción; Terrón, María C.; Luque, Daniel; Melero, José A.; McLellan, Jason S. PLoS Pathogens. 9/9/2016, Vol. 14 Issue 9, p1-21. 21p. DOI: 10.1371/journal.ppat.1005859.

Crystal structure and activity of Francisella novicida UDP-N-acetylglucosamine acyltransferase. Joo, Sang Hoon; Chung, Hak Suk. Biochemical & Biophysical Research Communications. Sep2016, Vol. 478 Issue 3, p1223-1229. 7p. DOI: 10.1016/j.bbrc.2016.08.098.

Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry. Shah, Manish B.; Jang, Hyun-Hee; Wilderman, P. Ross; Lee, David; Li, Sheng; Zhang, Qinghai; Stout, C. David; Halpert, James R. Biophysical Chemistry. Sep2016, Vol. 216, p1-8. 8p. DOI: 10.1016/j.bpc.2016.05.007.

Circular dichroism spectroscopy of membrane proteins. Miles, A. J.; Wallace, B. A. Chemical Society Reviews. 9/21/2016, Vol. 45 Issue 18, p4859-4872. 14p. DOI: 10.1039/c5cs00084j.

DNA/protein binding, cytotoxicity and catecholase activity studies of a piperazinyl moiety ligand based nickel(II) complex. Mistri, Soumen; Puschmann, Horst; Manna, Subal Chandra. Polyhedron. Sep2016, Vol. 115, p155-163. 9p. DOI: 10.1016/j.poly.2016.05.003.

AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy. Kärtner, F.X.; Ahr, F.; Calendron, A.-L.; Çankaya, H.; Carbajo, S.; Chang, G.; Cirmi, G.; Dörner, K.; Dorda, U.; Fallahi, A.; Hartin, A.; Hemmer, M.; Hobbs, R.; Hua, Y.; Huang, W.R.; Letrun, R.; Matlis, N.; Mazalova, V.; Mücke, O.D.; Nanni, E. Nuclear Instruments & Methods in Physics Research Section A. Sep2016, Vol. 829, p24-29. 6p. DOI: 10.1016/j.nima.2016.02.080.

Crystal structure of Arabidopsis thaliana calmodulin7 and insight into its mode of DNA binding. Kumar, Sanjeev; Mazumder, Mohit; Gupta, Nisha; Chattopadhyay, Sudip; Gourinath, Samudrala. FEBS Letters. Sep2016, Vol. 590 Issue 17, p3029-3039. 11p. DOI: 10.1002/1873-3468.12349.

The Structure of the Plakin Domain of Plectin Reveals an Extended Rod-like Shape. Ortega, Esther; Manso, José A.; Buey, Rubén M.; Carballido, Ana M.; Carabias, Arturo; Sonnenberg, Arnoud; de Pereda, José M. Journal of Biological Chemistry. 9/2/2016, Vol. 291 Issue 36, p18643-18662. 25p. DOI: 10.1074/jbc.M116.732909.

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; Case, David A.; York, Darrin M.; Adams, Paul D.; Warren, Gregory L. Acta Crystallographica Section D: Structural Biology. Sep2016, Vol. 72 Issue 9, p1062-1072. 10p. DOI: 10.1107/S2059798316012225.

Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome. Melnikov, Sergey; Mailliot, Justine; Shin, Byung-Sik; Rigger, Lukas; Yusupova, Gulnara; Micura, Ronald; Dever, Thomas E.; Yusupov, Marat. Journal of Molecular Biology. Sep2016, Vol. 428 Issue 18, p3570-3576. 7p. DOI: 10.1016/j.jmb.2016.05.011.

Role of N-terminal region of Escherichia coli maltodextrin glucosidase in folding and function of the protein. Pastor, Ashutosh; Singh, Amit K.; Shukla, Prakash K.; Equbal, Md. Javed; Malik, Shikha T.; Singh, Tej P.; Chaudhuri, Tapan K. BBA - Proteins & Proteomics. Sep2016, Vol. 1864 Issue 9, p1138-1151. 14p. DOI: 10.1016/j.bbapap.2016.06.008.

Crystal structure of VapC21 from Mycobacterium tuberculosis at 1.31 Å resolution. Jardim, Paulo; Santos, Isadora Cristina da Silva; Barbosa, João Alexandre Ribeiro Gonçalves; de Freitas, Sônia Maria; Valadares, Napoleão Fonseca. Biochemical & Biophysical Research Communications. Sep2016, Vol. 478 Issue 3, p1370-1375. 6p. DOI: 10.1016/j.bbrc.2016.08.130.

Improving Protein Crystal Quality via Mechanical Vibration. Qin-Qin Lu; Bin Zhang; Liang Tao; Lu Xu; Da Chen; Jing Zhu; Da-Chuan Yin. Crystal Growth & Design. Sep2016, Vol. 16 Issue 9, p4869-4876. 8p. DOI: 10.1021/acs.cgd.6b00227.

Membrane protein crystallization in micelles conjugated by nucleoside base-pairing: A different concept. Hosamani, Basavaprabhu; Kale, Raju R.; Sharma, Hemlata; Wachtel, Ellen; Kesselman, Ellina; Danino, Dganit; Friedman, Noga; Sheves, Mordechai; Namboothiri, Irishi N.N.; Patchornik, Guy. Journal of Structural Biology. Sep2016, Vol. 195 Issue 3, p379-386. 8p. DOI: 10.1016/j.jsb.2016.06.021.

Importance of Determination of Crystal Quality in Protein Crystals when Performing High-Resolution Structural Analysis. Haruhiko Koizumi; Ryo Suzuki; Masaru Tachibana; Katsuo Tsukamoto; Izumi Yoshizaki; Seijiro Fukuyama; Yoshihisa Suzuki; Satoshi Uda; Kenichi Kojima. Crystal Growth & Design. Sep2016, Vol. 16 Issue 9, p4905-4909. 5p. DOI: 10.1021/acs.cgd.6b00457.

Synthesis, crystal structure, Hirshfeld surface analysis and DNA binding properties of interactions with lattice pyrazinamide and its zinc(II) coordination polymer. Liu, Qing-Ling; Yang, Li-Jing; Luo, Yang-Hui; Jiang, Ye-Hao; Sun, Bai-Wang. Research on Chemical Intermediates. Sep2016, Vol. 42 Issue 9, p6947-6957. 11p. DOI: 10.1007/s11164-016-2506-y.

Concentration-Induced Association in a Protein System Caused by a Highly Directional Patch Attraction. Weimin Li; Persson, Björn A.; Lund, Mikael; Bergenholtz, Johan; Zackrisson Oskolkova, Malin. Journal of Physical Chemistry B. Sep2016, Vol. 120 Issue 34, p8953-8959. 7p. DOI: 10.1021/acs.jpcb.6b06873.

The Structure of the Plakin Domain of Plectin Reveals an Extended Rod-like Shape. Ortega, Esther; Manso, José A.; Buey, Rubén M.; Carballido, Ana M.; Carabias, Arturo; Sonnenberg, Arnoud; de Pereda, José M. Journal of Biological Chemistry. 9/2/2016, Vol. 291 Issue 36, p18643-18662. 25p. DOI: 10.1074/jbc.M116.732909.

Thermal stability of extracellular hemoglobin of Rhinodrilus alatus (HbRa): DLS and SAXS studies. Carvalho, José; Carvalho, Francisco; Santiago, Patrícia; Tabak, Marcel. European Biophysics Journal. Sep2016, Vol. 45 Issue 6, p549-563. 15p. DOI: 10.1007/s00249-016-1121-6.

Chemistry of Metal-organic Frameworks Monitored by Advanced X-ray Diffraction and Scattering Techniques. Mazaj, Matja Ž; Kaucic, Venceslav; Logar, Nataša Zabukovec. Acta Chimica Slovenica. 2016, Vol. 63 Issue 3, p440-458. 19p. 7 Diagrams, 1 Chart, 1 Graph. DOI: 10.17344/acsi.2016.2610.

Book reviews

NeuroTribes: The Legacy of Autism and the Future of Neurodiversity by Steve Silberman, Penguin Random House, New York, 2015, 543 pages, ISBN 978-1-58333-467-6.

My daughter Jeanette gave me this book when I last visited her in May, thinking I would enjoy it. She was right – NeuroTribes is fascinating. The author sets out to provide a comprehensive view of autism as we understand it today and does it well. Silberman begins with his introduction to the title subject through a Geek Cruise he sailed in 2000. The personalities of the hundred or so developers he interacted with on the cruise led him to research and write this book.

Silberman provides a short biography of the discoverer of hydrogen, Henry Cavendish, who showed all the symptoms of an autistic person: inattention to other people, regimented routine and singular focus on a problem, to name a few. Paul Dirac, who predicted the existence of the positron, is offered as another example of a historical figure with what we consider the modern markers of autism. I learned he was on the autistic spectrum when I reviewed Graham Farmelo's biography a few years back. Silberman fast-forwards into the modern era with a case study of a boy named Leo Rosa. Leo's parents worked endlessly to try to help him through diet and therapy to find these only alleviated symptoms caused by the autistic behavior, not autism itself.

Then, Silberman rewinds to the early 20^th century to look at the work of Hans Asperger at the Heilpädagogik Station in Vienna. Asperger had worked out many of the details we understand about autism today, but this information was lost in the Anschluss and subsequent purge of Viennese medicine. Asperger stayed in Vienna during WWII, but his work was suspect after the war ended because of the Nazi influence in Austria.

After the war, Leo Kanner, a psychotherapist in the United States, developed the model of autism that became the standard for many years. He proposed that autism was the result of toxic parenting. Silberman then takes a moment and clarifies what behaviors are associated with autism, citing radio hobbyists as a group that embraced technical prowess with real human contact. A similar situation occurred when computers became available and the same personalities that handled the radio so well came to work with this new technology.

Silberman's history of autism and its role in fostering the idea of neurodiversity is perhaps best summarized by this quote from Temple Grandin in the book:

"Aware adults with autism and their parents are often angry about autism. They may ask why nature or God created such horrible conditions as autism, manic depression and schizophrenia. However, if the genes that caused these conditions were eliminated there might be a terrible price to pay. It is possible that persons with bits of these traits are more creative, or possibly even geniuses. If science eliminated these genes, maybe the whole world would be taken over by accountants."

Dark Matter by Blake Crouch, Penguin Random House, New York, 2016, 352 pages: 978-1101904220.

I listened to an interview with the author, Blake Crouch, on Science Friday. Then, when I saw copies of the book all over the place, I picked one up for myself. The author took 10 years to write this book because he spent considerable time with scientists in order to make the idea of traversing the multiverse plausible. The premise is that the antagonist has developed a human version of Schrödinger's Cat and uses the device to traverse space, but not time. This a fun summer read but don't think too hard or the ideas of the multiverse and quantum coherence/decoherence are likely to give you a headache.

Reviews by Joseph D. Ferrara, Ph.D.
Deputy Director, X-ray Research Laboratory, Rigaku