Crystallography in the news

October 3, 2014. Chemistry students experience life as X-ray crystallographers and explore the X-ray factor while spending a day in the labs of Professor Jon Cooper at the Royal Free Hospital campus of the University College of London.

October 5, 2014. A new crystallographic technique developed at the University of Leeds is set to transform scientists' ability to observe how molecules work. They describe a new way of doing time-resolved crystallography. This "pump-probe" method uses clever math (a Hadamard transform) to open up the field to much less powerful light sources than were needed with earlier methods.

October 8, 2014. A group of researchers at the B1 CHESS beamline, led by staff scientist Zhongwu Wang, used innovative X-ray crystallography methods to explore the growth of nanocrystals into supercrystals. It involved the simultaneous collection of data on the ordering and orientation of lead sulfide nanocrystals and supercrystals using both wide-angle (WAXS) and small-angle (SAXS) X-ray scattering, which typically are done one at the time.

October 9, 2014. Researchers at the University of Virginia School of Medicine have solved a key protein structure within the Ebola virus. Through X-ray crystallography, Professor Zygmunt Derewenda of the Department of Molecular Physiology and Biological Physics and his team uncovered the structure of the Ebola nucleoprotein, the protein that packages the infectious material.

October 10, 2014. Scientists from Rutgers University and the Emory University School of Medicine determined the molecular structure of one specific section of envelope protein E2, known as the ectodomain core, that is directly involved in how the hepatitis C virus (HCV) penetrates the host cell membrane, an early step toward vaccine and therapies.

October 14, 2014. Scientists can now study the motion of HIV proteins on the surface of the virus, opening up new possibilities for fighting the disease. A team at Weill Cornell Medical College used single-molecule fluorescence resonance energy transfer (smFRET) imaging to get a real-time view of how the proteins attack and infect human immune cells.

October 19, 2014. Deep sea creatures inspire a new method of destroying cancer-causing pollutants. Professor David Leys of the Manchester Institute of Biotechnology has spent 15 years studying microbes that use vitamin B12 to reduce the toxicity of polychlorinated biphenyals (PCBs), dioxins and other dangerous substances. The work employed X-ray crystallography to produce a 3D image showing how halogens are removed from dangerous chemicals.

October 20, 2014. Using techniques that illuminate subtle changes in individual proteins, chemistry researchers at Cornell have uncovered new insight into the underlying causes of Amyotrophic Lateral Sclerosis (ALS). Both pulsed dipolar electron spin resonance (ESR) spectroscopy and small-angle X-ray scattering (SAXS) were employed in the work.

October 21, 2014. Five more companies will set up shop on or near the University at Buffalo campuses under START-UP NY, the innovative tax incentive program created by Gov. Andrew M. Cuomo. One of these companies, HarkerBio - a start-up company that provides an X-ray crystallography-based technology platform, expects to create 10 jobs and invest $500,000. It will collaborate with UB’s Center for Computational Research and open an office at Hauptman-Woodward Medical Research Institute on the Buffalo Niagara Medical Campus.

October 22, 2014. Hybrid methods to solve structures of molecular machines have created a storage headache for the Protein Data Bank. This month, leaders of the four organiza­tions that host the data bank held a workshop in Hinxton, UK, to hatch a plan to ensure that hybrid models and their insights into fundamental biology and disease do not get lost.

October 23, 2014. The brightest synchrotron light source in the world has delivered its first X-ray beams. The National Synchrotron Light Source II, at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory, detected its first photons, beginning a new phase of the facility's operations. Scientific experiments at NSLS-II are expected to begin before the end of the year.

October 26, 2014. Researchers led by Christian Degen, professor at the Laboratory for Solid State Physics at ETH Zurich, developed a different and vastly more sensitive measurement technique for magnetic resonance imaging (MRI) signals. For the first time, a single hydrogen atom has been detected using high-resolution MRI. The group is working on significantly increasing the resolution of the technique, with the goal of eventually imaging at the level of single molecules.

October 27, 2014. Researchers at the University of Illinois, led by Wilfred van der Donk and Satish K. Nair, report that they have made a breakthrough in understanding how a powerful antibiotic agent is made in nature. Their discovery solves a decades-old mystery, and opens up new avenues of research into thousands of similar molecules, many of which are likely to be medically useful.

Product spotlight: PILATUS 1M

Upgrade your R-AXIS to a PILATUS 1M and bring a whole new dimension to your laboratory. Hybrid Pixel Array Detectors (HPAD) have proven to be an effective means of increasing speed and throughput at synchrotron beamlines around the world. Now you can bring the power of this detector technology into the home lab. By utilizing your existing X-ray generator, optic, goniometer and sled, it is possible to cost effectively bring a new level of performance to your in-house research needs. An R-AXIS IV++ or R-AXIS HTC can easily be replaced with a PILATUS 1M that will allow shutterless data collection, and the extremely low noise characteristics will allow you to extend your home lab resolution with longer exposures. For more information >

Lab spotlight: Dr. Mair Churchill at the University of Colorado
in Denver, Department of Pharmacology

Mair's lab is interested in understanding the molecular basis of essential processes that regulate gene expression. They use biophysical, biochemical methods, and structural methods, including X-ray crystallography. Their insights into these fundamental mechanisms will contribute to a better understanding and ability to regulate gene expression processes involved in human diseases from cancer and heart disease to bacterial infections and will assist in drug development efforts.


Their studies focus on the following questions:

•  How is chromatin structure modulated for DNA-dependent processes?
•  How do transcription factors and pioneering factors activate gene expression?
•  How are genes coordinately regulated by quorum sensing in bacterial pathogens?

Useful link: VAMM VAMM is a coarse-grained force field and molecular mechanics package developed by Anil Korkut and Wayne Hendrickson for calculating large scale conformational transition pathways, energy minimization, molecular dynamics based on the virtual interactions of C-alpha atoms. VAMM force field is a knowledge based force field and formulated to capture features dependent on secondary structure and residue-specific contact information in proteins.

New at Rigaku Reagents Rigaku Reagents is now offering the JCSG Core Suite 1-4 Screens in deep well blocks! The 384 crystallization formulations were selected by the Joint Center for Structural Genomics, based on their highest hit rates in initial screening. For more information >

A drunken search in crystallization space. Fazio, Vincent J.; Peat, Thomas S.; Newman, Janet. Acta Crystallographica: Section F, Structural Biology Communications. Oct2014, Vol. 70 Issue 10, p1303-1311. 9p. DOI: 10.1107/S2053230X1401841X.

Crystallography using an X-ray free-electron laser. Patterson, Bruce D. Crystallography Reviews. Oct-Dec2014, Vol. 20 Issue 4, p242-294. 53p. DOI: 10.1080/0889311X.2014.939649.

Control of RecBCD Enzyme Activity by DNA Binding- and Chi Hotspot-Dependent Conformational Changes. Taylor, Andrew F.; Amundsen, Susan K.; Guttman, Miklos; Lee, Kelly K.; Luo, Jie; Ranish, Jeffrey; Smith, Gerald R. Journal of Molecular Biology. Oct2014, Vol. 426 Issue 21, p3479-3499. 21p. DOI: 10.1016/j.jmb.2014.07.017.

Low-dose X-ray radiation induces structural alterations in proteins. Borshchevskiy, Valentin; Round, Ekaterina; Erofeev, Ivan; Weik, Martin; Ishchenko, Andrii; Gushchin, Ivan; Mishin, Alexey; Willbold, Dieter; Büldt, Georg; Gordeliy, Valentin. Acta Crystallographica: Section D. Oct2014, Vol. 70 Issue 10, p2675-2685. 11p. DOI: 10.1107/S1399004714017295.

2D and 3D crystallization of a bacterial homologue of human vitamin C membrane transport proteins. Jeckelmann, Jean-Marc; Harder, Daniel; Ucurum, Zöhre; Fotiadis, Dimitrios. Journal of Structural Biology. Oct2014, Vol. 188 Issue 1, p87-91. 5p. DOI: 10.1016/j.jsb.2014.08.004.

High-Resolution Structure of a Membrane Protein Transferred from Amphipol to a Lipidic Mesophase. Polovinkin, V.; Gushchin, I.; Sintsov, M.; Round, E.; Balandin, T.; Chervakov, P.; Schevchenko, V.; Utrobin, P.; Popov, A.; Borshchevskiy, V.; Mishin, A.; Kuklin, A.; Willbold, D.; Chupin, V.; Popot, J.-L.; Gordeliy, V. Journal of Membrane Biology. Oct2014, Vol. 247 Issue 9/10, p997-1004. 8p. DOI: 10.1007/s00232-014-9700-x.

The many structural faces of calmodulin: a multitasking molecular jackknife. Kursula, Petri. Amino Acids. Oct2014, Vol. 46 Issue 10, p2295-2304. 10p. DOI: 10.1007/s00726-014-1795-y.

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. Terwilliger, Thomas C.; Bricogne, Gerard. Acta Crystallographica: Section D. Oct2014, Vol. 70 Issue 10, p2533-2543. 11p. DOI: 10.1107/S1399004714017040.

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering. Patel, Hitesh; Grüning, Björn A.; Günther, Stefan; Merfort, Irmgard. Bioinformatics. Oct2014, Vol. 30 Issue 20, p2978-2980. 3p. DOI: 10.1093/bioinformatics/btu424

Novel diamond X-ray crystal optics for synchrotrons and X-ray free-electron lasers. Stoupin, Stanislav. Diamond & Related Materials. Oct2014, Vol. 49, p39-47. 9p. DOI: 10.1016/j.diamond.2014.08.002.

Direct imaging electron microscopy (EM) methods in modern structural biology: Overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules. Miyaguchi, Katsuyuki. Biology of the Cell (Wiley-Blackwell). Oct2014, Vol. 106 Issue 10, p323-345. 23p. DOI: 10.1111/boc.201300081.

Sub-100-ps structural dynamics of horse heart myoglobin probed by time-resolved X-ray solution scattering. Oang, Key Young; Kim, Kyung Hwan; Jo, Junbeom; Kim, Youngmin; Kim, Jong Goo; Kim, Tae Wu; Jun, Sunhong; Kim, Jeongho; Ihee, Hyotcherl. Chemical Physics. Oct2014, Vol. 442, p137-142. 6p. DOI: 10.1016/j.chemphys.2014.03.004.

The Effect of Protein PEGylation on Physical Stability in Liquid Formulation. Holm, Louise Stenstrup; Mcumber, Aaron; Rasmussen, Jakob Ewald; Obiols-Rabasa, Marc; Thulstrup, Peter W.; Kasimova, Marina R.; Randolph, Theodore W.; van de Weert, Marco. Journal of Pharmaceutical Sciences. Oct2014, Vol. 103 Issue 10, p3043-3054. 12p. 1 Diagram, 2 Charts, 4 Graphs. DOI: 10.1002/jps.24094.

Operation of the Australian Store.Synchrotron for macromolecular crystallography. Meyer, Grischa R.; Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T.; McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M.; Bond, Charles S.; Buckle, Ashley M.; Androulakis, Steve. Acta Crystallographica: Section D. Oct2014, Vol. 70 Issue 10, p2510-2519. 10p. DOI: 10.1107/S1399004714016174.

Protein/Lipid Coaggregates are Formed During α-Synuclein-Induced Disruption of Lipid Bilayers. van Maarschalkerweerd, Andreas; Vetri, Valeria; Langkilde, Annette Eva; Foderà, Vito; Vestergaard, Bente. Biomacromolecules. Oct2014, Vol. 15 Issue 10, p3643-3654. 12p. DOI: 10.1021/bm500937p.

Solving the RNA polymerase I structural puzzle. Moreno-Morcillo, María; Taylor, Nicholas M. I.; Gruene, Tim; Legrand, Pierre; Rashid, Umar J.; Ruiz, Federico M.; Steuerwald, Ulrich; Müller, Christoph W.; Fernández-Tornero, Carlos. Acta Crystallographica: Section D. Oct2014, Vol. 70 Issue 10, p2570-2582. 13p. DOI: 10.1107/S1399004714015788.

Structure based design of novel 6,5 heterobicyclic mitogen-activated protein kinase kinase (MEK) inhibitors leading to the discovery of imidazo[1,5-a] pyrazine G-479. Robarge, Kirk D.; Lee, Wendy; Eigenbrot, Charles; Ultsch, Mark; Wiesmann, Christian; Heald, Robert; Price, Steve; Hewitt, Joanne; Jackson, Philip; Savy, Pascal; Burton, Brenda; Choo, Edna F.; Pang, Jodie; Boggs, Jason; Yang, April; Yang, Xioaye; Baumgardner, Matthew. Bioorganic & Medicinal Chemistry Letters. Oct2014, Vol. 24 Issue 19, p4714-4723. 10p. DOI: 10.1016/j.bmcl.2014.08.008.

Multi-crystal native SAD analysis at 6 keV. Liu, Qun; Guo, Youzhong; Chang, Yanqi; Cai, Zheng; Assur, Zahra; Mancia, Filippo; Greene, Mark I.; Hendrickson, Wayne A. Acta Crystallographica: Section D. Oct2014, Vol. 70 Issue 10, p2544-2557. 14p. DOI: 10.1107/S1399004714013376.

Small angle X-ray and neutron scattering from solutions of biological macromolecules. Snell, E. H. Crystallography Reviews. Oct-Dec2014, Vol. 20 Issue 4, p312-314. 3p. DOI: 10.1080/0889311X.2014.938442.

Structure of archaerhodopsin-2 at 1.8 Å resolution. Kouyama, Tsutomu; Fujii, Ryudo; Kanada, Soun; Nakanishi, Taichi; Chan, Siu Kit; Murakami, Midori. Acta Crystallographica: Section D. Oct2014, Vol. 70 Issue 10, p2692-2701. 10p. DOI: 10.1107/S1399004714017313.

Multiscale Conformational Heterogeneity in Staphylococcal Protein A: Possible Determinant of Functional Plasticity. Deis, Lindsay N.; Pemble, Charles W.; Qi, Yang; Hagarman, Andrew; Richardson, David C.; Richardson, Jane S.; Oas, Terrence G. Structure. Oct2014, Vol. 22 Issue 10, p1467-1477. 11p. DOI: 10.1016/j.str.2014.08.014.

Book review: The Science of Shakespeare: A New Look at the Playwright’s Universe

     by Dan Falk
     Thomas Dunne Books, New York, 384 pp, ISBN: 978-1250008770

Dan Falk’s latest work is an exciting exploration of the relationship between one of literature’s greatest playwrights and the scientific world of his time. Even though each chapter title is a quoted line from one of the Bard’s plays, Falk begins them by establishing the historical context of relevant scientific inventions and discoveries, and works his way towards connecting Shakespeare to these developments. He then returns to these specific lines in the plays that allude to either a crucial moment in scientific history or its reper­cussions in shaping a newfound scientific social consciousness. What drives the book is Falk’s tangible passion not only for the historical scientific context in which Shakespeare’s plays were written, but for the plays themselves.

In Chapter 9, titled “‘Does the world go round?’: Shakespeare and Galileo,” Falk explores the relationship between the work of the playwright and that of the astronomer. Interestingly, although Shakespeare’s birthplace in Stratford-upon-Avon is now a bustling tourist attraction, Galileo’s birthplace in Pisa is a private residence, marked by a small plaque and the Italian flag. The latter hardly seems fitting given Galileo’s myriad contributions to the fields of astronomy, physics, mathematics, engineering and philosophy.

Galileo is perhaps best remembered for developing an improved telescope and for the astronomical advancements he was subsequently able to make in support of Copernicus’ heliocentric theory. With his improved telescope, Galileo made a name for himself as the first person to identify three of Jupiter’s moons. This discovery revolutionized the field of astronomy, because it had previously been believed under the Aristotelian theory of cosmology that all celestial bodies orbited the Earth.

How does this relate to Shakespeare, you may wonder? One of Shakespeare’s later plays, Cymbeline, features Jupiter (the Roman god) descending from the heavens. Even though he is certainly apostrophized in many of Shakespeare’s other works, this is the only moment in which he makes a physical appearance onstage, which is certainly noteworthy since Cymbeline was written after the publication of Galileo’s discovery. Falk concedes that it cannot conclusively be proven that Shakespeare read Galileo’s research but, given Galileo’s notoriety as a challenger of Catholic doctrine, it seems unlikely that Shakespeare would not have heard of his work. Even if it is merely a coincidence, it is a fascinating one.

I found Falk’s book to be a quick and stimulating read, fast-paced and delightfully written.

Jeanette S. Ferrara    
Princeton University, Class of 2015