Crystallography in the News Product Spotlight: HKL-3000R

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Protein Crystallography Newsletter Volume 5, No. 7, July 2013 Crystallography in the news

In this issue: July 1, 2013. There's not much difference between what makes a man and what makes his beer—at least at the molecular level—according to a new study led by Crystallography in the news Professor John Schwabe at the University of Leicester. They discovered that a family of complexes that switch off gene expression is regulated by small signaling molecules New Rigaku webinar series called inositol phosphates. Upcoming event Product spotlight: HKL-3000R July 11, 2013. UK scientists plan to build a chromosome for the world's first synthetic yeast. Once all parts of the genome are complete, scientists can design new strains of Lab spotlight: Wolberger lab the yeast Saccharomyces cerevisiae to make products including chemicals, vaccines and Useful links for crystallography biofuels. Minister for Universities and Science David Willetts announced nearly £1M in funding for the UK arm of an international consortium attempting to build a synthetic Science video of the month version of the yeast genome by 2017. Crystallographers in the news July 16, 2013. A group of researchers led by Witold K. Surewicz of Case Western Survey of the month Reserve University studying the crystal structure of a snippet of the human prion has Monthly crystallographic papers found clues to how oligomers of the proteins could coax others to misfold. Book review July 16, 2013. Chemists of Radboud Univ. Nijmegen have found that a uniquely shaped enzyme that has never been seen before in biology is real: two interlocked ring structures, known as catenanes. This locked protein structure is maintained via weak non-covalent interactions. New Rigaku Webinar Series Nature, properties and July 17, 2013. An international team led by scientists at The Scripps Research Institute genesis of protein crystals. (TSRI) has determined and analyzed the three-dimensional atomic structure of the human glucagon receptor. The receptor, found mainly on liver and kidney cells, helps Presenter: Dr. Bernhard Rupp, k.k Hofkristallamt, regulate glucose levels in the bloodstream and is the target of potential therapeutic USA/Innsbruck Medical University, Austria. agents for type 2 diabetes. Time: Tuesday, August 6th, 2013, 8am PST July 25, 2013. Google celebrated the life and legacy of Rosalind Franklin on the Protein crystallization is the anniversary of her 93rd birthday with a special doodle on their search engine self-assembly of protein homepages. Born in 1920 in London, Franklin earned a Ph.D. in physical chemistry from molecules into an ordered, Cambridge University. She learned crystallography and X-ray diffraction, techniques that periodic structure, the protein she applied to DNA fibers. crystal. Protein molecules, however, are large, complex, and flexible macromolecules and most proteins are Product spotlight: HKL-3000R therefore difficult to crystallize.

To understand how to find HKL-3000R represents a new approach in conditions that allow crystal crystallographic software that integrates data formation, we must first collection, data reduction, phasing and model understand the physico- building into a single package. This approach chemical nature of proteins and significantly accelerates the process of structure how to modify their solubility determination and on average minimizes the and local surface property number of crystals, data sets and time required for distribution. structure solution.

Once we understand what conditions must be fulfilled for crystallization to occur, HKL-3000R controls the data collection instrument. the question is how to efficiently sample the Data collection strategy calculation for single and multiple axes goniometers. magnitude of possible reagent combinations that Raw image data reduction and analysis by industry standard HKL-2000. might provide the right conditions. The initial screening or sampling then informs us how to proceed Structure solution pipeline uses industry standard software packages (CCP4, further and how to optimize crystal growth, and often shelx, Arp/Warp, COOT, SOLVE/RESOLVE, etc.). also indicates that further examination and in most cases, modification of the protein itself may be Communication with standard databases (PDB, SwissProt). necessary to achieve successful crystallization. REGISTER Ask for more information. Upcoming Event Lab in the spotlight: Wolberger lab

The 71st Annual Pittsburgh Professor Cynthia Wolberger Diffraction Conference will Department of Biophysics and Biophysical Chemistry be being held in Buffalo, NY at Johns Hopkins Univ. School of Medicine, Baltimore, MD the Hauptman-Woodward Investigator, HHMI Medical Research Institute from the evening of the 18th of September to the afternoon of the 20th. The Wolberger lab is interested in the structural and Preliminary details are now available. Program topics mechanistic basis for transcriptional regulation and include crystallization approaches for recalcitrant ubiquitin signaling. Protein function is dynamically proteins and protein complexes, structural biology from an industrial perspective, macromolecular design regulated in the cell by the attachment and subsequent and DNA nanotechnology, technology developments removal of covalent posttranslational modifications. The for diffraction methods and a small molecule diffrac- modifications can be small, as in the case of acetylation, tion session. Meeting registration and discount hotel or quite large, as in the case of a polyubiquitin chain. reservation deadlines are the 16th and 21st of Acetylation and ubiquitination both occur in chromatin, the nucleoprotein complex into August. For more information contact the which eukaryotic DNA is packaged. organizers. Acetylation of the histone proteins in chromatin is associated with activation of transcription, whereas ubiquitination can be either an activating or a repressive mark, depending on which histone protein is modified. Ubiquitination of chromatin also plays a Lab in the Spotlight role in the response to DNA double-strand breaks, helping to recruit proteins that are required for DNA repair. The Wolberger group is interested in the molecular basis for these events, which ensure the integrity and expression of the genome. The lab uses X-ray crystallography, enzymology, and a variety of biophysical tools to gain insights into the mechanisms underlying these essential cellular processes.

Useful links: CHAPTER TWENTY-NINE

Chapter 29: Overexpression and Purification of Integral Membrane Proteins in Yeast. Franklin A. Hays, Zygy Roe-Zurz, and Robert M. Stroud. Methods in Enzymology, 2010, Vol. 470, p695-707.

Wolberger lab Selected recent crystallographic papers

Structure of the Repulsive Guidance Molecule (RGM)-Neogenin Signaling Hub. Bell, Christian H.; Healey, Eleanor; van Erp, Susan; Bishop, Benjamin; Chenxiang Tang; Gilbert, Robert J.C.; Aricescu, A. Radu; Pasterkamp, R. Jeroen; Siebold, Christian. Survey of the Month Science. 7/5/2013, Vol. 341 Issue 6141, p77-80. 4p. http://dx.doi.org/10.1126/science.1232322.

Structural characterization of human histidine triad nucleotide-binding protein 2, a member of the histidine triad superfamily. Maize, Kimberly M.; Wagner, Carston R.; Finzel, Barry C. FEBS Journal. Jul2013, Vol. 280 Issue 14, p3389-3398. 10p. http://dx.doi.org/10.1111/febs.12330.

Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models. Olson, Mark A.; Lee, Michael S. Journal of Computational Chemistry. Jul2013, Vol. 34 Issue 20, p1785-1793. 10p. 1 Chart, 4 Graphs.

http://dx.doi.org/10.1002/jcc.23325.

Can Protein Conformers Be Fractionated by Crystallization? Aoshuang Xu; Fenglei Li; Robinson, Howard; Yeung, Edward S. Analytical Chemistry. 7/2/2013, Vol. 85 Issue 13, p6372-6377. 6p. http://dx.doi.org/10.1021/ac400762x.

Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases. Udi, Yael; Fragai, Marco; Grossman, Moran; Mitternacht, Simon; Arad-Yellin, Rina; Calderone, Vito; Melikian, Maxime; Toccafondi, Mirco; Berezovsky, Igor N.; Luchinat, Claudio; Sagi, Irit. Journal of Molecular Biology. Jul2013, Vol. 425 Issue 13, p2330-2346. 17p. http://www.ncbi.nlm.nih.gov/pubmed/23583775.

Macromolecular juggling by ubiquitylation enzymes. Lorenz, Sonja; Cantor, Aaron J.; Rape, Michael; Kuriyan, John. BMC Biology. 2013, Vol. 11 Issue 1, p1-12. 12p. 1 Color Photograph, 4 Diagrams. http://dx.doi.org/10.1186/1741-7007-11-65.

ΔΔPT: a comprehensive toolbox for the analysis of protein motion. Rodgers, Thomas L.; Burnell, David; Townsend, Phil D.; Pohl, Ehmke; Cann, Martin J.; Wilson, Mark R.; McLeish, Tom C. B. BMC Bioinformatics. 2013, Vol. 14 Issue 1, p1-9. 9p. 1 Color Photograph, 1 Diagram, 1 Chart, 2 Graphs. http://dx.doi.org/10.1186/1471-2105-14- Photograph, 1 Diagram, 1 Chart, 2 Graphs. http://dx.doi.org/10.1186/1471-2105-14- http://www.surveymonkey.com/s/rigaku 183. Structure of the human cohesin inhibitor Wapl. Zhuqing Ouyang; Ge Zheng; Jianhua Song; Borek, Dominika M.; Otwinowski, Zbyszek; Brautigam, Chad A.; Tomchick, Diana R.; Rankin, Susannah; Hongtao Yu. Proceedings of the National Academy of Sciences Last Month's Survey Results of the United States of America. 7/9/2013, Vol. 110 Issue 28, p11355-11360. 6p. When was the last time you backed up your http://dx.doi.org/10.1073/pnas.1304594110. data? Microcrystal manipulation with laser tweezers. Wagner, Armin; Duman, Ramona; Stevens, Bob; Ward, Andy. Acta Crystallographica: Section D. Jul2013, Vol. 69 Issue 7, p1297-1302. 6p. http://dx.doi.org/10.1107/S090744491300958X.

A strategy for selecting the pH of protein solutions to enhance crystallization. Zhang, Chen-Yan; Wu, Zi-Qing; Yin, Da-Chuan; Zhou, Bo-Ru; Guo, Yun-Zhu; Lu, Hui-Meng; Zhou, Ren-Bin; Shang, Peng. Acta Crystallographica: Section F. Jul2013, Vol. 69 Issue 7, p821-826. 6p. http://dx.doi.org/10.1107/S1744309113013651.

Preliminary crystallographic analysis of the N-terminal PDZ-like domain of periaxin, an abundant peripheral nerve protein linked to human neuropathies. Han, Huijong; Kursula, Petri. Acta Crystallographica: Section F. Jul2013, Vol. 69 Issue 7, p804-808. 5p. http://dx.doi.org/10.1107/S1744309113016266.

Mimer: an automated spreadsheet-based crystallization screening system. Brodersen, Ditlev Egeskov; Andersen, Gregers Rom; Andersen, Christian Brix Folsted. Acta Crystallographica: Section F. Jul2013, Vol. 69 Issue 7, p815-820. 6p. http://dx.doi.org/10.1107/S1744309113014425. Science Video Robust structural analysis of native biological macromolecules from multi-crystal The Structures of Life anomalous diffraction data. Liu, Qun; Liu, Qinglian; Hendrickson, Wayne A. Acta Crystallographica: Section D. Jul2013, Vol. 69 Issue 7, p1314-1332. 19p. http://dx.doi.org/10.1107/S0907444913001479.

Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine? Newman, Janet; Burton, Denis R.; Caria, Sofia; Desbois, Sebastien; Gee, Christine L.; Fazio, Vincent J.; Kvansakul, Marc; Marshall, Bevan; Mills, Grant; Richter, Viviane; Seabrook, Shane A.; Wu, Mingbo; Peat, Thomas S. Acta Crystallographica: Section F. Jul2013, Vol. 69 Issue 7, p712-718. 7p. http://dx.doi.org/10.1107/S1744309113014152.

Book review:

Visualizing the Invisible The NIH/NIGMS video reveals how structural biology By Peter B. Moore provides insight into health and disease and is useful in developing new medications. Oxford University Press, 2012. ISBN: 978-0-190976709-0.

This book is devoted to using scattering of waves by physical objects to generate images of those objects. It is by no means complete, but covers just about everything Crystallographers in the News relevant to structural biology. The scales measured range from a few microns (cells) down to an Ångström or so (molecules).

The Protein Society Meeting in Boston Many years ago, I listened to a dynamic lecture by Peter Moore at a conference at CCNY. I was riveted by the presentation of the work done at Yale on the ribosome. The preface indicates that this book was created from the course the author teaches on instrumentation at Yale. As I read, I tried to imagine Professor Moore as he lectured at CCNY. I thought this would capture the essence of the course itself and give a better picture of the use of the book as a textbook. I think Moore accomplished his goal.

There are a few typos in this first edition, but I did not find any mistakes in the equations—and there are a lot of equations. Some are derived and some are merely presented as fact, but ample information is provided to derive results on one's own if so inclined. The end of each chapter contains a problem set and a series of appendices for those interested in detailed derivations of some of the concepts.

C hris Hill, C y nthia Wolberger, Ly nne Regan (President of The The book is divided into five parts. Part One covers the basics of scattering from Protein Society ) electrons, atoms, and then molecules. The concept of how the Fourier transform applies to scattering is introduced in Chapter 2. The final chapter of the first part Professor Sheena Radford of the University of Leeds covers the process of scattering by solid materials and brings forth the concepts of received the Carl Brändén Award, which honors a phase, velocity changes, absorption and dispersion. Finally, that particles can scatter like protein scientist who has made significant contri- waves is introduced. butions to the science and/or education. Rigaku sponsors the award each year. Two crystallographers Part Two covers crystallography and provides a good description of the basics of shared the Dorothy Hodgkin Award this year, Part Two covers crystallography and provides a good description of the basics of shared the Dorothy Hodgkin Award this year, lattices and the resulting diffraction pattern. Once diffraction is described, the author Professor Chris Hill of the University of Utah and covers the various solutions to the phase problem as applied to macromolecular Professor Cynthia Wolberger of Johns Hopkins crystallography. Chapter 7 provides a good description of electron density maps and University Medical Center. their interpretation. Part Three covers scattering from materials that are not crystalline. Two topics are treated in detail: coherent diffraction imaging and small angle scattering, with the latter receiving the most attention.

Part Four is devoted to the light microscope. The author covers the basics of lenses and how they form images. Next, Moore describes how light microscopes work and their limitations. This provides a natural segue into the higher resolution electron microscope, which is covered in Part Five. Here the author covers how electron lenses work, how electron microscopes create images from the hardware itself, and how refinements from downstream processing improve the images. The very last chapter covers three dimensional reconstruction and electron diffraction.

Here is a quick overview of my summer reading list:

For entertainment I recommend Joyland by Stephen King and NOS4A2 by Joe Hill, King's son. I picked up Bad Monkey by Carl Hiaasen for some laughs and Inferno by Dan Brown. Jeanette says the latter wasn't as entertaining as the author's previous books so I have put off starting it. Jared Diamond's latest The World Until Yesterday was enlightening and suggests we might all be a little happier and little healthier in a simpler world. I have Cooked by Michael Pollan and Plutocrats by Chrystia Freeland in my to- read stack. I really enjoyed Our Inner Ape by Frans De Waal a few years ago, so I picked up The Bonobo and the Atheist when I heard his interview on SciFri. So far, it is quite interesting. I am also working on Antifragile by Nicholas Taleb, author of The Black Swan, a book I reviewed here a couple of years ago.

Joseph D. Ferrara Chief Science Officer

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