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Protein Crystallography Newsletter
Volume 7, No. 1, January 2015
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In this issue:


Science Video
Wayne Hendrickson

video

Wayne Hendrickson (Columbia University) presented "Form Addressing Action for Membrane Proteins" as part of the Symposium "A Celebration of Open Access in Structural Biology: Recognizing the career and achievements of Professor Helen M. Berman". The public symposium was held on September 26, 2013 at Rutgers, The State University of New Jersey.

video



Upcoming Events

Macromolecular training class at Rigaku, February 18-25, 2015 at The Woodlands, TX. Class outline and form.

59th Biophysical Society Meeting, Feb 7-11, 2015, in Baltimore, MD.

40th Lorne Conf. on Protein Structure & Function, Feb 8-12, 2015 in Mantra Lorne, Victoria, Australia.

5th Winter School of Soft X-rays in Macromolecular Crystallography, Feb 28 - Mar 3, 2015 in Athens, GA.

Hybrid Methods in Structural Biology - Keystone Symposium, Mar 4-8 2015, in Tahoe City, CA.



Survey of the Month

1/2015 survey

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Last Month's Survey

If you could pick your Ph.D. advisor from a list of past Nobel Prize winners, who would it be?

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Crystallography in the news

January 2, 2015. Scientists, led by Michael G. Rossmann, Hanley Distinguished Professor of Biological Sciences at Purdue University, may have found a new technique to treat a virus that may cause possible paralysis. Researchers have discovered a class of compounds that could be effective in combating infections caused by enterovirus D68, which has stricken children with serious respiratory infections and may be associated with polio-like symptoms.

January 7, 2015. A new intermediate step and unexpected enzymatic activity in a metabolic pathway in the body, which could lead to new drug design for psychiatric and neurodegenerative diseases, has been discovered by researchers at Georgia State University. The research team has been studying a metabolic path called the tryptophan kynurenine pathway, which is linked to psychiatric and neurodegenerative disorders

January 13, 2015. Howard Hughes Medical Institute (HHMI) scientists have new structures of an essential cellular recycling machine that depict its structure with near atomic-level detail. The structures, which show a protein called NSF alone and interacting with its target, form a protein complex called SNARE when membranes fuse together.

January 15, 2015. US scientists have used X-ray crystallography to focus on an almost ubiquitous metabolic enzyme, nicotinamide nucleotide transhydrogenase, found in most life forms but with medically relevant links to diseases as disparate as diabetes and cancer.

January 16, 2015. Diane M. Simeone, M.D., director of the Pancreatic Cancer Center at the University of Michigan Comprehensive Cancer Center, has published crystallographic work that helps explain why pancreatic cancer is so lethal, with fewer than a third of patients surviving even early stage disease.

January 19, 2015. UK-based C4X Discovery Holdings has entered into a research agreement with drug discovery company Evotec. Under the agreement, C4XD's proprietary NMR-based technology and conformational design expertise will combine with Evotec's biology and chemistry expertise.

January 22, 2015. A major hurdle in structural biology and pharmacology is growing crystals to determine the structure of the biomolecules and pharmaceuticals under study. Researchers at the University of Tübingen, working with colleagues from Oxford and Grenoble, have now observed a key step in the nucleation and growth of some protein crystals.

January 22, 2015. Researchers at University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences and the Bridge Institute at the University of Southern California report the first crystal structure of the cellular receptor CXCR4 bound to an immune signaling protein called a chemokine.

January 22, 2015. Researchers in the US have devised a novel strategy for mapping multiple nuclear spins in a single molecule using quantum sensors in diamond. The approach, which is still theoretical, would in principle allow detailed interrogation at the atomic scale of structures such as the binding sites of proteins, which are not amenable to bulk analytical methods such as x-ray crystallography or nuclear magnetic resonance imaging.


pilatus3r1mTechnique spotlight: PILATUS3 R 1M

The PILATUS3 R 1M is a perfect replacement for people who currently have R-AXIS detectors and the want to continue to utilize their existing stage, optics and X-ray source. pilatus3r1m_example

To illustrate the speed and measurement quality of such a set up, data were collected for a lysozyme crystal on the PILATUS3 R 1M configured with an FR-X microfocus rotating anode generator for a total of 6 minutes. Following scaling, the overall redundancy was 11.9. The structure was easily solved using S-SAD method in HKL-3000R. HKL-3000R used SHELXC and SHELXD to find sites using data to 2.0 Å resolution. A full report is available.

Learn more



Lab spotlight: Otwinowski Lab / CUI  

CUIZbyszek Otwinowski
Professor, Department of Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd., ND10.214
Dallas, Texas 75390-9038


CUIOtwinowski's research addresses all aspects of phase estimates through interference measurements, direct methods, and dynamic simulations in the crystal lattice. The methods for the generation of a 3-dimensional molecular image will combine diverse sources of information, namely experimental (e.g., Multiple Anomalous Diffraction) and theoretical (predictions of the expected result). This combined process has mathematical similarity to the process of automated reasoning and pattern recognition.

The particular biological process of interest to this laboratory is protein folding. Proteins function in the globular, folded state; but they are produced in the elongated, unfolded state. For many proteins, the transition to folded state is accomplished with help from chaperonin proteins. Understanding the structure and function of the 800 kilodalton chaperonin GroEL requires finding out how this chaperonin can bind a large class of unfolded proteins. The structural challenge is to explain how a disordered state can be bound specifically.



Useful link: CheckMyMetal

CheckMyMetal (CMM): Metal Binding Site Validation Server. The CMM server is developed in Wladek Minor's lab. Citing CheckMyMetal (CMM): Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. Zheng,H., Chordia,M.D., Cooper,D.R., Chruszcz,M., Müller,P., Sheldrick,G.M., Minor,W. (2014) Nature Protocols, 9(1), 156-70.

The service is based on several well-established concepts reported previously: bond valence (1), VECSUM (2), metal binding sites (3), coordination geometries (4), assignment of sodium versus water (5), metal binding environment (6) in protein structures.



Selected recent crystallographic papers

Protein crystallography from the perspective of technology developments. Su, Xiao-Dong; Zhang, Heng; Terwilliger, Thomas C.; Liljas, Anders; Xiao, Junyu; Dong, Yuhui. Crystallography Reviews. Jan2015, Vol. 21 Issue 1/2, p122-153. 32p. DOI: 10.1080/0889311X.2014.973868.

Mechanistic insight from the crystal structure of mitochondrial complex I. Zickermann, Volker; Wirth, Christophe; Nasiri, Hamid; Siegmund, Karin; Schwalbe, Harald; Hunte, Carola; Brandt, Ulrich. Science. 1/2/2015, Vol. 347 Issue 6217, p44-49. 6p. DOI: 10.1126/science.1259859.

Conformation and interactions of dopamine hydrochloride in solution. Callear, Samantha K.; Johnston, Andrew; McLain, Sylvia E.; Imberti, Silvia. Journal of Chemical Physics. 2015, Vol. 142 Issue 1, p1-10. 10p. 4 Diagrams, 2 Charts, 7 Graphs. DOI: 10.1063/1.4904291.

Comprehensive large-scale assessment of intrinsic protein disorder. Walsh, Ian; Giollo, Manuel; Di Domenico, Tomás; Ferrari, Carlo; Zimmermann, Olav; Tosatto, Silvio C. E. Bioinformatics. Jan2015, Vol. 31 Issue 2, p201-208. 8p. DOI: 10.1093/bioinformatics/btu625.

Terazosin activates Pgk1 and Hsp90 to promote stress resistance. Chen, Xinping; Zhao, Chunyue; Li, Xiaolong; Wang, Tao; Li, Yizhou; Cao, Cheng; Ding, Yuehe; Dong, Mengqiu; Finci, Lorenzo; Wang, Jia-huai; Li, Xiaoyu; Liu, Lei. Nature Chemical Biology. Jan2015, Vol. 11 Issue 1, p19-25. 7p. 1 Diagram, 4 Graphs. DOI: 10.1038/nchembio.1657.

Heme binds to an intrinsically disordered region of Bach2 and alters its conformation. Watanabe-Matsui, Miki; Matsumoto, Takashi; Matsui, Toshitaka; Ikeda-Saito, Masao; Muto, Akihiko; Murayama, Kazutaka; Igarashi, Kazuhiko. Archives of Biochemistry & Biophysics. Jan2015, Vol. 565, p25-31. 7p. DOI: 10.1016/j.abb.2014.11.005.

Grease matrix as a versatile carrier of proteins for serial crystallography. Sugahara, Michihiro; Mizohata, Eiichi; Nango, Eriko; Suzuki, Mamoru; Tanaka, Tomoyuki; Masuda, Tetsuya; Tanaka, Rie; Shimamura, Tatsuro; Tanaka, Yoshiki; Suno, Chiyo; Ihara, Kentaro; Pan, Dongqing; Kakinouchi, Keisuke; Sugiyama, Shigeru; Murata, Michio; Inoue, Tsuyoshi; Tono, Kensuke; Song, Changyong; Park, Jaehyun; Kameshima, Takashi. Nature Methods. Jan2015, Vol. 12 Issue 1, p61-63. 3p. DOI: 10.1038/nmeth.3172.

Nuclear receptor full-length architectures: confronting myth and illusion with high resolution. Rastinejad, Fraydoon; Ollendorff, Vincent; Polikarpov, Igor. Trends in Biochemical Sciences. Jan2015, Vol. 40 Issue 1, p16-24. 9p. DOI: 10.1016/j.tibs.2014.10.011.

A Monte Carlo Method for Generating Side Chain Structural Ensembles. Bhowmick, Asmit; Head-Gordon, Teresa. Structure. Jan2015, Vol. 23 Issue 1, p44-55. 12p. DOI: 10.1016/j.str.2014.10.011.

Modulation of non-NMDA receptor gating by auxiliary subunits. Howe, James R. Journal of Physiology. Jan2015, Vol. 593 Issue 1, p61-72. 12p. DOI: 10.1113/jphysiol.2014.273904.

A guide to the crystallographic analysis of icosahedral viruses. McPherson, Alexander; Larson, Steven B. Crystallography Reviews. Jan-Apr2015, Vol. 21 Issue 1/2, p3-56. 54p. DOI: 10.1080/0889311X.2014.963572.

'Shooting gallery' for membrane proteins provides new insights into complexities of their function and structural dynamics. Martinac, Boris; Vandenberg, Jamie. Journal of Physiology. Jan2015, Vol. 593 Issue 2, p353-354. 2p. DOI: 10.1113/jphysiol.2014.286559.

Structural basis for sialic acid-mediated self-recognition by complement factor H. Blaum, Bärbel S; Hannan, Jonathan P; Herbert, Andrew P; Kavanagh, David; Uhrín, DuÅ¡an; Stehle, Thilo. Nature Chemical Biology. Jan2015, Vol. 11 Issue 1, p77-82. 6p. 3 Diagrams, 1 Graph. DOI: 10.1038/nchembio.1696.

Celebrating the past, looking to the future. Billinge, Simon J. L.; Miao, Jianwei. Acta Crystallographica. Section A, Foundations & Advances. Jan2015, Vol. 71 Issue 1, p1-2. 2p. DOI: 10.1107/S2053273314027685.

Structures from tiny crystals. Doerr, Allison. Nature Methods. Jan2015, Vol. 12 Issue 1, p37-37. 1p. DOI: 10.1038/nmeth.3238.

Direct phasing of protein crystals with high solvent content. He, Hongxing; Su, Wu-Pei. Acta Crystallographica. Section A, Foundations & Advances. Jan2015, Vol. 71 Issue 1, p92-98. 7p. DOI: 10.1107/S2053273314024097.

Oxidation Catalysis by Rationally Designed Artificial Metalloenzymes. Marchi-Delapierre, Caroline; Rondot, Laurianne; Cavazza, Christine; Ménage, Stéphane. Israel Journal of Chemistry. Jan2015, Vol. 55 Issue 1, p61-75. 15p. DOI: 10.1002/ijch.201400110.

Energy optimization of a regular macromolecular crystallography beamline for ultra-high-resolution crystallography. Rosenbaum, Gerd; Ginell, Stephan L.; Chen, Julian C.-H. Journal of Synchrotron Radiation. Jan2015, Vol. 22 Issue 1, p172-174. 3p. DOI: 10.1107/S1600577514022619.

A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Hagelueken, Gregor; Clarke, Bradley R; Huang, Hexian; Tuukkanen, Anne; Danciu, Iulia; Svergun, Dmitri I; Hussain, Rohanah; Liu, Huanting; Whitfield, Chris; Naismith, James H. Nature Structural & Molecular Biology. Jan2015, Vol. 22 Issue 1, p50-56. 7p. DOI: 10.1038/nsmb.2935.

The Amyloid Precursor Protein Shows a pH-Dependent Conformational Switch in Its E1 Domain. Hoefgen, Sandra; Dahms, Sven O.; Oertwig, Kathrin; Than, Manuel E. Journal of Molecular Biology. Jan2015, Vol. 427 Issue 2, p433-442. 10p. DOI: 10.1016/j.jmb.2014.12.005.

Upgrade of MacCHESS facility for X-ray scattering of biological macromolecules in solution. Acerbo, Alvin Samuel; Cook, Michael J.; Gillilan, Richard Edward. Journal of Synchrotron Radiation. Jan2015, Vol. 22 Issue 1, p180-186. 7p. DOI: 10.1107/S1600577514020360.

Structure of the immature HIV-1 capsid in intact virus particles at 8.8Å resolution. Schur, Florian K. M.; Hagen, Wim J. H.; Rumlová, Michaela; Ruml, TomáÅ¡; Müller, Barbara; Kräusslich, Hans-Georg; Briggs, John A. G. Nature. 1/22/2015, Vol. 517 Issue 7535, p505-508. 4p. DOI: 10.1038/nature13838.

Virus crystallography and structural virology: a personal perspective. Rossmann, Michael G. Crystallography Reviews. Jan2015, Vol. 21 Issue 1/2, p57-102. 46p. DOI: 10.1080/0889311X.2014.957282.



Book review: X Rays and Crystal Structure

     by W. H. Bragg and W. L. Bragg
     G. Bell and Sons, London, 1915.

This is the 100th anniversary of the publishing of this title and thus appropriate for January 2015. I found an original edition of it on Amazon for a reasonable price--about $40 including shipping from the UK. However, you can read the book in its entirety online by searching for "Bragg 1915" at Google Books. This book was published the year after the start of World War I and only three years after the discovery of X-ray diffraction by Max von Laue. It appeared about six months before W. L. Bragg (the son) was sent to France. While he was there, working out how to locate German artillery positions by "sound-ranging," he learned he had won the 1915 Nobel Prize with his father (W. H.). W. L. was 25 and is still the youngest Nobel Laureate in the sciences.

The preface was written by W. H. in 1914. Here he notes the publication of the book was delayed by "the times" and, as a result, he wrote the preface himself. It is not clear why; perhaps because he was the elder scientist. In the last paragraph, he states "I am anxious to make one point clear, viz., that my son is responsible for the 'reflection' idea which has made it possible to advance, as well as much the greater portion of the work of unraveling crystal structure to which the advance has led." This makes it very clear who Bragg's law nλ=2d sinθ is named after: W. L. Bragg.

Chapter 1 is an introduction to X-rays and provides a glimpse into the problem of the dual particle/wave nature of light (and X-rays) and how it was unresolved as of 1915; in fact, it would not be resolved until 1924 by de Broglie. The Braggs also provide an introduction to von Laue's work that showed that the wavelength of X-rays is on the same order of the distances between atoms in crystals so that ordered arrays behave like diffraction gratings. This provides the entrée to Chapter 2, Diffraction of Waves.

In Chapter 2, the Braggs describe using the wave theory of light, the diffraction of X-rays by a lattice of particles, deriving Bragg's law. Chapter 3 provides a discussion of the spectrometer W.H. used for measuring diffraction data, a device we would immediately recognize as a forerunner of the four circle diffractometer many of us used early in our careers. The authors use the term "spectra" to describe both the set of wavelengths that are emitted by a source and the reflections created when Bragg's law is satisfied.

Chapter 4 delves into the properties of X-rays, focusing primarily on the work by Barkla on absorption. The concept of scattering power is touched upon. It is worth noting that the concept of the scattering factor had not yet been applied to diffraction. Chapter 5 covers the concept of crystal structure in the classic sense of a macroscopic solid with well-defined faces that are unique for each compound. Six crystal systems are given, as trigonal and hexagonal are merged into one system, hexagonal. A brief description of symmetry is also provided.

Chapter 6 provides a detailed description of the then current state of knowledge regarding X-ray spectra. The relationship between wavelength and atomic number is developed. At the end of the chapter, the spectra for a source observed by diffraction from the diamond (111) reflection is shown and we clearly see the α1/ α2 split, the reason for which was not known at the time. The next chapters are the most interesting. Here, the Braggs develop crystal structure analysis. Chapters 7, 8 and 10 are "The Analysis of Crystal Structure," Parts 1, 2 and 3 respectively, with the intervening Chapter 9 titled "The Relation between Crystal Symmetry and the Arrangement of Atoms".

Chapter 7 starts off with a comparison of the structures of NaCl and KCl. The authors reach the conclusion that they are similar based on the metrics of the diffraction angles. The Braggs observe that the intensities of the 111 reflections for the two materials are related to the atomic weight of the atoms. In Chapter 8, the structures of the homologous series of carbonates MgCO3, CaCO3, MnCO3, FeCO3 and ZnCO3 are described and the Braggs solidify the relationship of scattering power to atomic weight: "We conclude that the alternate planes [Fe CO3] become equal in scattering power when their masses per unit area are equal".* Just two pages later, the idea of constructive and destructive interference is used to approximate the relationship of the intensities of the 100, 110 and 111 reflections of NaCl. This new information is used to solve the structure of FeS, which is rhombohedral, not cubic. Is this the first structure solved by phasing?

Chapter 9 describes the basics of symmetry. This is a necessary prelude to Chapter 10, which attempts to describe the structure of more complicated materials like SiO2, S8, Fe2O3, Al2O3 and some spinels. The temperature factor is described in Chapter 11, as is absorption as it applies to the diffracted radiation. The Braggs start to see the relationship between scattering angle and intensity, stating, "Possibly the scattering by a single atom depends on the angle of scattering, though this does not seem likely to account for the effect [inverse relationship between intensity and angle] which seems the same for all atoms. It is strange that no explanation is forthcoming of so simple and obvious an effect. It must certainly be answered if progress is not to be delayed." Clearly they had grasped the importance of the scattering factor but did not understand it yet. The final chapter is "The Analysis of Laue Photographs," which applies Bragg's law to the interpretation of Laue diffraction patterns.

In summary, what the Braggs knew at the beginning of 1915 was that X-rays were diffracted by the planes in a crystal lattice, the angle of the diffraction followed Bragg's law, the scattering power of a plane was proportional to the atomic weight, that the position of the atom in the unit cell affected the intensity of the reflection by changing the phase relationships, and temperature and absorption were effects that needed correction.

* The italics are theirs not mine.

Joseph D. Ferrara, Ph.D.    
Chief Science Officer    

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