Crystallography in the news

March 1, 2016. Wesleyan University conferred tenure to Associate Professor of Molecular Biology and Biochemistry Rich Olson, who employs X-ray crystallography to discover how otherwise benign bacteria transform into dangerous human pathogens.

March 2, 2016. University of Copenhagen's Department of Chemistry researchers have used X-ray crystallography to shed light on the lytic polysaccharide monooxygenases (LPMOs) enzymes' interaction with cellulose. In order to do this, the cellulose fragments needed to be bound into crystals of the enzyme.

March 8, 2016. The Protein Society, the premiere international society dedicated to supporting protein research, announces the winners of The 2016 Protein Society Awards. The awards will be conferred at the 30th Anniversary Symposium of The Protein Society (July 16-19, 2016, Baltimore, Maryland USA).

March 11, 2016. The Royal Society of Chemistry undertook a survey to gauge public attitudes in the UK towards chemistry. The survey revealed that the public in general was somewhat ambivalent to chemistry and was unable to link chemistry with positive examples of its application.

March 15, 2016. Concern about the overall employment picture for chemical professionals in the US has prompted the American Chemical Society (ACS) to examine the issue, under the direction of president Donna Nelson. When Nelson was running for ACS president in 2014, she sent emails to members asking which issues mattered most to them. The 1500 responses she received confirmed that jobs are the biggest concern for ACS members.

March 15, 2016. In experiments carried out partly at the Department of Energy's SLAC National Accelerator Laboratory, scientists from the University of California, San Francisco have determined in atomic detail how a potential drug molecule fits into and blocks a channel in cell membranes that Ebola and related "filoviruses" need to infect victims' cells.

March 15, 2016 Enrico Di Cera, M.D., chair of biochemistry and molecular biology at Saint Louis University, is an author of a new paper that says that the Structural Biology Grid Consortium has developed a repository, the Structural Biology Data Grid, to deposit, search and download structural biology data sets. In the current study, researchers found that the repository was effective in allowing researchers to reproduce earlier findings, letting work in the field progress.

March 17, 2016. Scientists at UC Berkeley from the Komeili lab, along with collaborators in the Hurley and Chang groups, have now shown that a bacterial protein called MamO has been transformed from a common protease to an inactive enzyme that helps to build magnetic nanoparticles using a novel metal-binding motif.

March 17, 2016. Warmest congratulations to Tracy Clinton and Michael Thompson, the recipients of the Protein Society's Year 2015 "Best Paper" awards.

March 21, 2016. Researchers at the University of Copenhagen have discovered a previously unknown weakness; an "Achilles heel", of bacteria. Their discovery, of a long-lifetime proton pump leak state, a crucial step in bacteria''s energy metabolism, may be the first step in developing an entirely novel form of antibiotics.

Crystallographers in the spotlight

Before it became a medicine – In a series of 3 videos, Pfizer describes what goes on behind the scenes in a pharmaceutical company.

Will Somers, VP of Global Biotherapeutic Technologies at Pfizer and renowned structural biologist, is one of the speakers in the video series.

For more about the Pfizer three part series.

The Carl Brändén Award

The Carl Brändén Award, sponsored by Rigaku Corporation, honors an outstanding protein scientist who has also made exceptional contributions in the areas of education and/or service to the field. The 2016 recipient of this award is Dr. Gary Pielak (University of North Carolina at Chapel Hill). Dr. Pielak is a long-standing member of the Protein Society and has served as conference organizer twice. The former Rotating Program Director of the National Science Foundation has advanced the field of protein chemistry through pioneering research in unraveling protein biophysics in living cells. Dr. Pielak and his students developed innovative quantitative techniques to measure protein stability and diffusion in crowded samples that interfere with standard measurement techniques. He has also made major advances in elucidating how the intracellular environment impacts both globular and intrinsically disordered proteins in surprising ways. Dr. Pielak has revolutionized our understanding of how proteins work where they actually function—inside cells—and not in the artificial environment of the test tube.

The award will be conferred at the 30th Anniversary Symposium of the Protein Society (July 16-19, 2016, Baltimore, Maryland USA).

Product spotlight: XtaLAB mini

The Rigaku XtaLAB mini 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 will enhance research productivity by offering affordable structure analysis capability without the necessity of relying on a departmental facility. With the XtaLAB mini, 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.

The XtaLAB mini is controlled by CrysAlis^Pro software, one of the most popular data collection and processing packages. CrysAlis^Pro is often referred to as "user-inspired software". Rigaku Oxford Diffraction's software team makes a concerted effort to incorporate features and areas of functionality based on our customers' ideas and feedback.

For more about the XtaLAB mini.

Lab in the spotlight

Anna Marie Pyle
William Edward Gilbert Prof of Molecular,
Cellular & Developmental Biology
Investigator Howard Hughes Med Inst
Prof Chemistry, Yale University

The Pyle laboratory uses a diverse set of biochemical and biophysical techniques, including crystallography and chemical probing, to understand the structural complexity of RNA architecture. Dr. Pyle pioneered the study of RNA helicase enzymes and other RNA-stimulated ATPases that serve as translocases, RNA remodeling enzymes, folding cofactors and signaling enzymes in the cell. Her experimental work is complemented by efforts to develop new computational tools for modeling, analyzing and predicting RNA structure.

Useful link: Discrete RNA Libraries from Pseudo-Torsional Space

Author: Elisabeth Humphris
Description: Libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone.
Reference: Humphris E and Pyle AM. Discrete RNA Libraries from Pseudo-Torsional Space. J Mol Biol,(2012).
Download: RNA Libraries

Use of Multiple Cryoprotectants to Improve Diffraction Quality from Protein Crystals. Miki Senda; Takeru Hayashi; Masanori Hatakeyama; Koh Takeuchi; Sasaki, Atsuo T.; Toshiya Senda. Crystal Growth & Design. Mar2016, Vol. 16 Issue 3, p1565-1571. 7p. DOI: 10.1021/acs.cgd.5b01692.

Identification of a novel cell death-inducing domain reveals that fungal amyloid-controlled programmed cell death is related to necroptosis. Daskalov, Asen; Habenstein, Birgit; Sabaté, Raimon; Berbon, Mélanie; Martinez, Denis; Chaignepain, Stéphane; Coulary-Salin, Bénédicte; Hofmann, Kay; Loquet, Antoine; Saupe, Sven J. Proceedings of the National Academy of Sciences of the United States of America. 3/8/2016, Vol. 113 Issue 10, p2720-2725. 6p. DOI: 10.1073/pnas.1522361113.

Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase. Im, Ha Na; Kim, Hyoun Sook; An, Doo Ri; Jang, Jun Young; Kim, Jieun; Yoon, Hye-Jin; Yang, Jin Kuk; Suh, Se Won. Journal of Structural Biology. Mar2016, Vol. 193 Issue 3, p172-180. 9p. DOI: 10.1016/j.jsb.2016.01.002.

ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses. Ming-Yan Cheung; Xiaorong Li; Rui Miao; Yu-Hang Fong; Kwan-Pok Li; Yuk-Lin Yung; Mei-Hui Yu; Kam-Bo Wong; Zhongzhou Chen; Hon-Ming Lam. Proceedings of the National Academy of Sciences of the United States of America. 3/8/2016, Vol. 113 Issue 10, p2648-2653. 6p. DOI: 10.1073/pnas.1522966113.

Sensitivity of lysozyme crystallization to temperature variation. Liu, Yong-Ming; Li, Hai-Sheng; Wu, Zi-Qing; Chen, Rui-Qing; Lu, Qin-Qin; Guo, Yun-Zhu; Zhang, Chen-Yan; Yin, Da-Chuan. CrystEngComm. 3/7/2016, Vol. 18 Issue 9, p1609-1617. 9p. DOI: 10.1039/c6ce00060f.

Cisplatin encapsulation within a ferritin nanocage: a high-resolution crystallographic study. Pontillo, Nicola; Pane, Francesca; Messori, Luigi; Amoresano, Angela; Merlino, Antonello. Chemical Communications. 3/18/2016, Vol. 52 Issue 22, p4136-4139. 4p. DOI: 10.1039/c5cc10365g.

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase. Schneider, Lisa K.; Einsle, Oliver. Biochemistry. 3/15/2016, Vol. 55 Issue 10, p1433-1440. 8p. DOI: 10.1021/acs.biochem.5b01278.

Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine. Balaev, Vladislav V.; Lashkov, Alexander A.; Gabdulkhakov, Azat G.; Dontsova, Maria V.; Seregina, Tatiana A.; Mironov, Alexander S.; Betzel, Christian; Mikhailov, Al'bert M. Acta Crystallographica: Section F, Structural Biology Communications. Mar2016, Vol. 72 Issue 3, p224-233. 9p. DOI: 10.1107/S2053230X1600162X.

Structure of Thermobifida fusca DyP-type peroxidase and activity towards Kraft lignin and lignin model compounds. Rahmanpour, Rahman; Rea, Dean; Jamshidi, Shirin; Fülöp, Vilmos; Bugg, Timothy D.H. Archives of Biochemistry & Biophysics. Mar2016, Vol. 594, p54-60. 7p. DOI: 10.1016/j.abb.2016.02.019.

Folding of Protein L with Implications for Collapse in the Denatured State Ensemble. Maity, Hiranmay; Reddy, Govardhan. Journal of the American Chemical Society. 3/2/2016, Vol. 138 Issue 8, p2609-2616. 8p. DOI: 10.1021/jacs.5b11300.

Quaternary Structure of Fur Proteins, a New Subfamily of Tetrameric Proteins. Pérard, Julien; Covès, Jacques; Castellan, Mathieu; Solard, Charles; Savard, Myriam; Miras, Roger; Galop, Sandra; Signor, Luca; Crouzy, Serge; Michaud-Soret, Isabelle; de Rosny, Eve. Biochemistry. 3/15/2016, Vol. 55 Issue 10, p1503-1515. 13p. DOI: 10.1021/acs.biochem.5b01061.

An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding. Melchior, John T.; Walker, Ryan G.; Morris, Jamie; Jones, Martin K.; Segrest, Jere P.; Lima, Diogo B.; Carvalho, Paulo C.; Gozzo, Fábio C.; Castleberry, Mark; Thompson, Thomas B.; Davidson, W. Sean. Journal of Biological Chemistry. 3/4/2016, Vol. 291 Issue 11, p5439-5451. 13p. DOI: 10.1074/jbc.M115.706093.

Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research. Sousa, Bruno L.; Silva-Filho, José C.; Kumar, Prashant; Graewert, Melissa A.; Pereira, Ronniery I.; Cunha, Rodrigo M.S.; Nascimento, Kyria S.; Bezerra, Gustavo A.; Delatorre, Plánio; Djinovic-Carugo, Kristina; Nagano, Celso S.; Gruber, Karl; Cavada, Benildo S. International Journal of Biochemistry & Cell Biology. Mar2016, Vol. 72, p27-39. 13p. DOI: 10.1016/j.biocel.2015.12.016.

Synthesis, X-ray crystal structure, DNA/protein binding and DNA cleavage studies of novel copper(ii) complexes of N-substituted isatin thiosemicarbazone ligands. Muralisankar, Mathiyan; Bhuvanesh, Nattamai S. P.; Sreekanth, Anandaram. New Journal of Chemistry. Mar2016, Vol. 40 Issue 3, p2661-2679. 19p. DOI: 10.1039/c5nj02806j.

A Pore Idea: the ion conduction pathway of TMEM16/ANO proteins is composed partly of lipid. Whitlock, Jarred; Hartzell, H. Pflugers Archiv European Journal of Physiology. Mar2016, Vol. 468 Issue 3, p455-473. 19p. DOI: 10.1007/s00424-015-1777-2.

Membranes on nanopores for multiplexed single-transporter analyses. Urban, Michael; Tampé, Robert. Microchimica Acta. Mar2016, Vol. 183 Issue 3, p965-971. 7p. DOI: 10.1007/s00604-015-1676-4.

Book review:

This month I read two memoirs from physicians: Oliver Sacks, a neurologist who lived a long life, and Paul Kalanthi, a neurosurgeon who barely finished his residency, both of whom passed away last year.

On the Move: A Life by Oliver Sacks, Knopf, New York City, 2015, 416 pages, ISBN: 978-0385352543.

I remember when Sacks' book Awakenings came out in 1973. I was not old enough to read it, but my mother, who was also a physician practicing in New York City, talked about it with great respect at the dinner table. While I have read other books by him, I have still not read Awakenings (although I know I should).

On the Move came out 4 months before Sacks passed away due to a metastasized ocular melanoma in August 2015. The author describes his late childhood and early teens, his coming out, his study of medicine, and his love of motorcycles. He traces his path from Oxford to Montreal to San Francisco to Los Angeles and finally to New York City. He details his compassion for his patients as a neurologist and his ability to tell stories both through his expository writing and this autobiography. There are many interesting anecdotes; for example, his squat record at Muscle Beach in the early 60s and the time he strapped a dying patient to his bike to show her the sunrise at the Grand Canyon. It was his time at Beth Abraham in New York that allowed him to treat patients with post-encephalitic disease with L-dopa and led to his rise to fame. The book ends only eight months before his death, offering a nearly complete autobiographical portrait. This book has some explicit descriptions and I would not recommend it for youngsters.

When Breath Becomes Air by Paul Kalanithi, Random House, New York, 2016, 256 pages, ISBN: 978-0812988406.

Paul Kalanithi was a resident neurosurgeon at Stanford Medical Center. He died March 9, 2015 of stage IV metastatic lung cancer. The prologue describes his first inkling that he might be sick, even though his tests came back negative. The first chapter then jumps backward in time, describing his youth moving from Bronxville, New York to Kingman, Arizona with his family and growing up in this forgotten valley; his days as an undergrad at Stanford; a year at Cambridge; and medical school at Yale where he met his wife, Lucy. After medical school they took residency positions in the Bay area: he at Stanford, she at USCF. Paul specialized in neurosurgery and started his residency at Stanford. The second chapter details the progression of his cancer and his daughter's birth. He officially completed his residency, but could not attend the ceremony because he was too ill. As his health declined, he began writing the book and completed it as best he could. Lucy provides the final chapter, written posthumously.

Review by Joseph D. Ferrara, Ph.D.
Chief Science Officer, Rigaku