Monthly Archives: February 2016

Vitaly Citovsky

Bar-Ziv, A., Levy, Y., Citovsky, V., & Gafni, Y. (2015). The Tomato yellow leaf curl virus (TYLCV) V2 protein inhibits enzymatic activity of the host papain-like cysteine protease CYP1. Biochem. Biophys. Res. Comm. 460, 525-529.

Lacroix, B. & Citovsky, V. (2015) Genetically modified organisms, plant transformation by Agrobacterium. In Discoveries in Modern Science: Exploration, Invention, Technology (J. Trefil, ed.), Farmington Hills: Macmillan, pp. 425-431.

Yuan, C., Lazarowitz, S.G., & Citovsky, V. (2015) Identification of a functional plasmodesmal localization signal in a plant viral cell-to-cell movement protein. mBio 7, e02052-15.

Lacroix, B. & Citovsky, V. (2015) Nopaline-type Ti plasmid of Agrobacterium encodes a VirF-like functional F-box protein. Sci. Rep. 5, 16610.

García-Cano, E., Magori, S., Lazarowitz, S.G., & Citovsky, V. (2015) Interaction of Arabidopsis trihelix-domain transcription factors VFP3 and VFP5 with Agrobacterium virulence protein VirF. PLOS ONE 10, e014212.

Nancy Hollingsworth

Liu, Y., W. Gaines, T. Callender, V. Busygina, A. Oke, P. Sung, J. Fung and N. M. Hollingsworth (2014) Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks.  PLoS Genet.  10:e1004005 doi:10.1371/journalpgen.1004005

Suhandynata, R., J. Liang, C. P. Albuquerque, H. Zhou and N. M. Hollingsworth (2014) A method for sporulating budding yeast cells that allows for unbiased identification of kinase substrates using stable isotope labeling by amino acids in cell culture.  G3 4: 2125-2135.

Chen, X., R. T. Suhandynata, R. Sandhu, B. Rockmill, N. Mohibullah, H. Niu, J. Liang, H-C Lo, D. E. Miller, H. Zhou, G. V. Börner, and N. M. Hollingsworth.  (2015) Phosphorylation of the synaptonemal complex protein Zip1 regulates the crossover/noncrossover decision during yeast meiosis.  PLoS Biol 13(12): e1002329. doi: 10.1371/journal.pbio.1002329

Hollingsworth, N. M. (2016) Mek1/Mre4 is a master regulator of meiotic recombination in budding yeast.  Microbial Cell (in press).

Hulin Li

Sun J, Yuan Y, Stillman B, C Speck, Li H. Structure and Function of Replication Initiation Factors. 2016, pp 427-441, Chapter 21 in “The Initiation of DNA Replication in Eukaryotes”, Edited by Daniel Kaplan, published by Springer 2016.

1. Bai L, Hu K, Wang T, Jastrab JB, Darwin KH, Li H.  Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A, in print.2. Yuan Z, Bai L, Sun J, Georgescu R, Liu J, O’Donnell ME, Li H. Atomic structure of the eukaryotic replicative CMG helicase by cryo-EM and implication to DNA unwinding, Nat Struct Mol Biol. 2016 Feb 8. doi: 10.1038/nsmb.3170
3.Liu W, Tarawa M, Xin H, Wang T, Emamy H, Li H, Yager KG, Starr FW, Tkachenko AV, Gang O. Diamond family of nanoparticle superlattices. Science, 2016 Feb 5;351(6273):582-6. doi: 10.1126/science.aad2080.
4. Tian Y, Zhang Y, Wang T, Li H, Gang O. Lattice Engineering via Nanoparticle-DNA Frameworks. Nature Materials, 2016 Feb 22. doi: 10.1038/nmat4571.
5. Eswaramoorthy S, Sun J, Li H, Singh BR, Swaminathan S. Molecular Assembly of Clostridium botulinum progenitor M complex of type E. Scientific reports. 2015; 5:17795.6. Sun J, Shi Y, Georgescu RE, Yuan Z, Chait BT, Li H, O’Donnell ME. The Architecture of a Eukaryotic Replisome. Nat Struct Mol Biol. 2015; 22(12):976-82.
7. Yu H, Takeuchi M, LeBarron J, Kantharia J, London E, Bakker H, Haltiwanger RS, Li H, Takeuchi H. Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Nat Chem Biol. 2015 Nov;11(11):847-54.
8. Chang F, Riera A, Evrin C, Sun J, Li H, Speck C, Weinreich M. Cdc6 ATPase activity disengages Cdc6 from the pre-replicative complex to promote DNA replication. Elife. 2015 Aug 25;4.
9. Werneburg G, Henderson NS, Portnoy EB, Sarowar S, Hultgren SJ, Li H, and Thanassi DG. The Pilus Usher Uses Domain Masking to Control Protein-Protein Interactions During Pilus Biogenesis and Functions as an Oligomer In Vivo. Nat Struct Mol Biol., 2015 Jul;22(7):540-6.
10. Jastrab JB, Wang T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Chatterjee C, Ovaa H, Gygi SP, Li H, and Darwin KH. An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2015, 112, E1763-72.
11. Tian Y, Wang T, Liu W, Xin H, Li H, Ke Y, Shih W, Gang O. Mesoscale 3D Nanoparticle Clusters with Prescribed Architectures. Nature Nanotechnology 2015 Jul;10(7):637-44
12. Sun J, Fernandez-Cid A, Riera A, Zuanning Yuan, Stillman B, Speck C, Li H. Structural and mechanistic insights into licensing of DNA replication. Genes Dev, 2014, 28, 2291-303.
13. Samel SA, Fernández-Cid A, Sun J, Riera A, Tognetti S, Herrera MC, Li H, Speck C. A unique DNA entry gate serves for regulated loading of the eukaryotic replicative helicase MCM2-7 onto DNA. Genes Dev. 2014, 28, 1653-66.
14. Burgie ES, Wang T, Bussell AN, Walker JM, Li H, Vierstra RD. Crystallographic and electron microscopic analyses of Deinococcus radiodurans phytochrome reveal a large-scale reorientation of the output module relative to the sensory module during photoconversion. J Biol Chem. 2014, 289, 24573-24587.
15. Sanson B, Wang T, Sun J, Wang L, Kaczocha M, Ojima I, Deutsch D, Li H. Crystallographic study of FABP5 as an intracellular endocannabinoid transporter. Acta Crystallogr D Biol Crystallogr. 2014, 70, 290-8.

 

Erwin London

Lin, Q., and London, E. (2015) Lin “Ordered Raft Domains Induced by Outer Leaflet Sphingomyelin in Cholesterol-Rich Asymmetric Vesicles” Biophys. J., 108, 2212-2022.

London, E. (2015) “Membrane Fusion: A New Role For  Membrane Domains?” Nature Chemical Biology, 11, 383 – 384.

Farnoud, A, Toledo, A.M., Konopka J.B., Del Poeta, M., London, E. (2015) “Raft-Like Membrane Domains in Pathogenic Microorganisms”, Current Topics in Membranes, Volume 75 “Membrane Domains” (A. Kenworthy, Editor), Academic Press/Elsevier, Amsterdam, pages 233-268.

Lin, Q., Wang, T., Li. H, and London, E. (2015) “Decreasing Transmembrane Segment Length Greatly Decreases Perfringolysin O Pore Size”, J. Memb. Biol. 248, 517-527.

Kim, J., and London, E. (2015) “Using sterol substitution to probe the role of membrane domains in membrane functions” Lipids 50, 721-734.

Pathak, P. and London, E. (2015) “Effect of Membrane Lipid Composition Upon the Formation of Ultra-Nanodomains”, Biophys. J., 109, 1630-1638.

Yu, H., Takeuchi, M., LeBarron, J., Kantharia, J., London, E., Bakker, H., Haltiwanger, R.S., Li, H., Takeuchi, H. (2015) “Structures of a Notch-modifying xylosyltransferase support an SNi-like retaining mechanism”, Nature Chemical Biology, 11,847-854.

Aaron Neiman

Jin, L., Zhang, K., Xu, Y., Sternglanz, R., Neiman, A.M. (2015).  Sequestration of mRNAs Modulates the Timing of Translation during Meiosis in Budding Yeast.  Mol Cell Biol. 35:3448-3458.

Park, J.-S., Halegoua, S., Kishida, S., and Neiman, A. M. (2015).  A conserved function in phosphatidylinositol metabolism for mammalian Vps13 family proteins.  PLoS One, 10:e0124836

 Jin, L. and Neiman, A. M. (2015) Post-transcriptional regulation in budding yeast meiosis Curr Genet. epub 17Nov

Lonnie Wollmuth

Alsaloum, M., R. Kazi, Q. Gan, J. Amin, and P. Wollmuth (2016) A molecular determinant of subtype-specific desensitization in ionotropic glutamate receptors. Journal of Neuroscience. In press.

Gan, Q., Dai, H-X. Zhou, and L. P. Wollmuth (2016) The transmembrane domain mediates tetramerization of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Journal of Biological Chemistry. In press.

Gan, Q., C. L. Salussolia, and P. Wollmuth (2015) Assembly of AMPA receptors: mechanisms and regulation. The Journal of Physiology. Invited review. 593:39-48.

Wollmuth, L. P (2015) Is cholesterol good or bad for your brain? – NMDARs have a say. The Journal of Physiology. Invited commentary.

Salussolia, C. L., Q. Gan, and P. Wollmuth (2015) Assaying AMPA receptor oligomerization. In: Ionotropic glutamate receptor technologies, G. Popescu, editor.  Humana Press.  Volume 106:3-14.

Kazi, R., M. Daniel, and P. Wollmuth (2015) Characterizing the thermodynamics of NMDA receptor pore opening. In: Ionotropic glutamate receptor technologies, G. Popescu, editor.  Humana Press.  Volume 106:145-162.

2015 Departmental Roster

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Faculty

Paul Bingham

Deborah Brown

David Bynum

Vitaly Citovsky

Kevin Czaplinski

Neta Dean 

Dale Deutsch 

Raafat M. El-Maghrabi 

Jarrod French 

Liang Gao

Peter Gergen

Steven Glynn

Yussuf A. Hannun

Bernadette Holdener

Nancy Hollingsworth

Martin Kaczocha

Wali Karzai

Sasha Levy

Huilin Li 

Erwin London

Edward Luk 

Harvard Lyman

Kenneth Marcu

Benjamin Martin

David Matus 

Aaron Neiman

Nisson Schechter

Keith Sheppard

Sanford Simon

Steven Smith

Rolf Sternglanz

Gerald Thomsen

Lonnie Wollmuth

 

Administrative Staff

 

 

Postdocs and Research Scientists

Jamie Blundell

Yuanheng Cai

Tracy Callender

Xiangyu Chen

Mathew Dunn

Elena Garcia-Cano

William Gillis

R. Antonio Herrera

Yasuno Iwaaki

Shinako Kakuda

Yakov Ido Keren

Naoki Kimata

Benoit Lacroix

Guangtao Li

Preeti Mehta

Sivan Osenberg

Anne Ostermeyer-Fay

Jae-Sook Park

Richard Row

Lihong Wan

Renhong Wu

Xiaohong Yu

Cheng Yuan

Xiaofeng Zhang

Martine Ziliox

 

Technical Staff

Gregory Rudomen, Director of Laboratories

Christy Au

Brian Benz

Teddy Betts

Neal Bhattacharji

Cameron Burnett

Shijun Cheng

Michael Dahan

Jasbir Dalal

Christy Felice

Danielle J. Francois

Rich Grady

Hao Chi Hsu

Regina Kim

Daniel Labuz

Dana L. Laikhram

Allison Marullo

Luke McGoldrick

Leor Needleman

Benjamin Rajan

Dhruv Nitin Ray

Sade Seidu

Joseph Sweeny

Megumi Takeuchi

Sara Tewksbury

Liqun Wang

Huijun Yang

Wan Zhang

Kai Zheng

 

Visiting Scholars/Scientists

Patricia Bossert

Hyewon Chung

Richard Elinson

Hagit Hak

Sondra Lazarowitz

Irfan Sadiq

Luyao Wang

Michael Yoder

Ping Zhu

 

Volunteers and Affiliates

Kafi Belfon

Shaun Charkowick

Daniel Chen

Jenny Gan

Kristie Haman

Scott Lew

Sarah Lewis

Robert Morabito

David Matus recognized as NCI Scientist of the Month

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Evolutionary developmental biologist David Q. Matus, Ph.D., is an assistant professor in the Biochemistry and Cell Biology Department at Stony Brook University in New York. He is interested in cellular invasion, a behavior observed in some normal cells during development and a hallmark of metastatic cancer cells.

Dr. Matus began his scientific career—and met his wife, Deirdre, also a biomedical scientist—while training dolphins in Hawaii as part of an internship on dolphin cognition. He decided to stay at University of Hawaii for graduate school, studying gene networks in sea anemones in the lab of Mark Q. Martindale, Ph.D.

 

See More: http://www.cancer.gov/research/nci-role/spotlight/profiles/david-matus

SBU Wins $1.4 Million NIH Grant to Support Underrepresented Undergrad and Doctoral Researchers 

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STONY BROOK, N.Y., August 29, 2014 – Stony Brook University’s (SBU) Center for Inclusive Education (CIE) has been awarded a $1.4 million grant from the National Institutes of Health (NIH) for its Initiative for Maximizing Student Development (IMSD) program. The grant will help increase the number of underrepresented individuals completing undergraduate and doctoral degrees in the biomedical sciences, further supporting SBU’s efforts in expanding and diversifying its undergrad and graduate programs. This grant marks the fifth high visibility, and competitive, award received by the CIE totaling $8.5 million in funds and support for 165 students and postdoctoral scholars.

“The center’s receipt of this $1.4 million grant from the NIH is indicative of their success in integrating research, education and professional development for underrepresented students in the biomedical sciences, “ said Provost and Senior Vice President for Academic Affairs, Dennis N. Assanis. “It will further enable us to provide the programming and resources necessary for these students to transition through the pipeline and, working with our world-renowned faculty, foster the inter-generational transmission of knowledge and skills needed for ground-breaking research and discovery.”

The IMSD project had been named MERGE: Maximizing Excellence in Research and Graduate Education (IMSD-MERGE). Over the next five years IMSD-MERGE will provide direct financial support to 50 scholars in the biomedical sciences: 25 undergraduates and 25 doctoral fellows. In addition to this direct research support, IMSD-MERGE will provide more broadly accessible academic enrichment services, constructive mentoring experiences, and rigorous professional development to SBU’s academic community. IMSD-MERGE welcomed its first cohort of 10 scholars this summer.

“The IMSD-MERGE program brings to Stony Brook innovative initiatives that will fortify efforts already underway to address critical junctures in student’s educational experiences. IMSD-MERGE will bolster student’s confidence, capacity, and comprehension of the research endeavor to prepare them for careers as research scholars and faculty,” said Dr. Peter Gergen, Professor of Biochemistry and Director of Undergraduate Biology who is the Principal Investigator and Project Director of IMSD MERGE.

IMSD-MERGE will introduce several new efforts at SBU including:

  • A Summer Heads Up Program for incoming students to help prepare them for courses required of their programs. The two-week immersion program offers activities that demand critical reading of scientific literature.
  • A Bio-Math learning center for undergraduate students to provide academic enrichment support to freshman and sophomore biomedical science majors and bolster their proficiency in their calculus prerequisite courses.
  • Entering Mentoring workshop for undergraduates, graduates, and faculty. They will participate in workshop sessions developing their communication skills, listening ability, and mentoring capacities.

“What sets IMSD-MERGE apart from other projects at Stony Brook is its dual focus on advancing the research and academic talents of both undergraduate and graduate students,” said Stony Brook University President Samuel L. Stanley Jr., MD. “With IMSD-MERGE, we are truly reaching across the campus community, including students and faculty alike, giving everyone opportunities to strengthen their skills as scholars, researchers, and mentors.”

Nina Maung-Gaona, CIE Director and Assistant Dean for Diversity in the Graduate School, as well as Co-Principal Investigator on the project adds, “With the ISMD-MERGE project, the CIE is both enhancing the quality of support it provides to our graduate scholars and expanding our community to include a larger number underrepresented researchers at the undergraduate level. By connecting these two, often separated campus groups, we are strengthening the transformative research relationships between students and faculty and creating a seamless pipeline.”

As mentioned, this grant is one of five received by the CIE that help increase the competitiveness and progression of the underrepresented scholars. Other grants include a five-year $ 3.3 million grant from the NIH’s National Institute of General Medical Sciences (NIGMS) and a $1.4 million grant from the National Science Foundation

For more information visit the Center for Inclusive Education website: http://www.stonybrook.edu/cie.

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Alida Almonte
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631-632-6310
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MCB-BSB (PhD Program)

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The Molecular and Cellular Biology (MCB) and the Biochemistry and Structural Biology (BSB) programs continue to do well. Erwin London started his ninth year as Director of BSB, while Wali Karzai started his fourth year at the helm of MCB. In the Fall 2015 class, we had 10 new students entering the MCB program and 6 new students entering the BSB program.

The MCSB training grant students for 2015-2016 are MCB students Matthew Elmes, Eric Paulissen, Matthew Simons and Gregory Carbonetti and BSB students Johnna St. Clair and Roger Shek.   Andreyah Pope was chosen to be an affiliate of the training grant (a participant in training grant activities but with financial support from other grants).   Jinelle Wint and Andreyah Pope were chosen to participate in IMSD-Merge, an NIH funded program for underrepresented minorities.  Joe Matarlo (BSB) was awarded a Turner Dissertation Fellowship.

The speaker at this year’s Student Invited Seminar, organized by Neha Puri and Michael Tramantano, was Craig Townsend from Johns Hopkins University.   His talk was entitled “Biosynthesis of b-Lactam Antibiotics and the Force of Convergent Evoluntion”.

The MCB program held its annual Second Year Student Symposium in June at the Hilton Garden Inn. Second year students were given their opportunity hone their presentation skills and showcase the research work to their colleagues and MCB program faculty.

The annual MCB-BSB retreat was held in September at the very scenic Lombardi’s on the Sound. Several MCB and BSB faculty were invited to speak and present their work. Speakers included Brian Sheridan, Dave Matus, Mark Bowen, Jiang Chen, and Steve Glynn. All 4th year MCB and BSB students presented their posters, which generated much interest among the attendees. Best poster awards at the retreat were given to Kuan Hu and Anthony Rampello.  Matt Elmes, Matt Simons, Greg Carbonetti, and Johnna St. Clair received awards for outstanding service to the MCB and BSB graduate programs.

Both MCB and BSB students attended a symposium on “Life Science Career Choices- Beyond Tenured Track Research” at the campus Hilton Garden Inn.  The speakers were Michael Rosconi, Senior Scientist Regeneron Pharmaceutical, Gregory Caputo, Chair Department of Chemistry Rowan University.  Paul Meers, Rutgers University, Franklin Abrams, Patent Attorney, Susan Malenbaum, Associate Director at Boehringer Ingelheim, and Juanita Sharpe, Assistant Vice Provost, Virginia Commonwealth University.   They discussed their career paths spanning faculty life in a University with an emphasis on teaching, to the biotechnology industry to patent law, to University administration.  Students had an opportunity for both questions and extended discussion at a reception after the meeting.

 

Wali Karzai, MCB Program Director & Erwin London, BSB Program Director

 

Master of Science Graduate Program BCB

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The Biochemistry and Cell Biology MS program hit its fifth year mark in 2014. We are proud of our students, faculty, and alumni for their efforts in making our BCB MS program a success.  We measure success by the quality of training our students attain, by the productivity our students bring to the labs in which they perform research, and by their ability to get .  This year, which reflects our overall five-year average, 90% of our graduates completed their MS in three semesters and were accepted in Ph.D., MD or DDS programs.  This cohort of ten students represents our largest graduating class yet. Half of the these students will continue doctoral research in Ph.D. programs at Cornell, Stony Brook, , and Bloomington.  We also congratulate three of our 2014 graduates who are off to Medical School.

This year’s incoming class of nine promises to be equally successful.  These students are currently performing research in areas spanning Biochemistry, Cell Biology, Biochemistry, Genetics, and Neurobiology, in labs at Stony Brook, Brookhaven, and Cold Spring Harbor. The enthusiasm of our faculty to recruit BCB MS students is a testament to the quality of this program. We have outstanding faculty who are committed to training outstanding students.  Our mission is to provide students with a fundamental theoretical and practical understanding of biochemistry and cell biology, that will prepare them for opportunities in real life sciences.

Neta Dean, Program Director

Institute for Stem Education

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The Center for Science and Mathematics Education (CESAME), which is housed in the Biochemistry Department, was founded by David Bynum in 2007, and has grown to become a national leader in STEM education research, teacher education, and community outreach. CESAME has been an incubator of innovative, interdisciplinary STEM education collaborations with the university and its surrounding communities. CESAME is now directed by Biochemistry and Cell Biology faculty member Keith Sheppard. CESAME has made notable contributions to STEM teaching, research, and policy at the university since 2007 including: • Generating over $ 7.5M in external grant funding. • Hiring three new tenure-track faculty members (Keith Sheppard, Angela Kelly and Ross Nehm) who collectively produce substantial amounts of high-impact discipline-based science education research; additionally, there are 10 affiliated faculty members in 8 STEM departments, 4 instructors and 3 administrative staff. • Creating a Ph.D. Program in Science Education in 2010, which currently enrolls 35 students. Doctoral courses were offered at Stony Brook Manhattan for the first time this year. • Faculty are active in state and national STEM educational policy activities, serving on editorial boards, writing policy statements, serving on advisory panels, meeting with key state leadership staff, and testifying at state-level education commissions. CESAME is a major provider of high quality STEM Teacher Education: • Offering a full complement of B.S. and M.A.T. programs in all STEM education fields and is one of the major producers of STEM teachers in the state. • Developing 24 graduate courses, of which 21 are currently active, and 7 undergraduate courses. • CESAME recently became the regional hub for the New York State Science and Mathematics Master Teacher program CESAME is a leading provider of high quality STEM outreach and student support: • CESAME has awarded $4.4M in fellowships and scholarships to post-doctoral, graduate, undergraduate, and high school students who have been actively involved in research or teaching in STEM disciplines. • Over 5,500 students attend our Teaching Labs annually; 85% of Long Island school districts have participated. Labs are offered in biology, geoscience, chemistry, sustainable chemistry and physics. Summer camps are offered in all disciplines of sciences, mathematics, and engineering. • CESAME sponsors Science Open Nights for the public and the annual Celebration of Undergraduate Research and Creative Activity. • CESAME has established research and professional development partnerships with the wider scientific community at Cold Spring Harbor Laboratories, Brookhaven National Laboratories, STEM Hub, American Museum of Natural History New York Botanical Garden, as well as NYS schools and community colleges. • CESAME annually hosts the Protein Modeling Challenge for regional high schools and also North American Computational Linguistics Olympiad.

Mechanism That Unwinds DNA May Function Like an Oil Rig “Pumpjack”

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Stony Brook researchers and colleagues use high-resolution imaging of proteins to develop the theory

A team of scientists led by Stony Brook University biochemist Huilin Li, PhD, have proposed that DNA is unwound by a type of “pumpjack” mechanism, similar to the way one operates on an oil rig. Their finding, published in Nature Structural & Molecular Biology, is based on new close-up images of the proteins that unwind DNA inside the nucleus of a yeast cell and could offer insight into ways that DNA replication can go awry and trigger disease.

dna

Members of the research team, from front: Zuanning Yuan, Stony Brook University graduate student; Huilin Li, Professor of Biochemistry and Cell Biology; and Lin Bai and Jingchuan Sun, postdoctoral scientist and research scientist, respectively, at Brookhaven National Lab. (Photo: BNL)

“DNA replication is a major source of errors that can lead to cancer,” explained Li, a Professor in the Department of Biochemistry & Cell Biology at Stony Brook University, a scientist at Brookhaven Lab, and lead author of the paper. “The entire genome—all 46 chromosomes—gets replicated every few hours in dividing human cells,” Li said, “so studying the details of how this process works may help us understand how errors occur.”

The investigative team includes scientists from Stony Brook University, the U.S. Department of Energy’s Brookhaven National Laboratory, Rockefeller University, and the University of Texas. Their research builds on previous collaborative work led by Dr. Li. In 2015, they produced the first-ever images of the complete DNA-copying protein complex, called the replisome. That study revealed a surprise about the location of the DNA-copying enzymes—DNA polymerases.

In the new paper, titled “Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation,” the research team focused on the atomic-level details of the “helicase” portion of the protein complex—the part that encircles and splits the DNA double helix so the polymerases can synthesize two daughter strands by copying from the two separated parental strands of the “twisted ladder.”

The scientists produced high-resolution images of the helicase using a technique known as cryo-electron microscopy (cryo-EM). One advantage of this method is that the proteins can be studied in solution, which is how they exist in the cells.

“You don’t have to produce crystals that would lock the proteins in one position,” Li said, adding that this is essential because the helicase is a molecular “machine” made of 11 connected proteins that must be flexible to work. “You have to be able to see how the molecule moves to understand its function.”

dna

Two images showing the structure of the helicase protein complex from above. (a) A surface-rendered three-dimensional electron density map as obtained by cryo-EM. (b) A computer-generated “ribbon diagram” of the atomic model built based on the density map. The helicase has three major components: the Mcm2-7 hexamer ring in green, which encircles the DNA strand; the Cdc45 protein in magenta; and the GINS 4-protein complex in marine blue. Cdc45 and GINS recruit and tether other replisome components to the helicase, including the DNA polymerases that copy each strand of the DNA.

“The whole mechanism operates similar to an old style pumpjack oil rig, with one part of the protein complex forming a stable platform, and another part rocking back and forth,” Li explained. “Each rocking motion could nudge the DNA strands apart and move the helicase along the double helix in a linear fashion,” he suggested.

Using computer software to sort out the images revealed that the helicase has two distinct conformations—one with components stacked in a compact way, and one where part of the structure is tilted relative to a more “fixed” base.

The atomic-level view allowed the scientists to map out the locations of the individual amino acids that make up the helicase complex in each conformation. Then, combining those maps with existing biochemical knowledge, they came up with a mechanism for how the helicase works.

“One part binds and releases energy from a molecule called ATP. It converts the chemical energy into a mechanical force that changes the shape of the helicase,” Li said. After kicking out the spent ATP, the helicase complex goes back to its original shape so a new ATP molecule can come in and start the process again.

“It looks and operates similar to an old style pumpjack oil rig, with one part of the protein complex forming a stable platform, and another part rocking back and forth,” Li said. Each rocking motion could nudge the DNA strands apart and move the helicase along the double helix in a linear fashion, he suggested.

This linear translocation mechanism appears to be quite different from the way helicases are thought to operate in more primitive organisms such as bacteria, where the entire complex is believed to rotate around the DNA, Li said. But there is some biochemical evidence to support the idea of linear motion, including the fact that the helicase can still function even when the ATP hydrolysis activity of some, but not all, of the components is knocked out by mutation.

“We acknowledge that this proposal may be controversial and it is not really proven at this point, but the structure gives an indication of how this protein complex works and we are trying to make sense of it,” he said.

The study was funded by the U.S. National Institutes of Health and the Howard Hughes Medical Institute (HHMI), with additional support from the Brookhaven Lab Biology Department. High-resolution cryo-EM data were collected at HHMI and the University of Texas Health Science Center.

Notes From Chairman

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2015 has been a year of changes in the Department of Biochemistry and Cell Biology.  One big change was the departure of Bob Haltiwanger, chairman of the department since 2007, who was recruited away to the University of Georgia.  The Department thrived under Bob’s leadership, including the hiring of seven new faculty members.  He is greatly missed, but we wish him well in his new surroundings. Bob’s departure necessitated another change, I have stepped in as Department chair.  I hope to see the Department continue to grow as it has under Bob.

In addition to Bob’s move, there were multiple retirements this year. Harvard Lyman, David Bynum, and Ken Marcu take with them over 100 years of experience educating and working with the students of Stony Brook.  Though all these departures are keenly felt, there have been many positive developments in the department this year as well.  The Department continued its healthy growth both in our educational mission and our research mission.  The number of students in our undergraduate courses continues to climb and this summer we will roll out our first online Biochemistry course.  Our Master’s program, begun in 2011, accepted its largest entering class ever.  On the research side, funding from research grants continues to grow and there were several exciting advances and faculty awards.

These developments are highlighted in our new and improved Newsletter.  The Newsletter is accessible through the Departmental website.  It will be updated frequently and contains a page for Alumni news.  We hope the Newsletter will not only help alumni keep in touch with the Department, but also with each other.  Please let us know what you are up to.