Biochemistry and Molecular Biophysics
E-Newsletter

View this email in your browser Spring Issue 2016

CONTENTS

Alumni Endowed Professorship Installation Ceremony

Elson Fellowship Fund

Student Awards

Thesis Examinations

Chili Cookoff! And the winner is ...

Welcome to New BMB Arrivals

Research Awards

Upcoming Events and Latest Publications

NEWS

Alumni Endowed Professorship Installation Ceremony

On July 11, 2016, Dr. Linda Pike was installed as the Alumni Endowed Professor of Biochemistry and Molecular Biophysics. The Installation was held in the Eric P. Newman Education Center. Dean David Perlmutter and Dr. John Cooper presided over the installation ceremony. After the opening remarks and installation Dr. Pike presented a seminar entitled “Parsley, Sage, Rosemary, and Thyme: The Fine ErbBs.”

Click Here to read more

Elson Fellowship Endowment Fund

The colleagues, friends and trainees of Dr. Elliot L. Elson have expressed a wish to establish an endowed education and training fund to honor him and his extraordinary impact on both the Washington University School of Medicine and molecular biophysics. His teaching and research contributions have been far-reaching and numerous.

The Elliot L. Elson Education Training Endowment will be used to support opportunities for students and the very best post-doctoral trainees in the Department of Biochemistry and Molecular Biophysics.

If you would like to help contribute to this endowment fund, please click here.

Student Awards

2016 NSF Graduate Fellowship Recipient

Yansel Nuñez was recently awarded an NSF graduate fellowship. Yansel received a B.S. in biology from Seton Hall University. After graduation, he spent a year working at the NIH in their Intramural Research Training program. In 2014, he matriculated at Washington University in the Molecular Cell Biology graduate program. He joined Dr. Linda Pike’s laboratory where his thesis research focuses on EGF receptor structure and function.

CBSE Graduate Student Scholar Named

Maxwell Zimmerman, a Computational & Molecular Biophysics student in the laboratory of Dr. Greg Bowman, has been selected as a 2016-2017 CBSE Graduate Student Scholar. Maxwell was recognized for the early promise he has shown in the development of novel sampling algorithms that are aiding feature-based sampling of high dimensional conformational spaces.

Maxwell has also been selected as a three year Monsanto Fellow which will give him a unique opportunity to interact with Monsanto scientists in a variety of venues.

Thesis Examinations in the Department

Joseph Stodola defended his PhD thesis entitled "Timing the Steps of Okazaki Fragment Maturation" on May 2, 2016. Joe was in the program of Biochemistry and completed his thesis in the laboratory of Dr. Peter Burgers.

Chao Wu defended his PhD thesis entitled "Structure and Dynamics of a Small Multidrop Resistance Transporter" on March 30, 2016. Chao was in the program of Computational and Molecular Biophysics and completed his thesis in the laboratory of Dr. Katherine Henzler-Wildman.

Chi Zhang defended his PhD thesis entitled "Engineering Cre Recombinase for Genome Editing" on March 30, 2016. Chi was in the program in Computational and Systems Biology and completed his thesis work in the laboratory of Dr. Jim Havranek.

Chili Cookoff

On February 19th, we held our Annual Chili Cook-off. The competition was intense and the chili was good! The 2016 Chili Cook-off winner was: The Lohman lab. Congratulations! Photos

BMB Department Welcomes...

Thomas Frederick-Postdoctoral Research Associate in Dr. Greg Bowman's lab.

Shuang Li-Postdoctoral Research Associate in Dr. Weikai Li's lab.

Amarendar Reddy Maddirala-Postdoctoral Research Associate in Dr. Jim Janetka's lab.

Marlene Mekel-Staff Scientist in Dr. John Cooper's lab.

Tanumoy Mondol-Postdoctoral Research Associate in Dr. Peter Burgers' lab.

Min Shinn-Graduate Student in Dr. Tim Lohman's lab.

Research Awards

Gregory Bowman, PhD, Assistant Professor of Biochemistry and Molecular Biophysics received a new five-year grant from the National Science Foundation for his research entitled "CAREER: FAST Methods for Protein Folding and Design".

Gregory Bowman, PhD, Assistant Professor of Biochemistry and Molecular Biophysics received a BWF Ad Hoc grant in support of a workshop entitled “The 2016 Workshop on Kinetics and Markov State Models (MSMs) in Drug Design" to be held May 19-20 at the Novartis Institutes for Biomedical Research in Cambridge, Massachusetts.

Peter M. Burgers, PhD, Marvin A. Brennecke Professor of Biological Chemistry, Department of Biochemistry and Molecular Biophysics received a five-year MIRA grant from the National Institute of General Medical Sciences for his research entitled "Mechanisms of DNA Replication and Maintenance in Eukaryotes".

John A Cooper, MD, PhD, Wittcoff Professor and Head of Biochemistry and Molecular Biophysics received a new five-year MIRA grant from National Institute of General Medical Sciences for his research entitled “Actin Assembly and Cell Motility: Mechanisms and Regulation”.

Timothy M. Lohman, PhD, Marvin A. Brennecke Professor of Biophysics, Department of Biochemistry and Molecular Biophysics received a four-year grant from the National Institute of General Medical Sciences for his research entitled "SSB Protein/DNA Interactions".

Forward

Upcoming Events:

September 6, 2016
BMB Seminar
Dr. Jim Janetka
WUSTL
"A fresh “out of the cell” look at bacteria and tumors: Targeting pathogenic mechanisms in cancer and infection"

September 13, 2016
Biophysical Evening Seminar
Dr. John Tainer
The University of Texas, M. D. Anderson Cancer Center
"TBA"

September 20, 2016
BMB Seminar
Dr. Kim Stroka
University of Maryland, College Park
"Evaluation of Blood-Brain Barrier Mechanobiology using Biomimetic Models"

October 4, 2016
BMB Seminar
Dr. Lucia Strader
Washington University in Saint Louis
"ARF Transcription Factors: Protein aggregation as a regulator of gene transcription"

October 11, 2016
BMB Seminar
Dr. Rama Ranganathan
UT Southwestern Medical Center at Dallas
"TBA"

October 18, 2016
BMB Seminar
Dr. Jeff Peng
University of Notre Dame
"TBA"

November 1, 2016
BMB Seminar
Dr. Dave Thomas
University of Minnesota
"TBA"

November 8, 2016
BMB Seminar
Dr. Selba Kutluay
Washington University in Saint Louis
“HIV-1 integrase binds the viral RNA genome and is essential during virion morphogenesis"

November 15, 2016
BMB Seminar
Dr. Michelle Arkin
University of California - San Francisco
"TBA"

November 29, 2016
BMB Seminar
Dr. Maria Kontoyianni
Southern Illinois University, Edwardsville
"TBA"

Latest Publications:

Pascolutti, R., Sun, X., Kao, J., Maute, R., Ring, A.M., Bowman, G.R. and Kruse, A.C. Structure and dynamics of PD-L1 and an ultra high-affinity PD-1 receptor mutant. Structure (E-pub ahead of print.) (2016).

Stojkovic, G., Makarova, A.V., Wanrooij, P.H., Forslund, J., Burgers, P.M., and Wanrooij, S. Oxidative DNA damage stalls the human mitochondrial replisome. Sci Rep 6: 28942 (2016).

Cho, J.E, Huang, S.N., Burgers, P.M., Shuman, S., Pommier, Y. and Jinks-Robertson, S. Parallel analysis of ribonucleotide-dependent deletions produced by yeast Top1 in vitro and in vivo. Nucleic Acids Res. (E-pub ahead of print.) (2016).

Sawicka, M., Wanrooij, P.H., Darbari, V.C., Tannous, E., Hailemariam, S., Bose, D., Makarova, A.V., Burgers, P.M. and Xhang, X. The dimeric architecture of checkpoint kinases Mec1ATR and Tel1ATM reveal a common structural organization. J Biol Chem 291:13436-13437 (2016).

Stodola, J.L., Stith, C.M. and Burgers, P.M. Proficient replication of the yeast genome by a viral DNA polymerase. J Biol Chem 291:11698-11705 (2016).

Stodola, J.L. and Burgers, P.M. Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale. Nat Struct Mol Biol 23:402-408 (2016).

Burgers, P.M., Gordenin, D. and Kunkel, T.A. Who is leading the replication fork, pol epsilon or pol delta? Mol Cell. 61:492-493 (2016).

Koc, K.N., Singh, S.P., Stodola, J.L., Burgers, P.M. and Galletto, R. Pif1 removes a Rap1-dependent barrier to the stand displacement activity of DNA polymerase delta. Nucleic Acids Res. 44:3811-3819 (2016).

Wang, X., Galletta, B.J., Cooper, J.A. and Carlsson, A.E. Actin-regulator feedback interactions during endocytosis. Biophys J 110:1430-1443 (2016).

Xu X, Wang X, Todd EM, Jaeger ER, Vella JL, Mooren OL, Feng Y, Hu J, Cooper JA, Morley SC, Huang YH. Mst1 Kinase Regulates the Actin-Bundling Protein L-Plastin To Promote T Cell Migration. J Immunol. 2016 Jul 27. pii: 1600874. [Epub ahead of print]

Babaei, B., Davarian, A., Lee, S.L., Pryse, K.M., McConnaughey, W.B., Elson, E.L. and Genin, G.M. Remodeling by fibroblasts alters the rate-dependent mechanical properties of collagen. Acta Biomater. S1742-7061:30130-30131 (2016).

Li, Y., Huang, G., Li, M., Wang, L., Elson, E.L., Jian Lu, T., Genin, G.M. and Xu, F. An approach to quantifying 3D responses of cells to extreme strain. Sci Rep. 6:19550 (2016).

Elson, E.L. and Genin, G.M. Tissue constructs: Platforms for basic research and drug discovery. Interface Focus 6:20150095 (2016).

Xiao, Z., Banan, B., Xu, M., Jia, J., Manning, P.T., Hiebsch, R.R., Gunasekaran, M., Upadhya, G.A., Frazier, W.A., Mohanakumar, T., LIn, Y. and Chapman, W.C. Attenuation of ischemia-reperfusion injury and improvement of survival in recipients of steatotic rat livers using CD47 monoclonal antibody. Transplantation 100:1480-1489 (2016).

Mondal, T., Wang, H., DeKoster, G.T., Baban, B., Gross, M.L. and Frieden, C. ApoE: In vitro studies of a small molecule effector. Biochemistry 55:2613-2621 (2016).

Rammohan, J., Ruiz Manzano, A., Garner, A.L., Prusa, J., Stallings, C.L. and Galburt, E.A. Cooperative stabilization of Mycobacterium tuberculosis rrnAP3 promoter open complexes by RbpA and CarD. Nucleic Acids Res. (E-pub ahead of print.) (2016).

Lisica, A., Engel, C., Jahnel, M., Roldan, E., Galburt, E.A., Cramer, P. and Grill, S.W. Mechanisms of backtrack recovery by RNA polymerases I and II. PNAS 113:2946-2951 (2016).

Sokoloski, J.E., Kozlov, A.G., Galletto, R. and Lohman, T.M. Chemo-mechanical pushing of proteins along single-stranded DNA. P.N.A.S., USA (E-pub ahead of print.) (2016).

Singh, S.P., Koc, K.N., Stodola, J.L. and Galletto, R. A monomer of Pif1 unwinds double-stranded DNA and it is regulated by the nature of the non-translocating strand at the 3'-end. J Mol Biol. 428:1053-1067 (2016).

Greenberg, M.J., Arpag, G., Tuzel, E. and Ostap, E.M. A perspective on the role of myosins as mechanosensors. Biophysical Journal 110:2568-2576 (2016).

Woody, M.S., Lewis, J.H., Greenberg, M.J., Goldman, Y.E., and Ostap, E.M. MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood
Estimation. Biophysical Journal, 111:273-282 (2016).

Bergonzo, C., Hall, K.B., Cheatham, T.E. Divalent ion dependent conformational changes in an RNA stem-loop observed by molecular dynamics. J Chem Theory Comput. 12:3382-3389 (2016).

Smith, J.A., Xu, G., Feng, R., Janetka, J.W., Moeller, K.D. C-Glycosides, Array-based Addressable Libraries, and the Versatility of Constant Current Electrochemistry. ElectroAnalysis, 28:1-11, 2016.

Han, Z., Harris, P.K.W., Karmakar, P., Kim, T., Owusu, B.Y., Wildman, S.A., Klampfer, L. and Janetka, J.W. alpha-Ketobenzothiazole serine protease inhibitors of aberrant HGF/c-MET and MSP/RON kinase pathway signaling in cancer. ChemMedChem 11:585-599 (2016).

Simpson, C., Jones, N.G., Hull-Ryde, E.A., Kireev, D.B., Stashko, M., Tang, K., Janetka, J., Wildman, S.A., Zuercher, W.J., Schapira, M., Hui, R., Janzen, W.P. and Sibley, L.D. Identification of small molecule inhibitors that block the Toxoplasma gondii rhoptry kinase ROP18. ACS Infect. Dis. 2:194-206 (2015).

Jarvis, C., Han, Z., Kalas, V., Klein, R., Pinkner, J.S., Ford, B., Binkley, J., Cusumano, C.K., Cusumano, Z., Mydock-McGrane, L., Hultgren, S.J. and Janetka, J.W. Antivirulence isoquinolone mannosides: Optimization of the biaryl aglycone for FimH lectin binding affinity and efficacy in the treatment of chronic UTI. Chem Med Chem 11:367-373 (2016).

Wang, Q., Heizer, E., Rosa, B.A., Wildman, S.A., Janetka, J.W. and Mitreva, M. Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. Infection, Genetics and Evolution S1567-1348:30025-30029 (2016).

Krishna, U., Romero-Gallo, J., Suarez, G., Azah, A., Krezel, A.M., Varga, M.G., Forsyth, M.H. and Peek, R.M. Jr. Genetic evolution of a Helicobacter pylori acid-sensing histidine kinase and gastric disease. J Infect Dis. (E-pub ahead of print.) (2016).

Shu, Q., Krezel, A.M., Cusumano, Z.T., Pinkner, J.S., Klein, R., Hultgren, S.J. and Frieden, C. Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation. Proc Natl Acad Sci, USA 113:7130-7135 (2016).

Li, W. Bringing bioactive compounds into membranes: The UbiA superfamily of intramembrane aromatic prenyltransferases. Trends Biochem Sci 41:356-370 (2016).

Simon, M., Sokoloski, J., Hao, L., Weiland, E. and Lohman, T.M. Processive DNA Unwinding by RecBCD helicase in the absence of canonical motor translocation. J Molecular Biology (E-pub ahead of print.) (2016).

Chowdhury, F., Li, I., Ngo, T., Leslie, B., Kim, B., Sokoloski, J., Weiland, E., Wang, X., Chemla, Y., Lohman, T., and Ha, T. Defining single molecular forces required for Notch activation using nano yoyo. Nano Letters (E-pub ahead of print.) (2016).

Waldman, V., Weiland, E., Kozlov, A. and Lohman, T. Is fully wrapped SSB-DNA complex essential for E. coli survival? Nucleic Acids Research (E-pub ahead of print.) (2016).

Ronan, T., Macdonald-Obermann, J.L., Huelsmann, L., Bessman, N.J., Naegle, K.M. and Pike, L.J. Different EGF receptor agonists produce unique signatures for the recruitment of downstream signaling protein. J Biol Chem 291:5528-5540 (2016).