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Biochemistry and Molecular Biophysics
E-Newsletter


View this email in your browser                                                                                      Spring/Summer Issue 2020

 
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CONTENTS

Faculty News

Student Awards

Thesis Examinations

Welcome to New BMB Arrivals

Research Awards

Seminar Schedule

Latest Publications
NEWS
Faculty Spotlight - Dr. Linda Pike

Snapshot of a Scientist
 
As a five-year-old child, Dr. Linda Pike explored the cellular world through the eyepiece of a microscope and learned about chemical reactions involved in photo film development. Her lifelong love of chemistry was influenced by her father, a chemical engineer, who had Linda memorizing chemical names and symbols before kindergarten.  At a very young age, Pike was destined to be a scientist. 
 
“My father did photography as a hobby, and he used to take us down to the dark room with him,” Pike said. “We would watch the film develop and then the pictures coming up out of the dark. It was like magic.”
 
From the time she finished high school, she was driven to study the interface of biology and chemistry.  A few years into her undergraduate education in chemistry at the University of Delaware, Pike set her goals on obtaining her PhD and becoming an academic professor.  And that is exactly what she did.

To continue reading, please click here.

Dr. Greg Bowman Featured in The Source

Folding@home’s fight against COVID-19 enlists big tech, gamers, pro soccer

When the crowdsourced supercomputing project Folding@home first announced a shift to coronavirus research and asked for new volunteers to run its software and expand its computing capacity, organizations and citizen scientists from all walks of life heeded the call. Now, about four months later, the number of volunteers has increased a hundredfold.

To continue reading, please
 click here.

Congratulations to Dr. Jim Janetka, whose promotion to Professor was officially approved on September 11, 2020.

For more information on Dr. Jim Janetka, click here.

Dr. Natalie Niemi

Dr. Natalie Niemi joined the Department on July 1, 2020, as an Assistant Professor on the Investigator Track. Her lab will investigate how mitochondria are built, regulated, and maintained across physiological contexts. They blend biochemistry, systems biology, and physiology to understand mechanisms of mitochondrial regulation and how they influence metabolism and organellar function. Using insights gained from our molecular studies, the Niemi lab aims to understand how mitochondrial dysfunction contributes to mammalian pathophysiology, with the long-term goal of translating our discoveries into new therapeutic options to restore mitochondrial function in human disease.

For more information on Dr. Natalie Niemi, click here.

Student Awards
2020 Ceil M. DeGutis Prize awarded to:
Ms. Cohan is a Ph.D. Candidate in Biomedical Engineering at the McKelvey School of Engineering. Ms. Cohan was nominated for this award by her thesis mentor, Dr. Rohit Pappu. In her thesis work, she utilizes a variety of computational and experimental techniques to understand how intrinsically disordered regions (IDRs) might impact the molecular functions of bacterial proteins.
Mr. Jonathan Lin completed his PhD thesis in the lab of Dr. Rajendra Apte in the Department of Ophthalmology and Visual Sciences. His research led to the discovery that NAD+ intermediate molecules can enhance the metabolism of the neurosensory retina and thus has therapeutic potential for preventing photoreceptor neurodegeneration. He graduated from Washington University in St. Louis this past May with an MD/PhD under the Medical Scientist Training Program (MSTP). He will pursue his postgraduate education in the Transitional Year Residency at MetroWest Medical Center followed by Ophthalmology Residency at Harvard Medical School/Mass, Eye and Ear Infirmary.
2020 MilliporeSigma Fellowship awarded to:

Ms. Jasmine Cubuk is a fourth-year graduate student in the Biochemistry, Biophysics, and Structural Biology (BBSB) program. She is doing her PhD thesis work in the lab of Dr. Andrea Soranno, where she studies how sequence composition of intrinsically disordered regions within a protein can affect interactions with both proteins and nucleic acids using single-molecule fluorescence spectroscopy.

Jasmine joined the BBSB program after receiving her B.S. from Stockton University in Galloway, NJ with a major in biochemistry & molecular biology and a minor in holistic health. Prior to starting her Ph.D. work, Jasmine studied polymer synthesis and how polymer interactions contribute to optimized hydrogel formation.

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Mr. Jhullian Alston (JJ) is a fourth-year graduate student in the Biochemistry, Biophysics, and Structural Biology (BBSB) program. He is completing his Ph.D. thesis work jointly between the labs of Dr. Andrea Soranno and Dr. Alex Holehouse, where he combines computational biophysics with single-molecule fluorescence spectroscopy to understand how intrinsically disordered regions within a protein can affect interactions with both proteins and nucleic acids.

Jhullian joined the BBSB program after receiving his B.A. in Biology from The University of Maryland, Baltimore County where he was a Meyerhoff and MARC Scholar. Prior to starting his Ph.D. work, Jhullian had a diverse research background, studying nerve injury after radical prostatectomy, developing mouse models of prostate cancer, using CRISPR to develop fusion proteins in P. falciparum and C. elegans, and investigating the effects of O-GlcNAcylation.

To continue reading, please
click here.

PhD Thesis Examinations
Justin Porter in the Computational and Systems Biology program in the laboratory of Dr. Greg Bowman. His thesis was entitled "Conformational ensemble encodes functional properties of beta lactamases, myosin motors, and other biological macromolecules".
Min Kyung Shinn in the Physics program in the laboratory of Dr. Timothy Lohman. Her thesis was entitled "Specificity of SSB binding to its Interacting Proteins and Multiple Allosteric Effects of SSB C-terminal Tail on Assembly and DNA Binding of E. coli RecOR Proteins".
Sukrit Singh in the Computational and Molecular Biophysics program in the laboratory of Dr. Greg Bowman. His thesis was entitled "Understanding and exploiting protein allostery and dynamics using molecular simulations".
Melanie Sparks in the Biochemistry. Biophysics and Structural Biology program in the laboratory of Drs. Peter Burgers and Roberto Galletto. Her thesis was entitled "Bumpy Road Ahead: Overcoming DNA replication obstacles one barrier at a time".
BMB Department Welcomes...
Jonathan Borowsky-Undergraduate Student in Dr. Greg Bowman's lab.
Emily Hunter-Staff Scientist in Dr. Natalie Niemi's lab.
Catherine Kuhn-Research Technician I in Dr. Greg Bowman's lab.
Michaela Morhaus-Research Technician II in Dr. Natalie Niemi's lab.
Mariah Norman-Research Technician II in Dr. Jim Janetka's lab.
Wenhao (Owen) Ouyang-Undergraduate Student in Dr. Andrea Soranno's lab.
Ishan Taneja-Bioinformatics Research Assistant in Dr. Alex Holehouse's lab.
Research Awards

August 21st, 2020 – Carl Frieden, PhD, Professor of Biochemistry and Molecular Biophysics, received a new one-year grant award from BrightFocus Foundation for his research entitled “Understanding apoE”.


July 10th, 2020 – Rui Zhang, PhD, Assistant Professor of Biochemistry and Molecular Biophysics received a new five-year grant award from the National Institute of General Medical Sciences for his research entitled “Structural and functional studies of axonemal microtubule inner proteins (MIPs)”.


May 14. 2020 - Gregory Bowman, PhD, Associate Professor of Biochemistry and Molecular Biophysics received a new one-year grant award from the National Science Foundation for his research entitled RAPID: Folding@home and COVID-19”.


April 24, 2020 - Timothy M. Lohman, PhD, Marvin A. Brennecke Professor of Biophysics and Professor of Biochemistry and Molecular Biophysics received a new five-year MIRA grant award totalling $3,771,457 from National Institute of General Medical Sciences for his research entitled Mechanisms of Helicases, Translocases and SSB Proteins involved in Genome Maintenance
 
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2020 Fall Seminar Schedule:

September 22, 2020

BMB Seminar
Dr. Washington University in Saint Louis
University of California, San Diego
"Mechanoperception in the Green Lineage"



September 24, 2020

BMB Seminar
Dr. Anthony O'Donoghue
University of California, San Diego
"Uncovering the optimal substrate sequence of proteases for development of inhibitors and diagnostics"



September 29, 2020

BMB Seminar
Dr. Gabriel Rocklin
Northwestern University
"The structural basis for protein energy landscapes in a de novo designed proteome"



October 8, 2020

BMB Seminar
Dr. Naoko Mizuno
National Institutes of Health - National Heart, Lung and Blood Institute
"Molecular understanding of cell shape formation"



October 13, 2020

BMB Seminar
Dr. Kory Lavine
Washington University
"Viral and Immune Pathogenesis of COVID-19 Myocarditis"



October 20, 2020

BMB Seminar
Dr. Yuan He
Northwestern University
"Structural visualization of molecular machines on genes using cryo-EM"



October 27, 2020

BMB Seminar
Dr. Nathan Baker
University of Washington and Pacific Northwest National Laboratory
"Managing uncertainty in computational biophysics"



November 12, 2020

BMB Seminar - Gerty and Carl Cori Lecture
Dr. Tom Rapoport
Harvard Medical School
"Mechanism of ER-Associated Protein Degradation (“ERAD”)"



November 17, 2020

BMB Seminar
Dr. Simon Scheuring
Weill Cornell Medicine
High-Speed Atomic Force Microscopy: A forceful Tool for Molecular Biophysics"



November 24, 2020

BMB Seminar
Dr. Magnus Kjærgaard
Aarhus University in Denmark
"TBA"



December 1, 2020

BMB Seminar
Dr. Danuta Szczesna-Cordary
University of Miami Miller School of Medicine
"Genetic cardiomyopathies associated with mutations in myosin light chains:
underlying mechanisms and potential treatments"



December 8, 2020

BMB Seminar
Dr. Lillian Chong
University of Pittsburgh
"The Art of Possibility: Weighted Ensemble Simulations of Long-timescale Kinetics"



(All seminars will be presented over Zoom. If you would like the zoom link for a specific seminar or if you would like to be added to our seminar notification email list, please email torresm@wustl.edu.)



Latest Publications (in date order):
 

Melanie A. Sparks, Peter M. Burgers, & Roberto Galletto. (2020). “Pif1, RPA and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis” J Biol Chem. 2020 Sep 10;jbc.RA120.015699. doi: 10.1074/jbc.RA120.015699. Online ahead of print. (Abstract)



Kory J. Lavine & Michael J. Greenberg. (2020). “Beyond genomics-technological advances improving the molecular characterization and precision treatment of heart failure” Heart Fail Rev. 2020 Sep 3. doi: 10.1007/s10741-020-10021-5. Online ahead of print. (Abstract)



Mathivanan Chinnaraj, David A. Barrios, Carl Frieden, Tomasz Heyduk, Robert Flaumenhaft, & Nicola Pozzi. (2020). “Bioorthogonal Chemistry Enables Single-Molecule FRET Measurements of Catalytically Active Protein Disulfide Isomerase” Chembiochem. 2020 Aug 28. doi: 10.1002/cbic.202000537. Online ahead of print. (Abstract)



Weikai Li, Russell E. Bishop, & Filippo Mancia. (2020). “Integral Membrane Enzymes (2020)” J Mol Biol. 2020 Aug 21;432(18):4943-4945. doi: 10.1016/j.jmb.2020.07.022. Epub 2020 Jul 30. (Abstract)



Yihu Yang, Xiaoran Roger Liu, Zev J. Greenberg, Fengbo Zhou, Peng He, Lingling Fan, Shixuan Liu, Guomin Shen, Takeshi Egawa, Michael L. Gross, Laura G. Schuettpelz, & Weikai Li (2020). “Open conformation of tetraspanins shapes interaction partner networks on cell membranes” EMBO J (2020) e105246. 2020-08-16. doi: 10.15252/embj.2020105246. (Abstract)



Wenwen Gao, Yaqi Xu, Hongli Liu, Meng Gao, Qing Cao, Yiyi Wang, Longteng Cui, Rong Huang, Yan Shen, Sanqiang Li, Haiping Yang, Yixiang Chen, Chaokun Li, Haichuan Yu, Weikai Li, & Guomin Shen. (2020). “Characterization of missense mutations in the signal peptide and propeptide of FIX in hemophilia B by a cell-based assay” Blood Adv. 2020 Aug 11;4(15):3659-3667. doi: 10.1182/bloodadvances.2020002520. (Abstract)



Rachel Bezalel-Buch, Young K. Cheun, Upasana Roy, Orlando D. Schärer, & Peter M. Burgers (2020). “Bypass of DNA interstrand crosslinks by a Rev1-DNA polymerase ζ complex” Nucleic Acids Res. 2020 Jul 7;gkaa580. doi: 10.1093/nar/gkaa580. Online ahead of print. (Abstract)



Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, & Gregory R. Bowman (2020). “Citizen Scientists Create an Exascale Computer to Combat COVID-19” bioRxiv. 2020 Jun 28;2020.06.27.175430. doi: 10.1101/2020.06.27.175430. Preprint (Abstract)



Katarzyna Dubiel, Camille Henry, Lisanne M. Spenkelink, Alexander G. Kozlov, Elizabeth A. Wood, Slobodan Jergic, Nicholas E. Dixon, Antoine M. van Oijen, Michael M. Cox, Timothy M. Lohman, Steven J. Sandler, & James L. Keck (2020). “Development of a Single-Stranded DNA-binding Protein Fluorescent Fusion Toolbox” Nucleic Acids Res. 2020 Jun 19;48(11):6053-6067. doi: 10.1093/nar/gkaa320. (Abstract)



Jasmine Cubuk, Jhullian J. Alston, J. Jeremías Incicco, Sukrit Singh, Melissa D. Stuchell-Brereton, Michael D. Ward, Maxwell I. Zimmerman, Neha Vithani, Daniel Griffith, Jason A. Wagoner, Gregory R. BowmanKathleen B. HallAndrea Soranno, & Alex S. Holehouse. (2020). “The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA” bioRxiv. 2020 Jun 18;2020.06.17.158121. doi: 10.1101/2020.06.17.158121. Preprint (Abstract)



Shuang Li, Shixuan Liu, Xiaoran Roger Liu, Mengru Mira Zhang, and Weikai Li. (2020). “Competitive tight-binding inhibition of VKORC1 underlies warfarin dosage variation and antidotal efficacy” Blood Adv. 2020 May 26; 4(10): 2202–2212. Published online 2020 May 20. doi: 10.1182/bloodadvances.2020001750 (Abstract)



Jason D Fernandes, Sarvenaz Sarabipour, Christopher T Smith, Natalie M Niemi, Nafisa M Jadavji, Ariangela J Kozik, Alex S Holehouse, Vikas Pejaver, Orsolya Symmons, Alexandre W Bisson Filho, & Amanda Haage (2020). “A survey-based analysis of the academic job market” Elife. 2020 Jun 12;9:e54097. doi: 10.7554/eLife.54097. Online ahead of print. (Abstract)



Eliza A. Ruben, Prafull S. Gandhi, Zhiwei Chen, Sarah K. Koester, Gregory T. DeKosterCarl Frieden, & Enrico Di Cera. (2020). “19 F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2” J Biol Chem. 2020 Jun 12;295(24):8227-8235. doi: 10.1074/jbc.RA120.013419. Epub 2020 May 1. (Abstract)



James W Janetka, Allen T Hopper, Ziping Yang, Jennifer Barks, Mary Savari Dhason, Qiuling Wang, & L David Sibley (2020). “Optimizing Pyrazolopyrimidine Inhibitors of Calcium Dependent Protein Kinase 1 for Treatment of Acute and Chronic Toxoplasmosis” J Med Chem. 2020 Jun 11;63(11):6144-6163. doi: 10.1021/acs.jmedchem.0c00419. Epub 2020 Jun 1. (Abstract)



Justin R. Porter, Artur Meller, Maxwell I. Zimmerman, Michael J. Greenberg, & Gregory R. Bowman (2020). “Conformational Distributions of Isolated Myosin Motor Domains Encode Their Mechanochemical Properties” Elife. 2020 May 29;9:e55132. doi: 10.7554/eLife.55132. (Abstract)



Shuang Li, Shixuan Liu, Yihu Yang, & Weikai Li (2020). “Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases” J Mol Biol. 2020 May 20; S0022-2836(20)30350-8. doi: 10.1016/j.jmb.2020.05.009. Online ahead of print. (Abstract)



James Brett Case, Paul W Rothlauf, Rita E Chen, Zhuoming Liu, Haiyan Zhao, Arthur S Kim, Louis-Marie Bloyet, Qiru Zeng, Stephen Tahan, Lindsay Droit, Ma Xenia G Ilagan, Michael A Tartell, Gaya Amarasinghe, Jeffrey P Henderson, Shane Miersch, Mart Ustav, Sachdev Sidhu, Herbert W Virgin, David Wang, Siyuan Ding, Davide Corti, Elitza S Theel, Daved H Fremont, Michael S Diamond, & Sean P J Whelan (2020). “Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2” bioRxiv. 2020 May 18;2020.05.18.102038. doi: 10.1101/2020.05.18.102038. Preprint (Abstract)


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