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Biochemistry and Molecular Biophysics
E-Newsletter


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Logo for the Dept of Biochemistry and Molecular Biophysics at Washington University in St. Louis, MO
A gathering of present and past members of the Biochemistry
department to celebrate the 80th birthday of Carl Cori in 1976.
CONTENTS

Gerty & Carl Cori Lecture

Faculty News

Student Awards

Thesis Examinations

Events

Welcome to New BMB Arrivals

Research Awards

Latest Publications

Seminar Schedule
NEWS
The 2018 Gerty & Carl Cori Lecture
Tania Baker, PhD, from Massachusetts Institute of Technology, presented the 2018 Carl and Gerty Cori Lecture on September 25, 2018, in Connor Auditorium, Farrell Learning and Teaching Center. Dr. Baker's seminar was entitled "AAA+ Unfoldase Motors: Powerful Protein Destroyers and Activators”. Following the reception, faculty held a dinner for Dr. Baker at Cafe Napoli Restaurant in Clayton.

For more information on Dr. Tania Baker, please click here.
John Majors Symposium
On Friday, October 19th, 2018, a symposium in remembrance of Dr. John Majors was held in Moore Auditorium on the medical campus of Washington University. Many colleagues, friends and family members from the university community, as well as from across the country, were in attendance. Drs. Peter Burgers, Mark Johnston, Charlie Rice, and Harold Varmus all gave heartfelt talks about John’s influence in biophysics as well as speaking about the different hobbies (i.e., backpacking and golf) and interests John had outside of the lab. It was great to hear about the many sides of John that were not widely known. By the end of the day, everyone had learned something new about John.

The night concluded with a dinner at the Eric P. Newman Center on the medical campus. John’s nephew, Craig Hollow, and niece, Joleen Hollow-Bist, shared their experiences with John as an uncle. Many others shared personal stories about John and his influence on their life and work. Sonja Hunter and Kim Gerick, mentees of John, made a beautiful tribute slide show displaying personal pictures of John Majors’ life with family, friends, and colleagues.

If you would like to view that slide show presentation, click here.

Thank you to everyone who came from near and far to help us honor our friend and colleague John Majors.

A memorial fund has been established in Dr. John Majors’ name.

To make a donation online, please visit: https://alumni.wustl.edu/JohnMajors

To read John Majors’ Obituary – Click here.

Click on the following to view more photos or a slideshow of the photos taken at the event.
Symposium in Honor of Dr. Jim Janetka
The American Chemical Society in Saint Louis awarded Dr. Jim Janetka with the Saint Louis Award. This award is presented to an individual who has made outstanding contributions to the profession of chemistry and demonstrated potential to further the advancement of the chemical profession.  The award symposium was held on November 2, 2018 on the Washington University of Saint Louis campus.  Various speakers where invited to present in the afternoon, followed by a reception and banquet at the Glen Echo Country Club. Congratulations Dr. Janetka.  
Dr. Pike awarded Professor of the Year
On November 15th, the Distinguished Service Teaching Awards ceremony honored faculty that exhibited exemplary teaching skills from the 2017-2018 school year. The Class of 2021 awarded Dr. Linda Pike with Professor of the Year. Congratulations Dr. Pike!
Congratulations to Drs. Hall and Pike!
Drs. Kathleen Hall and Linda Pike were selected as new fellows by the American Association for the Advancement of Science (AAAS), the world’s largest general scientific society.
The AAAS selects fellows in recognition of their distinguished efforts to advance science and its applications, and has selected eleven faculty members at Washington University in St. Louis – the most in a decade-and-a-half. (more…)
On January 14th, 2019, Dr. Michael Kinch spoke to PBS Living St. Louis about his book on the history of vaccines and the controversies of the past and the present, as well as the successes.

You can view the Living St. Louis video here.
Student Awards
2018 Elson Fellowship in Honor of Dr. Elliot Elson
Congratulations to Sarah Clippinger for being selected for the 2018 Elson Fellowship. 

For more information on Sarah Clippinger, please click here.
2018 David F. Silbert Summer Fellowship Awarded to:
During the summer of 2018, Mr. John LeClair, a second-year medical student, performed research with Drs. Lisa McKenzie and Milan Chheda in the Department of Medicine, Medical Oncology.  His project was entitled “Characterizing the role of CHD4 in glioblastoma treatment response”.
During the summer of 2018, Ms. Meng (Mary) Zhu, a second-year medical student, performed research with Drs. Matthew Walter and Michael Alberti in the Department of Medicine, Bone Marrow Transplant.  Her project was entitled “Mutant U2AF1(Q157P) expression alters hematopoiesis in vivo”.
PhD Thesis Examinations
Robb Welty in the program of Computational and Molecular Biophysics in the laboratory of Dr. Kathleen Hall. His thesis was entitled "Kinetic Modeling of RNA Folding and Allostery".
Fengbo Zhou in the program of Computational and Molecular Biophysics in the laboratory of Dr. Weikai Li. His thesis was entitled "Mass spectrometry footprinting analysis and molecular dynamics simulation for structural studies on transmembrane proteins".
Events
Holiday Party
On December 8th, 2018, the BMB Department celebrated its annual Holiday Party at Saratoga Lanes in Maplewood, MO. Everyone enjoyed bowling, pool and a visit from Santa.
 
Click on the following to view more photos or a slideshow of the photos taken at the event.

 
Biochemistry, Biophysics & Structural Biology Graduate Program Retreat
On November 15 and 16, 2018, the BBSB hosted their 25th Annual Graduate Student Retreat at the Cedar Creek Conference Center in New Haven, MO. Drs. Michael Greenberg and Meredith Jackrel were the two main speakers on Thursday evening. Dr. Greenberg spoke on "The Molecular and Cellular Biophysics of Heart Disease", and Dr. Jackrel spoke on "Protein Disappregases to Counter Protein Misfolding".

The best student talk awards were given to Katherine Basore for her talk entitled "Structural insights into alphavirus-receptor interactions" and Justin Miller for his talk entitled "Prodrugs...activate! Towards rationale design of lipophilic prodrugs.
Chili Cookoff
On October 26th, 2018, the BMB Department held our 4th Annual Chili Cook-off. Because it was close to Halloween, this year’s event also included a costume contest!

The winner with the best Chili was the Robertson lab!

The Lohman lab won best costume – they all “dressed up” as Dr. Lohman!
BMB Department Welcomes...
Samantha Barrick-Postdoctoral Research Associate in Dr. Michael Greenberg's lab.
Ken Buss-Departmental Accounting Assistant.
Rahul Chadda-Senior Scientist in Dr. Janice Robertson's lab.
Matthew Cruz-Graduate Student in Dr. Greg Bowman's lab.
Jasmine Cubuk-Graduate Student in Dr. Andrea Soranno's lab.
Juan Jeremias-Postdoctoral Research Associate in Dr. Andrea Soranno's lab.
Matthew Mahoney-Research Specialist in Dr. Jim Janetka's lab.
Kacey Mersch-Graduate Student in Dr. Janice Robertson's lab.
Olivia Murray-Staff Scientist in Dr. John Cooper's lab.
Guomin Shen-Visiting Researcher in Dr. Weikai Li's lab.
Neha Vithani-Postdoctoral Research Associate in Dr. Greg Bowman's lab.
Jorine Voss-Postdoctoral Research Associate in Dr. Jim Janetka's lab.
Xiangli Wang-Postdoctoral Research Associate in Dr. Rui Zhang's lab.
Zhe Zeng-Postdoctoral Research Associate in Dr.Weikai Li's lab.
Research Awards
January 31, 2019 - Weikai Li, PhD, assistant professor of biochemistry and molecular biophysics, along with Michael L. Gross, PhD, professor of chemistry, immunology, and medicine, received a new four year grant award from the National Institute of General Medical Sciences for their research entitled “New chemical probes enable Mass Spectrometry-based footprinting of human protein structure in lipid membranes and cells”.

January 23, 2019 - Justin Porter, a Computational & Systems Biology student in the Bowman laboratory, received a three year National Research Service Award from the National Heart, Lung, and Blood Institute for his research entitled “Physics-based precision medicine: computationally phenotyping myosin isoforms and cardiomyopathy mutations”.

January 17, 2019 - Andrea Soranno, PhD, Assistant Professor of Biochemistry and Molecular Biophysics received a new three year Research Grant Award from the Alzheimer’s Association (AARG) for his work entitled Conformational analysis of ApoE isoforms and their role in AD mechanism.

January 9th, 2019 – Weikai Li, PhD, assistant professor of biochemistry and molecular biophysics received a four year renewal from the National Heart, Lung, and Blood Institute for his research entitled “Structural and Functional Basis of the Vitamin K Cycle”.

December 27th, 2018 – Weikai Li, PhD, assistant professor of biochemistry and molecular biophysics, along with Rui Zhang, PhD, assistant professor of biochemistry and molecular biophysics received a new three year, grant award from the W. M. Keck foundation for their research entitled “Terminal coupling enabled structure determination of human membrane proteins at atomic resolution”.

October 19th, 2018 – Andrea Soranno, PhD, Assistant Professor of Biochemistry and Molecular Biophysics received a New Investigator Award in Alzheimer’s Disease from the American Federation for Aging Research (AFAR), Inc. for his work entitled “Identifying Neurotoxic Conformers in the Structural Ensemble of apoE”.



 
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Upcoming Seminars:

February 4, 2019

BMB Seminar
Dr. Alex Holehouse
WUSM
"Linking sequence, ensemble, and phase behavior in low complexity domains"


February 12, 2019

BMB Seminar
Dr. Michael Vahey
WUSM
"Fluorescence approaches to understanding influenza A virus assembly and transmission"


February 19, 2019

BMB Seminar
Dr. Jon Silva
WUSM
"Precision Antiarrhythmic Medicine: The Devil is in the Molecular Details"


February 26, 2019

BMB Seminar
Dr. Joe Ippolito
WUSM
"Sex differences in cancer metabolism: a new angle to precision medicine"


March 12, 2019

BMB Seminar
Dr. Jason Held
WUSM
"Context-dependent control of cellular redox biology and signaling"


March 19, 2019

BMB Seminar
Dr. Jeff Hass
Bayer Crop Science
"From Atoms to the Field: Protecting Crops from Insects"


March 26, 2019

BMB Seminar
Dr. Linda Columbus
Univ. of Virginia, School of Medicine
"From Lipid/detergent - protein interactions to host -pathogen interactions, how do membrane proteins work?"


April 2, 2019

BMB Seminar
Dr. Robert Piper
University of Iowa Health Care
"TBA"


April 9, 2019

BMB Seminar
Dr. Elizabeth Tran
Purdue University
"Gene Expression through Studies of the RNA Helicase Dbp2/DDX5"


April 16, 2019

BMB Seminar
Dr. Stuart Campbell
Yale University
"TBA"


April 23, 2019

BMB Seminar
Dr. Peng Yuan
WUSM
"Opening of transient receptor potential ion channels"


April 30, 2019

BMB Seminar
Dr. Colin Nichols
WUSM
"Potassium channel proteins as ionic conduits: Just how do ions get through them?"


May 7, 2019

BMB Seminar
Dr. Tracy Johnson
University of California, Los Angeles
"TBA"


May 14, 2019

BMB Seminar
Dr. Michael Greenberg
WUSM
"Dissecting the Mechanism of Familial Cardiomyopathies from the Ground Up"


Latest Publications (in date order):


Welty R., Pabit S.A., Katz A.M., Calvey G.D., Pollack L., & Hall K.B. “Divalent ions tune the kinetics of a bacterial GTPase Center rRNA folding transition from secondary to tertiary structure.” RNA. 2018 Dec. 24(12):1828-1838. doi: 10.1261/rna.068361.118. (
Abstract)


Knoverek C.R., Amarasinghe G.K., & Bowman G.R. “Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.” Trends Biochem Sci. 2018 Dec 13. pii: S0968-0004(18)30248-2. doi: 10.1016/j.tibs.2018.11.007. [Epub ahead of print] (
Abstract)


Maddirala A., Klein R.D., Pinkner J., Kalas V., Hultgren S.J., & Janetka J.W. “Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through iterative rational drug design.” J Med Chem. 2018 Dec 12. doi: 10.1021/acs.jmedchem.8b01561. [Epub ahead of print] (
Abstract)


Dubiel K., Myers A.R., Kozlov A.G., Yang O., Zhang J., Ha T., Lohman T.M., & Keck J.L. “Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins.” J Mol Biol. 2018 Nov 22. pii: S0022-2836(18)31046-5. doi: 10.1016/j.jmb.2018.11.019. [Epub ahead of print] (
Abstract)


Galburt E.A. “The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression.” Proc Natl Acad Sci U S A. 2018 Nov 21. pii: 201809454. doi: 10.1073/pnas.1809454115. [Epub ahead of print] (
Abstract)


Zimmerman M.I., Porter J.R., Sun X., Silva R.R., & Bowman G.R. “Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.” J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500.(
Abstract)


Kiehart D.P. & Cooper J.A. “Contractile protein biochemistry in the Pollard Lab in Baltimore.” Biophys Rev. 2018 Nov 8. doi: 10.1007/s12551-018-0477-5. [Epub ahead of print] (
Abstract)


Yen M., Qi Z., Chen X., Cooper J.A., Mitra R.D., & Onken M.D. “Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma.” BMC Med Genomics. 2018 Nov 6;11(1):97. doi: 10.1186/s12920-018-0424-0. (
Abstract)


Dahan D., Tsirkas I., Dovrat D., Sparks M.A., Singh S.P., Galletto R., & Aharoni A. “Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures.” Nucleic Acids Res. 2018 Nov 5. doi: 10.1093/nar/gky1065. [Epub ahead of print] (
Abstract)


Robertson J.L. “The lipid bilayer membrane and its protein constituents.” J Gen Physiol. 2018 Nov 5;150(11):1472-1483. doi: 10.1085/jgp.201812153. (
Abstract)


Johnston A.B., Hilton D.M., McConnell P., Johnson B., Harris M.T., Simone A., Amarasinghe G.K., Cooper J.A., & Goode B.L. “A novel mode of capping protein-regulation by twinfilin.” Elife. 2018 Oct 23;7. pii: e41313. doi: 10.7554/eLife.41313. (
Abstract)


Sun X., Singh S., Blumer K.J., & Bowman G.R. “Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding.” Elife. 2018 Oct 5;7. pii: e38465. doi: 10.7554/eLife.38465. (
Abstract)


Axelrod D., Elson E.L., Schlessinger J., & Koppel D.E. “Reminiscences on the “Classic” 1976 FRAP Article in Biophysical Journal.” Biophys J. 2018 Oct 2;115(7):1156-1159. doi: 10.1016/j.bpj.2018.08.037. (
Abstract)


Woody M.S., Greenberg M.J., Barua B., Winkelmann D.A., Goldman Y.E., & Ostap E.M. “Positive cardiac inotrope omecamtiv mecarbil activates muscle despite suppressing the myosin working stroke.” Nat Commun. 2018 Sep 21;9(1):3838. doi: 10.1038/s41467-018-06193-2. (
Abstract)


Greenberg M.J., Daily N.J., Wang A., Conway M.K., & Wakatsuki T. “Genetic and Tissue Engineering Approaches to Modeling the Mechanics of Human Heart Failure for Drug Discovery.” Front Cardiovasc Med. 2018 Sep 19;5:120. doi: 10.3389/fcvm.2018.00120. eCollection 2018. (
Abstract)


Geronimo C.L., Singh S.P., Galletto R., & Zakian V.A. “The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity.” Nucleic Acids Res. 2018 Sep 19;46(16):8357-8370. doi: 10.1093/nar/gky655. (
Abstract)


Rezaei-Ghaleh N., Parigi G., Soranno A., Holla A., Becker S., Schuler B., Luchinat C., & Zweckstetter M. “Local and Global Dynamics in Intrinsically Disordered Synuclein.” Angew Chem Int Ed Engl. 2018 Sep 5. doi: 10.1002/anie.201808172. [Epub ahead of print] (
Abstract)


Onken M.D., Makepeace C.M., Kaltenbronn K.M., Kanai S.M., Todd T.D., Wang S., Broekelmann T.J., Rao P.K., Cooper J.A., & Blumer K.J. “Targeting nucleotide exchange to inhibit constitutively active G protein α subunits in cancer cells.” Sci Signal. 2018 Sep 4;11(546). pii: eaao6852. doi: 10.1126/scisignal.aao6852. (
Abstract)


Macdonald-Obermann J.L. & Pike L.J. “Allosteric regulation of epidermal growth factor (EGF) receptor ligand binding by tyrosine kinase inhibitors.” J Biol Chem.2018 Aug 31;293(35):13401-13414. doi: 10.1074/jbc.RA118.004139. (
Abstract)


Ordabayev Y.A., Nguyen B., Niedziela-Majka A., & Lohman T.M. “Regulation of UvrD Helicase Activity by MutL.” J Mol Biol. 2018 Aug 29. pii: S0022-2836(18)30591-6. doi: 10.1016/j.jmb.2018.08.022. (
Abstract)


Sukumar N., Liu S., Li W., Mathews F.S., Mitra B., & Kandavelu P. “Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2Å resolution.” Biochimie. 2018 Jul 30. pii: S0300-9084(18)30212-8. doi: 10.1016/j.biochi.2018.07.017. (
Abstract)


Onken M, Makepeace CM, Wang S, Kaltenbronn KM, Kanai SM, Broekelmann TJ, Cooper JA, & Blumer KJ. “Pharmacologic targeting of Gq reveals new pathways in uveal melanoma” AACR, July 2018, Volume 78, Issue 13 Supplement (
Abstract)


Klein R.D., Shu Q., Cusumano Z.T., Nagamatsu K., Gualberto N.C., Lynch A.J.L., Wu C., Wang W., Jain N., Pinkner J.S., Amarasinghe G.K., Hultgren S.J., Frieden C., & Chapman M.R. “Structure-Function Analysis of the Curli Accessory Protein CsgE Defines Surfaces Essential for Coordinating Amyloid Fiber Formation.” MBio.2018 Jul 17;9(4). pii: e01349-18. doi: 10.1128/mBio.01349-18. (
Abstract)


Song J.G., King M.R., Zhang R., Kadzik R.S., Thawani A., & Petry S. “Mechanism of how augmin directly targets the γ-tubulin ring complex to microtubules.” J Cell Biol. 2018 Jul 2;217(7):2417-2428. doi: 10.1083/jcb.201711090. (
Abstract)


Singh S.P., Kukshal V., De Bona P., Antony E., & Galletto R. “The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers.” Nucleic Acids Res.2018 Jun 21. doi: 10.1093/nar/gky530. (
Abstract)

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