Joseph E. Wedekind Short CV

Joseph E. Wedekind, Ph.D. 
Professor 
Department of Biochemistry & Biophysics
Center for AIDS Research and Center for RNA Biology
601 Elmwood Avenue, MC 712
University of Rochester School of Medicine & Dentistry
Rochester, New York 14642
e-mail: joseph.wedekind@rochester.edu
https://www.urmc.rochester.edu/labs/wedekind.aspx 

EDUCATION

Ph.D., Biochemistry 1995 (Structural Enzymology)  University of Wisconsin, Madison

B.S. Biochemistry 1990 University of California, Riverside

EXPERIENCE

2002 – present
Department of Biochemistry & Biophysics, University of Rochester, New York 
Professor (2014 – present), Associate Professor (2006 – 2014, tenured 2010), Assistant Professor (2002-2006)

1999 – 2002
Department of Biochemistry & Molecular Biology, Rosalind Franklin University, Illinois
Assistant Professor

1995-1999
Department of Structural Biology, Stanford University, California
Post-Doctoral Research Fellow (Prof. David B. McKay)

1990-1995
Institute for Enzyme Research, University of Wisconsin at Madison
Graduate Research Assistant (Advisor: Prof. Ivan Rayment; co-advisor: Prof. Perry A Frey)

1988-1990
Department of Biochemistry, University of California at Riverside
Undergraduate Research Assistant (Prof. Alexander McPherson Jr.)

1989
Department of Pathology, University of Southern California, Los Angeles
Edmondson Summer Research Fellow (Prof. Alan Epstein)

1986-1989 
United States Department of Agriculture and Department of Entomology, Riverside, California
Federal Work Study Program (Prof. Dan Gonzalez)

HONORS

SERVICE

ONGOING RESEARCH SUPPORT

R01 AI150463     Wedekind (PI)     08/01/17 – 07/31/21
NIH/NIAID
Cyclic Peptide Inhibitors of HIV-1 Proliferation
Goals: The goal of this project is to develop novel constrained peptides that target HIV-1 TAR based on our library of lab-evolved TAR Binding Proteins (TBPs). The novel co-crystal structure of TAR in complex with variant TBP6.7 suggests a minimal lab-evolved β2-β3 peptide is sufficient for binding. We will optimize this peptide, followed by testing for anti-viral activity. We will also work to identify other novel peptides that bind TAR based on our TBP library. The results should provide new compounds that block viral infectivity, leading to a functional cure.
Role: PI 

R01 GM63162      Wedekind (PI)     07/01/17 – 06/30/21
NIH/NIGMS
Mechanisms of Action of Non-Coding RNA Molecules
Goals: The major goal of this project is to elucidate riboswitch signal-transduction pathways for the family of translational preQ1 riboswitches. We will use: (i) crystallography and calorimetry to characterize on-path mutants, (ii) an innovative live-cell chemical modification analysis coupled to a GFP reporter assay, and (iii) single-molecule kinetic analysis of RNA transient structure (SiMKARTS) to probe Shine-Dalgarno sequence accessibility. The results will reveal unprecedented structure-function relationships that integrate atomic-resolution structural and biophysical information with effector-mediated RNA conformational changes in live cells.
Role: PI

3R01GM063162-15S1     Wedekind (PI)     09/01/19 – 08/31/20
NIH/NIGMS
Mechanisms of Action of Non-Coding RNA Molecules
Goals: This equipment supplement was awarded to support the acquisition of a Sorvall LYNX 6000 superspeed centrifuge with six accompanying carbon fiber and titanium rotors.
Role: PI

T32AI049815     Wedekind (PI)     07/01/11 – 06/30/21
NIH/NIAID
Training in HIV Replication and Pathogenesis
Major Goal: This program seeks to train predoctoral students for careers as outstanding research scientists in the field of HIV/AIDS.
Role: PI

PUBLICATIONS

78 Total (71 manuscripts + 7 book chapters https://www.urmc.rochester.edu/people/23504899joseph-e-wedekind/publications)

h-index = 34; i10 = 61 (https://scholar.google.com/citations?user=-FWrFpoAAAAJ&hl=en)  

Selected Publications

SS Chavali, R Bonn-Breach, JE Wedekind* (2019) Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery. J. Biol. Chem. 294, 9326-9341. [featured in JBC Reviews roundup]. 

IA Belashov, DW Crawford, CE Cavender, P Dai, PC Beardslee, DH Mathews, BL Pentelute, BR McNaughton, JE Wedekind* (2018) Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Nucl. Acids Res. 46, 6401-6415. [Breakthrough article & cover]. 

JA Liberman, KC Suddala, A Aytenfisu, D Chan, IA Belashov, M Salim, DH Mathews, RC Spitale, NG Walter, JE Wedekind* (2015) Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc. Nat’l Acad. Sci. 112, E3485-E3494. [PNAS Plus manuscript] 

JA Liberman, M Salim, J Krucinska, JE Wedekind* (2013) Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat. Chem. Biol. 9, 353-355. [cover art] 

M Guo, RC Spitale, R Volpini, J Krucinska, G Cristalli, PR Carey, JE Wedekind* (2009) Direct Raman Measurement of an Elevated Base pKa in the Active Site of a Small Ribozyme in a Precatalytic Conformation. J. Am. Chem. Soc. 131, 12908-12909 [C&E News Highlight]. 

JE Wedekind*, R Gillilan, A Janda, J Krucinska, JD Salter, RP Bennett, J Raina, HC Smith (2006) Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits. J. Biol. Chem. 281, 38122-38126. [accelerated publication]. 

AK Ghosh, PR Sridhar, S Leshchenko, AK Hussain, J Li, AY Kovalevsky, DE Walters, JE Wedekind, V Grum-Tokars, D Das, Y Koh, K Maeda, H Gatanaga, IT Weber, H Mitsuya (2006) Structure-based design of novel HIV-1 protease inhibitors to combat drug resistance. J. Med. Chem. 49, 5252-5261. 

K Xie, MP Sowden, GSC Dance, AT Torelli, HC Smith, JE Wedekind* (2004) The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activationinduced deaminase and APOBEC-1. Proc. Nat’l Acad. Sci. 101, 8114-8119. 

JE Wedekind, DB McKay (1999) Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis. Nat. Struct. Molec Biol. 6, 261-268. [commentary by E. Westhof]. 

PC Babbitt, MS Hasson, JE Wedekind, DRJ Palmer, WC Barrett, GH Reed, I Rayment, G D Ringe, GL Kenyon, JA Gerlt (1996) The enolase superfamily: a general strategy for enzymecatalyzed abstraction of the α-protons of carboxylic acids. Biochemistry 35, 16489-16501. 

JE Wedekind, PA Frey, I Rayment (1996) The Structure of Nucleotidylated Histidine-166 of Galactose-1-phosphate Uridylyltransferase Provides Insight into Phosphoryl Group Transfer, Biochemistry 35, 11560-11569.