Joseph E. Wedekind, Ph.D.

Contact Information

Phone Numbers

Research Labs

The Wedekind lab uses biophysical, biochemical and cell-based techniques to investigate: (i) bacterial riboswitches, and (ii) lab-evolved proteins that target HIV-1 RNA.

Visit The Wedekind lab uses biophysical, biochemical and cell-based techniques to investigate: (i) bacterial riboswitches, and (ii) lab-evolved proteins that target HIV-1 RNA. Lab Website

Locations

University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester, NY 14642

Faculty Appointments

Professor - Department of Biochemistry and Biophysics (SMD)

Biography

Research

The Wedekind lab investigates the mechanisms of action of non-protein-coding (nc)RNAs. We are interested especially in the elegant, three-dimensional architectures of these RNAs, and how they bind to specific small molecules or peptides, leading to conformations that alter biological function. Model systems include: (i) metabolite-sensing riboswitches that regulate protein translation, and (ii) the application of lab-evolved proteins to target HIV-1 RNA. This work is relevant to the development of new antibiotics and anti-retroviral therapies. This work is funded by NIH/NIGMS grants R01 GM063162 and R01 GM123864.

Our lab employs a variety of biochemical, biophysical, and structural approaches, such as X-ray crystallography. We greatly acknowledge NIH/NCRR award S10 RR026501 for supporting this instrumentation. For access or further information see: https://www.urmc.rochester.edu/structural-biology-biophysics.aspx

Credentials

Education

1990
B.Sc. | University of California at Riverside
Biochemistry (Magna Cum Laude)

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

Post-doctoral Training & Residency

1995 - 1999
RNA Biophysics, Dept. of Structural Biology, Stanford University School of Medicine. 1995-1999

Awards

2018 - 2022
Member, MSFB Study Section
Sponsor: Center for Scientific Review, NIH/PHS

2017 - 2019
Secretary, Medical Faculty Council
Location: University of Rochester SMD

2015
Faculty Teaching Award in Biophysics
Sponsor: University of Rochester SMD
Location: Dept. Biochemistry & Biophysics

2011 - 2016
Editorial Board Member, The Journal of Biological Chemistry
Sponsor: ASBMB

2010 - 2012
Executive Committee Member, CHESS Users' Group
Sponsor: Cornell High Energy Synchrotron Source, Ithaca NY

2010
Faculty Teaching Award in Biophysics
Location: University of Rochester SMD | Dept. Biochemistry & Biophysics

2007 - 2009
Elected Secretary (The Board of Directors)
Sponsor: The Pittsburgh Diffraction Society
Location: Pittsburgh, PA

2005
Faculty Teaching Award in Biophysics
Location: University of Rochester SMD | Dept. Biochemistry & Biophysics

1996 - 1999
Life Sciences Research Foundation Fellow
Sponsor: Burroughs Wellcome Fund
Location: Dept. Structural Biology, Stanford, CA

1996
Individual NRSA Post-doctoral Fellowship (declined)
Sponsor: NIH
Location: Stanford, CA

1996
Leukemia and Lymphoma Society Post-Doctoral Award (declined)
Sponsor: Leukemia and Lymphoma Society
Location: Stanford, CA

1995 - 1996
Dean's Fellow
Location: Stanford University School of Medicine

1992 - 1995
NIH Biophysics Training Grant Recipient
Sponsor: NIH/NIGMS

1990
Elected Member, Phi Beta Kappa
Location: Iota Chapter of California

1989
Edmondson Summer Research Fellow
Sponsor: Dept. of Pathology
Location: University of Southern California

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Patents

Patent Title: Nucleic Acid Binding Compounds and Methods of Use
Patent #: 9,212,205
Issue Date: Dec 15, 2015
Country: United States
Invented By: Peter Gareiss, Brian R McNaughton, Benjamin Locke Miller, Krzysztof Sobczak, Charles A Thornton, Joseph E Wedekind

Patent Title: Methods and Compositions Related to the Structure and Function of APOBEC3G
Patent #: 8,999,317
Issue Date: Apr 07, 2015
Country: United States
Invented By: Ryan P Bennett, Harold C Smith, Joseph E Wedekind

Patent Title: Methods and Compositions Related to the Structure and Function of APOBEC3G
Patent #: 2104516
Issue Date: Jan 07, 2015
Country: Europe
Invented By: Harold C Smith, Joseph E Wedekind

Patent Title: Methods and Compositions Related to the Structure and Function of APOBEC3G
Patent #: DE2104516
Issue Date: Jan 07, 2015
Country: Germany
Invented By: Harold C Smith, Joseph E Wedekind

Patent Title: Methods and Compositions Related to the Structure and Function of APOBEC3G
Patent #: GB2104516
Issue Date: Jan 07, 2015
Country: United Kingdom
Invented By: Harold C Smith, Joseph E Wedekind

Patent Title: Context-Dependent-Inhibitors of Cytidine Deaminases and Uses Thereof
Patent #: 8,158,770
Issue Date: Apr 17, 2012
Country: United States
Invented By: Harold C Smith, Joseph E Wedekind

Patent Title: Anti-HIV Peptides
Patent #: 10,538,556
Issue Date: Jan 21, 2020
Country: United States
Invented By: Ivan A Belashov, David Crawford, Brian R McNaughton, Joseph E Wedekind

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Publications

Journal Articles

11/10/2020
Chavali SS, Cavender CE, Mathews DH, Wedekind JE. "Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove." Journal of the American Chemical Society.. 2020 Nov 10; Epub 2020 Nov 10.

10/13/2020
Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE. "Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors." The Journal of biological chemistry.. 2020 Oct 13; Epub 2020 Oct 13.

6/29/2020
Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE. "Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation." Nucleic acids research.. 2020 Jun 29; Epub 2020 Jun 29.

Books & Chapters

2015
Chapter Title: Tails of Three Knotty Switches: How PreQ1 Riboswitch Structures Control Protein Translation
Book Title: eLifeSciences
Author List: Belashov I.A., Dutta D., Salim M., Wedekind J.E.
Published By: John Wiley & Sons, Inc 2015

2014
Chapter Title: Metal Dependence of Ligand Binding and Heavy-Atom Derivatization of Evolutionarily Distinct PreQ1 Riboswitches
Book Title: Chemical Biology of Nucleic Acids
Author List: Joseph E. Wedekind, Joseph A. Liberman, Jermaine L. Jenkins, Mohammad Salim
Published By: Springer 2014

2010
Chapter Title: Structural aspects of metal ion binding in small natural and artificial RNA enzymes
Book Title: Metal Ions in Life Sciences: Structural and Catalytic Roles of Metals in RNA
Author List: J.E. Wedekind
Edited By: A. Sigel, S. Sigel, R. Sigel
Published By: Wiley-Blackwell 2010

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