Joseph E Wedekind

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. pmc Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits
    Joseph E Wedekind
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Biol Chem 281:38122-6. 2006
  2. pmc APOBEC3G subunits self-associate via the C-terminal deaminase domain
    Ryan P Bennett
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 283:33329-36. 2008
  3. pmc Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold
    Joseph A Liberman
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
    Nat Chem Biol 9:353-5. 2013
  4. pmc Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme
    Celeste MacElrevey
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    RNA 14:1600-16. 2008
  5. pmc Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme
    Andrew T Torelli
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue Box 712, Rochester, New York 14642, USA
    Biochem Biophys Res Commun 371:154-8. 2008
  6. pmc The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain
    Robert C Spitale
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 284:11012-6. 2009
  7. pmc Identification of an imino group indispensable for cleavage by a small ribozyme
    Robert C Spitale
    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627 0216, USA
    J Am Chem Soc 131:6093-5. 2009
  8. pmc Exploring ribozyme conformational changes with X-ray crystallography
    Robert C Spitale
    Department of Chemistry, Biological Chemistry Cluster, Rochester, NY 14627 0216, USA
    Methods 49:87-100. 2009
  9. pmc Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer
    Jason Salter
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    Biochemistry 45:686-700. 2006
  10. doi request reprint Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding
    Ryan P Bennett
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 283:7320-7. 2008

Collaborators

  • Harold C Smith
  • Rosaria Volpini
  • Michael R Green
  • Clara L Kielkopf
  • Paul R Carey
  • Jacques Robert
  • Mark Skasko
  • David M Lehmann
  • Xiang Liu
  • Baek Kim
  • Hashim M Al-Hashimi
  • Jolanta Krucinska
  • Joseph A Liberman
  • Robert C Spitale
  • Andrew T Torelli
  • Jason D Salter
  • Ryan P Bennett
  • Celeste MacElrevey
  • Jermaine L Jenkins
  • Varuni K Jamburuthugoda
  • Geoffrey M Lippa
  • Shabnam Alam
  • Kefang Xie
  • Krishna C Suddala
  • Mark P Sowden
  • Wenhua Wang
  • Mohammad Salim
  • Vahe Bandarian
  • Gloria Cristalli
  • Moriah G Heller
  • Jason Salter
  • H Travis Ichikawa
  • Valerie Grum-Tokars
  • Geoffrey S C Dance
  • Franz Gruswitz
  • Jessica L Goodman
  • Jun Feng
  • Alexandre Maucuer
  • William J Bauer
  • Nils G Walter
  • Valérie Manceau
  • Charles L Brooks
  • Karen R Thickman
  • Anthony M Mustoe
  • Scott D Kennedy
  • Catherine D Eichhorn
  • Ankit Gupta
  • Arlie J Rinaldi
  • Yuanyuan Chen
  • Ivan A Belashov
  • Man Guo
  • Reid M McCarty
  • Jay Raina
  • Michael V Mungillo
  • Jose M Santos-Velazquez
  • Darwin J Operario
  • Pauline Chugh
  • Robert A Bambara
  • Vladimir Presnyak
  • ERIKA A SZYMANSKI
  • Vandana Purohit
  • Amanda J Pelly
  • Pinwei Huang
  • Elie Diner
  • Jurgen Bachl
  • Joshua A Lees
  • Shauna H Marr
  • Andrea Bottaro
  • Mary Frishman
  • Melisa L Kundracik
  • Dongdong Guo
  • Shuh Chyung Song
  • Steven L Spitalnik
  • Barry M Goldstein
  • Perry A Frey
  • Susan Wang
  • Frank J Ruzicka

Detail Information

Publications37

  1. pmc Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits
    Joseph E Wedekind
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Biol Chem 281:38122-6. 2006
    ..These observations imply that the disruption of cellular HMM particles may require regulation of protein-RNA, as well as protein-protein interactions, which has implications for therapeutic development...
  2. pmc APOBEC3G subunits self-associate via the C-terminal deaminase domain
    Ryan P Bennett
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 283:33329-36. 2008
    ..These findings corroborate the small angle x-ray scattering structural model and are instructive for development of high throughput screens that target specific domains and their functions to identify HIV/AIDS therapeutics...
  3. pmc Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold
    Joseph A Liberman
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
    Nat Chem Biol 9:353-5. 2013
    ..The results account for translational control mediated by the preQ1-II riboswitch class and expand the known repertoire of ligand-binding modes used by regulatory RNAs...
  4. pmc Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme
    Celeste MacElrevey
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    RNA 14:1600-16. 2008
    ..These findings demonstrate the importance of the Ade38 Watson-Crick face in attaining a reaction-intermediate state and the sensitivity of the RNA fold to restructuring when electrostatic and shape features fail to complement...
  5. pmc Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme
    Andrew T Torelli
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue Box 712, Rochester, New York 14642, USA
    Biochem Biophys Res Commun 371:154-8. 2008
    ..The advantages of 2',5'-linkages to investigate phosphoryl-transfer reactions are discussed, and argue for their expanded use in structural studies...
  6. pmc The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain
    Robert C Spitale
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 284:11012-6. 2009
    ..The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated...
  7. pmc Identification of an imino group indispensable for cleavage by a small ribozyme
    Robert C Spitale
    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627 0216, USA
    J Am Chem Soc 131:6093-5. 2009
    ..This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships...
  8. pmc Exploring ribozyme conformational changes with X-ray crystallography
    Robert C Spitale
    Department of Chemistry, Biological Chemistry Cluster, Rochester, NY 14627 0216, USA
    Methods 49:87-100. 2009
    ..The methods are broadly applicable to other RNA systems...
  9. pmc Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer
    Jason Salter
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    Biochemistry 45:686-700. 2006
    ..Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction...
  10. doi request reprint Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding
    Ryan P Bennett
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 283:7320-7. 2008
    ..The CRS lies in a region involved in both Gag and Vif interactions; therefore, identification of this motif has important implications for the design of therapeutics that target HIV-1 while maintaining antiviral and cellular functions...
  11. doi request reprint Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure
    Krishna C Suddala
    Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA
    Nucleic Acids Res 41:10462-75. 2013
    ....
  12. ncbi request reprint Structural phylogenetic analysis of activation-induced deaminase function
    H Travis Ichikawa
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Immunol 177:355-61. 2006
    ....
  13. pmc APOBEC-1 and AID are nucleo-cytoplasmic trafficking proteins but APOBEC3G cannot traffic
    Ryan P Bennett
    Department of Biochemistry, Box 712, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Biochem Biophys Res Commun 350:214-9. 2006
    ..We demonstrate that hA3G is not a nucleo-cytoplasmic shuttling protein like APOBEC-1 and AID, but is strongly retained in the cytoplasm through a mechanism that involves both the N and C-terminal regions of the protein...
  14. pmc A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization
    Andrew T Torelli
    Department of Biochemistry and Biophysics, Rochester, NY 14642, USA
    RNA 13:1052-70. 2007
    ..Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds...
  15. pmc A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme
    Celeste MacElrevey
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    Acta Crystallogr D Biol Crystallogr 63:812-25. 2007
    ..The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects...
  16. pmc Riboswitch structure in the ligand-free state
    Joseph A Liberman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
    Wiley Interdiscip Rev RNA 3:369-84. 2012
    ..An understanding of these topics is essential to comprehend riboswitch gene regulation at the molecular level, which has already provided a basis to understand the mechanism of action of natural antimicrobials...
  17. pmc Functional characterization of APOBEC-1 complementation factor phosphorylation sites
    David M Lehmann
    Environmental Health Sciences Center, Department of Toxicology, University of Rochester, Rochester, NY 14642, USA
    Biochim Biophys Acta 1773:408-18. 2007
    ..These data suggest that phosphorylation of ACF by PKC may be a key regulatory mechanism of apoB mRNA editing in rat hepatocytes...
  18. pmc Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core
    Robert C Spitale
    Department of Biochemistry and Biophysics, 601 Elmwood Avenue, Box 712, Rochester New York 14642, USA
    Biochemistry 48:7777-9. 2009
    ..We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA...
  19. pmc The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1
    Kefang Xie
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 101:8114-9. 2004
    ..Most importantly, the results suggested both AID and APOBEC-1 are equally likely to bind single-stranded DNA or RNA, which has implications for the identification of natural AID targets...
  20. pmc A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function
    Jason D Salter
    Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA
    Biochemistry 48:10685-7. 2009
    ..Overall, the results provide physical restraints for the A3G quaternary structure that have implications for modulating antiviral function...
  21. pmc Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex
    Wenhua Wang
    Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Structure 21:197-208. 2013
    ..We further determine that SPSP phosphorylation and the SF1/U2AF⁶⁵ interface are essential in vivo. These results offer a structural prototype for phosphorylation-dependent control of pre-mRNA splicing factors...
  22. pmc A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis
    Joseph A Liberman
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA
    J Am Chem Soc 134:16933-6. 2012
    ..Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity...
  23. pmc Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage
    Varuni K Jamburuthugoda
    Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    J Biol Chem 283:9206-16. 2008
    ..This can restrict ground state dNTP binding and lead to inefficient DNA synthesis particularly at low dNTP concentrations, ultimately contributing to viral replication failure in macrophage and instability in vivo of the M184I mutation...
  24. ncbi request reprint Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition
    Kefang Xie
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Acta Crystallogr D Biol Crystallogr 61:1386-94. 2005
    ..These results suggest a model for recognition of the glycopeptide antigen that accounts for the deleterious effect of the G91S substitution...
  25. pmc Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation
    Jermaine L Jenkins
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Biol Chem 286:24626-37. 2011
    ..These observations are distinct from transcriptional preQ(1) riboswitches of the same class that exhibit strictly ligand-dependent folding. Implications for gene regulation are discussed...
  26. pmc Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design
    Celeste MacElrevey
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:1049-53. 2005
    ..5, c = 63.5 A. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported...
  27. ncbi request reprint Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family
    Jessica L Goodman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Box 712, Rochester, New York 14642, USA
    Biochemistry 43:13883-91. 2004
    ..A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins...
  28. pmc Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world
    Joseph A Liberman
    Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
    Curr Opin Struct Biol 21:327-34. 2011
    ..The results showcase the breadth of functionality attainable from ncRNAs, as well as molecular features notable for antibacterial design...
  29. pmc Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex
    Jason D Salter
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
    Biochemistry 51:8702-4. 2012
    ..An additional interface between Cul5 and an N-terminal region of Vif appears to be plausible, which has therapeutic design implications...
  30. doi request reprint Crystallographic analysis of small ribozymes and riboswitches
    Geoffrey M Lippa
    Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
    Methods Mol Biol 848:159-84. 2012
    ..The methods presented provide a guide for comparable investigations of noncoding RNA molecules including a 48-solution, "first choice" RNA crystal screen compiled from our prior successes with commercially available screens...
  31. ncbi request reprint Activation induced deaminase: the importance of being specific
    Harold C Smith
    Department of Biochemistry and Biophysics, The James P Wilmot Cancer Center, USA
    Trends Genet 20:224-7. 2004
    ..Recently, the biological relevance of assaying mammalian enzymes for DNA deaminase activity using Escherichia coli DNA as a reporter has been questioned, representing another round in the ongoing debate...
  32. ncbi request reprint Metal ion binding and function in natural and artificial small RNA enzymes from a structural perspective
    Joseph E Wedekind
    Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Met Ions Life Sci 9:299-345. 2011
    ..When metal ion binding isn't possible, ribozymes make due by ionizing their bases, or by recruiting cofactors that augment their chemical functionality...
  33. ncbi request reprint Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn
    Shabnam Alam
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    Biochemistry 44:14396-408. 2005
    ..A comparison of all three new structures has implications for the catalytically relevant conformation of the S-turn and suggests a rationale for the distinctive metal dependence of each mutant...
  34. ncbi request reprint Kinetic evidence for interaction of human immunodeficiency virus type 1 reverse transcriptase with the 3'-OH of the incoming dTTP substrate
    Varuni K Jamburuthugoda
    Department of Biochemistry and Biophysics, University of Rochester, 601 Elmwood Avenue, Box 672, Rochester, New York 14642, USA
    Biochemistry 44:10635-43. 2005
    ..The kinetic data presented in this report demonstrate the functional role of the Q151 residue in HIV-1 RT interaction with dTTP and its analogues containing chemical modifications at the 3'-C of the sugar moiety...
  35. pmc Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine
    Robert C Spitale
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA
    J Org Chem 72:8551-4. 2007
    ....
  36. ncbi request reprint Coupling of MBP fusion protein cleavage with sparse matrix crystallization screens to overcome problematic protein solubility
    Franz Gruswitz
    University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Biotechniques 39:476, 478, 480. 2005
  37. ncbi request reprint Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business
    Joseph E Wedekind
    Department of Biochemistry and Biophysics, University of Rochester, School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY 14623, USA
    Trends Genet 19:207-16. 2003
    ..In light of the hypothesis that these proteins might represent novel mRNA editing systems that could affect proteome diversity, we consider their structure, expression and relevance to biomedically significant processes or pathologies...