Joseph E. Wedekind, Ph.D.

Joseph E. Wedekind, Ph.D.

Contact Information

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

Office: (585) 273-4516
Fax: (585) 275-6007

Journal Articles

Showing all 64 journal articles available.

Jenkins JL, Wedekind JE. "The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures." Methods in molecular biology. 2016 1490:265-80.
2015 Nov 6
Dutta D, Wedekind JE. "Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units." Journal of molecular biology. 2015 Nov 6; 427(22):3469-72. Epub 2015 Aug 06.
2015 Nov
Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH. "Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics." RNA. 2015 Nov; 21(11):1898-907. Epub 2015 Sep 14.
2015 Jul 7
Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE. "Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics." Proceedings of the National Academy of Sciences of the United States of America. 2015 Jul 7; 112(27):E3485-94. Epub 2015 Jun 23.
2014 Jun 4
Heldenbrand H, Janowski PA, Giamba?u G, Giese TJ, Wedekind JE, York DM. "Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path." Journal of the American Chemical Society. 2014 Jun 4; 136(22):7789-92. Epub 2014 May 23.
Liberman JA, Bogue JT, Jenkins JL, Salim M, Wedekind JE. "ITC analysis of ligand binding to preQ? riboswitches." Methods in enzymology. 2014 549:435-50.
2013 Dec
Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL, Walter NG. "Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure." Nucleic acids research. 2013 Dec; 41(22):10462-75. Epub 2013 Sep 03.
2013 Sep 23
Can M, Krucinska J, Zoppellaro G, Andersen NH, Wedekind JE, Hersleth HP, Andersson KK, Bren KL. "Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure." Chembiochem : a European journal of chemical biology. 2013 Sep 23; 14(14):1828-38. Epub 2013 Jul 31.
2013 Jun
Liberman JA, Salim M, Krucinska J, Wedekind JE. "Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold." Nature chemical biology. 2013 Jun; 9(6):353-5. Epub 2013 Apr 14.
2013 Feb 5
Wang W, Maucuer A, Gupta A, Manceau V, Thickman KR, Bauer WJ, Kennedy SD, Wedekind JE, Green MR, Kielkopf CL. "Structure of phosphorylated SF1 bound to U2AF?? in an essential splicing factor complex." Structure. 2013 Feb 5; 21(2):197-208. Epub 2012 Dec 27.
2012 Nov 6
Salter JD, Lippa GM, Belashov IA, Wedekind JE. "Core-binding factor ? increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex." Biochemistry. 2012 Nov 6; 51(44):8702-4. Epub 2012 Oct 25.
2012 Oct 25
Banáš P, Sklenovský P, Wedekind JE, Sponer J, Otyepka M. "Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study." The journal of physical chemistry. B. 2012 Oct 25; 116(42):12721-34. Epub 2012 Oct 12.
2012 Oct 17
Liberman JA, Guo M, Jenkins JL, Krucinska J, Chen Y, Carey PR, Wedekind JE. "A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis." Journal of the American Chemical Society. 2012 Oct 17; 134(41):16933-6. Epub 2012 Oct 03.
Liberman JA, Wedekind JE. "Riboswitch structure in the ligand-free state." Wiley interdisciplinary reviews. RNA. 2012 3(3):369-84. Epub 2011 Sep 28.
Lippa GM, Liberman JA, Jenkins JL, Krucinska J, Salim M, Wedekind JE. "Crystallographic analysis of small ribozymes and riboswitches." Methods in molecular biology. 2012 848:159-84.
2011 Jul 15
Jenkins JL, Krucinska J, McCarty RM, Bandarian V, Wedekind JE. "Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation." The Journal of biological chemistry. 2011 Jul 15; 286(28):24626-37. Epub 2011 May 18.
2011 Jun
Liberman JA, Wedekind JE. "Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world." Current opinion in structural biology. 2011 Jun; 21(3):327-34. Epub 2011 Apr 27.
2010 Jul 14
Wedekind JE. "The apo riboswitch as a molecular hydra." Structure. 2010 Jul 14; 18(7):757-8.
2009 Nov 17
Salter JD, Krucinska J, Raina J, Smith HC, Wedekind JE. "A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function." Biochemistry. 2009 Nov 17; 48(45):10685-7.
2009 Oct
Spitale RC, Wedekind JE. "Exploring ribozyme conformational changes with X-ray crystallography." Methods : a companion to Methods in enzymology. 2009 Oct; 49(2):87-100. Epub 2009 Jun 24.
2009 Sep 16
Guo M, Spitale RC, Volpini R, Krucinska J, Cristalli G, Carey PR, Wedekind JE. "Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation." Journal of the American Chemical Society. 2009 Sep 16; 131(36):12908-9.
2009 Aug 25
Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE. "Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core." Biochemistry. 2009 Aug 25; 48(33):7777-9.
2009 May 6
Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE. "Identification of an imino group indispensable for cleavage by a small ribozyme." Journal of the American Chemical Society. 2009 May 6; 131(17):6093-5.
2009 Apr 24
Spitale RC, Torelli AT, Krucinska J, Bandarian V, Wedekind JE. "The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain." The Journal of biological chemistry. 2009 Apr 24; 284(17):11012-6. Epub 2009 Mar 04.
2008 Nov 28
Bennett RP, Salter JD, Liu X, Wedekind JE, Smith HC. "APOBEC3G subunits self-associate via the C-terminal deaminase domain." The Journal of biological chemistry. 2008 Nov 28; 283(48):33329-36. Epub 2008 Oct 08.
2008 Aug
MacElrevey C, Salter JD, Krucinska J, Wedekind JE. "Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme." RNA. 2008 Aug; 14(8):1600-16. Epub 2008 Jul 02.
2008 Jun 20
Torelli AT, Spitale RC, Krucinska J, Wedekind JE. "Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme." Biochemical and biophysical research communications. 2008 Jun 20; 371(1):154-8. Epub 2008 Apr 16.
2008 Apr 4
Jamburuthugoda VK, Santos-Velazquez JM, Skasko M, Operario DJ, Purohit V, Chugh P, Szymanski EA, Wedekind JE, Bambara RA, Kim B. "Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage." The Journal of biological chemistry. 2008 Apr 4; 283(14):9206-16. Epub 2008 Jan 24.
2008 Mar 21
Bennett RP, Presnyak V, Wedekind JE, Smith HC. "Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding." The Journal of biological chemistry. 2008 Mar 21; 283(12):7320-7. Epub 2007 Dec 28.
2007 Oct 26
Spitale RC, Heller MG, Pelly AJ, Wedekind JE. "Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine." The Journal of organic chemistry. 2007 Oct 26; 72(22):8551-4. Epub 2007 Sep 29.
2007 Jul
Torelli AT, Krucinska J, Wedekind JE. "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." RNA. 2007 Jul; 13(7):1052-70. Epub 2007 May 08.
2007 Jul
MacElrevey C, Spitale RC, Krucinska J, Wedekind JE. "A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme." Acta crystallographica. Section D, Biological crystallography. 2007 Jul; 63(Pt 7):812-25. Epub 2007 Jun 15.
2007 Mar
Lehmann DM, Galloway CA, MacElrevey C, Sowden MP, Wedekind JE, Smith HC. "Functional characterization of APOBEC-1 complementation factor phosphorylation sites." Biochimica et biophysica acta. 2007 Mar; 1773(3):408-18. Epub 2006 Dec 08.
2006 Dec 15
Wedekind JE, Gillilan R, Janda A, Krucinska J, Salter JD, Bennett RP, Raina J, Smith HC. "Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits." The Journal of biological chemistry. 2006 Dec 15; 281(50):38122-6. Epub 2006 Oct 31.
2006 Nov 10
Bennett RP, Diner E, Sowden MP, Lees JA, Wedekind JE, Smith HC. "APOBEC-1 and AID are nucleo-cytoplasmic trafficking proteins but APOBEC3G cannot traffic." Biochemical and biophysical research communications. 2006 Nov 10; 350(1):214-9. Epub 2006 Sep 18.
2006 Aug 24
Ghosh AK, Sridhar PR, Leshchenko S, Hussain AK, Li J, Kovalevsky AY, Walters DE, Wedekind JE, Grum-Tokars V, Das D, Koh Y, Maeda K, Gatanaga H, Weber IT, Mitsuya H. "Structure-based design of novel HIV-1 protease inhibitors to combat drug resistance." Journal of medicinal chemistry. 2006 Aug 24; 49(17):5252-61.
2006 Jul 1
Ichikawa HT, Sowden MP, Torelli AT, Bachl J, Huang P, Dance GS, Marr SH, Robert J, Wedekind JE, Smith HC, Bottaro A. "Structural phylogenetic analysis of activation-induced deaminase function." The Journal of immunology : official journal of the American Association of Immunologists. 2006 Jul 1; 177(1):355-61.
2006 May 23
Chaves FA, Richards KA, Torelli A, Wedekind J, Sant AJ. "Peptide-binding motifs for the I-Ad MHC class II molecule: alternate pH-dependent binding behavior." Biochemistry. 2006 May 23; 45(20):6426-33.
2006 Jan 24
Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE. "Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer." Biochemistry. 2006 Jan 24; 45(3):686-700.
2005 Dec 1
MacElrevey C, Wedekind JE. "Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design." Acta crystallographica. Section F, Structural biology and crystallization communications. 2005 Dec 1; 61(Pt 12):1049-53. Epub 2005 Nov 12.
2005 Nov 8
Alam S, Grum-Tokars V, Krucinska J, Kundracik ML, Wedekind JE. "Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn." Biochemistry. 2005 Nov 8; 44(44):14396-408.
2005 Oct
Xie K, Song SC, Spitalnik SL, Wedekind JE. "Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition." Acta crystallographica. Section D, Biological crystallography. 2005 Oct; 61(Pt 10):1386-94. Epub 2005 Sep 28.
2005 Oct
Gruswitz F, Frishman M, Goldstein BM, Wedekind JE. "Coupling of MBP fusion protein cleavage with sparse matrix crystallization screens to overcome problematic protein solubility." BioTechniques. 2005 Oct; 39(4):476, 478, 480.
2005 Aug 9
Jamburuthugoda VK, Guo D, Wedekind JE, Kim B. "Kinetic evidence for interaction of human immunodeficiency virus type 1 reverse transcriptase with the 3'-OH of the incoming dTTP substrate." Biochemistry. 2005 Aug 9; 44(31):10635-43.
2004 Nov 9
Goodman JL, Wang S, Alam S, Ruzicka FJ, Frey PA, Wedekind JE. "Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family." Biochemistry. 2004 Nov 9; 43(44):13883-91.
2004 May 25
Xie K, Sowden MP, Dance GS, Torelli AT, Smith HC, Wedekind JE. "The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1." Proceedings of the National Academy of Sciences of the United States of America. 2004 May 25; 101(21):8114-9. Epub 2004 May 17.
2004 May
Alam S, Wang SC, Ruzicka FJ, Frey PA, Wedekind JE. "Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase from Pseudomonas putida." Acta crystallographica. Section D, Biological crystallography. 2004 May; 60(Pt 5):941-4. Epub 2004 Apr 21.
2004 Apr
Song SC, Xie K, Czerwinski M, Spitalnik SL, Wedekind JE. "Purification, crystallization and X-ray diffraction analysis of a recombinant Fab that recognizes a human blood-group antigen." Acta crystallographica. Section D, Biological crystallography. 2004 Apr; 60(Pt 4):788-91. Epub 2004 Mar 23.
2003 Aug 19
Wedekind JE, McKay DB. "Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation." Biochemistry. 2003 Aug 19; 42(32):9554-63.
2003 Apr
Wedekind JE, Dance GS, Sowden MP, Smith HC. "Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business." Trends in genetics : TIG. 2003 Apr; 19(4):207-16.
2003 Jan
Grum-Tokars V, Milovanovic M, Wedekind JE. "Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme." Acta crystallographica. Section D, Biological crystallography. 2003 Jan; 59(Pt 1):142-5. Epub 2002 Dec 19.
2001 Dec 7
Wedekind JE, Trame CB, Dorywalska M, Koehl P, Raschke TM, McKee M, FitzGerald D, Collier RJ, McKay DB. "Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity." Journal of molecular biology. 2001 Dec 7; 314(4):823-37.
Wedekind JE, McKay DB. "Purification, crystallization, and X-ray diffraction analysis of small ribozymes." Methods in enzymology. 2000 317:149-68.
1999 Mar
Wedekind JE, McKay DB. "Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis." Nature structural biology. 1999 Mar; 6(3):261-8.
Wedekind JE, McKay DB. "Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis." Annual review of biophysics and biomolecular structure. 1998 27:475-502.
1996 Dec 24
Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. "The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids." Biochemistry. 1996 Dec 24; 35(51):16489-501.
1996 Dec
Reed GH, Poyner RR, Larsen TM, Wedekind JE, Rayment I. "Structural and mechanistic studies of enolase." Current opinion in structural biology. 1996 Dec; 6(6):736-43.
1996 Sep 10
Wedekind JE, Frey PA, Rayment I. "The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer." Biochemistry. 1996 Sep 10; 35(36):11560-9.
1996 Apr 9
Larsen TM, Wedekind JE, Rayment I, Reed GH. "A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution." Biochemistry. 1996 Apr 9; 35(14):4349-58.
1995 Sep 5
Wedekind JE, Frey PA, Rayment I. "Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 A resolution." Biochemistry. 1995 Sep 5; 34(35):11049-61.
1995 Apr 25
Ruzicka FJ, Wedekind JE, Kim J, Rayment I, Frey PA. "Galactose-1-phosphate uridylyltransferase from Escherichia coli, a zinc and iron metalloenzyme." Biochemistry. 1995 Apr 25; 34(16):5610-7.
1995 Apr 4
Wedekind JE, Reed GH, Rayment I. "Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution." Biochemistry. 1995 Apr 4; 34(13):4325-30.
1994 Aug 9
Wedekind JE, Poyner RR, Reed GH, Rayment I. "Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution." Biochemistry. 1994 Aug 9; 33(31):9333-42.
1994 May 1
Wedekind JE, Frey PA, Rayment I. "Crystallization and preliminary crystallographic analysis of galactose-1-phosphate uridylyltransferase from Escherichia coli." Acta crystallographica. Section D, Biological crystallography. 1994 May 1; 50(Pt 3):329-31.


Belashov I.A., Dutta D., Salim M., Wedekind J.E.. "Tails of Three Knotty Switches: How PreQ1 Riboswitch Structures Control Protein Translation". eLifeSciences. : John Wiley & Sons, Inc, 2015.
Joseph E. Wedekind, Joseph A. Liberman, Jermaine L. Jenkins, Mohammad Salim. "Metal Dependence of Ligand Binding and Heavy-Atom Derivatization of Evolutionarily Distinct PreQ1 Riboswitches". Chemical Biology of Nucleic Acids. : Springer, 2014. 423-440
J.E. Wedekind. "Structural aspects of metal ion binding in small natural and artificial RNA enzymes". Metal Ions in Life Sciences: Structural and Catalytic Roles of Metals in RNA. A. Sigel, S. Sigel, R. Sigel. : Wiley-Blackwell, 2010.
J.E. Wedekind & P.A Beal. "Mechanism of action and structural aspects of ADARS (A-to-I) and APOBEC-related (C-to-U) deaminases". In DNA and RNA modification Enzymes: Comparative Structure, Mechanism, Functions. H. Grosjean. : Landes BioSciences, 2009. 1-682
C. McElrevey, J.E. Wedekind. "Chemistry, Phylogeny and Structure of the APOBEC Family". RNA and DNA Editing: Molecular Mechanisms and their Integration into Biological. Harold C. Smith. New Jersey: Wiley Interscience, 2008. 369-430
Smith* HC, Wedekind* JE, Xie K, Sowden MP. "Mammalian C to U Editing". Topics in Current Genetics: "Fine-Tuning of RNA Functions by Modification and Ed. H. Grosjean. : Springer-Verlag, Berlin, 2005. 1610-2096
McKay, D.B & Wedekind, J.E.. "Small Ribozymes". The RNA World. R. Gesteland, T. Cech, J.F. Atkins. Cold Spring Harbor, New York: Cold Spring Harbor, 1999. 265-286