Joseph E. Wedekind, Ph. D. - Publications

Affiliations: 
Biochemistry University of Rochester, Rochester, NY 
Area:
x-ray crystallography, ncRNA structure, APOBEC3G
Website:
http://www.urmc.rochester.edu/people/23504899-joseph-e-wedekind

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Warnasooriya C, Ling C, Belashov IA, Salim M, Wedekind JE, Ermolenko DN. Observation of preQ-II riboswitch dynamics using single-molecule FRET. Rna Biology. PMID 30328747 DOI: 10.1080/15476286.2018.1536591  0.56
2018 Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. 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. Nucleic Acids Research. PMID 29961805 DOI: 10.1093/nar/gky529  0.56
2018 Dutta D, Belashov IA, Wedekind JE. Coupling GFP Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria. Biochemistry. PMID 29897738 DOI: 10.1021/acs.biochem.8b00316  0.56
2017 Wedekind JE, Dutta D, Belashov IA, Jenkins JL. Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes. The Journal of Biological Chemistry. PMID 28455443 DOI: 10.1074/jbc.R117.787713  0.56
2015 Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH. Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. Rna (New York, N.Y.). 21: 1898-907. PMID 26370581 DOI: 10.1261/rna.051367.115  1
2015 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. PMID 26255959 DOI: 10.1016/j.jmb.2015.08.001  1
2015 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. PMID 26106162 DOI: 10.1073/pnas.1503955112  1
2014 Liberman JA, Bogue JT, Jenkins JL, Salim M, Wedekind JE. ITC analysis of ligand binding to preQ₁ riboswitches. Methods in Enzymology. 549: 435-50. PMID 25432759 DOI: 10.1016/B978-0-12-801122-5.00018-0  1
2014 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. 136: 7789-92. PMID 24842535 DOI: 10.1021/ja500180q  1
2013 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. 41: 10462-75. PMID 24003028 DOI: 10.1093/nar/gkt798  1
2013 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. 14: 1828-38. PMID 23908017 DOI: 10.1002/cbic.201300118  1
2013 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. 9: 353-5. PMID 23584677 DOI: 10.1038/nchembio.1231  1
2013 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 U2AF⁶⁵ in an essential splicing factor complex. Structure (London, England : 1993). 21: 197-208. PMID 23273425 DOI: 10.1016/j.str.2012.10.020  1
2012 Salter JD, Lippa GM, Belashov IA, Wedekind JE. Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry. 51: 8702-4. PMID 23098073 DOI: 10.1021/bi301244z  1
2012 Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M. Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. The Journal of Physical Chemistry. B. 116: 12721-34. PMID 22998634 DOI: 10.1021/jp309230v  1
2012 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. 134: 16933-6. PMID 22989273 DOI: 10.1021/ja3070528  1
2012 Lippa GM, Liberman JA, Jenkins JL, Krucinska J, Salim M, Wedekind JE. Crystallographic analysis of small ribozymes and riboswitches. Methods in Molecular Biology (Clifton, N.J.). 848: 159-84. PMID 22315069 DOI: 10.1007/978-1-61779-545-9_11  1
2012 Liberman JA, Wedekind JE. Riboswitch structure in the ligand-free state. Wiley Interdisciplinary Reviews. Rna. 3: 369-84. PMID 21957061 DOI: 10.1002/wrna.114  1
2011 Wedekind JE. Metal ion binding and function in natural and artificial small RNA enzymes from a structural perspective. Metal Ions in Life Sciences. 9: 299-345. PMID 22010277  1
2011 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. 286: 24626-37. PMID 21592962 DOI: 10.1074/jbc.M111.230375  1
2011 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. 21: 327-34. PMID 21530235 DOI: 10.1016/j.sbi.2011.03.016  1
2010 Wedekind JE. The apo riboswitch as a molecular hydra. Structure (London, England : 1993). 18: 757-8. PMID 20637410 DOI: 10.1016/j.str.2010.06.003  1
2010 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 pre-catalytic conformation Aip Conference Proceedings. 1267: 627-628. DOI: 10.1063/1.3482715  1
2009 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. 48: 10685-7. PMID 19839647 DOI: 10.1021/bi901642c  1
2009 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. 131: 12908-9. PMID 19702306 DOI: 10.1021/ja9060883  1
2009 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. 48: 7777-9. PMID 19634899 DOI: 10.1021/bi9011622  1
2009 Spitale RC, Wedekind JE. Exploring ribozyme conformational changes with X-ray crystallography. Methods (San Diego, Calif.). 49: 87-100. PMID 19559088 DOI: 10.1016/j.ymeth.2009.06.003  1
2009 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. 131: 6093-5. PMID 19354216 DOI: 10.1021/ja900450h  1
2009 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. 284: 11012-6. PMID 19261617 DOI: 10.1074/jbc.C900024200  1
2008 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. 283: 33329-36. PMID 18842592 DOI: 10.1074/jbc.M803726200  1
2008 MacElrevey C, Salter JD, Krucinska J, Wedekind JE. Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. Rna (New York, N.Y.). 14: 1600-16. PMID 18596253 DOI: 10.1261/rna.1055308  1
2008 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. 371: 154-8. PMID 18423397 DOI: 10.1016/j.bbrc.2008.04.036  1
2008 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. 283: 9206-16. PMID 18218633 DOI: 10.1074/jbc.M710149200  1
2008 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. 283: 7320-7. PMID 18165230 DOI: 10.1074/jbc.M708567200  1
2007 Spitale RC, Heller MG, Pelly AJ, Wedekind JE. Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine. The Journal of Organic Chemistry. 72: 8551-4. PMID 17902696 DOI: 10.1021/jo7015778  1
2007 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. 63: 812-25. PMID 17582172 DOI: 10.1107/S090744490702464X  1
2007 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 (New York, N.Y.). 13: 1052-70. PMID 17488874 DOI: 10.1261/rna.510807  1
2007 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. 1773: 408-18. PMID 17229474 DOI: 10.1016/j.bbamcr.2006.11.019  1
2007 Macelrevey C, Wedekind JE. Chemistry, Phylogeny, and Three-Dimensional Structure of the APOBEC Protein Family Rna and Dna Editing: Molecular Mechanisms and Their Integration Into Biological Systems. 369-419. DOI: 10.1002/9780470262269.ch16  1
2006 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. 281: 38122-6. PMID 17079235 DOI: 10.1074/jbc.C600253200  1
2006 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. 350: 214-9. PMID 16999936 DOI: 10.1016/j.bbrc.2006.09.032  1
2006 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. 49: 5252-61. PMID 16913714 DOI: 10.1021/jm060561m  1
2006 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. Journal of Immunology (Baltimore, Md. : 1950). 177: 355-61. PMID 16785531  1
2006 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. 45: 6426-6433. PMID 16700553 DOI: 10.1021/bi060194g  1
2006 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. 45: 686-700. PMID 16411744 DOI: 10.1021/bi051887k  1
2005 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. 61: 1049-53. PMID 16511232 DOI: 10.1107/S1744309105035888  1
2005 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. 44: 14396-408. PMID 16262240 DOI: 10.1021/bi051550i  1
2005 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. 39: 476, 478, 480. PMID 16235558 DOI: 10.2144/000112033  1
2005 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. 61: 1386-94. PMID 16204891 DOI: 10.1107/S0907444905023851  1
2005 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. 44: 10635-43. PMID 16060672 DOI: 10.1021/bi050611+  1
2004 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. 43: 13883-91. PMID 15518536 DOI: 10.1021/bi048207i  1
2004 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. 101: 8114-9. PMID 15148397 DOI: 10.1073/pnas.0400493101  1
2004 Smith HC, Bottaro A, Sowden MP, Wedekind JE. Activation induced deaminase: the importance of being specific. Trends in Genetics : Tig. 20: 224-7. PMID 15145573 DOI: 10.1016/j.tig.2004.03.012  1
2004 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. 60: 941-4. PMID 15103146 DOI: 10.1107/S0907444904005256  1
2004 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. 60: 788-91. PMID 15039587 DOI: 10.1107/S0907444904002963  1
2003 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. 42: 9554-63. PMID 12911297 DOI: 10.1021/bi0300783  1
2003 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. 19: 207-16. PMID 12683974 DOI: 10.1016/S0168-9525(03)00054-4  1
2003 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. 59: 142-5. PMID 12499551 DOI: 10.1107/S0907444902019066  1
2001 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. 314: 823-37. PMID 11734000 DOI: 10.1006/jmbi.2001.5195  1
2000 Wedekind JE, McKay DB. Purification, crystallization, and X-ray diffraction analysis of small ribozymes. Methods in Enzymology. 317: 149-68. PMID 10829279  1
1999 Wedekind JE, McKay DB. Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis. Nature Structural Biology. 6: 261-8. PMID 10074945 DOI: 10.1038/6700  1
1998 Wedekind JE, McKay DB. Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis. Annual Review of Biophysics and Biomolecular Structure. 27: 475-502. PMID 9646875 DOI: 10.1146/annurev.biophys.27.1.475  1
1996 Reed GH, Poyner RR, Larsen TM, Wedekind JE, Rayment I. Structural and mechanistic studies of enolase. Current Opinion in Structural Biology. 6: 736-43. PMID 8994873 DOI: 10.1016/S0959-440X(96)80002-9  1
1996 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. 35: 16489-501. PMID 8987982 DOI: 10.1021/bi9616413  1
1996 Wedekind JE, Frey PA, Rayment I. The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer. Biochemistry. 35: 11560-9. PMID 8794735 DOI: 10.1021/bi9612677  1
1996 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. 35: 4349-58. PMID 8605183 DOI: 10.1021/bi952859c  1
1995 Ruzicka FJ, Wedekind JE, Kim J, Rayment I, Frey PA. Galactose-1-phosphate uridylyltransferase from Escherichia coli, a zinc and iron metalloenzyme. Biochemistry. 34: 5610-7. PMID 7727423  1
1995 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. 34: 4325-30. PMID 7703246  1
1995 Wedekind JE, Frey PA, Rayment I. Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 A resolution. Biochemistry. 34: 11049-61. PMID 7669762  1
1994 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. 50: 329-31. PMID 15299446 DOI: 10.1107/S0907444993012958  1
1994 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. 33: 9333-42. PMID 8049235  1
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