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

74 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
2022 Schroeder GM, Cavender CE, Blau ME, Jenkins JL, Mathews DH, Wedekind JE. A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nature Communications. 13: 199. PMID 35017488 DOI: 10.1038/s41467-021-27790-8  0.344
2021 Srivastava Y, Bonn-Breach R, Chavali SS, Lippa GM, Jenkins JL, Wedekind JE. Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing. Crystals. 11. PMID 33777416 DOI: 10.3390/cryst11030273  0.786
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. 295: 16470-16486. PMID 33453887 DOI: 10.1074/jbc.RA120.015444  0.312
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. PMID 33170672 DOI: 10.1021/jacs.0c09689  0.381
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. PMID 33051202 DOI: 10.1074/jbc.RA120.015444  0.312
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. PMID 32597951 DOI: 10.1093/Nar/Gkaa546  0.401
2019 Bonn-Breach R, Gu Y, Jenkins J, Fasan R, Wedekind J. Structure of Sonic Hedgehog protein in complex with zinc(II) and magnesium(II) reveals ion-coordination plasticity relevant to peptide drug design. Acta Crystallographica. Section D, Structural Biology. 75: 969-979. PMID 31692471 DOI: 10.1107/S2059798319012890  0.397
2019 Dutta D, Wedekind JE. Nucleobase mutants of a bacterial preQ-II riboswitch that uncouple metabolite sensing from gene regulation. The Journal of Biological Chemistry. PMID 31659117 DOI: 10.1074/Jbc.Ra119.010755  0.387
2019 Chavali SS, Bonn-Breach R, Wedekind JE. Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery. The Journal of Biological Chemistry. PMID 31080171 DOI: 10.1074/Jbc.Rev119.006860  0.426
2019 Chavali SS, Belashov IA, Jenkins J, Wedekind JE. Structural characterization of lab-evolved proteins reveals signature sequences required for high-affinity binding to HIV-1 TAR RNA Acta Crystallographica Section a Foundations and Advances. 75: a132-a132. DOI: 10.1107/S0108767319098672  0.408
2019 Shashank Chavali S, Belashov I, Jenkins J, Wedekind J. Structural Characterization of a Peptide Derived from a Lab-Evolved Protein that Targets HIV-1 TAR RNA Biophysical Journal. 116: 501a-502a. DOI: 10.1016/J.Bpj.2018.11.2706  0.364
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  0.422
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  0.423
2018 Wedekind JE, Belashov IA, Crawford DW, Lavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR. Structure of HIV-1 TAR in complex with a lab-evolved protein provides insight into RNA recognition and synthesis of a constrained peptide that impairs transcription Acta Crystallographica Section a Foundations and Advances. 74: a345-a345. DOI: 10.1107/S0108767318096551  0.383
2018 Cavender CE, Belashov IA, Wedekind JE, Mathews DH. Conformational Dynamics of the HIV-1 Trans-Activation Response Element RNA Hairpin Bound to a Lab-Evolved Peptide Biophysical Journal. 114: 337a. DOI: 10.1016/J.Bpj.2017.11.1886  0.334
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  0.31
2016 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 (Clifton, N.J.). 1490: 265-80. PMID 27665605 DOI: 10.1007/978-1-4939-6433-8_17  0.44
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  0.382
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  0.425
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  0.337
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  0.34
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  0.436
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  0.409
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  0.408
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  0.731
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  0.412
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  0.394
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  0.774
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 DOI: 10.1039/9781849732512-00299  0.463
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  0.399
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  0.387
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  0.383
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  0.309
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  0.455
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  0.469
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  0.453
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  0.388
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  0.756
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  0.448
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  0.377
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  0.785
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  0.464
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  0.726
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  0.731
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  0.336
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  0.353
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  0.32
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 DOI: 10.4049/Jimmunol.177.1.355  0.31
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  0.408
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  0.777
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  0.466
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  0.761
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  0.536
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+  0.344
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  0.451
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  0.651
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  0.394
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  0.582
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  0.624
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  0.527
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  0.6
2000 Wedekind JE, McKay DB. Purification, crystallization, and X-ray diffraction analysis of small ribozymes. Methods in Enzymology. 317: 149-68. PMID 10829279 DOI: 10.1016/S0076-6879(00)17013-2  0.663
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  0.66
1999 McKay DB, Wedekind JE. 11 Small Ribozymes Cold Spring Harbor Monograph Archive. 37: 265-286. DOI: 10.1101/087969589.37.265  0.42
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  0.662
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  0.583
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  0.562
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  0.589
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  0.611
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 DOI: 10.1021/Bi00016A036  0.523
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 DOI: 10.1021/Bi00013A022  0.592
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 DOI: 10.1021/Bi00035A010  0.606
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  0.558
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 DOI: 10.1021/Bi00197A038  0.604
Show low-probability matches.