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Joseph E. Wedekind, Ph.D.


Showing all 77 journal articles & 7 books available

Journal Articles

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.. 2022 Jan 11; 13(1):199. Epub 2022 Jan 11.

Chavali SS, Mali SM, Bonn R, Saseendran A, Bennett RP, Smith HC, Fasan R, Wedekind JE. "Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells." The Journal of biological chemistry.. 2021 Nov 9; :101390. Epub 2021 Nov 09.

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.. 2021 Mar; 11(3)Epub 2021 Mar 10.

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 Dec 4; 295(49):16470-16486.

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.

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.

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.. 2019 Nov 1; 75(Pt 11):969-979. Epub 2019 Oct 30.

Dutta D, Wedekind JE. "Nucleobase mutants of a bacterial preQ-II riboswitch that uncouple metabolite sensing from gene regulation." The Journal of biological chemistry.. 2019 Oct 28; Epub 2019 Oct 28.

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.. 2019 May 12; Epub 2019 May 12.

Warnasooriya C, Ling C, Belashov IA, Salim M, Wedekind JE, Ermolenko DN. "Observation of preQ-II riboswitch dynamics using single-molecule FRET." RNA biology.. 2018 Oct 17; :1-7. Epub 2018 Oct 17.

Dutta D, Belashov IA, Wedekind JE. "Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria." Biochemistry.. 2018 Aug 7; 57(31):4620-4628. Epub 2018 Jun 26.

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.. 2018 Jul 27; 46(13):6401-6415.

Wedekind JE, Dutta D, Belashov IA, Jenkins JL. "Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes." The Journal of biological chemistry.. 2017 Jun 9; 292(23):9441-9450. Epub 2017 Apr 28.

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.

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):3469-3472. Epub 2015 Aug 06.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Wedekind JE. "The apo riboswitch as a molecular hydra." Structure.. 2010 Jul 14; 18(7):757-8.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Books & Chapters

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, Inc2015

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: Springer2014

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-Blackwell2010

Chapter Title: Mechanism of action and structural aspects of ADARS (A-to-I) and APOBEC-related (C-to-U) deaminases
Book Title: In DNA and RNA modification Enzymes: Comparative Structure, Mechanism, Functions
Author List: J.E. Wedekind & P.A Beal
Edited By: H. Grosjean
Published By: Landes BioSciences2009

Chapter Title: Chemistry, Phylogeny and Structure of the APOBEC Family
Book Title: RNA and DNA Editing: Molecular Mechanisms and their Integration into Biological
Author List: C. McElrevey, J.E. Wedekind
Edited By: Harold C. Smith
Published By: Wiley Interscience2008 in New Jersey

Chapter Title: Mammalian C to U Editing
Book Title: Topics in Current Genetics: "Fine-Tuning of RNA Functions by Modification and Ed
Author List: Smith* HC, Wedekind* JE, Xie K, Sowden MP
Edited By: H. Grosjean
Published By: Springer-Verlag, Berlin2005

Chapter Title: Small Ribozymes
Book Title: The RNA World
Author List: McKay, D.B & Wedekind, J.E.
Edited By: R. Gesteland, T. Cech, J.F. Atkins
Published By: Cold Spring Harbor1999 in Cold Spring Harbor, New York