URMC / Labs / Wedekind Lab / Publications Publications Schroeder GMKiliushik DJenkins JLWedekind JE Structure and function analysis of a type III preQ1-I riboswitch from E. coli reveals direct metabolite-sensing by the Shine-Dalgarno sequence.; The Journal of biological chemistry. 2023 Sep 01. Kretsch RCAndersen ESBujnicki JMChiu WDas RLuo BMasquida BMcRae EKSSchroeder GMSu ZWedekind JEXu LZhang KZheludev INMoult JKryshtafovych A RNA target highlights in CASP15: Evaluation of predicted models by structure providers.; Proteins. 2023 Jul 19. Wedekind JE RNA in the loop: Probing T-loop/T-loop receptor interactions as mediators of long-range RNA contacts that influence gene regulation.; Journal of molecular biology. 2023 Apr 06. Schroeder GMAkinyemi OMalik JFocht CMPritchett EMBaker CDMcSally JPJenkins JLMathews DHWedekind JE A riboswitch separated from its ribosome-binding site still regulates translation.; Nucleic acids research. 2023 Feb 10. Srivastava YBlau MEJenkins JLWedekind JE Full-Length NAD+-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate.; Biochemistry. 2023 Jan 10. Cavender CESchroeder GMMathews DHWedekind JE Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model.; Methods in molecular biology (Clifton, N.J.); Vol 2568, pp. 53-73. 2023. Schroeder GMCavender CEBlau MEJenkins JLMathews DHWedekind JE A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.; Nature communications; Vol 13(1). 2022 Jan 11. Chavali SSMali SMBonn RSaseendran ABennett RPSmith HCFasan RWedekind 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 09. Srivastava YBonn-Breach RChavali SSLippa GMJenkins JLWedekind JE Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.; Crystals; Vol 11(3). 2021 Mar. Chavali SSMali SMJenkins JLFasan RWedekind 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; Vol 295(49). 2020 Dec 04. Chavali SSCavender CEMathews DHWedekind 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. Schroeder GMDutta DCavender CEJenkins JLPritchett EMBaker CDAshton JMMathews DHWedekind 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. Bonn-Breach RGu YJenkins JFasan RWedekind 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; Vol 75(Pt 11). 2019 Nov 01. Dutta DWedekind JE Nucleobase mutants of a bacterial preQ1-II riboswitch that uncouple metabolite sensing from gene regulation.; The Journal of biological chemistry. 2019 Oct 28. Chavali SSBonn-Breach RWedekind 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. Warnasooriya CLing CBelashov IASalim MWedekind JEErmolenko DN Observation of preQ1-II riboswitch dynamics using single-molecule FRET.; RNA biology. 2018 Oct 17. Belashov IACrawford DWCavender CEDai PBeardslee PCMathews DHPentelute BLMcNaughton BRWedekind 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 Jun 29. Dutta DBelashov IAWedekind JE Coupling GFP Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.; Biochemistry. 2018 Jun 13. Wedekind JEDutta DBelashov IAJenkins JL Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes.; The Journal of biological chemistry. 2017 Apr 28. Jenkins JLWedekind 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.); Vol 1490. 2016. Dutta DWedekind JE Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units.; Journal of molecular biology; Vol 427(22). 2015 Nov 6. Aytenfisu AHLiberman JAWedekind JEMathews DH Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.; RNA (New York, N.Y.); Vol 21(11). 2015 Nov. Liberman JASuddala KCAytenfisu AChan DBelashov IASalim MMathews DHSpitale RCWalter NGWedekind 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; Vol 112(27). 2015 Jul 7. Heldenbrand HJanowski PAGiambaşu GGiese TJWedekind JEYork 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; Vol 136(22). 2014 Jun 4. Liberman JABogue JTJenkins JLSalim MWedekind JE ITC analysis of ligand binding to preQ₁ riboswitches.; Methods in enzymology; Vol 549. 2014. Suddala KCRinaldi AJFeng JMustoe AMEichhorn CDLiberman JAWedekind JEAl-Hashimi HMBrooks CLWalter 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; Vol 41(22). 2013 Dec. Can MKrucinska JZoppellaro GAndersen NHWedekind JEHersleth HPAndersson KKBren KL Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure.; Chembiochem : a European journal of chemical biology; Vol 14(14). 2013 Sep 23. Liberman JASalim MKrucinska JWedekind JE Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold.; Nature chemical biology; Vol 9(6). 2013 Jun. Wang WMaucuer AGupta AManceau VThickman KRBauer WJKennedy SDWedekind JEGreen MRKielkopf CL Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex.; Structure (London, England : 1993); Vol 21(2). 2013 Feb 5. Salter JDLippa GMBelashov IAWedekind JE Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex.; Biochemistry; Vol 51(44). 2012 Nov 6. Banáš PSklenovský PWedekind JEŠponer JOtyepka M Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.; The journal of physical chemistry. B; Vol 116(42). 2012 Oct 25. Liberman JAGuo MJenkins JLKrucinska JChen YCarey PRWedekind JE A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.; Journal of the American Chemical Society; Vol 134(41). 2012 Oct 17. Liberman JAWedekind JE Riboswitch structure in the ligand-free state.; Wiley interdisciplinary reviews. RNA; Vol 3(3). 2012 May. Lippa GMLiberman JAJenkins JLKrucinska JSalim MWedekind JE Crystallographic analysis of small ribozymes and riboswitches.; Methods in molecular biology (Clifton, N.J.); Vol 848. 2012. Jenkins JLKrucinska JMcCarty RMBandarian VWedekind JE Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation.; The Journal of biological chemistry; Vol 286(28). 2011 Jul 15. Liberman JAWedekind JE Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world.; Current opinion in structural biology; Vol 21(3). 2011 Jun. Wedekind JE The apo riboswitch as a molecular hydra.; Structure (London, England : 1993); Vol 18(7). 2010 Jul 14. Salter JDKrucinska JRaina JSmith HCWedekind JE A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function.; Biochemistry; Vol 48(45). 2009 Nov 17. Spitale RCWedekind JE Exploring ribozyme conformational changes with X-ray crystallography.; Methods (San Diego, Calif.); Vol 49(2). 2009 Oct. Guo MSpitale RCVolpini RKrucinska JCristalli GCarey PRWedekind 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; Vol 131(36). 2009 Sep 16. Spitale RCVolpini RMungillo MVKrucinska JCristalli GWedekind JE Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.; Biochemistry; Vol 48(33). 2009 Aug 25. Spitale RCVolpini RHeller MGKrucinska JCristalli GWedekind JE Identification of an imino group indispensable for cleavage by a small ribozyme.; Journal of the American Chemical Society; Vol 131(17). 2009 May 6. Spitale RCTorelli ATKrucinska JBandarian VWedekind JE The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.; The Journal of biological chemistry; Vol 284(17). 2009 Apr 24. Bennett RPSalter JDLiu XWedekind JESmith HC APOBEC3G subunits self-associate via the C-terminal deaminase domain.; The Journal of biological chemistry; Vol 283(48). 2008 Nov 28. MacElrevey CSalter JDKrucinska JWedekind JE Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.; RNA (New York, N.Y.); Vol 14(8). 2008 Aug. Torelli ATSpitale RCKrucinska JWedekind JE Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.; Biochemical and biophysical research communications; Vol 371(1). 2008 Jun 20. Jamburuthugoda VKSantos-Velazquez JMSkasko MOperario DJPurohit VChugh PSzymanski EAWedekind JEBambara RAKim 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; Vol 283(14). 2008 Apr 4. Bennett RPPresnyak VWedekind JESmith 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; Vol 283(12). 2008 Mar 21. Spitale RCHeller MGPelly AJWedekind JE Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine.; The Journal of organic chemistry; Vol 72(22). 2007 Oct 26. MacElrevey CSpitale RCKrucinska JWedekind 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; Vol 63(Pt 7). 2007 Jul.