URMC / Labs / Wedekind Lab / Publications Publications Wedekind JEDutta DBelashov IAJenkins JL (2017 Apr 28). Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes. The Journal of biological chemistry. Jenkins JLWedekind JE (2016). The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures. Methods in molecular biology (Clifton, N.J.). Dutta DWedekind JE (2015 Nov 6). Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units. Journal of molecular biology. Aytenfisu AHLiberman JAWedekind JEMathews DH (2015 Nov). Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. RNA (New York, N.Y.). Liberman JASuddala KCAytenfisu AChan DBelashov IASalim MMathews DHSpitale RCWalter NGWedekind JE (2015 Jul 7). 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. Heldenbrand HJanowski PAGiambaşu GGiese TJWedekind JEYork DM (2014 Jun 4). 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. Liberman JABogue JTJenkins JLSalim MWedekind JE (2014). ITC analysis of ligand binding to preQ₁ riboswitches. Methods in enzymology. Suddala KCRinaldi AJFeng JMustoe AMEichhorn CDLiberman JAWedekind JEAl-Hashimi HMBrooks CLWalter NG (2013 Dec). 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. Can MKrucinska JZoppellaro GAndersen NHWedekind JEHersleth HPAndersson KKBren KL (2013 Sep 23). Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure. Chembiochem : a European journal of chemical biology. Liberman JASalim MKrucinska JWedekind JE (2013 Jun). Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nature chemical biology. Wang WMaucuer AGupta AManceau VThickman KRBauer WJKennedy SDWedekind JEGreen MRKielkopf CL (2013 Feb 5). Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure (London, England : 1993). Salter JDLippa GMBelashov IAWedekind JE (2012 Nov 6). Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry. Banáš PSklenovský PWedekind JEŠponer JOtyepka M (2012 Oct 25). Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. The journal of physical chemistry. B. Liberman JAGuo MJenkins JLKrucinska JChen YCarey PRWedekind JE (2012 Oct 17). A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis. Journal of the American Chemical Society. Liberman JAWedekind JE (2012 May). Riboswitch structure in the ligand-free state. Wiley interdisciplinary reviews. RNA. Lippa GMLiberman JAJenkins JLKrucinska JSalim MWedekind JE (2012). Crystallographic analysis of small ribozymes and riboswitches. Methods in molecular biology (Clifton, N.J.). Jenkins JLKrucinska JMcCarty RMBandarian VWedekind JE (2011 Jul 15). Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. The Journal of biological chemistry. Liberman JAWedekind JE (2011 Jun). Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world. Current opinion in structural biology. Wedekind JE (2010 Jul 14). The apo riboswitch as a molecular hydra. Structure (London, England : 1993). Salter JDKrucinska JRaina JSmith HCWedekind JE (2009 Nov 17). A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function. Biochemistry. Spitale RCWedekind JE (2009 Oct). Exploring ribozyme conformational changes with X-ray crystallography. Methods (San Diego, Calif.). Guo MSpitale RCVolpini RKrucinska JCristalli GCarey PRWedekind JE (2009 Sep 16). 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. Spitale RCVolpini RMungillo MVKrucinska JCristalli GWedekind JE (2009 Aug 25). Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry. Spitale RCVolpini RHeller MGKrucinska JCristalli GWedekind JE (2009 May 6). Identification of an imino group indispensable for cleavage by a small ribozyme. Journal of the American Chemical Society. Spitale RCTorelli ATKrucinska JBandarian VWedekind JE (2009 Apr 24). The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. The Journal of biological chemistry. Bennett RPSalter JDLiu XWedekind JESmith HC (2008 Nov 28). APOBEC3G subunits self-associate via the C-terminal deaminase domain. The Journal of biological chemistry. MacElrevey CSalter JDKrucinska JWedekind JE (2008 Aug). Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. RNA (New York, N.Y.). Torelli ATSpitale RCKrucinska JWedekind JE (2008 Jun 20). Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochemical and biophysical research communications. Jamburuthugoda VKSantos-Velazquez JMSkasko MOperario DJPurohit VChugh PSzymanski EAWedekind JEBambara RAKim B (2008 Apr 4). 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. Bennett RPPresnyak VWedekind JESmith HC (2008 Mar 21). 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. Spitale RCHeller MGPelly AJWedekind JE (2007 Oct 26). Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine. The Journal of organic chemistry. Torelli ATKrucinska JWedekind JE (2007 Jul). 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.). MacElrevey CSpitale RCKrucinska JWedekind JE (2007 Jul). A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Acta crystallographica. Section D, Biological crystallography. Lehmann DMGalloway CAMacElrevey CSowden MPWedekind JESmith HC (2007 Mar). Functional characterization of APOBEC-1 complementation factor phosphorylation sites. Biochimica et biophysica acta. Wedekind JEGillilan RJanda AKrucinska JSalter JDBennett RPRaina JSmith HC (2006 Dec 15). Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits. The Journal of biological chemistry. Bennett RPDiner ESowden MPLees JAWedekind JESmith HC (2006 Nov 10). APOBEC-1 and AID are nucleo-cytoplasmic trafficking proteins but APOBEC3G cannot traffic. Biochemical and biophysical research communications. Ghosh AKSridhar PRLeshchenko SHussain AKLi JKovalevsky AYWalters DEWedekind JEGrum-Tokars VDas DKoh YMaeda KGatanaga HWeber ITMitsuya H (2006 Aug 24). Structure-based design of novel HIV-1 protease inhibitors to combat drug resistance. Journal of medicinal chemistry. Ichikawa HTSowden MPTorelli ATBachl JHuang PDance GSMarr SHRobert JWedekind JESmith HCBottaro A (2006 Jul 1). Structural phylogenetic analysis of activation-induced deaminase function. Journal of immunology (Baltimore, Md. : 1950). Chaves FARichards KATorelli AWedekind JSant AJ (2006 May 23). Peptide-binding motifs for the I-Ad MHC class II molecule: alternate pH-dependent binding behavior. Biochemistry. Salter JKrucinska JAlam SGrum-Tokars VWedekind JE (2006 Jan 24). Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry. MacElrevey CWedekind JE (2005 Dec 1). 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. Alam SGrum-Tokars VKrucinska JKundracik MLWedekind JE (2005 Nov 8). 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. Gruswitz FFrishman MGoldstein BMWedekind JE (2005 Oct). Coupling of MBP fusion protein cleavage with sparse matrix crystallization screens to overcome problematic protein solubility. BioTechniques. Xie KSong SCSpitalnik SLWedekind JE (2005 Oct). Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition. Acta crystallographica. Section D, Biological crystallography. Jamburuthugoda VKGuo DWedekind JEKim B (2005 Aug 9). Kinetic evidence for interaction of human immunodeficiency virus type 1 reverse transcriptase with the 3'-OH of the incoming dTTP substrate. Biochemistry. Goodman JLWang SAlam SRuzicka FJFrey PAWedekind JE (2004 Nov 09). Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family. Biochemistry. Xie KSowden MPDance GSTorelli ATSmith HCWedekind JE (2004 May 25). 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. Alam SWang SCRuzicka FJFrey PAWedekind JE (2004 May). Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase from Pseudomonas putida. Acta crystallographica. Section D, Biological crystallography. Song SCXie KCzerwinski MSpitalnik SLWedekind JE (2004 Apr). Purification, crystallization and X-ray diffraction analysis of a recombinant Fab that recognizes a human blood-group antigen. Acta crystallographica. Section D, Biological crystallography. Wedekind JEMcKay DB (2003 Aug 19). 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.