Publications

• 1. Kiliushik D
  2. Goenner C
  3. Law M
  4. Schroeder GM
  5. Srivastava Y
  6. Jenkins JL
  7. Wedekind JE
  Knotty is nice: metabolite binding and RNA-mediated gene regulation by the preQ1 riboswitch family.; The Journal of biological chemistry. 2024 Oct 30.
• 1. Iannuzzelli JA
  2. Bonn R
  3. Hong AS
  4. Anitha AS
  5. Jenkins JL
  6. Wedekind JE
  7. Fasan R
  Cyclic peptides targeting the SARS-CoV-2 programmed ribosomal frameshifting RNA from a multiplexed phage display library.; Chemical science. 2024 Oct 17.
• 1. Srivastava Y
  2. Akinyemi O
  3. Rohe TC
  4. Pritchett EM
  5. Baker CD
  6. Sharma A
  7. Jenkins JL
  8. Mathews DH
  9. Wedekind JE
  Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.; Nucleic acids research. 2024 Oct 16.
• 1. Schroeder GM
  2. Kiliushik D
  3. Jenkins JL
  4. Wedekind 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.
• 1. Kretsch RC
  2. Andersen ES
  3. Bujnicki JM
  4. Chiu W
  5. Das R
  6. Luo B
  7. Masquida B
  8. McRae EKS
  9. Schroeder GM
  10. Su Z
  11. Wedekind JE
  12. Xu L
  13. Zhang K
  14. Zheludev IN
  15. Moult J
  16. Kryshtafovych A
  RNA target highlights in CASP15: Evaluation of predicted models by structure providers.; Proteins. 2023 Jul 19.
• 1. 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.
• 1. Schroeder GM
  2. Akinyemi O
  3. Malik J
  4. Focht CM
  5. Pritchett EM
  6. Baker CD
  7. McSally JP
  8. Jenkins JL
  9. Mathews DH
  10. Wedekind JE
  A riboswitch separated from its ribosome-binding site still regulates translation.; Nucleic acids research. 2023 Feb 10.
• 1. Srivastava Y
  2. Blau ME
  3. Jenkins JL
  4. Wedekind JE
  Full-Length NAD+-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate.; Biochemistry. 2023 Jan 10.
• 1. Cavender CE
  2. Schroeder GM
  3. Mathews DH
  4. Wedekind 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.
• 1. Schroeder GM
  2. Cavender CE
  3. Blau ME
  4. Jenkins JL
  5. Mathews DH
  6. Wedekind JE
  A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.; Nature communications; Vol 13(1). 2022 Jan 11.
• 1. Chavali SS
  2. Mali SM
  3. Bonn R
  4. Saseendran A
  5. Bennett RP
  6. Smith HC
  7. Fasan R
  8. 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 09.
• 1. Srivastava Y
  2. Bonn-Breach R
  3. Chavali SS
  4. Lippa GM
  5. Jenkins JL
  6. Wedekind JE
  Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.; Crystals; Vol 11(3). 2021 Mar.
• 1. Chavali SS
  2. Mali SM
  3. Jenkins JL
  4. Fasan R
  5. 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; Vol 295(49). 2020 Dec 04.
• 1. Chavali SS
  2. Cavender CE
  3. Mathews DH
  4. 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.
• 1. Schroeder GM
  2. Dutta D
  3. Cavender CE
  4. Jenkins JL
  5. Pritchett EM
  6. Baker CD
  7. Ashton JM
  8. Mathews DH
  9. 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.
• 1. Bonn-Breach R
  2. Gu Y
  3. Jenkins J
  4. Fasan R
  5. 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; Vol 75(Pt 11). 2019 Nov 01.
• 1. Dutta D
  2. Wedekind JE
  Nucleobase mutants of a bacterial preQ1-II riboswitch that uncouple metabolite sensing from gene regulation.; The Journal of biological chemistry. 2019 Oct 28.
• 1. Chavali SS
  2. Bonn-Breach R
  3. 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.
• 1. Warnasooriya C
  2. Ling C
  3. Belashov IA
  4. Salim M
  5. Wedekind JE
  6. Ermolenko DN
  Observation of preQ1-II riboswitch dynamics using single-molecule FRET.; RNA biology. 2018 Oct 17.
• 1. Belashov IA
  2. Crawford DW
  3. Cavender CE
  4. Dai P
  5. Beardslee PC
  6. Mathews DH
  7. Pentelute BL
  8. McNaughton BR
  9. 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 Jun 29.
• 1. Dutta D
  2. Belashov IA
  3. Wedekind JE
  Coupling GFP Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.; Biochemistry. 2018 Jun 13.
• 1. Wedekind JE
  2. Dutta D
  3. Belashov IA
  4. Jenkins JL
  Metalloriboswitches: RNA-Based Inorganic Ion Sensors that Regulate Genes.; The Journal of biological chemistry. 2017 Apr 28.
• 1. Jenkins JL
  2. 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.); Vol 1490. 2016.
• 1. Dutta D
  2. 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; Vol 427(22). 2015 Nov 6.
• 1. Aytenfisu AH
  2. Liberman JA
  3. Wedekind JE
  4. Mathews DH
  Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.; RNA (New York, N.Y.); Vol 21(11). 2015 Nov.
• 1. Liberman JA
  2. Suddala KC
  3. Aytenfisu A
  4. Chan D
  5. Belashov IA
  6. Salim M
  7. Mathews DH
  8. Spitale RC
  9. Walter NG
  10. 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; Vol 112(27). 2015 Jul 7.
• 1. Heldenbrand H
  2. Janowski PA
  3. Giambaşu G
  4. Giese TJ
  5. Wedekind JE
  6. 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; Vol 136(22). 2014 Jun 4.
• 1. Liberman JA
  2. Bogue JT
  3. Jenkins JL
  4. Salim M
  5. Wedekind JE
  ITC analysis of ligand binding to preQ₁ riboswitches.; Methods in enzymology; Vol 549. 2014.
• 1. Suddala KC
  2. Rinaldi AJ
  3. Feng J
  4. Mustoe AM
  5. Eichhorn CD
  6. Liberman JA
  7. Wedekind JE
  8. Al-Hashimi HM
  9. Brooks CL
  10. 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; Vol 41(22). 2013 Dec.
• 1. Can M
  2. Krucinska J
  3. Zoppellaro G
  4. Andersen NH
  5. Wedekind JE
  6. Hersleth HP
  7. Andersson KK
  8. Bren 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.
• 1. Liberman JA
  2. Salim M
  3. Krucinska J
  4. Wedekind JE
  Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold.; Nature chemical biology; Vol 9(6). 2013 Jun.
• 1. Wang W
  2. Maucuer A
  3. Gupta A
  4. Manceau V
  5. Thickman KR
  6. Bauer WJ
  7. Kennedy SD
  8. Wedekind JE
  9. Green MR
  10. Kielkopf CL
  Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex.; Structure (London, England : 1993); Vol 21(2). 2013 Feb 5.
• 1. Salter JD
  2. Lippa GM
  3. Belashov IA
  4. Wedekind 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.
• 1. Banáš P
  2. Sklenovský P
  3. Wedekind JE
  4. Šponer J
  5. Otyepka M
  Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.; The journal of physical chemistry. B; Vol 116(42). 2012 Oct 25.
• 1. Liberman JA
  2. Guo M
  3. Jenkins JL
  4. Krucinska J
  5. Chen Y
  6. Carey PR
  7. Wedekind 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.
• 1. Liberman JA
  2. Wedekind JE
  Riboswitch structure in the ligand-free state.; Wiley interdisciplinary reviews. RNA; Vol 3(3). 2012 May.
• 1. Lippa GM
  2. Liberman JA
  3. Jenkins JL
  4. Krucinska J
  5. Salim M
  6. Wedekind JE
  Crystallographic analysis of small ribozymes and riboswitches.; Methods in molecular biology (Clifton, N.J.); Vol 848. 2012.
• 1. Jenkins JL
  2. Krucinska J
  3. McCarty RM
  4. Bandarian V
  5. Wedekind 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.
• 1. Liberman JA
  2. Wedekind 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.
• 1. Wedekind JE
  The apo riboswitch as a molecular hydra.; Structure (London, England : 1993); Vol 18(7). 2010 Jul 14.
• 1. Salter JD
  2. Krucinska J
  3. Raina J
  4. Smith HC
  5. Wedekind 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.
• 1. Spitale RC
  2. Wedekind JE
  Exploring ribozyme conformational changes with X-ray crystallography.; Methods (San Diego, Calif.); Vol 49(2). 2009 Oct.
• 1. Guo M
  2. Spitale RC
  3. Volpini R
  4. Krucinska J
  5. Cristalli G
  6. Carey PR
  7. 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; Vol 131(36). 2009 Sep 16.
• 1. Spitale RC
  2. Volpini R
  3. Mungillo MV
  4. Krucinska J
  5. Cristalli G
  6. 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; Vol 48(33). 2009 Aug 25.
• 1. Spitale RC
  2. Volpini R
  3. Heller MG
  4. Krucinska J
  5. Cristalli G
  6. Wedekind 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.
• 1. Spitale RC
  2. Torelli AT
  3. Krucinska J
  4. Bandarian V
  5. Wedekind 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.
• 1. Bennett RP
  2. Salter JD
  3. Liu X
  4. Wedekind JE
  5. Smith HC
  APOBEC3G subunits self-associate via the C-terminal deaminase domain.; The Journal of biological chemistry; Vol 283(48). 2008 Nov 28.
• 1. MacElrevey C
  2. Salter JD
  3. Krucinska J
  4. Wedekind 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.
• 1. Torelli AT
  2. Spitale RC
  3. Krucinska J
  4. Wedekind JE
  Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.; Biochemical and biophysical research communications; Vol 371(1). 2008 Jun 20.
• 1. Jamburuthugoda VK
  2. Santos-Velazquez JM
  3. Skasko M
  4. Operario DJ
  5. Purohit V
  6. Chugh P
  7. Szymanski EA
  8. Wedekind JE
  9. Bambara RA
  10. 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; Vol 283(14). 2008 Apr 4.