URMC / Labs / Wedekind Lab / Publications

Publications from the Wedekind Lab

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.