HDV ribozyme

Inverse thio effects in the hepatitis delta ribozyme reveal that the reaction pathway is controlled by metal ion charge density

191. P. Thaplyal, A. Ganguly, S. Hammes-Schiffer, and P. C. Bevilacqua, “Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density,” Biochemistry 54, 2160-2175 (2015).

Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme

170. P. Thaplyal, A. Ganguly, B. L. Golden, and S. Hammes-Schiffer, “Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme,” Biochemistry 52, 6499-6514 (2013).

Identification of the catalytic Mg2+ ion in the hepatitis delta virus ribozyme

162. J. Chen, A. Ganguly, Z. Miswan, S. Hammes-Schiffer, P. C. Bevilacqua, and B. L. Golden, “Identification of the catalytic Mg2+ ion in the hepatitis delta virus ribozyme, ” Biochemistry 52, 557-567 (2013).

An Integrated Picture of HDV Ribozyme Catalysis

158. B. L. Golden, S. Hammes-Schiffer, P. R. Carey, P. C. Bevilacqua, “An Integrated Picture of HDV Ribozyme Catalysis,” pp. 135-167 in Biophysics of RNA Folding, ed. R. Russell (Springer, New York, 2013).

Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism

150. A. Ganguly, P. C. Bevilacqua, and S. Hammes-Schiffer, “Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism,” J. Phys. Chem. Lett. 2, 2906-2911 (2011).

Mechanistic strategies in the HDV ribozyme: Chelated and diffuse metal ion interactions and active site protonation

141. N. Veeraraghavan, A. Ganguly, B. L. Golden, P. C. Bevilacqua, and S. Hammes-Schiffer, “Mechanistic strategies in the HDV ribozyme: Chelated and diffuse metal ion interactions and active site protonation,” J. Phys.Chem. B 115, 8346-8357 (2011).

Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions

137. N. Veeraraghavan, A. Ganguly, J.-H. Chen, P. C. Bevilacqua, S. Hammes-Schiffer, and B. L. Golden, “Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions,”Biochemistry 50, 2672-2682 (2011).

Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments

129. N. Veeraraghavan, P. C. Bevilacqua, and S. Hammes-Schiffer, “Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments,” J. Mol. Biol. 402, 278-291 (2010).