TY - JOUR
T1 - Investigation of the pKa of the nucleophilic O2' of the hairpin ribozyme
AU - Veenis, Andrew J.
AU - Li, Pengfei
AU - Soudackov, Alexander V.
AU - Hammes-Schiffer, Sharon
AU - Bevilacqua, Philip C.
N1 - Funding Information:
The authors thank Darrin York and Abir Ganguly for their advice and for providing the parameters for an N1-protonated adenine. The authors thank Jacob Sieg for assistance in getting started with R and David Stevens for assistance in getting started with AMBER. This work was supported in part by the National Institutes of Health Grants R35 GM139449 (P.L., A.V.S., and S.H-S.) and R35 GM127064 (A.J.V. and P.C.B.). This work was also supported in part by the start-up funds from Loyola University Chicago (P.L.) and by the National Aeronautics and Space Administration under Grant No. 80NSSC20M0097 issued through the PA Space Grant Consortium (A.J.V.). Computations using Gaussian for this research were performed on the Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar supercomputer. This content is solely the responsibility of the authors and does not necessarily represent the views of the Institute for Computational and Data Sciences. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number ACI-1548562. Specifically, this work used XSEDE SDSC Dell Cluster with NVIDIA V100 GPUs NVLINK and HDR IB (Expanse GPU) at the San Diego Supercomputer Center at UC San Diego through allocation TG-CHE210018.
Funding Information:
The authors thank Darrin York and Abir Ganguly for their advice and for providing the parameters for an N1-protonated adenine. The authors thank Jacob Sieg for assistance in getting started with R and David Stevens for assistance in getting started with AMBER. This work was supported in part by the National Institutes of Health Grants R35 GM139449 (P.L., A.V.S., and S.H-S.) and R35 GM127064 (A.J.V. and P.C.B.). This work was also supported in part by the start-up funds from Loyola University Chicago (P.L.) and by the National Aeronautics and Space Administration under Grant No. 80NSSC20M0097 issued through the PA Space Grant Consortium (A.J.V.). Computations using Gaussian83 for this research were performed on the Pennsylvania State University's Institute for Computational and Data Sciences' Roar supercomputer. This content is solely the responsibility of the authors and does not necessarily represent the views of the Institute for Computational and Data Sciences. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number ACI-1548562.84 Specifically, this work used XSEDE SDSC Dell Cluster with NVIDIA V100 GPUs NVLINK and HDR IB (Expanse GPU) at the San Diego Supercomputer Center at UC San Diego through allocation TG-CHE210018.
Publisher Copyright:
© 2021 American Chemical Society
PY - 2021/11/4
Y1 - 2021/11/4
N2 - Small ribozymes cleave their RNA phosphodiester backbone by catalyzing a transphosphorylation reaction wherein a specific O2' functions as the nucleophile. While deprotonation of this alcohol through its acidification would increase its nucleophilicity, little is known about the pKa of this O2' in small ribozymes, in part because high pKa's are not readily accessible experimentally. Herein, we turn to molecular dynamics to calculate the pKa of the nucleophilic O2' in the hairpin ribozyme and to study interactions within the active site that may impact its value. We estimate the pKa of the nucleophilic O2' in the wild-type hairpin ribozyme to be 18.5 ± 0.8, which is higher than the reference compound, and identify a correlation between proper positioning of the O2' for nucleophilic attack and elevation of its pKa. We find that monovalent ions may play a role in depression of the O2' pKa, while the exocyclic amine appears to be important for organizing the ribozyme active site. Overall, this study suggests that the pKa of the O2' is raised in the ground state and lowers during the course of the reaction owing to positioning and metal ion interactions.
AB - Small ribozymes cleave their RNA phosphodiester backbone by catalyzing a transphosphorylation reaction wherein a specific O2' functions as the nucleophile. While deprotonation of this alcohol through its acidification would increase its nucleophilicity, little is known about the pKa of this O2' in small ribozymes, in part because high pKa's are not readily accessible experimentally. Herein, we turn to molecular dynamics to calculate the pKa of the nucleophilic O2' in the hairpin ribozyme and to study interactions within the active site that may impact its value. We estimate the pKa of the nucleophilic O2' in the wild-type hairpin ribozyme to be 18.5 ± 0.8, which is higher than the reference compound, and identify a correlation between proper positioning of the O2' for nucleophilic attack and elevation of its pKa. We find that monovalent ions may play a role in depression of the O2' pKa, while the exocyclic amine appears to be important for organizing the ribozyme active site. Overall, this study suggests that the pKa of the O2' is raised in the ground state and lowers during the course of the reaction owing to positioning and metal ion interactions.
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U2 - 10.1021/acs.jpcb.1c06546
DO - 10.1021/acs.jpcb.1c06546
M3 - Article
C2 - 34695361
AN - SCOPUS:85118954576
VL - 125
SP - 11869
EP - 11883
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
SN - 1520-6106
IS - 43
ER -