Protonation-dependent base flipping in the catalytic triad of a small RNA

Zhaoxi Sun; Xiaohui Wang; John Z.H. Zhang

doi:10.1016/j.cplett.2017.07.003

Protonation-dependent base flipping in the catalytic triad of a small RNA

Zhaoxi Sun, Xiaohui Wang, John Z.H. Zhang

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35° and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA⁺ base pair is formed under acidic condition.

Original language	English (US)
Pages (from-to)	239-244
Number of pages	6
Journal	Chemical Physics Letters
Volume	684
DOIs	https://doi.org/10.1016/j.cplett.2017.07.003
State	Published - 2017

ASJC Scopus subject areas

General Physics and Astronomy
Physical and Theoretical Chemistry

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10.1016/j.cplett.2017.07.003

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title = "Protonation-dependent base flipping in the catalytic triad of a small RNA",

abstract = "Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35° and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA+ base pair is formed under acidic condition.",

author = "Zhaoxi Sun and Xiaohui Wang and Zhang, {John Z.H.}",

note = "Funding Information: This work was supported by graduate scientific research innovation funding project of East China Normal University and National Natural Science Foundation of China (Grant No. 21433004). Publisher Copyright: {\textcopyright} 2017 Elsevier B.V.",

year = "2017",

doi = "10.1016/j.cplett.2017.07.003",

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AU - Sun, Zhaoxi

AU - Wang, Xiaohui

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N1 - Funding Information: This work was supported by graduate scientific research innovation funding project of East China Normal University and National Natural Science Foundation of China (Grant No. 21433004). Publisher Copyright: © 2017 Elsevier B.V.

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Y1 - 2017

N2 - Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35° and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA+ base pair is formed under acidic condition.

AB - Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35° and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA+ base pair is formed under acidic condition.

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JO - Chemical Physics Letters

JF - Chemical Physics Letters

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Protonation-dependent base flipping in the catalytic triad of a small RNA

Abstract

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