Fast coarse-grained model for RNA titration.

TitleFast coarse-grained model for RNA titration.
Publication TypeJournal Article
Year of Publication2017
Authorsda Silva FLuis Barro, Derreumaux P, Pasquali S
JournalJ Chem Phys
Volume146
Issue3
Pagination035101
Date Published2017 Jan 21
ISSN1089-7690
KeywordsAzotobacter vinelandii, Introns, Models, Chemical, Molecular Dynamics Simulation, Monte Carlo Method, Protein Structure, Secondary, Protons, RNA, RNA, Catalytic, Titrimetry
Abstract

A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKshifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

DOI10.1063/1.4972986
Alternate JournalJ Chem Phys
Citation Key2017|2041
PubMed ID28109220