title: Fast coarse-grained model for RNA titration.
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 pKashifts. 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.
authors.affiliation: Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ave. do café, s/no, BR-14040-903 Ribeirão Preto, São Paulo, Brazil.
authors.forename: Fernando Luís
authors.identifier: 0000000325262085
authors.initials: FL
authors.lastname: Barroso da Silva
authors.affiliation: Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.affiliation: Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Samuela
authors.initials: S
authors.lastname: Pasquali
mesh_terms: D016948:Azotobacter vinelandii / Q000201:enzymology; D007438:Introns; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D017433:Protein Structure, Secondary; D011522:Protons; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry; D017186:Titrimetry
chemical_list: D011522:Protons; D016337:RNA, Catalytic; D012313:RNA