Fast coarse-grained model for RNA titration

Autor(es)

Barroso da Silva, Fernando Luis ; Derreumaux, Philippe ; Pasquali, Samuela

• Tipo de documento: Artigo Científico
• Fonte: Journal of Chemical Physics; v. 146, n. 3 JAN 21 2017.
• Citações Web of Science: 6

Resumo

A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Huckel 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 pK(a) shifts. 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. Published by AIP Publishing. (AU)

• Processo FAPESP: 10/50425-0 - Mecanismos moleculars fundamentais responsaveis pela complexacao de proteinas. de parametros fisico-quimicos as aplicacoes em tecnologia de alimentos e farmaceutica.
• Beneficiário: Fernando Luis Barroso da Silva
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 15/16116-3 - Mecanismos moleculares de origem eletrostática responsáveis pela complexação de proteínas
• Beneficiário: Fernando Luis Barroso da Silva
• Modalidade de apoio: Auxílio à Pesquisa - Regular