Fast coarse-grained model for RNA titration

被引：9

作者：

Barroso da Silva, Fernando Luis ^{[1
,2
,3
]}

Derreumaux, Philippe ^{[2
,3
]}

Pasquali, Samuela ^{[2
,3
,4
,5
]}

机构：

[1] Univ Sao Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Dept Fis & Quim, Ave Cafe S-N, BR-14040903 Ribeirao Preto, SP, Brazil

[2] Univ Paris Diderot Paris 7, CNRS, Lab Biochim Theor, Inst Biol Phys Chim,UPR 9080, 13 Rue Pierre & Marie Curie, F-75005 Paris, France

[3] Univ Sorbonne Paris Cite, 13 Rue Pierre & Marie Curie, F-75005 Paris, France

[4] Univ Paris 05, Fac Sci Pharmaceut & Biol, Lab Cristallog, 4 Ave Observ, F-75006 Paris, France

[5] Univ Paris 05, Fac Sci Pharmaceut & Biol, RMN Biol, CNRS,UMR 8015, 4 Ave Observ, F-75006 Paris, France

来源：

JOURNAL OF CHEMICAL PHYSICS | 2017年 / 146卷 / 03期

基金：

巴西圣保罗研究基金会;

关键词：

PH MOLECULAR-DYNAMICS; CONSTANT PH; CHARGE REGULATION; MONTE-CARLO; POISSON-BOLTZMANN; TITRATABLE WATER; PROTEINS; DNA; BINDING; PROTONATION;

D O I：

10.1063/1.4972986

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页数：9

共 64 条

[1] Constant-pH molecular dynamics using stochastic titration [J].