Open AccessCoarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations
Author(s) -
Matúš Rebič,
Francesca Mocci,
Jozef Uličný,
Alexander P. Lyubartsev,
Aatto Laaksonen
Publication year - 2017
Publication title -
acs omega
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.779
H-Index - 40
ISSN - 2470-1343
DOI - 10.1021/acsomega.6b00419
Subject(s) - monte carlo method , salt (chemistry) , molecular dynamics , biopolymer , statistical physics , inverse , ionic bonding , elasticity (physics) , chemistry , materials science , chemical physics , biological system , physics , computational chemistry , mathematics , thermodynamics , ion , geometry , statistics , composite material , polymer , organic chemistry , biology
We present a coarse-grained (CG) model of a rodlike higher-order quadruplex with explicit monovalent salts, which was developed from radial distribution functions of an underlying reference atomistic molecular dynamics simulation using inverse Monte Carlo technique. This work improves our previous CG model and extends its applicability beyond the minimal salt conditions, allowing its use at variable ionic strengths. The strategies necessary for the model development are clearly explained and discussed. The effects of the number of stacked quadruplexes and varied salt concentration on the elasticity of the rodlike higher-order quadruplex structures are analyzed. The CG model reproduces the deformations of the terminal parts in agreement with experimental observations without introducing any special parameters for terminal beads and reveals slight differences in the rise and twist of the G-quartet arrangement along the studied biopolymer. The conclusions of our study can be generalized for other G-quartet-based structures.