|A Coarse-grained Model for Double-helix Molecules in Solution: Spontaneous Helix Formation and Equilibrium Properties
|Year of Publication
|Tepper, HL, Voth, GA
|J Chem Phys
|Base Pairing Computer Simulation DNA/*chemistry Hydrophobic and Hydrophilic Interactions *Models, Molecular Nucleic Acid Conformation Solutions Solvents/chemistry
A new reductionist coarse-grained model is presented for double-helix molecules in solution. As with such models for lipid bilayers and micelles, the level of description is both particulate and mesoscopic. The particulate (bead-and-spring) nature of the model makes for a simple implementation in standard molecular dynamics simulation codes and allows for investigation of thermomechanic properties without preimposing any (form of) response function. The mesoscopic level of description–where groups of atoms are condensed into coarse-grained beads–causes long-range interactions to be effectively screened, which greatly enhances the efficiency and scalability of simulations. Without imposing local or global order parameters, a linear initial configuration of the model molecule spontaneously assembles into a double helix due to the interplay between three contributions: hydrophobic/hydrophilic interactions between base pairs, backbone, and solvent; phosphate-phosphate repulsion along the backbone; and favorable base-pair stacking energy. We present results for the process of helix formation as well as for the equilibrium properties of the final state, and investigate how both depend on the input parameters. The current model holds promise for two routes of investigation: First, within a limited set of generic parameters, the effect of local (atomic-scale) perturbations on overall helical properties can be systematically studied. Second, since the efficiency allows for a direct simulation of both small and large (>100 base pairs) systems, the model presents a testground for systematic coarse-graining methods.