One-bead coarse-grained model for RNA dynamics.
We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.
Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico.
Mario
M
Villada-Balbuena
Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico.
Mauricio D
0000000231747540
MD
Carbajal-Tinoco
D000465:Algorithms; D008274:Magnesium / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
D012313:RNA; D008274:Magnesium