Potencial de Fuerza Media Asociado a la Interacción entre la Proteína Ribosómica S8 y su Aptámero de ARN.

Abstract

The dissociation process of the complex between S8 ribosomal protein and its RNA aptamer was studied with Molecular Dynamics simulations. By sampling the configurations accessed by the complex during the forced dissociation, the corresponding potential of mean force (PMF) was determined. First, the complex was placed in a water box large enough to simulate the dissociation. After the system reached equilibrium, the dissociation was induced by applying an external force with constant speed of 0.25 (Å/ps) in the z direction. Such force was applied on the Cα of THR35, LYS54, LYS113 and SER130 aminoacids of the S8 ribosomal protein. The application of the external force induced the dissociation of the complex in 160 ps. In order to obtain the PMF, the reaction coordinate ξ was defined as the distance between the RNA and protein centers of mass along the z-axis. ξ was sampled on 12 intervals (windows) between 22.4 and 36.8 Å. The PMF calculated by the weighted histogram analysis method WHAM, revealed that the energy cost required to dissociate the complex was 21.3 kcal/mol. Finally, the existence of regions of constant PMF revealed the presence of contacts critical for the formation of the complex. The identified critical contacts are formed by the protein residues ALA114, SER132, GLN80 & THR27 with their RNA counterpart , CYT17, ADE24, URA5 & ADE4, respectively