A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.

ABSTRACT: Cooperative interactions play an important role in recognition and binding in macromolecular systems. In this study, we find that cross-correlated atomic fluctuations can be used to identify cooperative networks in a protein-RNA system. The dynamics of the RRM-containing protein U1A-stem loop 2 RNA complex have been calculated theoretically from a 10 ns molecular dynamics (MD) simulation. The simulation was analyzed by calculating the covariance matrix of all atomic fluctuations. These matrix elements are then presented in the form of a two-dimensional grid, which displays fluctuations on a per residue basis. The results indicate the presence of strong, selective cross-correlated fluctuations throughout the RRM in U1A-RNA. The atomic fluctuations correspond well with previous biophysical s

SUBMITTER: Kormos BL 

PROVIDER: S-EPMC1994251 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature