Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

ABSTRACT: U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interac

SUBMITTER: Ghaemi Z 

PROVIDER: S-EPMC6044910 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature