Analyzing the flexibility of RNA structures by constraint counting.

ABSTRACT: RNA requires conformational dynamics to undergo its diverse functional roles. Here, a new topological network representation of RNA structures is presented that allows analyzing RNA flexibility/rigidity based on constraint counting. The method extends the FIRST approach, which identifies flexible and rigid regions in atomic detail in a single, static, three-dimensional molecular framework. Initially, the network rigidity of a canonical A-form RNA is analyzed by counting on constraints of network elements of increasing size. These considerations demonstrate that it is the inclusion of hydrophobic contacts into the RNA topological network that is crucial for an accurate flexibility prediction. The counting also explains why a protein-based parameterization results in overly rigid RNA structu

SUBMITTER: Fulle S 

PROVIDER: S-EPMC2480660 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature