Analysis of Interactions and Dissection of Interfaces Involved in RNA-Protein Recognition

RNA-protein recognition is an important component of many cellular processes, such as gene expression, protein synthesis, replication of many viruses, etc. Primary to the understanding of the functional implications of RNA-protein interactions is an in-depth analysis of the molecular mechanisms by which proteins identify and discriminate between specific RNA molecules. To gain some insight into the structural and physicochemical interactions that happen when a protein binds to RNA, an analysis of a non-redundant dataset of 61 RNA-protein complexes is presented. Between the two components, 2056 Å2 of surface area is buried and the larger interfaces tend to be made up of multiple patches. The interfaces can be dissected into core and rim regions and distinct preferences of residues in the two regions are evident. The residues in the core have smaller sequence entropy as compared to the rim, indicating greater sequence conservation. Interfaces have been classified based on the composition of the secondary structural elements found therein. Various physicochemical parameters have been used to compare the protein-RNA interfaces with those found in protein-protein and protein- DNA complexes.