PRince: a web server for structural and physicochemical analysis of protein-RNA interface

Abstract

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

Figure 1.

Graphical representation of the protein-RNA interface formed by ribosomal protein L25 and 5S rRNA fragment (PDB id, 1DFU). (A) Interface region along with the water molecules. Atoms belong to protein, RNA and interface water molecules are colored blue, red and cyan, respectively. (B) Surface region of the protein and RNA are colored in blue and red, respectively, while their interface region is colored in green.