Computational analysis of RNA-protein interaction interfaces via the Voronoi diagram.

Cellular functions are mediated by various biological processes including biomolecular interactions, such as protein-protein, DNA-protein and RNA-protein interactions in which RNA-Protein interactions are indispensable for many biological processes like cell development and viral replication. Unlike the protein-protein and protein-DNA interactions, accurate mechanisms and structures of the RNA-Protein complexes are not fully understood. A large amount of theoretical evidence have shown during the past several years that computational geometry is the first pace in understanding the binding profiles and plays a key role in the study of intricate biological structures, interactions and complexes. In this paper, RNA-Protein interaction interface surface is computed via the weighted Voronoi diagram of atoms. Using two filter operations provides a natural definition for interface atoms as classic methods. Unbounded parts of Voronoi facets that are far from the complex are trimmed using modified convex hull of atom centers. This algorithm is implemented to a database with different RNA-Protein complexes extracted from Protein Data Bank (PDB). Afterward, the features of interfaces have been computed and compared with classic method. The results show high correlation coefficients between interface size in the Voronoi model and the classical model based on solvent accessibility, as well as high accuracy and precision in comparison to classical model.

Computational structure analysis of biomacromolecule complexes by interface geometry.

The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model.