Amino Acids Surface Patterns in Protein Domain Functionality Analysis

Abstract

Surface characterization of peptides may provide useful information about functionality and potential interactions with other molecules. A description of a protein site through a surface that models the shape conferred by the exposed residues is an effective tool for the analysis and modeling of proteins that may highlight similarities and relationships not detectable through comparisons at the levels of primary, secondary, and tertiary structure. This study concerns the development of a tool that extracts the residues that concur to the shape modeling of the surface of a protein or a portion of it. This task is accomplished without taking into account the order of amino acids in the primary structure but only according to the selection of a portion of the protein indicated through geometric parameters or an explicit list of amino acids belonging to the site of interest. Using this software, it is possible to identify some surface patterns that could be analyzed both in comparison with the functional domains of specific protein families or for study of particular interaction sites in macromolecular complexes.