Computational Investigation of Structural Interfaces of Protein Complexes with Short Linear Motifs

Abstract

Protein complexes with short linear motifs (SLiMs) are known to play important regulatory functions in eukaryotes. In this investigation, I have studied the structures deposited in PDB with SLiMs. The structures were grouped into three broad categories of protein-protein, protein-peptide, and the rest as others. Protein-peptide complexes were found to be most highly represented. The interfaces were evaluated for geometric features and conformational variables. It was observed that protein-protein and protein-peptide complexes show characteristic differences in residue pairings, which were quantified by evaluating normalized contact residue pairing frequencies. Interface residues adopt characteristic canonical residue conformations in the Ramachandran space, with a pronounced preference for positive ϕ conformations. It was observed that phosphorylated residues have an unusual propensity to adopt the positive ϕ conformations at the interface.

Keywords: Ramachandran map; propensity; protein−peptide interactions; short linear motif (SLiM).