Large contact surface interactions between proteins detected by time series analysis methods: Case study on C-phycocyanins

Abstract

A purely sequence-dependent approach to the modeling of protein–protein interaction was applied to the study of C-phycocyanin αβ dimers. The interacting pairs (α and β subunits) share an almost complete structural homology, together with a general lack of sequence superposition; thus, they constitute a particularly relevant example for protein–protein interaction prediction. The present analysis is based on a description posited at an intermediate level between sequence and structure, that is, the hydrophobicity patterning along the chains. Based on the description of the sequence hydrophobicity patterns through a battery of nonlinear tools (recurrence quantification analysis and other sequence complexity descriptors), we were able to generate an explicit equation modeling α and β monomers interaction; the model consisted of canonical correlation between the hydrophobicity autocorrelation structures of the interacting pairs. The general implications of this holistic approach to the modeling of protein–protein interactions, which considers the protein primary structures as a whole, are discussed. Proteins 2003;51:299–310. © 2003 Wiley-Liss, Inc.