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

Alessandro Giuliani, Romualdo Benigni, Mauro Colafranceschi, Indu Chandrashekar, Sudha M. Cowsik

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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.

Original languageEnglish
Pages (from-to)299-310
Number of pages12
JournalProteins: Structure, Function and Bioinformatics
Issue number2
Publication statusPublished - 1 May 2003
Externally publishedYes


  • Bioinformatics
  • Principal component analysis
  • Protein-protein interaction
  • Recurrence quantification analysis
  • Singular value decomposition

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