Jones, Susan; (1996) Protein-protein interactions. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Protein-protein interactions are fundamental to many biological processes. This work updates the current knowledge of the nature of these interactions using the 3-dimensional co-ordinates of protein complexes deposited in the Brookhaven Protein Data Bank (PDB). The characterisation of interfaces within a data set of 32 homo-dimers is presented, including the analysis of interface size, shape complementarity, amino acid composition, polarity and segmentation. The interfaces in these complexes were observed to be, in general, circular, hydrophobic patches on the surface of proteins, which were planar, and segmented with respect to the amino acid sequence. Interface properties were also analysed in different types of protein-protein complex, including dimers, trimers, enzyme-inhibitors, and antibody-proteins. These were classified as permanent (where the components only occur and function in a complexed state), and 'optional' (where the components also exist independently). The 'optional' complexes were less hydrophobic, and contained more inter-molecular hydrogen bonds. These complexes also had smaller and less well packed interfaces than those that only exist in the complexed state. Protein-protein interface properties were also used to differentiate the observed interface from other sites on the protein surface. Circular and contiguous patches of amino acid residues were defmed on the surface of protein structures. For all surface patches defined, 6 properties (solvation potential, residue interface propensity, planarity, hydrophobicity, accessible surface area, and protrusion) were calculated, and compared to those of the observed interface. Using this method, homo-dimer interfaces were found to be those patches that were the most planar, hydrophobic, surface accessible and protruding. This method of patch analysis was used in a predictive algorithm, to locate putative interaction sites on the surface of isolated protomers. The algorithm proved successful in the prediction of such sites in homo-dimers and enzyme- inhibitor complexes.

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