Interfac rim core

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Conservation and relative importance of residues across protein-protein interfaces

Mainak Guharoy and Pinak Chakrabarti

The role of hydrophobic residues in protein-protein recognition and the formation of multimeric protein assembly has long been recognized. A quantitative enumeration of the hydrophobic patches on the interface was achieved by dissecting it into core and rim regions, the former containing residues with some atoms fully buried in the interface, whereas the latter only contains atoms that retain partial accessibility. The core possesses more hydrophobic residues and has a composition that is distinct from the rim or the rest of the protein surface. With the division into core and rim residues one can ask the question of whether as two groups these residues have different contributions to binding energy, and consequently have different evolutionary pressure for their conservation. The degree of conservation of each interface residue can be defined in terms of sequence entropy at that position in the polypeptide chain across all of the homologous proteins.

Calculation of Mean Sequence Entropies for the Core and Rim. The amino acid residues comprising the interface were segregated into core and rim based on the solvent accessibility of their constituent atoms in the bound state, the former type of residues having fully buried atoms, whereas the latter contain atoms that remain partially exposed to solvent. 


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Dissecting protein–protein recognition sites

When the interface buries <2000 Å2 of protein surface, the recognition sites usually form a single patch on the surface of each component protein. In contrast, larger interfaces are generally multipatch, with at least one pair of patches that are equivalent in size to a single-patch interface. Each recognition site, or patch within a site, contains a core made of buried interface atoms, surrounded by a rim of atoms that remain accessible to solvent in the complex.

The interface area is the area buried in the interaction, measured as the sum of the solvent accessible surface area (ASA) of the two component proteins, less that of the complex.

Lo Conte et al.12 noted that most of the protein–protein complexes bury a surface area in the range of 1200–2000 Ų and defined their interfaces as “standard size.”



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The atomic structure of protein-protein recognition sites


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core interface, rim interface, and non-interface residues