Surface complementarity of buried protein residues

摘要

The surface fit of residues buried in protein interiors has been estimated using a surface complementarity function (S-m). For a perfect match between two surfaces, S-m gives a value of 1.0. When all dot surface points were considered irrespective of having been contributed by main-chain or side-chain atoms, buried residues gave an average S-m of 0.60, ranging from 0.57 to 0.63 for the 20 amino acids. This indicated the ability of all residues, i.e. polar, apolar, or charged to pack with the same measure of complementarity in protein interiors. Further, the same calculation performed with surface points from side-chain atoms alone gave a lower global average of 0.47, implying the importance of main-chain atoms in internal packing. The lower value of surface complementarity obtained in this case also showed that the side-chains of buried residues need not invariably be involved in a 'jigsaw puzzle'-like complementarity with other side-chains of the polypeptide chain and can occasionally show serious packing defects, though they play a predominant role in packing compared to the main-chain atoms. However, the combination of both side- and main-chain atoms ensures a high average S-m of 0.60 (calculated with all atoms), indicating high steric fit for all residues upon burial. [References: 35]