Dissecting subunit interfaces in homodimeric proteins

• DOI: 10.1002/prot.10461
• Publication Date: 2003-10-22T19:34:13Z
• Authors: Ranjit Prasad Bah...; Pinak Chakrabarti; Francis Rodier; Joël Janin
• Keywords: Models, Molecular; Protein Subunits; 0303 health sciences; 03 medical and health sciences; Binding Sites; Amino Acids; Dimerization; Hydrophobic and Hydrophilic Interactions; Protein Binding

Abstract The subunit interfaces of 122 homodimers known three‐dimensional structure are analyzed and dissected into sets surface patches by clustering atoms at the interface; 70 single‐patch, others have up to six patches, often contributed different structural domains. average interface buries 1,940 Å 2 each monomer, contains one or two burying 600–1,600 , is 65% nonpolar includes 18 hydrogen bonds. However, range size hydrophobicity wide among interfaces. Each has a core made residues with buried in dimer, surrounded rim that remain accessible solvent. core, which constitutes 77% on average, an amino acid composition resembles protein interior except for presence arginine residues, whereas more like surface. These properties homodimers, permanent assemblies, compared those protein‐protein complexes where components associate after they independently folded. On twice larger than complexes, much less polar due large fraction belonging although compositions cores similar types Proteins 2003. © 2003 Wiley‐Liss, Inc.