Reassessing buried surface areas in protein-protein complexes.
The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3% greater than in their unbound state, and the BSA, 7% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.
Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700 054, India.
Devlina
D
Chakravarty
Mainak
M
Guharoy
Charles H
CH
Robert
Pinak
P
Chakrabarti
Joël
J
Janin
D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D006860:Hydrogen Bonding; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D000596:Amino Acids; D046912:Multiprotein Complexes; D011506:Proteins
binding free energy; conformation changes; protein-protein interaction; solvent accessible surface