Reassessing buried surface areas in protein–protein complexes

Protein Science - Tập 22 Số 10 - Trang 1453-1457 - 2013
Devlina Chakravarty1, Mainak Guharoy2, Charles H. Robert2, Pinak Chakrabarti3, Joël Janin4
1Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700 054, India
2CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico‐Chimique (IBPC), Université Paris Diderot Sorbonne Paris Cité Paris France
3Department of Biochemistry Bose Institute P‐1/12 CIT Scheme VIIM Kolkata 700 054 India
4IBBMC, CNRS UMR 8619 Université Paris‐Sud 11 Orsay France

Tóm tắt

AbstractThe 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.

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Protein Science

Tập 22 Số 10

1453-1457

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