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Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

by Sambit Kumar Mishra, Connor J Cooper, Jerry M Parks, Julie C Mitchell
Publication Type
Journal Name
The Journal of Physical Chemistry B
Publication Date
Page Numbers
6058 to 6067

Protein-protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. In this study, we propose a scoring function, KFC-E, that accounts for both conservation and co-evolution of putative binding hotspot residues at protein-protein interfaces. We tested KFC-E on two benchmark sets of unbound examples and three benchmark sets of bound examples, finding that KFC-E can correctly distinguish near-native hits from docking decoys in about half the cases where near-native solutions were present.