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

Mishra, Sambit Kumar; Cooper, Connor J.; Parks, Jerry M.; Mitchell, Julie C.

doi:10.1021/acs.jpcb.0c11525

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

Journal Article · Wed Jun 02 00:00:00 EDT 2021 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

DOI:https://doi.org/10.1021/acs.jpcb.0c11525· OSTI ID:1807273

Mishra, Sambit Kumar ^[1]; ^[1]; ^[1]; ^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

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. Here in this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1807273

Journal Information:: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Journal Name: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry Journal Issue: 23 Vol. 125; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
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binding modes
co-evolution
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hotspots

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

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