Exploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation (SILCS) methodology.

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TitleExploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation (SILCS) methodology.
Publication TypeJournal Article
Year of Publication2018
AuthorsYu, W, Jo, S, Lakkaraju, SKaushik, Weber, DJ, Mackerell, AD
JournalProteins
Date Published2018 Dec 23
ISSN1097-0134
Abstract

Protein docking methods are powerful computational tools to study protein-protein interactions (PPI). While a significant number of docking algorithms have been developed, they are usually based on rigid protein models or with limited considerations of protein flexibility and the desolvation effect is rarely considered in docking energy functions, which may lower the accuracy of the predictions. To address these issues, we introduce a PPI energy function based on the Site-Identification by Ligand Competitive Saturation (SILCS) framework and utilize the fast Fourier transform (FFT) correlation approach. The free energy content of the SILCS FragMaps represent an alternative to traditional energy grids and they can be efficiently utilized to guide FFT-based protein docking. Application of the approach to 8 diverse test cases, including 7 from Protein Docking Benchmark 5.0, showed the PPI prediction using SILCS approach (SILCS-PPI) to be competitive with several commonly used protein docking methods indicating that the method has the ability to both qualitatively and quantitatively inform the prediction of PPI. Results show the utility of the SILCS-PPI docking approach for determination of probability distributions of PPI interactions over the surface of both partner proteins, allowing for identification of alternate binding poses. Such binding poses are confirmed by experimental crystal contacts in our test cases. While more computationally demanding than available PPI docking technologies, we anticipate that the SILCS-PPI docking approach will offer an alternative methodology for improved evaluation of PPIs that could be used in a variety of fields from systems biology to excipient design for biologics-based drugs. This article is protected by copyright. All rights reserved.

DOI10.1002/prot.25650
Alternate JournalProteins
PubMed ID30582220