Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein–Protein Interfaces. Issue 7 (29th March 2019)

• Record Type: Journal Article
• Authors: Clark, Anthony J.; Negron, Christopher; Hauser, Kevin; Sun, Mengzhen; Wang, Lingle; Abel, Robert; Friesner, Richard A.
• Is Part Of: Journal of molecular biology. Volume 431:Issue 7(2019)
• Page Start: 1481
• Page End: 1493
• Publication Date: 2019-03-29
• Subjects: free energy perturbation -- antibodies -- protein-protein binding; mm-GB/SA molecular mechanics generalized Born surface area -- MM molecular mechanics -- FEP free energy perturbation -- MD molecular dynamics -- bNAb broadly neutralizing antibody -- RMSE root mean square error -- SKEMPI Structural database of Kinetics and Energetics of Mutant Protein Interactions -- fSASA fractional solvent accessible surface area; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2019.02.003
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Building on the substantial progress that has been made in using free energy perturbation (FEP) methods to predict the relative binding affinities of small molecule ligands to proteins, we have previously shown that results of similar quality can be obtained in predicting the effect of mutations on the binding affinity of protein–protein complexes. However, these results were restricted to mutations which did not change the net charge of the side chains due to known difficulties with modeling perturbations involving a change in charge in FEP. Various methods have been proposed to address this problem. Here we apply the co-alchemical water approach to study the efficacy of FEP calculations of charge changing mutations at the protein–protein interface for the antibody–gp120 system investigated previously and three additional complexes. We achieve an overall root mean square error of 1.2 kcal/mol on a set of 106 cases involving a change in net charge selected by a simple suitability filter using side-chain predictions and solvent accessible surface area to be relevant to a biologic optimization project. Reasonable, although less precise, results are also obtained for the 44 more challenging mutations that involve buried residues, which may in some cases require substantial reorganization of the local protein structure, which can extend beyond the scope of a typical FEP simulation. We believe that the proposed prediction protocol will be of sufficient efficiency and accuracy to guide protein engineering projects for which optimization and/or maintenance of a high degree of binding affinity is a key objective. Graphical Abstract: Unlabelled Image