Calculation of Relative Binding Free Energy for Mutations in Protein Complexes: The Alchemical Path

Abstract

Calculating the binding free energies, particularly the relative changes due to point mutations, for protein complexes has long been employed to complement experiments to explore roles and functions of specific residues on proteins during complex biological processes, such as protein-protein, ligand-receptor, and protein-DNA/RNA interactions. For instance, the free energy perturbation (FEP) method has been extensively used to estimate both the relative and absolute binding free energies of various protein complexes. In this chapter, we introduced some basic theoretical concepts of binding free energy calculations along with a detailed step-by-step guide for setting up, running, and analyzing FEP simulations in the context of popular NAMD and VMD software. The protocol comprised the preparation of the hybrid structure/topology and simulation setups required for both relative and absolute free energy calculations. Taking the sAPP–GABABR1a binary complex and the HLA-peptide-TCR tertiary complex as illustrative practical applications, the protocol however should be generally applicable to various biological complexes.