Druart, Karen; Palmai, Zoltan; Omarjee, Eyaz; Simonson, Thomas
Protein:Ligand Binding Free Energies: A Stringent Test for Computational Protein Design

A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl-tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate L-tyrosine (L-Tyr), compared to the analogs D-Tyr, p-acetyl-, and p-azido-phenylalanine (ac-Phe, az-Phe). We simulate L-and D-Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous "MD/GBSA" procedure: molecular dynamics with explicit solvent for structures and a Generalized Born-Surface Area model for binding free energies. Next, we consider L-Tyr, ac- and az-Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either L-Tyr or D-Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when L-Tyr is the ligand and a D-Tyr specific mutant when D-Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln. (C) 2015 Wiley Periodicals, Inc.


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