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.
Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France.
Karen
K
Druart
Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France.
Zoltan
Z
Palmai
Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France.
Eyaz
E
Omarjee
Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France.
Thomas
T
Simonson
D001665:Binding Sites / Q000187:drug effects; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D013816:Thermodynamics; D014443:Tyrosine / Q000737:chemistry* / Q000378:metabolism*; D014448:Tyrosine-tRNA Ligase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
D008024:Ligands; D050505:Mutant Proteins; D014443:Tyrosine; D014448:Tyrosine-tRNA Ligase
aminoacyl-tRNA synthetase; continuum electrostatics; molecular dynamics