De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Molecular recognition underpins all specific protein-ligand interactions and is essential for biomolecular functions. The prediction of canonical binding poses and distinguishing binders from nonbinders are much sought after goals. Here, we apply the generalized replica exchange with solute tempering method, gREST, combined with a flat-bottom potential to evaluate binder and nonbinder interactions with a T4 lysozyme Leu99Ala mutant. The buried hydrophobic cavity and possibility of coupled conformational changes in this protein make binding predictions difficult. The present gREST simulations, enabling enhanced flexibilities of the ligand and protein residues near the binding site, sample bindings in multiple poses, and correct portrayal of X-ray structures. The free-energy profiles of binders (benzene, ethylbenzene, and