LAUSR

Molecular recognition underpins all specific protein-ligand interactions and is essential for biomolecular functions. Prediction of canonical binding poses and distinguishing binders from non-binders 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 non-binder interaction with T4 lysozyme L99A 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 correctly portray X-ray structures. The free-energy profiles of binders (benzene, ethylbenzene, and n-hexylbenzene) are distinct from those of non-binders (phenol and benzaldehyde). Bindings of the two larger molecules seem to be associated with a structural change toward an excited conformation of the protein, which agrees with experimental findings. The protocol is generally applicable to various proteins having buried cavities with limited access for ligands with different shapes, sizes and chemical properties.