Noncovalent Interaction Origins of Substrate Discrimination in LinB: A Combined QM/MM and SAPT Analysis

Abstract

Abstract Noncovalent interactions (NCIs) play a fundamental role in ligand organization within enzyme active sites and are increasingly recognized as contributors to selective substrate recognition. The haloalkane dehalogenase LinB provides a suitable system for probing the physicochemical origins of selectivity, as structurally similar substrates exhibit markedly different reactivity. In this work, we investigated LinB-catalyzed dehalogenation pathways for 1,2-dibromopropane (DBP) and the closely related 1,2-dichloropropane (DCP), considering both C1 and C2 nucleophilic attack for each enantiomer. While minimum free-energy pathway calculations reproduced the experimentally observed DBP preference, they did not fully resolve the molecular origin of these selectivity trends within a reaction-coordinate framework. To address this limitation, we applied symmetry-adapted perturbation theory (SAPT) to ensembles of representative structures sampled along the reaction pathways. This interaction-level approach revealed that substrate discrimination arises from a finely balanced interplay of electrostatic attraction, dispersion stabilization, and exchange repulsion, rather than a single dominant factor. Active-site residues preorganize the binding pocket to favor DBP stabilization, whereas DCP experiences weaker stabilizing interactions and increased repulsion, resulting in higher barriers and reduced reactivity. Overall, this study demonstrates the utility of SAPT-based analysis of NCIs for elucidating nonmechanistic contributions to enzyme selectivity beyond conventional pathway approaches.