Genomic and structural insights into the atpB L173I substitution: modulation of the F₀ rotor architecture in Mycobacterium tuberculosis ATP synthase and altered Bedaquiline binding dynamics.

Abstract

The F₀F₁ ATP synthase of Mycobacterium tuberculosis (M. tuberculosis) is an essential membrane-embedded rotary motor responsible for ATP synthesis and maintenance of the proton motive force in bacteria. The transmembrane F₀ domain comprises the c-subunit (atpE) and the a-subunit (atpB). Their coordinated interactions are needed for proton translocation and torque generation. Bedaquiline (BDQ), FDA-approved diarylquinoline for the treatment of multidrug-resistant tuberculosis (MDR-TB), targets the F₀ motor by binding at the a-c interface and inhibiting rotary catalysis. To the best of our knowledge, this study represents the first attempt to analyze the effects of mutations in the atpB protein on its structural stability in the F₀ domain, thereby highlighting the novelty of this work. In this study, we integrated Indian whole-genome sequencing (WGS) datasets (PRJNA37907) with long-timescale (1000 ns) membrane-embedded molecular dynamics (MD) simulations. Among 57 atpB mutations identified from WGS analysis, L173I was selected for structural and MD analysis. L173I is located at the atpB-atpE interface near the BDQ-binding region, despite V177L and S184A showing higher prevalence. Comparative MD simulations encompassed four systems: wild-type apo, wild-type with BDQ, L173I apo, and L173I with BDQ. Structural interrogation revealed that the L173I substitution induces subtle destabilization of the global fold of the atpB-atpE complex relative to the apo state, while more critically attenuating inter-subunit contacts between the a-subunit and the c-ring. These perturbations provide a mechanistic rationale for reduced BDQ susceptibility, arising from altered interfacial dynamics rather than complete abrogation of drug binding. This integrative genomic-structural framework advances our understanding of ATP synthase-mediated resistance in M. tuberculosis.