Deciphering intrinsic inter-subunit couplings that lead to sequential hydrolysis of F1-ATPase ring

TL;DR

This study combines computational simulations and experimental data to uncover how intrinsic inter-subunit couplings in F1-ATPase promote its sequential hydrolysis, revealing the structural dynamics underlying its coordinated rotary mechanism.

Contribution

It identifies specific inter-subunit couplings and conformational changes that facilitate sequential hydrolysis in F1-ATPase, advancing understanding of its molecular coordination.

Findings

Sequential hydrolysis schemes were reproduced through simulations.

Neighbor-site ATP binding and hydrolysis facilitate product release.

Asymmetrical neighbor-site opening and charge hopping enable product release.

Abstract

The rotary sequential hydrolysis of metabolic machine F1-ATPase is a prominent feature to reveal high coordination among multiple chemical sites on the stator F1 ring, which also contributes to tight coupling between the chemical reaction and central {\gamma}-shaft rotation. High-speed AFM experiments discovered that the sequential hydrolysis was maintained on the F1 ring even in the absence of the {\gamma} rotor. To explore how the intrinsic sequential performance arises, we computationally investigated essential inter-subunit couplings on the hexameric ring of mitochondrial and bacterial F1. We first reproduced the sequential hydrolysis schemes as experimentally detected, by simulating tri-site ATP hydrolysis cycles on the F1 ring upon kinetically imposing inter-subunit couplings to substantially promote the hydrolysis products release. We found that it is key for certain ATP binding and hydrolysis events to facilitate the neighbor-site ADP and Pi release to support the sequential hydrolysis. The kinetically feasible couplings were then scrutinized through atomistic molecular dynamics simulations as well as coarse-grained simulations, in which we enforced targeted conformational changes for the ATP binding or hydrolysis. Notably, we detected the asymmetrical neighbor-site opening that would facilitate the ADP release upon the enforced ATP binding, and computationally captured the complete Pi release through charge hopping upon the enforced neighbor-site ATP hydrolysis. The ATP-hydrolysis triggered Pi release revealed in current TMD simulation confirms a recent prediction made from statistical analyses of single molecule experimental data in regard to the role ATP hydrolysis plays. Our studies, therefore, elucidate both the concerted chemical kinetics and underlying structural dynamics of the inter-subunit couplings that lead to the rotary sequential hydrolysis of the F1 ring.