# Molecular Mechanism of ATP Hydrolysis Catalyzed by p97: A QM/MM Study

## TL;DR

This study uses advanced simulations to uncover how the p97/VCP protein breaks down ATP, revealing a key role for a conserved amino acid in the process.

## Contribution

The first in silico study of ATP hydrolysis in p97/VCP or any AAA+ protein, revealing a catalytic mechanism involving a conserved glutamate.

## Key findings

- Glu305 from the Walker B motif acts as a catalytic base activating water for nucleophilic attack on the γ-phosphate.
- Phosphate bond formation and breakage occur concertedly in the first reaction step.
- Findings are validated against cryo-EM and NMR data for post-hydrolysis states.

## Abstract

A computational study
of p97/VCP ATPase using hybrid
quantum mechanics/molecular
mechanics (QM/MM) simulations is presented that explores the conformational
landscape of the active site and hydrolysis-competent states of the
crystallographic water molecules. Our investigation focuses on the
reaction mechanism, particularly the events of the rate-determining
first reaction step, which we study using extensive sampling with
the path well-tempered metadynamics extended-system adaptive biasing
force (WTM-eABF) enhanced sampling method. We identify the highly
conserved glutamate (Glu305) from the Walker B motif as a catalytic
base that activates the lytic water molecule for nucleophilic attack
on the γ-phosphate in the first reaction step, while the final
product is formed in a second step that involves proton transfer and
rearrangements in the Mg2+ coordination sphere. We show
that phosphate bond formation and breakage occur concertedly in the
first reaction step. The findings gained through versatile QM/MM approaches
are validated against recent cryo-EM and NMR data for the post-hydrolysis
protein state, elucidating the role of amino acids from conserved
motifs across the AAA+ protein family. To the best of our knowledge,
this is the first in silico exploration of ATP hydrolysis
in p97/VCP or any other AAA+ protein.