Dynamic Behavior and Substrate Interactions of the Polymyxin Resistance Determinant MCR‑1 Investigated by Molecular Dynamics Simulations in the Membrane Environment

TL;DR

This study uses molecular simulations to explore how the MCR-1 enzyme, which makes bacteria resistant to colistin, behaves in a membrane environment and interacts with its substrate.

Contribution

The study reveals dynamic behavior and substrate interactions of full-length MCR-1 in a membrane using molecular dynamics simulations.

Findings

MCR-1's domains show limited movement relative to each other in the membrane environment.

POPE can bind to the resting state of MCR-1 in an orientation suitable for PEtN transfer.

Stable binding of a second zinc requires restraints and involves Glu116, which is critical for colistin resistance.

Abstract

The Mobile Colistin Resistance (MCR) phosphoethanolamine
(PEtN)
transferase is a plasmid-borne enzyme responsible for colistin antibiotic
resistance in , the
most important antimicrobial-resistant bacterial pathogen worldwide.
Bacterial PEtN transferases like MCR comprise periplasmic catalytic
and integral membrane domains, with mechanistic understanding largely
based on studies of the former and limited information on the full-length
enzyme. Previous investigations of a PEtN transferase identified that the catalytic domain can effectively
dissociate from the transmembrane component and instead make extensive
contacts with the membrane surface. Here, we report molecular dynamics
simulations of a model of full-length MCR-1 in a representative membrane
comprising 80% of a PEtN donor substrate, palmitoyloleoyl phosphoethanolamine
(POPE), that explore the dynamic behavior of the enzyme and the impact
upon it of zinc stoichiometry and PEtN addition to the Thr285 acceptor
residue. The results identify only limited movement of the two domains
relative to one another, and that POPE can bind the likely “resting”
state of the enzyme (monozinc with unmodified Thr285) in an orientation
compatible with PEtN transfer to Thr285. Stable binding of a second
zinc equivalent occurred only with application of restraints and involved
Glu116 from the transmembrane domain. Mutation of this residue abolished
MCR-1-mediated protection of recombinant from colistin. Our data suggest domain motions in bacterial PEtN
transferases to be condition-dependent and support a proposed “ping-pong”
reaction mechanism, with the monozinc enzyme competent to undertake
the first stage.

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