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Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR

Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR
Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR

Covalent modification of outer membrane lipids of Gram-negative bacteria can impact the ability of the bacterium to develop resistance to antibiotics as well as modulating the immune response of the host. The enzyme LpxR from Salmonella typhimurium is known to deacylate lipopolysaccharide molecules of the outer membrane; however, the mechanism of action is unknown. Here, we employ molecular dynamics and Monte Carlo simulations to study the conformational dynamics and substrate binding of LpxR in representative outer membrane models as well as detergent micelles. We examine the roles of conserved residues and provide an understanding of how LpxR binds its substrate. Our simulations predict that the catalytic H122 must be Nε-protonated for a single water molecule to occupy the space between it and the scissile bond, with a free binding energy of −8.5 kcal mol−1. Furthermore, simulations of the protein within a micelle enable us to predict the structure of the putative “closed” protein. Our results highlight the need for including dynamics, a representative environment, and the consideration of multiple tautomeric and rotameric states of key residues in mechanistic studies; static structures alone do not tell the full story.

0006-3495
1-12
Saunders, Graham M.
0dc09f56-5dfd-457d-bb89-236e10a20ded
Bruce Macdonald, Hannah E.
8e3f96bf-6806-4dc9-bd25-5b7a5325c7a7
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Saunders, Graham M.
0dc09f56-5dfd-457d-bb89-236e10a20ded
Bruce Macdonald, Hannah E.
8e3f96bf-6806-4dc9-bd25-5b7a5325c7a7
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394

Saunders, Graham M., Bruce Macdonald, Hannah E., Essex, Jonathan W. and Khalid, Syma (2018) Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR. Biophysical Journal, 1-12. (doi:10.1016/j.bpj.2018.09.002).

Record type: Article

Abstract

Covalent modification of outer membrane lipids of Gram-negative bacteria can impact the ability of the bacterium to develop resistance to antibiotics as well as modulating the immune response of the host. The enzyme LpxR from Salmonella typhimurium is known to deacylate lipopolysaccharide molecules of the outer membrane; however, the mechanism of action is unknown. Here, we employ molecular dynamics and Monte Carlo simulations to study the conformational dynamics and substrate binding of LpxR in representative outer membrane models as well as detergent micelles. We examine the roles of conserved residues and provide an understanding of how LpxR binds its substrate. Our simulations predict that the catalytic H122 must be Nε-protonated for a single water molecule to occupy the space between it and the scissile bond, with a free binding energy of −8.5 kcal mol−1. Furthermore, simulations of the protein within a micelle enable us to predict the structure of the putative “closed” protein. Our results highlight the need for including dynamics, a representative environment, and the consideration of multiple tautomeric and rotameric states of key residues in mechanistic studies; static structures alone do not tell the full story.

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More information

Accepted/In Press date: 6 September 2018
e-pub ahead of print date: 13 September 2018

Identifiers

Local EPrints ID: 425070
URI: http://eprints.soton.ac.uk/id/eprint/425070
ISSN: 0006-3495
PURE UUID: 46fcfe54-42ed-4d35-88fe-e0fb5d4d1095
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 10 Oct 2018 16:30
Last modified: 15 Sep 2021 01:53

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