Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli

Abstract

The outer lipopolysaccharide (LPS) membrane of Gram-negative bacteria forms the main barrier for transport of antimicrobial molecules into the bacterial cell. In this study we develop coarse-grained models for the outer membrane of Escherichia coli in the Martini-3 framework. The coarse-grained model force field was parametrized and validated using all-atom simulations of symmetric membranes of lipid A and rough LPS as well as a complete asymmetric membrane of LPS with the Oantigen. The bonded parameters were obtained using an iterative refinement procedure with target bonded distributions obtained from all-atom simulations. The membrane thickness, area of the LPS, and density distributions for the different regions as well as the water and ion densities in Martini-3 simulations show excellent agreement with the all-atom data. Additionally the solvent accessible surface area for individual molecules in water was found to be in good agreement. The binding of calcium ions with phosphate and carboxylate moieties of LPS is accurately captured in the Martini-3 model, indicative of the integrity of the highly negatively charged LPS molecules in the outer membranes of Gram-negative bacteria. The melting transition of the coarse-grained lipid A membrane model was found to occur between 300 and 310 K, and the model captured variations in area per LPS, order parameter, and membrane thickness across the melting transition. Our study reveals that the proposed Martini-3 models for LPS are able to capture the physicochemical balance of the complex sugar architecture of the outer membrane of Escherichia coli. The coarse-grained models developed in this study would be useful for determining membrane protein interactions and permeation of potential antimicrobials through bacterial membranes at mesoscopic spatial and temporal scales.

Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations

“…Appropriately parametrized coarse-grained membrane and sugar representations would be required to capture translocation through the outer membrane and peptidoglycan environments. Improvements in the sugar interaction force fields in the latest Martini 3 models do address this aspect, allowing for improved Martini-based representations, as shown in our recent work of the Gram-negative outer membrane . Studies assessing the translocation free energies of molecules using these outer membrane models have yet to appear in the literature.…”

“…Hence, extensive testing of coarse-grained force fields such as Martini is needed. Since the outer membrane and the peptidoglycan layers of the bacterial cell envelope are composed of sugars, the accuracy of the recent Martini models for these components of the bacterial cell envelope needs to be tested against accurate all-atom force fields. ,− In what follows, we summarize the literature concerning MD simulations of different components of the bacterial cell envelope using all-atom, united-atom, and coarse-grained descriptions.…”

“…While the Martini force field has been widely used to study lipids, the interactions of sugar molecules were not accurately captured in earlier versions of the force field. , Using the recently developed Martini 3 force field, which overcomes the shortcoming of the sugar parametrization, Vaiwala and Ayappa developed coarse-grained models of the outer membrane of E. coli (Figure A,B). The parametrization was systematically evaluated for symmetric bilayers of lipid A and rough LPS as well as the asymmetric outer membrane composed of smooth LPS and phospholipids.…”

“…(C) Interaction energies for insertion of small molecules into Re-LPS. Panels (A) and (B) are adapted with permission from ref . Copyright 2023 American Chemical Society.…”