Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

Abstract

The outer membrane of Gram-negative bacteria is almost exclusively composed of lipopolysaccharide in its outer leaflet, whereas the inner leaflet contains a mixture of phospholipids. Lipopolysaccharide diffuses at least an order of magnitude slower than phospholipids, which can cause issues for molecular dynamics simulations in terms of adequate sampling. Here we test a number of simulation protocols for their ability to achieve convergence with reasonable computational effort using the MARTINI coarse-grained force-field. This is tested in the context both of potential of mean force (PMF) calculations for lipid extraction from membranes, and of lateral mixing within the membrane phase. We find that decoupling the cations that crosslink the lipopolysaccharide headgroups from the extracted lipid during PMF calculations is the best approach to achieve convergence comparable to that for phospholipid extraction. We also show that lateral lipopolysaccharide mixing/sorting is very slow and not readily addressable even with Hamiltonian replica exchange. We discuss why more sorting may be unrealistic for the short (microseconds) timescales we simulate and provide an outlook for future studies of lipopolysaccharide-containing membranes.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

“…Simulations of lipid bilayers containing products of lipid oxidations have found a decrease in permeability for the case of oxysterols [550] and tail oxidized phosphatidylcholine [481]. From the standpoint of pharmaceutical research, the most interesting are studies of membranes that form a boundary with an extracellular environment, including bacterial membranes [415,[610][611][612][613][614][615][616], the stratum corneum, i.e., the most external layer of the skin [617][618][619][620][621][622][623][624][625][626], membranes present in the eyes [557,[627][628][629][630][631], and the ocular mucous membrane [632], or lung surfactant monolayers [263,558,[633][634][635][636][637][638]. Specifically, MD simulations have been used in studies of enhancer effects on the permeability of the stratum corneum (e.g., [544]).…”

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

“…2− due to more hydrogen bond donors in PO 4 1− (Figure S12A). However, the overall stabilization of the leaflet integrity is maintained by the electrostatic interactions formed by salt bridges between Ca 2+ ions and phosphate groups of lipid A, indicated by a much larger number of salt bridges than that of interlipid A hydrogen bonds (Figure S12C).…”

“…Conventional all-atom molecular dynamics (MD) simulations suffer from slow and incomplete coverage of phase space, which can limit their applicability to slowly evolving systems. Thus, there is a great need to identify and implement methods to improve conformational sampling. − A major contributing factor to the slow coverage of phase space is the small integration time steps (1 or 2 fs) that are required to conserve the total energy . Hydrogen mass repartitioning (HMR) is a simulation technique that enables all-atom MD to employ a 4-fs time step by distributing a heavy atom mass to hydrogen atom(s) attached to the heavy atom.…”

What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?

“…Atomistic models of LPS now exist for the AMBER, GROMOS and CHARMM families of force fields, enabling simulations of more biologically representative models of the OM [1, 43–46]. These simulations have the caveat that the slow-moving nature of LPS necessitates much longer simulation times to achieve equilibrated systems and to observe significant dynamics [47, 48]. This can in part be mitigated by the use of CG models.…”