Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

Abstract

The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface

“…model reported by Noinaj et al (19): most of the b-barrel domain from crystal structure Protein Data Bank (PDB): 4N75 (20) and residues 715-740 from crystal structure PDB: 4C4V (18). The resultant full-length BamA model was embedded into an asymmetric bilayer whose acyl chain and headgroup composition was chosen to mimic a typical E. coli outer membrane (45) using the protocol implemented in CHARMM-GUI Membrane Builder (46,47) as previously described in (48) and also recently applied for OmpF simulations (49). The outer leaflet of the membrane was composed entirely of rough LPS with lipid A and R1 core (50), and the inner leaflet consisted of a mixture of PPPE, PVPG, and PVCL with a ratio of 15:4:1 (51), where PPPE is 16:0 (palmitoyl) -16:1 cis-9 (palmitoleoyl) phosphatidylethanolamine, PVPG is 16:0 (palmitoyl) -18:1 cis-11 (vacenoyl) phosphatidylglycerol, and PVCL is 1,1 0 -palmitoyl-2,2 0 -vacenoyl cardiolipin with a net charge of À2e.…”

Localized incorporation of outer membrane components in the pathogen Brucella abortus

“…The binding of LPS molecules to different OM porins was already reported for several other Gram-negative bacteria, e.g., E. coli (Rocque et al, 1987;Strittmatter & Galanos, 1987;Buehler et al, 1991;de Cock & Tommassen, 1996), Salmonella (Strittmatter & Galanos, 1987;Latsch et al, 1992;Hagge et al, 2002) or Yersinia (Strittmatter & Galanos, 1987;Vakorina et al, 2003). This is well described for OmpF, a major porin of E. coli (Bolla et al, 1988;Holzenburg et al, 1989;Diedrich et al, 1990;Buehler et al, 1991;Sen & Nikaido, 1991;Arunmanee et al, 2014Arunmanee et al, , 2016Patel et al, 2016) belonging to the same family as Omp2b. One selective advantage of clustering R-LPS and Omp2b could be to facilitate diffusion of compounds from the medium into the pores of the porin, as suggested by theoretical simulations using OmpF as a model (Patel et al, 2016).…”

“…This is well described for OmpF, a major porin of E. coli (Bolla et al, 1988;Holzenburg et al, 1989;Diedrich et al, 1990;Buehler et al, 1991;Sen & Nikaido, 1991;Arunmanee et al, 2014Arunmanee et al, , 2016Patel et al, 2016) belonging to the same family as Omp2b. One selective advantage of clustering R-LPS and Omp2b could be to facilitate diffusion of compounds from the medium into the pores of the porin, as suggested by theoretical simulations using OmpF as a model (Patel et al, 2016). We were able to show that Omp2b seems to have a preference of co-localizing with R-LPS, whereas there was no distinction between the different endogenous LPS types in previous in vivo studies (Rocque et al, 1987;Strittmatter & Galanos, 1987;Bolla et al, 1988;Holzenburg et al, 1989;Diedrich et al, 1990;Buehler et al, 1991;Latsch et al, 1992).…”

Challenges in structural approaches to cell modeling

“…Together Figs. 6 and 7 show the current progress of all-atom modeling and simulation of complex membrane systems [214-216] including LPS and GPI-anchor. It is also now possible to build various glycolipid models in Glycolipid Modeler in CHARMM-GUI (http://www.charmm-gui.org/input/glycolipid), and it will be possible to incorporate Glycolipid Modeler into Membrane Builder in the future to model realistic cellular membranes.…”