Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity

Abstract

Background Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments. Results To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly. Conclusions The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.

The hidden intricacies of aquaporins: Remarkable details in a common structural scaffold

“…Investigating CL interactions utilizing a multitude of E. coli inner membrane proteins in silico identified a typical CL binding site to harbor two to three basic residues in close proximity, at least one polar residue, and one or more aromatic residues slightly deeper within the membrane (173). Similar to EcAQPZ, CL was also found to bind preferentially to this cytoplasmic crevice at the contact of two neighboring BtAQP1 protomers, as evident from MD simulations using a native-like model of E. coli polar lipid extract (174). In the latter study, the rest of the cytoplasmic protein surface was covered with negatively charged phosphatidylglycerols, which were attracted by a number of positively charged residues (Lys7 1.-16 , Lys8 1.-15 , Arg12 1.-11 , Arg95 3.-11 , Arg243 6.25 , and Lys245 6.27 ), similarly to CL.…”

“…Monomeric Ec GLPF was also less resistant to proteolysis in E. coli (186), with a significantly stabilized tetrameric assembly in vivo (188). Additional stabilization via specific lipid interactions within the complex natural lipid composition (174) may have evolved in parallel to inter- and intra-protomer evolution. In any case, optimization of tetramer stability is a tradeoff with protein aggregation and protein folding, as protomer stability in the lipid bilayer is a prerequisite for AQ(G)P folding into the membrane and consequent tetramerization.…”

The energetic barrier to single-file water flow through narrow channels

“…Thus, the plot indicates a negligible entropy of activation for water diffusion across lipid bilayers and membrane channels. Below, we list the sources of the plotted data next to the abbreviations used in the figure: aquaporin-1, AQP1 (Horner et al 2015;Zeidel et al 1992); aquaporin-Z, AQPZ (Horner et al 2015;Pohl et al 2001); bacterial potassium channel, KcsA (Horner et al 2015;Saparov and Pohl 2004); gramicidin A, gA (Pohl and Saparov 2000;Boehler et al 1978); aquaporin-0, AQP0 (Zampighi et al 1995;Kumar et al 2012); palmitoyl oleoyl phosphatidylcholine, POPC (Huster et al 1997); dioleoyl phosphatidylcholine, DOPC (Huster et al 1997); polar lipid extract from Escherichia coli, E. coli PLE (Saparov and Pohl 2004;Pluhackova and Horner 2021); egg and plant phosphatidylcholine, Egg PC and Plant PC (Fettiplace and Haydon 1980); CNT, CN-1 (Tunuguntla et al 2017); CNT, CN-2 (Li et al 2020); aquafoldamer, AQF (Shen et al 2020).…”

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]).…”