Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers

Abstract

Understanding the forces that stabilize membrane proteins in their native states is one of the contemporary challenges of biophysics. To date, estimates of side chain partitioning free energies from water to the lipid environment show disparate values between experimental and computational measures. Resolving the disparities is particularly important for understanding the energetic contributions of polar and charged side chains to membrane protein function because of the roles these residue types play in many cellular functions. In general, computational free energy estimates of charged side chain partitioning into bilayers are much larger than experimental measurements. However, the lack of a protein-based experimental system that uses bilayers against which to vet these computational predictions has traditionally been a significant drawback. Moon & Fleming recently published a novel hydrophobicity scale that was derived experimentally by using a host-guest strategy to measure the side chain energetic perturbation due to mutation in the context of a native membrane protein inserted into a phospholipid bilayer. These values are still approximately an order of magnitude smaller than computational estimates derived from molecular dynamics calculations from several independent groups. Here we address this discrepancy by showing that the free energy differences between experiment and computation become much smaller if the appropriate comparisons are drawn, which suggests that the two fields may in fact be converging. In addition, we present an initial computational characterization of the Moon & Fleming experimental system used for the hydrophobicity scale: OmpLA in DLPC bilayers. The hydrophobicity scale used OmpLA position 210 as the guest site, and our preliminary results demonstrate that this position is buried in the center of the DLPC membrane, validating its usage in the experimental studies. We further showed that the introduction of charged Arg at position 210 is well tolerated in OmpLA and that the DLPC bilayers accommodate this perturbation by creating a water dimple that allows the Arg side chain to remain hydrated. Lipid head groups visit the dimple and can hydrogen bond with Arg, but these interactions are transient. Overall, our study demonstrates the unique advantages of this molecular system because it can be interrogated by both computational and experimental practitioners, and it sets the stage for free energy calculations in a system for which there is unambiguous experimental data.

Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm

“…The molecular dynamics calculations of OmpLA have been previously published (37). A similar protocol was used for PagP and OmpW in DLPC bilayers and is described in detail in SI Text.…”

Buried lysine, but not arginine, titrates and alters transmembrane helix tilt

“…Additionally, for cases in which the aqueous access to Arg may be impeded, structural manipulations to remove the obstruction can restore the accommodation of Arg within a bilayer (19). In relatively thin dilauroyl-phosphatidylcholine bilayer membranes, the cost of placing Arg within a transmembrane helix of outer membrane phospholipase is about 3.7 kcal/mol at pH 3.8 (13,16,18), whereas a somewhat larger cost was found for placing Lys at the same position at pH 3.8 (13). Within the context of the existing experiments and simulations, the pH dependence of side-chain ionization merits consideration.…”

“…Although some molecular dynamics simulations (10,11) have estimated larger energy barriers than translocon-mediated (12) or water-to-bilayer membrane protein-folding experiments (13) for moving Arg into the bilayer, careful consideration of experimental conditions and the underlying molecular context is leading to a convergence of findings from different methods (14)(15)(16). In particular, Arg side-chain snorkeling, helix off-center translocation, and membrane deformation all can contribute to maintaining (partial) hydration and thereby lowering the free energy for accommodating a charged residue within a lipid bilayer (14)(15)(16)(17)(18). Additionally, for cases in which the aqueous access to Arg may be impeded, structural manipulations to remove the obstruction can restore the accommodation of Arg within a bilayer (19).…”

Reduced Lipid Bilayer Thickness Regulates the Aggregation and Cytotoxicity of Amyloid-β

“…Both DOPC and POPC have been previously applied to examine the interactions between lipid bilayers and amyloidogenic proteins (8, 16 -19). DLPC bilayers have been used in the study of a variety of membrane proteins and were observed to stabilize some membrane proteins in vitro that are less tractable with other lipid bilayer systems, but they have not been used previously in the study of A␤ (20,21).…”