Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1.

The dynamic nature of lipid membranes presents significant challenges with respect to understanding the molecular basis of protein/membrane interactions. Consequently, there is relatively little known about the structural mechanisms by which membrane-binding proteins might distinguish subtle variations in lipid membrane composition and/or structure. We have previously developed a multidisciplinary approach that combines molecular dynamics simulation with interfacial x-ray scattering experiments to produce an atomistic model for phosphatidylserine recognition by the immune receptor Tim4. However, this approach requires a previously determined protein crystal structure in a membrane-bound conformation. Tim1, a Tim4 homolog with distinct differences in both immunological function and sensitivity to membrane composition, was crystalized in a closed-loop conformation that is unlikely to support membrane binding. Here we have used a previously described highly mobile membrane mimetic membrane in combination with a conventional lipid bilayer model to generate a membrane-bound configuration of Tim1 in silico. This refined structure provided a significantly improved fit of experimental x-ray reflectivity data. Moreover, the coupling of the x-ray reflectivity analysis with both highly mobile membrane mimetic membranes and conventional lipid bilayer molecular dynamics simulations yielded a dynamic model of phosphatidylserine membrane recognition by Tim1 with atomic-level detail. In addition to providing, to our knowledge, new insights into the molecular mechanisms that distinguish the various Tim receptors, these results demonstrate that in silico membrane-binding simulations can remove the requirement that the existing crystal structure be in the membrane-bound conformation for effective x-ray reflectivity analysis. Consequently, this refined methodology has the potential for much broader applicability with respect to defining the atomistic details of membrane-binding proteins.

Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4.

Recognition of phosphatidylserine (PS) lipids exposed on the extracellular leaflet of plasma membranes is implicated in both apoptotic cell removal and immune regulation. The PS receptor T cell immunoglobulin and mucin-domain-containing molecule 4 (Tim4) regulates T-cell immunity via phagocytosis of both apoptotic (high PS exposure) and nonapoptotic (intermediate PS exposure) activated T cells. The latter population must be removed at lower efficiency to sensitively control immune tolerance and memory cell population size, but the molecular basis for how Tim4 achieves this sensitivity is unknown. Using a combination of interfacial X-ray scattering, molecular dynamics simulations, and membrane binding assays, we demonstrate how Tim4 recognizes PS in the context of a lipid bilayer. Our data reveal that in addition to the known Ca(2+)-coordinated, single-PS binding pocket, Tim4 has four weaker sites of potential ionic interactions with PS lipids. This organization makes Tim4 sensitive to PS surface concentration in a manner capable of supporting differential recognition on the basis of PS exposure level. The structurally homologous, but functionally distinct, Tim1 and Tim3 are significantly less sensitive to PS surface density, likely reflecting the differences in immunological function between the Tim proteins. These results establish the potential for lipid membrane parameters, such as PS surface density, to play a critical role in facilitating selective recognition of PS-exposing cells. Furthermore, our multidisciplinary approach overcomes the difficulties associated with characterizing dynamic protein/membrane systems to reveal the molecular mechanisms underlying Tim4's recognition properties, and thereby provides an approach capable of providing atomic-level detail to uncover the nuances of protein/membrane interactions.

Liquid Surface X-ray Studies of Gold Nanoparticle-Phospholipid Films at the Air/Water Interface.

Amphiphilic phospholipids and nanoparticles functionalized with hydrophobic capping ligands have been extensively investigated for their capacity to self-assemble into Langmuir monolayers at the air/water interface. However, understanding of composite films consisting of both nanoparticles and phospholipids, and by extension, the complex interactions arising between nanomaterials and biological membranes, remains limited. In this work, dodecanethiol-capped gold nanoparticles (Au-NPs) with an average core diameter of 6 nm were incorporated into 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayers with surface densities ranging from 0.1 to 20% area coverage at a surface pressure of 30 mN/m. High resolution liquid surface X-ray scattering studies revealed a phase separation of the DPPC and Au-NP components of the composite film, as confirmed with atomic force microscopy after the film was transferred to a substrate. At low Au-NP content, the structural organization of the phase-separated film is best described as a DPPC film containing isolated islands of Au-NPs. However, increasing the Au-NP content beyond 5% area coverage transforms the structural organization of the composite film to a long-range interconnected network of Au-NP strands surrounding small seas of DPPC, where the density of the Au-NP network increases with increasing Au-NP content. The observed phase separation and structural organization of the phospholipid and nanoparticle components in these Langmuir monolayers are useful for understanding interactions of nanoparticles with biological membranes.

Thermodynamic and kinetic investigations of the release of oxidized phospholipids from lipid membranes and its effect on vascular integrity.

The lipid membrane not only provides a rich interface with an array of receptor signaling complexes with which a cell communicates, but it also serves as a source of lipid derived bioactive molecules. In pathologic conditions of acute lung injury (ALI) associated with activation of oxidative stress, unsaturated phosphatidyl cholines overlooking a luminal space undergo oxidation leading to generation of fragmented phospholipids such as 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (lysoPC), or 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC) full length oxygenation products (oxPAPC). Using Langmuir monolayers as models of the lipid bilayer, we evaluated the propensity of these phospholipids to solubilize from the cell membrane. The results suggest that lysoPC is rapidly released as it is produced, while oxPAPC has a longer membrane bound lifetime. After being released from cell membranes, these oxidized phospholipids exhibit potent agonist-like effects on neighboring cells. Therefore, we correlate the presence of the two phospholipid groups with the onset and resolution of increased vascular leakiness associated with ALI through testing their effect on vascular endothelial barrier integrity. Our work shows that cells respond differently to these two groups of products of phosphatidyl choline oxidation. LysoPC disrupts cell-cell junctions and increases endothelial permeability while oxPAPC enhances endothelial barrier. These data suggest a model whereby rapid release of lysoPC results in onset of ALI associated vascular leak, and the release of a reserve of oxPAPC as oxidative stress subsides restores the vascular barrier properties.