Trollmann, M. F. W. | bioRxiv Science

bioRxiv2024

Constant-pH MD Simulations of Lipids

Constant pH Molecular Dynamics (CpHMD) simulations represent a cutting-edge computational approach for studying biological systems with remarkable realism. Recent advancements have enhanced the accessibility and efficiency of CpHMD, significantly reducing the performance overhead compared to traditional constant-protonation MD simulations. This chapter guides the reader through the application of CpHMD to investigate the pH-dependent behavior of Cationic Ionizable Lipids (CILs) -- a critical component of Lipid Nanoparticles (LNPs), which are among the most promising platforms for drug delivery. LNPs, including those employed in mRNA-based vaccines, played a pivotal role in the global response to the SARS-CoV-2 pandemic, underscoring their potential in modern medicine. The chapter begins with a comprehensive introduction to the fundamental concepts of LNPs and provides a step-by-step protocol for setting up simulations of membranes containing CILs to calculate their apparent pKa. This parameter is crucial for governing the in vivo behavior of LNPs, where precise control is essential to optimize delivery efficiency while minimizing toxicity. By showcasing the ability of CpHMD simulations to unravel the intricate relationship between pH-dependent protonation, membrane structure, and lipid distribution, this chapter highlights their potential to inform the rational design of novel LNP formulations.

biophysics↗

bioRxiv2023

Role of lipid nanodomains for inhibitory FcγRIIb function

The inhibitory Fc{gamma} receptor Fc{gamma}RIIb is involved in immune regulation and is known to localize to specific regions of the plasma membrane called lipid rafts. Previous studies suggested a link between the altered lateral receptor localization within the plasma membrane and the functional impairment of the Fc{gamma}RIIb-I232T variant that is associated with systemic lupus erythematosus. Here, we conducted microsecond all-atom molecular dynamics simulations and IgG binding assays to investigate the lipid nano-environment of Fc{gamma}RIIb monomers and of the Fc{gamma}RIIb-I232T mutant within a plasma membrane model, the orientation of the Fc{gamma}RIIb ectodomain, and its accessibility to IgG ligands. In contrast to previously proposed models, our simulations indicated that Fc{gamma}RIIb does not favor a cholesterol-or a sphingolipid-enriched lipid environment. Interestingly, cholesterol was depleted for all studied Fc{gamma}RIIb variants within a 2-3 nm environment of the receptor, counteracting the usage of raft terminology for models on receptor functionality. Instead, the receptor interacts with lipids that have poly-unsaturated fatty acyl chains and with (poly-) anionic lipids within the cytosolic membrane leaflet. We also found that Fc{gamma}RIIb monomers adopt a conformation that is not suitable for binding to its IgG ligand, consistent with a lack of detectable binding of monomeric IgG in experiments on primary immune cells. However, our results propose that multivalent IgG complexes might stabilize Fc{gamma}RIIb in a binding-competent conformation. We suggest differences in receptor complex formation within the membrane as a plausible cause of the altered membrane localization or clustering and the altered suppressive function of the Fc{gamma}RIIb-I232T variant. Significance StatementOur study sheds new light on the molecular mechanisms underlying the regulation of immune signaling mediated by the inhibitory Fc{gamma} receptor (Fc{gamma}RIIb). By utilizing atomistic simulations and experimental assays, we demonstrate that Fc{gamma}RIIb interacts with specific lipids in the plasma membrane. Notably, our findings challenge the current view of membrane heterogeneity in immune cells, as Fc{gamma}RIIb is not localized in specialized membrane domains known as rafts. Rather, we propose that receptor complex formation modulates receptor localization and conformation, thereby enabling ligand binding. Our findings have important implications for understanding how immune receptors function and communicate with each other, and may provide new opportunities for developing therapeutic strategies targeting Fc{gamma}RIIb in diseases such as autoimmunity and cancer.

immunology↗