Biology subjects

Böckmann, R. A.

Publications and source records attributed to Böckmann, R. A..

4 recordsLinked to original sources

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↗

bioRxiv2024

Mechanistic Insight into pH-Driven Phase Transition of Lipid Nanoparticles

The functionality of lipid nanoparticles (LNPs) as delivery systems in mRNA-based therapeutics is intricately linked to the protonation behavior of their aminolipid components. This study employs large-scale constant-pH molecular dynamics (CpHMD) simulations to decode the environment-dependent pKa of aminolipids in the Comirnaty lipid formulation, providing a detailed view of their pH-dependent structural dynamics. Our results reveal a significant shift in the apparent pKa of the aminolipid ALC-0315, from an intrinsic value of 9.3 in water to 4.9 within the LNP environment. This shift arises from the interplay between lipid reorganization and local electrostatic interactions, resulting in distinct protonation states across the LNP core and surface. At low pH, protonated aminolipids dominate the LNP surface, promoting efficient mRNA encapsulation, whereas at neutral pH, deprotonated aminolipids migrate to the hydrophobic core, driving structural stabilization. Notably, the localized pKa of aminolipids varies significantly with their position, decreasing from near-surface regions (7 to 8) to the hydrophobic core ([≤]4). These findings elucidate the molecular mechanisms underpinning LNP phase transitions and highlight the key role of pKa shifts for the design of aminolipids and for optimizing LNP compositions for enhanced therapeutic delivery. This study bridges experimental observations with molecular-level insights, advancing the rational development of next-generation lipid-based nanocarriers.

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↗

bioRxiv2022

Lipid bicelles in the study of biomembrane characteristics

Simulations of lipid membranes typically make use of periodic boundary conditions to mimic macroscopically sized membranes and allow for comparison to experiments performed e.g. on planar lipid membranes or on unilamellar lipid vesicles. However, the lateral periodicity partly suppresses membrane fluctuations or membrane remodeling, processes that are of particular importance in the study of asymmetric membranes - i.e. membranes with integral or associated proteins and/or asymmetric lipid compositions. Here, we devised a simple albeit powerful lipid bicelle model system that (i) displays similar structural, dynamical and mechanical properties compared to infinite periodic lipid membrane systems, and allows (ii) for the study of asymmetric lipid bilayer systems, and (iii) the unperturbed formation of local spontaneous curvature induced by lipids or proteins in coarse-grained and all-atom molecular dynamics simulations. In addition, the system is characterized by largely unbiased thermal fluctuations as opposed to standard bilayer systems. Application of the bicelle system for an asymmetric lipid composition resembling the plasma membrane reveals that the cholesterol density for a tension-free plasma membrane with a vanishing spontaneous curvature is larger by 28% within the extracellular leaflet compared to the cytosolic leaflet. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/517649v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@56cb44org.highwire.dtl.DTLVardef@3b16faorg.highwire.dtl.DTLVardef@161a143org.highwire.dtl.DTLVardef@a248e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗