Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations

A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present. This suggested that the accumulation of glucose molecules near the headgroups influences the local lipid bilayer undulation and crimping of the lipid tails. We find that the area compressibility modulus increases with the glucose level, causing enhanced bilayer rigidity arising from the slow lateral diffusion of lipids. The restricted lipid motion at high glucose concentrations controls the sustainability of the curved bilayer surface. Calculations revealed that certain orientations of CO → of interfacial glucose with the PN → of lipid headgroups are preferred, which helps the glucose to form direct hydrogen bonds (HBs) with the lipid headgroups. Such lipid-glucose (LG) HBs relax slowly at low glucose concentrations and exhibit a higher lifetime, whereas fast structural relaxation of LG HBs with a shorter lifetime was noticed at a higher glucose level. In contrast, lipid-water (LW) HBs exhibited a higher lifetime at a higher glucose level, which gradually decreased with the glucose level lowering. The study interprets that the glucose concentration-driven LW and LG interactions are mutually inclusive. Our detailed analysis will exemplify small saccharide concentration-driven membrane stabilizing efficiency, which is, in general, helpful for drug delivery study.

Which Moiety Drives Gangliosides to Form Nanodomains?

Gangliosides are important glycosphingolipids involved in a multitude of physiological functions. From a physicochemical standpoint, this is related to their ability to self-organize into nanoscopic domains, even at molar concentrations of one per 1000 lipid molecules. Despite recent experimental and theoretical efforts suggesting that a hydrogen bonding network is crucial for nanodomain stability, the specific ganglioside moiety decisive for the development of these nanodomains has not yet been identified. Here, we combine an experimental technique achieving nanometer resolution (Förster resonance energy transfer analyzed by Monte Carlo simulations) with atomistic molecular dynamic simulations to demonstrate that the sialic acid (Sia) residue(s) at the oligosaccharide headgroup dominates the hydrogen bonding network between gangliosides, driving the formation of nanodomains even in the absence of cholesterol or sphingomyelin. Consequently, the clustering pattern of asialoGM₁, a Sia-depleted glycosphingolipid bearing three glyco moieties, is more similar to that of structurally distant sphingomyelin than that of the closely related gangliosides GM₁ and GD_1a with one and two Sia groups, respectively.

Structure of Galectin-3 bound to a model membrane containing ganglioside GM1

Galectin-3 (Gal-3) is a β-galactosidase-binding protein involved in various biological processes, including neuronal growth and adhesion. The pairing of Gal-3 with ganglioside GM1's pentasaccharide chain at the outer leaflet of the plasma membrane, which triggers downstream cell-signaling cascades, seems to be involved in these processes. A crucial feature of Gal-3 is its ability to form oligomers and supramolecular assemblies that connect various carbohydrate-decorated molecules. Although we know the atomistic structure of Gal-3 bound to small carbohydrate ligands, it remains unclear how Gal-3 binds GM1 in a membrane. Furthermore, the influence of this interaction on Gal-3's structure and oligomeric assembly has to be elucidated. In this study, we used X-ray reflectivity (XR) from a model membrane to determine the structure and surface coverage of Gal-3 bound to a membrane containing GM1. We observed that the carbohydrate recognition domain interacts with GM1's pentasaccharide, while the N-terminal domain is pointed away from the membrane, likely to facilitate protein-protein interactions. In a membrane containing 20 mol % GM1, Gal-3 covered ∼50% of the membrane surface with one Gal-3 molecule bound per 2130 Å2. We used molecular dynamics simulations and Voronoi tessellation algorithms to build an atomistic model of membrane-bound Gal-3, which is supported by the XR results. Overall, this work provides structural information describing how Gal-3 can bind GM1's pentasaccharide chain, a prerequisite for triggering regulatory processes in neuronal growth and adhesion.

Exploring Membrane Binding Targets of Disordered Human Tau Aggregates on Lipid Rafts Using Multiscale Molecular Dynamics Simulations

The self-aggregation of tau, a microtubule-binding protein, has been linked to the onset of Alzheimer's Disease. Recent studies indicate that the disordered tau aggregates, or oligomers, are more toxic than the ordered fibrils found in the intracellular neurofibrillary tangles of tau. At present, details of tau oligomer interactions with lipid rafts, a model of neuronal membranes, are not known. Using molecular dynamics simulations, the lipid-binding events, membrane-damage, and protein folding of tau oligomers on various lipid raft surfaces were investigated. Tau oligomers preferred to bind to the boundary domains (Lod) created by the coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains in the lipid rafts. Additionally, stronger binding of tau oligomers to the ganglioside (GM1) and phosphatidylserine (PS) domains, and subsequent protein-induced lipid chain order disruption and beta-sheet formation were detected. Our results suggest that GM1 and PS domains, located exclusively in the outer and inner leaflets, respectively, of the neuronal membranes, are specific membrane domain targets, whereas the Lod domains are non-specific targets, of tau oligomers binding to neurons. The molecular details of these specific and non-specific tau bindings to lipid rafts may provide new insights into understanding membrane-associated tauopathies leading to Alzheimer's Disease.

Multifaceted Computational Modeling in Glycoscience

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.

Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse

Although the quality of current additive all-atom force fields for carbohydrates has been demonstrated in many applications, occasional significant differences reported for the hydrodynamic behavior of specific polysaccharides modeled with different force fields is a cause for concern. In particular, irreversible conformational collapse has been noted for some polysaccharide simulations with the GLYCAM06j force field. Here, we investigate the cause of this phenomenon through comparative simulations of a range of saccharides with both the GLYCAM06j and the CHARMM36 carbohydrate force fields. We find that conformational collapse in GLYCAM06j occurs for saccharide chains containing the deoxy sugar α-l-rhamnose after relatively long simulation intervals. Further, we explore the mechanism of conformational collapse and show that this phenomenon arises because of the anomalous low energy in GLYCAM06j (as compared to quantum mechanical calculations) of a specific orientation of α-l-Rha to α-l-Rha glycosidic linkages, which are subsequently sustained by intramolecular interactions in the saccharide chain. We identify the lack of partial charges on aliphatic hydrogens in GLYCAM as the source of this anomaly, demonstrating that addition of small partial atomic charges on the aliphatic protons in rhamnose removes the conformational collapse phenomenon. This work reveals the large cumulative impact that small partial charges may have on the dynamic behavior of polysaccharides and indicates that future reparameterization of the GLYCAM06j force field should investigate the addition of partial charges on all aliphatic hydrogens.

Axonal plasma membrane-mediated toxicity of cholesterol in Alzheimer's disease: A microsecond molecular dynamics study

Alzheimer's disease is increasingly being recognized as an immune-mediated disease of brain. Since physiological brain health and brain immune function is dependent upon homeostatic neuronal membrane structure and function, alterations in membrane lipid biochemistry may predispose to disease. Brain is rich in cholesterol, and cholesterol metabolism dysfunction is a known risk factor for AD. Employing extensive microsecond all-atom molecular dynamics simulations, we investigated the properties of model neuronal membranes as a function of cholesterol concentration; phospholipid and phospholipid/cholesterol bilayers were also simulated to compare against available experimental data. Increased cholesterol concentrations compact and stiffen the lipid membrane, reducing permeability while modulating local water densities in the peri-membranous environment. Conversely, lower cholesterol mole fraction yields membranes with increased molecular disorder, enhanced fluidity, higher molecular tilting, and augmented interdigitation between bilayer leaflet lipids. Our findings provide a molecular insight on effect of cholesterol composition on various biochemical processes occurring at neuronal axon plasma membrane. These calculations also endeavor to establish a membrane-based link between cholesterol as an AD risk factor and possible AD pathology.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.