An atomistic characterization of high-density lipoproteins and the conserved "LN" region of apoA-I.

The physicochemical characteristics of the various subpopulations of high-density lipoproteins (HDLs) and, in particular, their surface properties determine their ability to scavenge lipids and interact with specific receptors and peptides. Five representative spheroidal HDL subpopulation models were mapped from a previously reported equilibrated coarse-grained (CG) description to an atomistic representation for subsequent molecular dynamics simulation. For each HDL model a range of finer-level analyses was undertaken, including the component-wise characterization of HDL surfaces, the average size and composition of hydrophobic surface patches, dynamic protein secondary structure monitoring, and the proclivity for solvent exposure of the proposed ß-amyloid (Aß) binding region of apolipoprotein A-I (apoA-I), "LN." This study reveals that previously characterized ellipsoidal HDL3a and HDL2a models revert to a more spherical geometry in an atomistic representation due to the enhanced conformational flexibility afforded to the apoA-I protein secondary structure, allowing for enhanced surface lipid packing and lower overall surface hydrophobicity. Indeed, the proportional surface hydrophobicity and apoA-I exposure reduced with increasing HDL size, consistent with previous characterizations. Furthermore, solvent exposure of the "LN" region of apoA-I was exclusively limited to the smallest HDL3c model within the timescale of the simulations, and typically corresponded to a distinct loss in secondary structure across the "LN" region to form part of a significant contiguous hydrophobic patch on the HDL surface. Taken together, these findings provide preliminary evidence for a subpopulation-specific interaction between HDL3c particles and circulating hydrophobic species such as Aß via the exposed "LN" region of apoA-I.

Unravelling the influence of surface lipids on the structure, dynamics and interactome of high-density lipoproteins.

Surface lipids influence the biological activities of high-density lipoproteins (HDLs) but their species-specific effects on HDL structure, dynamics, and surface interactome has remained unclear. Building upon the five-lipid species HDL models developed and characterised in previous work, representative models of the major HDL subpopulations found in human plasma containing apolipoprotein A-I (apoA-I) have been studied using molecular dynamics simulation to describe their varying degrees of surface lipidome complexity. Specifically, two additional sets of representative HDL subpopulation particles were developed, one with sphingomyelin (SM) and the other with SM, phosphatidylethanolamine, phosphatidylinositol, and ceramide in quantities reflecting average levels characterised for HDL subpopulations derived from normolipidemic patients. These lipid species were assessed in terms of HDL size, morphology, dynamics, and overall interactome. The findings reveal that the presence of a representative SM fraction marginally enhanced HDL interfacial curvature and surface monolayer rigidity, manifesting in tighter phospholipid packing and slower surface lipid dynamics relative to SM-deficient HDL models. Furthermore, the presence of SM resulted in a reduction in the solvent exposure of core lipids and cholesterol molecules, whilst also enhancing apolipoprotein conformational flexibility and its overall twisting across the HDL surface. The hydrophobicity of apoA-I-bound lipid patches and the proportion of apoA-I hydrophobic surface area is enhanced by the overall lipidation of apoA-I irrespective of lipid composition. These findings offer new insights into how the surface lipid composition of different HDL subpopulations can significantly impact the overall interactome of HDL particles, potentially influencing subpopulation-specific biological functions like lipid scavenging and receptor interactions.

Redefining the Molecular Interplay between Dimethyl Sulfoxide, Lipid Bilayers, and Dehydration.

The potentially damaging action of dimethyl sulfoxide (DMSO) on phospholipid bilayers remains a matter of controversy. We have conducted a series of long-scale molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers at various levels of hydration in the presence of variable quantities of DMSO. These simulations provide evidence for a non-destructive dehydrating mechanism of action for DMSO on DOPC bilayers across a wide concentration range and levels of hydration. Specifically, under full- and low-hydration conditions, the bilayer underwent a minor lateral contraction, coinciding with surface dehydration in the presence of dilute DMSO solutions (XDMSO < 0.3). At higher DMSO concentrations, this bilayer structure was retained despite a progressive deterioration of the hydration structure at the interface. A similar convergence of bilayer structural properties was observed under dehydration conditions for 0.3 < XDMSO < 0.7. Destabilization occurred for dehydrated bilayers in the presence of XDMSO ≥ 0.7, suggesting the existence of a DMSO concentration and/or dehydration threshold. However, such DMSO concentrations far exceed those established as toxic to other cellular components. Our findings represent a computational model for DMSO-DOPC interactions that is consistent with a range of experimental characterizations, offering new molecular insights into the cryoprotective mechanisms of action of DMSO.

Mechanisms of Interaction of Small Hydroxylated Cryosolvents with Dehydrated Model Cell Membranes: Stabilization vs Destruction.

The mechanism by which cryosolvents such as alcohols modify and penetrate cell membranes as a function of their concentration and hydration state remains poorly understood. We conducted molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayers in the presence of aqueous solutions of four common penetrating hydroxylated cryosolvents (methanol, ethylene glycol, propylene glycol, and glycerol) at varying concentration ranges and across three different hydration states. All cryosolvents were found to preferentially replace water at the bilayer interface, and a reduction in hydration state correlates with a higher proportion of cryosolvent at the interface for relative concentrations. Minor differences in chemical structure had a profound effect on cryosolvent-membrane interactions, as the lone methyl groups of methanol and propylene glycol enhanced their membrane localization and penetration, but with increasing concentrations acted to destabilize the membrane structure in a process heightened at higher hydration states. By contrast, ethylene glycol and glycerol promoted and retained membrane structural integrity by forming hydrogen-bonded lipid bridges via distally located hydroxyl groups. Glycerol exhibited the highest capacity to cross-link lipids at relative concentrations, as well as promoted a bilayer structure consistent with a fully hydrated bilayer in the absence of cryosolvent for all hydration states investigated.

Structure and intermolecular interactions in spheroidal high-density lipoprotein subpopulations.

Human serum high-density lipoproteins (HDLs) are a population of small, dense protein-lipid aggregates that are crucial for intravascular lipid trafficking and are protective against cardiovascular disease. The spheroidal HDL subfraction can be separated by size and density into five major subpopulations with distinct molecular compositions and unique biological functionalities: HDL3c, HDL3b, HDL3a, HDL2a and HDL2b. Representative molecular models of these five subpopulations were developed and characterised for the first time in the presence of multiple copies of its primary protein component apolipoprotein A-I (apoA-I) using coarse-grained molecular dynamics simulations. Each HDL model exhibited size, morphological and compositional profiles consistent with experimental observables. With increasing particle size the separation of core and surface molecules became progressively more defined, resulting in enhanced core lipid mixing, reduced core lipid exposure at the surface, and the formation of an interstitial region between core and surface molecules in HDL2b. Cholesterol molecules tended to localise around the central helix-5 of apoA-I, whilst triglyceride molecules predominantly interacted with aromatic, hydrophobic residues located within the terminal helix-10 across all subpopulation models. The three intermediate HDL models exhibited similar surface profiles despite having distinct molecular compositions. ApoA-I in trefoil, quatrefoil and pentafoil arrangements across the surface of HDL particles exhibited significant warping and twisting, but largely retained intermolecular contacts between adjacent apoA-I chains. Representative HDL subpopulations differed in particle size, morphology, intermolecular interaction profiles and lipid and protein dynamics. These findings reveal how different HDL subpopulations might exhibit distinct functional associations depending on particle size, form and composition.

Does Sucrose Change Its Mechanism of Stabilization of Lipid Bilayers during Desiccation? Influences of Hydration and Concentration.

Sugar-membrane interactions are believed to be responsible for cell preservation during desiccation and freezing, but the molecular mechanism by which they achieve this is still not well understood. The associated decrease of the main phase transition temperature of phospholipid bilayers is explained by two opposing views on the matter: the direct sugar-phospholipid interaction at the bilayer interface (water replacement hypothesis) and an entropy-driven phase transition with sugar molecules concentrating away from the lipid interface (hydration forces explanation). Both mechanisms are supported by experiments but molecular dynamics (MD) simulations have overwhelmingly shown the occurrence of direct sugar-phospholipid interactions. We have performed MD simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers at different water and sucrose contents. The behavior of sucrose was found to depend on both the sucrose and water contents: at high sucrose concentration and at low hydration, it is best described by the hydration forces explanation model, whereas at low sucrose concentration, it is consistent with the water replacement hypothesis model. These simulations reveal that at low concentration, sucrose molecules preferentially interact directly with the membrane interface while at high concentration, they preferentially accumulate in the intermembrane solution. The transition between the two modes of interaction is revealed for the first time as being governed by the saturation of the lipid bilayer interface with sucrose molecules, and this occurs more rapidly as the level of hydration decreases.

Influence of Bilayer Size and Number in Multi-Bilayer DOPC Simulations at Full and Low Hydration.

Biophysical studies of model cell membranes at full and low hydration are usually carried out using scattering measurements on multi-bilayer systems. Molecular simulations of lipid bilayers aimed at reproducing those experimental conditions are usually conducted using single bilayers with different amounts of water. These simulation conditions may lead to artifacts arising from size effects and self-interactions because of periodic boundary conditions. We have tested the influence of the size and number of bilayers on membrane properties using the Lipid14 force field for lipids in molecular dynamics simulations of 1,2-dioleoyl- sn-glycero-3-phosphocholine bilayers at full hydration (44 water molecules per lipid), low hydration (18 water molecules per lipid), and dehydration (9 water molecules per lipid). A number of additional simulations were conducted with the Slipids force field for comparison. We have found that the average area per lipid (APL), thickness, mass density profiles, and acyl tail order parameters are insensitive to the size and the number of bilayers for all hydration states. The Lipid14 force field can also successfully reproduce the experimentally observed decrease in APL and corresponding increase in bilayer thickness upon dehydration, reflecting the increase in ordering as the system becomes more gel-like. Additionally, decreasing hydration levels were associated with a trend away from normal lateral diffusion and toward more subdiffusive regimes across both force fields. In summary, at least for the Lipid14 force field, the use of a single bilayer with 128 phospholipid molecules provides an adequate representation of multi-bilayer systems at varying levels of hydration.

Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field.

Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecular systems; however, the parameters for DMSO published by Fox and Kollman in 1998 have only been tested for pure liquid DMSO. We have conducted an MD simulation study of DMSO in a water mixture and computed several structural and dynamical properties such as of the mean density, self-diffusion coefficient, hydrogen bonding and DMSO and water ordering. The AMBER force field of DMSO is seen to reproduce well most of the experimental properties of DMSO in water, with the mixture displaying strong and specific water ordering, as observed in experiments and multiple other MD simulations with other non-polarizable force fields. Graphical abstract Hydration structure within hydrogen-bonding distance around a DMSOmolecule.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

Role of the cell membrane interface in modulating production and uptake of Alzheimer's beta amyloid protein.

The beta amyloid protein (Aß) plays a central role in Alzheimer's disease (AD) pathogenesis and its interaction with cell membranes in known to promote mutually disruptive structural perturbations that contribute to amyloid deposition and neurodegeneration in the brain. In addition to protein aggregation at the membrane interface and disruption of membrane integrity, growing reports demonstrate an important role for the membrane in modulating Aß production and uptake into cells. The aim of this review is to highlight and summarize recent literature that have contributed insight into the implications of altered membrane composition on amyloid precursor protein (APP) proteolysis, production of Aß, its internalization in to cells via permeabilization and receptor mediated uptake. Here, we also review the various membrane model systems and experimental tools used for probing Aß-membrane interactions to investigate the key mechanistic aspects underlying the accumulation and toxicity of Aß in AD.

Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer.

Molecular dynamics (MD) simulations have been used to investigate the interactions of a variety of hydroxylated cryosolvents (glycerol, propylene glycol and ethylene glycol), methanol and dimethyl sulfoxide (DMSO) in aqueous solution with a 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) bilayer in its fluid phase at 323K. Each cryosolvent induced lateral expansion of the membrane leading to thinning of the bilayer and resulting in disordering of the lipid hydrocarbon chains. Propylene glycol and DMSO were observed to exhibit a greater disordering effect on the structure of the membrane than the other three alcohols. Closer examination exposed a number of effects on the lipid bilayer as a function of the molecular size and hydrogen bonding capacity of the cryosolvents. Analyses of hydrogen bonds revealed that increased concentrations of the polyhydroxylated cryosolvents induced the formation of a cross-linked cryosolvent layer across the surface of the membrane bilayer. This effect was most pronounced for glycerol at sufficiently high concentrations, which displayed a comparatively enhanced capacity to induce cross-linking of lipid headgroups resulting in the formation of extensive hydrogen bonding bridges and the promotion of a dense cryosolvent layer across the phospholipid bilayer.

The effects of cryosolvents on DOPC-ß-sitosterol bilayers determined from molecular dynamics simulations.

Polyhydroxylated alcohols and DMSO are common cryosolvents that can damage cell membranes at sufficiently high concentrations. The interaction of representative plant cell membranes composed of mixed 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)-ß-sitosterol bilayers, at a range of compositions, with a variety of cryosolvent molecules (DMSO, propylene glycol, ethylene glycol, glycerol, and methanol) has been investigated using molecular dynamics simulations. All the cryosolvents cause the bilayers to thin and become disordered; however, DMSO and propylene glycol have a greater disordering effect on the bilayer. Propylene glycol is shown to have the ability to cause the formation of pores in pure DOPC bilayers in a manner similar to that previously shown for DMSO. As the concentration of ß-sitosterol within the bilayer increases, the membranes become more resistant to the deleterious effects of the cryosolvents. All three polyhydroxylated species are observed to form hydrogen bonds to multiple phospholipid molecules, effectively acting as cross-linkers, with glycerol being the most effective cross-linker. Increases in the concentration of ß-sitosterol reduce overall hydrogen bonding of the bilayer with the cryosolvents as well as cross-linking, with glycerol and ethylene glycol being the most affected. The ability of all of these cryosolvents to affect the integrity of cell membranes appears to be the result of the balance of their ability to disorder lipid bilayers, to diffuse across them, and to interact with the lipid head groups.