Influence of docosahexaenoic acid on the interfacial behavior of cholesterol-containing lipid membranes: Interactions with small amphiphiles and hydration properties.

Cholesterol is known to significantly modify both the structural and the dynamical properties of lipid membranes. On one side, the presence of free cholesterol molecules has been determined to stiffen the membrane bilayer by stretching the hydrophobic tails. Additionally, recent experimental and computational findings have made evident the fact that cholesterol also alters the dynamics and the hydration properties of the polar head groups of DPPC model lipid membranes. In turn, we have recently shown that the Omega-3 fatty acid docosahexaenoic acid, DHA, counteracts the effect of cholesterol on DPPC membrane's mechanical properties by fluidizing the bilayer. However, such behavior represents in fact a global outcome dominated by the larger lipid hydrophobic tails that neither discriminates between the different parts of the membrane nor elucidates the effect on membrane hydration and binding properties. Thus, we now perform molecular dynamics simulations to scrutinize the influence of DHA on the interfacial behavior of cholesterol-containing lipid membranes by characterizing their hydration properties and their binding to amphiphiles. We find that while cholesterol destabilizes interactions with amphiphiles and slightly weakens the lipid's hydration layer, the incorporation of DHA practically restores the interfacial behavior of pure DPPC.

A certain proportion of docosahexaenoic acid tends to revert structural and dynamical effects of cholesterol on lipid membranes.

This work investigates how docosahexaenoic acid (DHA) modifies the effect of Cholesterol (Chol) on the structural and dynamical properties of dipalmitoylphosphatidylcholine (DPPC) membrane. We employ low-cost and non-invasive methods: zeta potential (ZP), conductivity, density, and ultrasound velocity, complemented by molecular dynamics simulations. Our studies reveal that 30% of DHA added to the DPPC-Chol system tends to revert Chol action on a model lipid bilayer. Results obtained in this work shed light on the effect of polyunsaturated fatty acids - particularly DHA - on lipid membranes, with potential preventive applications in many diseases, e.g. neuronal as, Alzheimer's disease, and viral, as Covid-19.

Effect of cholesterol on the hydration properties of ester and ether lipid membrane interphases.

Fluorescence spectroscopy and Molecular Dynamics results show that cholesterol reduces water along the chains in ether lipids by changing the water distribution pattern between tightly and loosely bound water molecules. Water distribution was followed by emission spectra and generalized polarization of 6-dodecanoyl-2-dimethyl aminonaphthalene (Laurdan) inserted in 1,2-dimiristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14: 0 Diether PC) membranes. Molecular Dynamics simulations indicate that the action of cholesterol could be different in ether PC in comparison to ester PC. In addition, Cholesterol seems to act "per se" as an additional hydration center in ether lipids. Regardless of the phase state, cholesterol both in DMPC and 14:0 Diether PC vesicles, changed the distribution of water molecules decreasing the dipole relaxation of the lipid interphase generating an increase in the non-relaxable population. Above 10% Cholesterol/14:0 Diether PC ratio vesicles' interphase present an environment around Laurdan molecules similar to that corresponding to ester PC.

Interaction of hydroxy-xanthones with phosphatidylcholines: The effector decreases compressibility and increases the fluidity of membranes.

This work reports the effect of hydroxy-xanthones (XAs) on 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers as determined by ultrasound velocimetry, densimetry and molecular dynamics simulations. XAs with different number of hydroxyl group were studied. Experimental results, in good agreement with molecular dynamics simulations, revealed that the presence of XAs in the systems studied increases fluidity while simultaneously decreses the compressibility of both membranes. This ´apparent contradiction´ ceases to exist when the particular geometrical structure of the xanthones is taken into account: the planar shape of their fused aromatic rings might allow them to pack efficiently among the hydrocarbon tails of the lipids, thus decreasing compressibility, while their presence weakens or disrupts methylene-methylene interchain interactions, thus increasing membrane fluidity and decreasing their melting temperature.

Experimental and computational studies of the effects of free DHA on a model phosphatidylcholine membrane.

Docosahexaenoic acid (DHA, 22:6) is a natural active compound that has raised considerable interest due to its several biological effects. In this work, effects of free DHA on the physicochemical properties of dipalmitoylphosphatidylcholine (DPPC) liposomes are investigated in terms of lipid membrane structure, by means of temperature-dependent zeta potential measurements, density studies and molecular dynamics simulations. Experimental results predict, in good agreement with simulations that DHA readily incorporates into DPPC liposomes, localizing at the lipid headgroup region. These data show that DHA induces changes in the lipid bilayer structure as well as in membrane fluidity.

"Chameleonic" backbone hydrogen bonds in protein binding and as drug targets.

We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.

Influence of temperature, anions and size distribution on the zeta potential of DMPC, DPPC and DMPE lipid vesicles.

The purpose of the work is to compare the influence of the multilamellarity, phase state, lipid head groups and ionic media on the origin of the surface potential of lipid membranes. With this aim, we present a new analysis of the zeta potential of multilamellar and unilamellar vesicles composed by phosphatidylcholines (PC) and phosphatidylethanolamines (PE) dispersed in water and ionic solutions of polarizable anions, at temperatures below and above the phase transition. In general, the adsorption of anions seems to explain the origin of the zeta potential in vesicles only above the transition temperature (Tc). In this case, the sign of the surface potential is ascribed to a partial orientation of head group moiety toward the aqueous phase. This is noticeable in PC head groups but not in PEs, due to the strong lateral interaction between PO and NH group in PE.

Relaxation pathway confinement in glassy dynamics.

We compute for an archetypical glass-forming system the excess of particle mobility distributions over the corresponding distribution of dynamic propensity, a quantity that measures the tendency of the particles to be mobile and reflects the local structural constraints. This enables us to demonstrate that, on supercooling, the dynamical trajectory in search for a relaxation event must deal with an increasing confinement of relaxation pathways. This "entropic funnel" of relaxation pathways built upon a restricted set of mobile particles is also made evident from the decay and further collapse of the associated Shannon entropy.

A unifying motif of intermolecular cooperativity in protein associations.

At the molecular level, most biological processes entail protein associations which in turn rely on a small fraction of interfacial residues called hot spots. Our theoretical analysis shows that hot spots share a unifying molecular attribute: they provide a third-body contribution to intermolecular cooperativity. Such motif, based on the wrapping of interfacial electrostatic interactions, is essential to maintain the integrity of the interface. Thus, our main result is to unravel the molecular nature of the protein association problem by revealing its underlying physics and thus by casting it in simple physical grounds. Such knowledge could then be exploited in rational drug design since the regions here indicated may serve as blueprints to engineer small molecules disruptive of protein-protein interfaces.

Temperature dependence of the structure of protein hydration water and the liquid-liquid transition.

We study the temperature dependence of the structure and orientation of the first hydration layers of the protein lysozyme and compare it with the situation for a model homogeneous hydrophobic surface, a graphene sheet. We show that in both cases these layers are significantly better structured than bulk water. The geometrical constraint of the interface makes the water molecules adjacent to the surface lose one water-water hydrogen bond and expel the fourth neighbors away from the surface, lowering local density. We show that a decrease in temperature improves the ordering of the hydration water molecules, preserving such a geometrical effect. For the case of graphene, this favors an ice Ih-like local structuring, similar to the water-air interface but in the opposite way along the c axis of the basal plane (while the vicinal water molecules of the air interface orient a hydrogen atom toward the surface, the oxygens of the water molecules close to the graphene plane orient a lone pair in such a direction). In turn, the case of the first hydration layers of the lysozyme molecule is shown to be more complicated, but still displaying signs of both kinds of behavior, together with a tendency of the proximal water molecules to hydrogen bond to the protein both as donors and as acceptors. Additionally, we make evident the existence of signatures of a liquid-liquid transition (Widom line crossing) in different structural parameters at the temperature corresponding to the dynamic transition incorrectly referred to as "the protein glass transition."

Behavior of water in contact with model hydrophobic cavities and tunnels and carbon nanotubes.

By means of molecular dynamics simulations we analyze the behavior of water in contact with model hydrophobic cavities and tunnels. We study the hydration and filling propensity of cavities and tunnels carved in alkane monolayers and, for comparison, we also study single-walled carbon nanotubes of similar size. Our results will determine the dependence of the filling propensity as a function of cavity size while revealing the dynamical nature of the process with alternation of filled and dry states. Concerning the tunnels built across the monolayer, we shall show that the minimum diameter in order to get filled is about twice as large as that for the carbon nanotubes, thus evidencing a more hydrophobic behavior. The existence of water-water hydrogen bonds, a necessary condition for penetration, will also be made evident.

Quantitative investigation of the two-state picture for water in the normal liquid and the supercooled regime.

Several evidences have helped to establish the two-state nature of liquid water. Thus, within the normal liquid and supercooled regimes water has been shown to consist of a mixture of well-structured, low-density molecules and unstructured, high-density ones. However, quantitative analyses have faced the burden of unambiguously determining both the presence and the fraction of each kind of water "species". A recent approach by combining a local structure index with potential-energy minimisations allows us to overcome this difficulty. Thus, in this work we extend such study and employ it to quantitatively determine the fraction of structured molecules as a function of temperature for different densities. This enables us to validate predictions of two-state models.

Structural and dynamical aspects of water in contact with a hydrophobic surface.

By means of molecular dynamics simulations we study the structure and dynamics of water molecules in contact with a model hydrophobic surface: a planar graphene-like layer. The analysis of the distributions of a local structural index indicates that the water molecules proximal to the graphene layer are considerably more structured than the rest and, thus, than the bulk. This structuring effect is lost in a few angstroms and is basically independent of temperature for a range studied comprising parts of both the normal liquid and supercooled states (240K to 320K). In turn, such structured water molecules present a dynamics that is slower than the bulk, as a consequence of their improved interactions with their first neighbors.

Determining the heterogeneity in time of the dynamics within a slowly relaxing region of a supercooled liquid: Role of sharp relaxation events.

Supercooled liquids have been shown to be dynamically heterogeneous with different regions of the system presenting dynamics that vary from each other even by orders of magnitude. Computer simulations have confirmed such a picture by detecting that the mobile particles in model glass formers are not homogeneously distributed within the system but arranged in clusters. More recently, the dynamics of small systems has been characterized by demonstrating that their structural relaxation is not homogeneous in time, in the sense that it does not evolve gradually but it is signed by rapid bursts of mobility characterized by relative compact clusters of mobile particles. These events (which have been named d clusters) are fast and sparse and trigger the transitions the system experiences between metabasins (MB) of its potential-energy surface. The MB residence times are much larger than the time scales of occurrence of the d clusters, and it has been suggested that the events that occur within them scarcely contribute to the structural relaxation of the system. Thus, the picture of glassy relaxation that emerges would indicate that at any time a supercooled liquid may present different spatial regions, each one characterized by different structural relaxation times. In turn, each of such regions would not relax smoothly or gradually but by means of sporadic sharp relaxation events. Here, we assess for a model glass former the relative relevance of the MB exploration events and of the d clusters both in small systems and within regions of large systems, to show that the structural relaxation at the region level is indeed extremely heterogeneous in time and utterly governed by the latter.

Evidence of a two-state picture for supercooled water and its connections with glassy dynamics.

The picture of liquid water as consisting of a mixture of molecules of two different structural states (structured, low-density molecules and unstructured, high-density ones) represents a belief that has been around for long time awaiting for a conclusive validation. While in the last years some indicators have indeed provided certain evidence for the existence of structurally different "species", a more definite bimodality in the distribution function of a sound structural quantity would be desired. In this context, our present work combines the use of a structural parameter with a minimization technique to yield neat bimodal distributions in a temperature range within the supercooled liquid regime, thus clearly revealing the presence of two populations of differently structured water molecules. Furthermore, we elucidate the role of the inter-conversion between the identified two kinds of states for the dynamics of structural relaxation, thus linking structural information to dynamics, a long-standing issue in glassy physics.

Time evolution of dynamic propensity in a model glass former: the interplay between structure and dynamics.

By means of the isoconfigurational method, we calculate the change in the propensity for motion that the structure of a glass-forming system experiences during its relaxation dynamics. The relaxation of such a system has been demonstrated to evolve by means of rapid crossings between metabasins of its potential energy surface (a metabasin being a group of mutually similar, closely related structures which differ markedly from other metabasins), as collectively relaxing units (d-clusters) take place. We now show that the spatial distribution of propensity in the system does not change significantly until one of these d-clusters takes place. However, the occurrence of a d-cluster clearly decorrelates the propensity of the particles, thus ending up with the dynamical influence of the structural features proper of the local metabasin. We also show an important match between particles that participate in d-clusters and that which show high changes in their propensity.

Space and time dynamical heterogeneity in glassy relaxation. The role of democratic clusters.

In this work we review recent computational advances in the understanding of the relaxation dynamics of supercooled glass-forming liquids. In such a supercooled regime these systems experience a striking dynamical slowing down which can be rationalized in terms of the picture of dynamical heterogeneities, wherein the dynamics can vary by orders of magnitude from one region of the sample to another and where the sizes and timescales of such slowly relaxing regions are expected to increase considerably as the temperature is decreased. We shall focus on the relaxation events at a microscopic level and describe the finding of the collective motions of particles responsible for the dynamical heterogeneities. In so doing, we shall demonstrate that the dynamics in different regions of the system is not only heterogeneous in space but also in time. In particular, we shall be interested in the events relevant to the long-time structural relaxation or α relaxation. In this regard, we shall focus on the discovery of cooperatively relaxing units involving the collective motion of relatively compact clusters of particles, called 'democratic clusters' or d-clusters. These events have been shown to trigger transitions between metabasins of the potential energy landscape (collections of similar configurations or structures) and to consist of the main steps in the α relaxation. Such events emerge in systems quite different in nature such as simple model glass formers and supercooled amorphous water. Additionally, another relevant issue in this context consists in the determination of a link between structure and dynamics. In this context, we describe the relationship between the d-cluster events and the constraints that the local structure poses on the relaxation dynamics, thus revealing their role in reformulating structural constraints.

Do short-time fluctuations predict the long-time dynamic heterogeneity in a supercooled liquid?

Recent investigations have demonstrated that the short-time fluctuations in a supercooled liquid can be used as predictors of the long-time dynamic propensity (that is, the regions of the sample with enhanced tendency to be mobile within time scales on the order of the alpha -relaxation time). This could mean that the long-time dynamics (the actual mobility of the particles at such long times) would be implicit in the short-time dynamics or else, that the long-time dynamic propensity [as defined in A. Widmer-Cooper and P. Harrowell, Phys. Rev. Lett. 96, 185701 (2006)], while providing a measure of the degree of jamming of the local structure, would only be sensitive to the short time behavior. The first scenario is in clear disagreement with our recent finding that the influence of the local structure on dynamics (as determined by the propensity for motion) is only local in time, fading out at times close to the metabasin lifetime, much before the alpha -relaxation time. Thus, in this work we show that the short-time fluctuations in supercooled liquids do in fact represent precursors to the dynamics at intermediate times commensurate with the metabasin lifetime (being thus able to predict the regions of the sample that will present high propensity for motion at such stage) but that the dynamical behavior at later times of the alpha relaxation is unpredictable, in agreement with a metabasin random walk scenario.

Connections between structural jamming, local metabasin features, and relaxation dynamics in a supercooled glassy liquid.

Dynamics in glass-forming liquids in the supercooled regime vary considerably from one point of the sample to another suggesting the existence of regions with different degrees of jamming. In fact, the existence of relatively compact regions with particles with an enhanced propensity for motion has been detected in model glassy systems. In turn, the structural relaxation has been shown to be accomplished by means of a series of fast transitions between metabasins in the potential energy landscape involving the collective motion of a substantial number of particles arranged in relatively compact clusters (democratic clusters or d clusters). In this work we shall complete this picture by identifying the connections between local structural jamming, metabasin confining strength, and d clusters. Thus we shall demonstrate that the degree of jamming of the local structure dictates the confining strength of the local metabasin and that the local high propensity regions and the d clusters are not only similar in nature but that they share a significant amount of particles.