Adsorption of pulmonary and exogeneous surfactants on SARS-CoV-2 spike protein.

COVID-19 is transmitted by airborne particles containing virions of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus virions represent nanoparticles enveloped by a lipid bilayer decorated by a "crown" of Spike protein protrusions. Virus transmission into the cells is induced by binding of Spike proteins with ACE2 receptors of alveolar epithelial cells. Active clinical search is ongoing for exogenous surfactants and biologically active chemicals capable of hindering virion-receptor binding. Here, we explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of adsorption of selected pulmonary surfactants, zwitterionic dipalmitoyl phosphatidyl choline and cholesterol, and exogeneous anionic surfactant, sodium dodecyl sulfate, on the S1-domain of the Spike protein. We show that surfactants form micellar aggregates that selectively adhere to the specific regions of the S1-domain that are responsible for binding with ACE2 receptors. We find distinctly higher cholesterol adsorption and stronger cholesterol-S1 interactions in comparison with other surfactants, that is consistent with the experimental observations of the effects of cholesterol on COVID-19 infection. Distribution of adsorbed surfactant along the protein residue chain is highly specific and inhomogeneous with preferential adsorption around specific amino acid sequences. We observe preferential adsorption of surfactants on cationic arginine and lysine residues in the receptor-binding domain (RBD) that play an important role in ACE2 binding and are present in higher amounts in Delta and Omicron variants, which may lead to blocking direct Spike-ACE2 interactions. Our findings of strong selective adhesion of surfactant aggregates to Spike proteins have important implications for informing clinical search for therapeutic surfactants for curing and preventing COVID-19 caused by SARS-CoV-2 and its variants.

Adsorption of Pulmonary and Exogeneous Surfactants on SARS-CoV-2 Spike Protein.

COVID-19 is transmitted by inhaling SARS-CoV-2 virions, which are enveloped by a lipid bilayer decorated by a "crown" of Spike protein protrusions. In the respiratory tract, virions interact with surfactant films composed of phospholipids and cholesterol that coat lung airways. Here, we explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of surfactant adsorption on Spike proteins. With examples of zwitterionic dipalmitoyl phosphatidyl choline, cholesterol, and anionic sodium dodecyl sulphate, we show that surfactants form micellar aggregates that selectively adhere to the specific regions of S1 domain of the Spike protein that are responsible for binding with ACE2 receptors and virus transmission into the cells. We find high cholesterol adsorption and preferential affinity of anionic surfactants to Arginine and Lysine residues within S1 receptor binding motif. These findings have important implications for informing the search for extraneous therapeutic surfactants for curing and preventing COVID-19 by SARS-CoV-2 and its variants.

Adsorption of Pulmonary and Exogeneous Surfactants on SARS-CoV-2 Spike Protein

COVID-19 is transmitted by inhaling SARS-CoV-2 virions, which are enveloped by a lipid bilayer decorated by a "crown" of Spike protein protrusions. In the respiratory tract, virions interact with surfactant films composed of phospholipids and cholesterol that coat lung airways. Here, we explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of surfactant adsorption on Spike proteins. With examples of zwitterionic dipalmitoyl phosphatidyl choline, cholesterol, and anionic sodium dodecyl sulphate, we show that surfactants form micellar aggregates that selectively adhere to the specific regions of S1 domain of the Spike protein that are responsible for binding with ACE2 receptors and virus transmission into the cells. We find high cholesterol adsorption and preferential affinity of anionic surfactants to Arginine and Lysine residues within S1 receptor binding motif. These findings have important implications for informing the search for extraneous therapeutic surfactants for curing and preventing COVID-19 by SARS-CoV-2 and its variants.

Dissipative particle dynamics simulations in colloid and Interface science: a review.

Dissipative particle dynamics (DPD) is one of the most efficient mesoscale coarse-grained methodologies for modeling soft matter systems. Here, we comprehensively review the progress in theoretical formulations, parametrization strategies, and applications of DPD over the last two decades. DPD bridges the gap between the microscopic atomistic and macroscopic continuum length and time scales. Numerous efforts have been performed to improve the computational efficiency and to develop advanced versions and modifications of the original DPD framework. The progress in the parametrization techniques that can reproduce the engineering properties of experimental systems attracted a lot of interest from the industrial community longing to use DPD to characterize, help design and optimize the practical products. While there are still areas for improvements, DPD has been efficiently applied to numerous colloidal and interfacial phenomena involving phase separations, self-assembly, and transport in polymeric, surfactant, nanoparticle, and biomolecules systems.

Effects of metal-polymer complexation on structure and transport properties of metal-substituted polyelectrolyte membranes.

Morphological and transport properties of hydrated metal-substituted Nafion membranes doped with metal ions of different valency and coordination strength are explored using coarse-grained dissipative particle dynamics simulations. To incorporate the effects of metal-polymer complexation, we introduce a novel metal ion complexation model, in which the charged central metal ion is surrounded by dummy sites that coordinate with ligands. The model parameters are determined by matching the metal-ligand running coordination numbers and the diffusion coefficients obtained from atomistic simulations and/or experiments. The increase of valency and coordination strength is found to strongly influence both the morphology and transport characteristics of the membrane at all hydration levels. The membrane segregation into hydrophobic and hydrophilic sub-phases is affected by metal-sulphonate coordination induced crosslinking at the hydrophilic/hydrophobic interface. The simulation results indicate that the interfacial crosslinking influences the interfacial tension and thereby affect the growth and coalescence of water clusters upon the increase of hydration. Multivalent complexation hinders water and ion mobility and causes anomalous sub-diffusion and dramatic decrease of the water permeability and ionic conductivity. Our DPD model is found efficient in elucidating the mechanisms of coordination-induced cross-linking and complexation and predicting on a semi-quantitative level the morphological and transport properties of metal-substituted Nafion membranes depending on the ion valency and coordination strength. The proposed model can be further advanced and adopted for other polyelectrolyte systems, such as sulfonated block-copolymers, polysaccharide solutions and composites, and biopolymer assemblies.

Stability of Lipid Coatings on Nanoparticle-Decorated Surfaces.

Lipid membranes supported on solid surfaces and nanoparticles find multiple applications in industrial and biomedical technologies. Here, we explore in silico the mechanisms of the interactions of lipid membranes with nanostructured surfaces with deposited nanoparticles and explain the characteristic particle size dependence of the uniformity and stability of lipid coatings observed in vitro. Simulations are performed to demonstrate the specifics of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid membrane adhesion to hydrophilic and hydrophobic nanoparticles ranging in size from 1.5 to 40 nm using an original coarse-grained molecular dynamics model with implicit solvent and large simulation boxes (scales up to 280 × 154 × 69 nm3). We find that one of the major factors that affects the uniformity and stability of lipid coatings is the disjoining pressure in the water hydration layer formed between the lipid membrane and hydrophilic solid surface. This effect is accounted for by introducing a special long-range lipid-solid interaction potential that mimics the effects of the disjoining pressure in thin water layers. Our simulations reveal the physical mechanisms of interactions of lipid bilayers with solid surfaces that are responsible for the experimentally observed nonmonotonic particle size dependence of the uniformity and stability of lipid coatings: particles smaller than the hydration layer thickness (<2-3 nm) or larger than ∼20 nm are partially or fully enfolded by a lipid bilayer, whereas particles of the intermediate size (5-20 nm) cause membrane perforation and pore formation. In contrast, hydrophobic nanoparticles, which repel the hydration layer, tend to be encapsulated within the hydrophobic interior of the membrane and coated by the lipid monolayer. The proposed model can be further extended and applied to a wide class of systems comprising nanoparticles and nanostructured substrates interacting with lipid and surfactant bilayers and monolayers.

Modeling Gas-Liquid Interfaces by Dissipative Particle Dynamics: Adsorption and Surface Tension of Cetyl Trimethyl Ammonium Bromide at the Air-Water Interface.

Adsorption of surfactants at gas-liquid interfaces that causes reduction in the surface tension is a classical problem in colloid and interface science with multiple practical applications in oil and gas recovery, separations, cosmetics, personal care, and biomedicine. Here, we develop an original coarse-grained model of the liquid-gas interface within the conventional dissipative particle dynamics (DPD) framework with the goal of quantitatively predicting the surface tension in the presence of surfactants. As a practical case-study example, we explore the adsorption of the cationic surfactant cetyl trimethyl ammonium bromide (CTAB) on the air-water interface. The gas phase is modeled as a DPD fluid composed of fictitious hard-core "gas" beads with exponentially decaying repulsive potentials to prevent penetration of the liquid phase components. A rigorous parametrization scheme is proposed based on matching the bulk and interfacial properties of water and octane taken as the reference compounds. Quantitative agreement between the simulated and experimental surface tension of CTAB solutions is found for a wide range of bulk surfactant concentrations (∼10-3 to ∼1 mmol/L) with the reduction of the surface tension from ∼72 mN/m (pure water) to the limiting value of ∼37.5 mN/m at the critical micelle concentration. The gas phase DPD model with the proposed parametrization scheme can be extended and applied to modeling various gas-liquid interfaces with surfactant and lipid monolayers, such as bubble suspensions, foams, froths, etc.

Adhesion and Separation of Nanoparticles on Polymer-Grafted Porous Substrates.

This work explores interactions of functionalized nanoparticles (NP) with polymer brushes (PB) in a binary mixture of good and poor solvents. NP-PB systems are used in multiple applications, and we are particularly interested in the problem of chromatographic separation of NPs on polymer-grafted porous columns. This process involves NP flow through the pore channels with walls covered by PBs. NP-PB adhesion is governed by adsorption of polymer chains to NP surface and entropic repulsion caused by the polymer chain confinement between NP and the channel wall. Both factors depend on the solvent composition, variation of which causes contraction or expansion of PB. Using dissipative particle dynamics simulations in conjunction with the ghost tweezers free energy calculation technique, we examine the free energy landscapes of functionalized NPs within PB-grafted channels depending on the solvent composition at different PB grafting densities and polymer-solvent affinities. The free energy landscape determines the probability of NP location at a given distance to the surface, positions of equilibrium adhesion states, and the Henry constant that characterizes adsorption equilibrium and NP partitioning between the stationary phase of PB and mobile phase of flowing solvent. We analyze NP transport through a polymer-grafted channel and calculate the mean velocity and retention time of NP depending on the NP size and solvent composition. We find that, with the increase of the bad (poor) solvent fraction and respective PB contraction, NP separation exhibits a transition from the hydrodynamic size exclusion regime with larger NPs having shorter retention time to the adsorption regime with smaller NPs having shorter retention time. The observed reversal of the sequence of elution is reminiscent of the critical condition in polymer chromatography at which the retention time is molecular weight independent. This finding suggests the possibility of the existence of an analogous special regime in nanoparticle chromatography at which NPs with like surface properties elute together regardless of their size. The latter has important practical implications: NPs can be separated by surface chemistry rather than by their size employing the gradient mode of elution with controlled variation of solvent composition.

CRMPs: critical molecules for neurite morphogenesis and neuropsychiatric diseases.

Neuronal polarity and spatial rearrangement of neuronal processes are central to the development of all mature nervous systems. Recent studies have highlighted the dynamic expression of Collapsin-Response-Mediator Proteins (CRMPs) in neuronal dendritic/axonal compartments, described their interaction with cytoskeleton proteins, identified their ability to activate L- and N-type voltage-gated calcium channels (VGCCs) and delineated their crucial role as signaling molecules essential for neuron differentiation and neural network development and maintenance. In addition, evidence obtained from genome-wide/genetic linkage/proteomic/translational approaches revealed that CRMP expression is altered in human pathologies including mental (schizophrenia and mood disorders) and neurological (Alzheimer's, prion encephalopathy, epilepsy and others) disorders. Changes in CRMPs levels have been observed after psychotropic treatments, and disrupting CRMP2 binding to calcium channels blocked neuropathic pain. These observations, altogether with those obtained from genetically modified mice targeting individual CRMPs and RNA interference approaches, pave the way for considering CRMPs as potential early disease markers and modulation of their activity as therapeutic strategy for disorders associated with neurite abnormalities.

Shock Wave Induced Collapse of Arrays of Nanobubbles Located Next to a Lipid Membrane: Coarse-Grained Computer Simulations.

We used molecular dynamics simulations to study creation of pores in lipid bilayer membranes by inducing shock waves in systems containing arrays of nanobubbles next to these membranes. Shock waves impinged on the bubbles imploding them and produced nanojets that subsequently hit the bilayers making pores in them. Our simulations were performed using the MARTINI coarse-grained force field. The emphasis in our study was on the interaction of shock waves with two-bubble arrays when the bubbles were placed in different alignments. We observed that the largest damage to the bilayer was produced when two bubbles were positioned in a serial alignment and the bubbles touched each other. When two touching each other bubbles were located parallel to the membrane surface and at the same distance from the surface, the membrane damage was reduced, compared to the damage done by explosion of two independent nanobubbles. When two nanobubbles were placed in slanted configurations, the damage was intermediate between damages produced by two bubbles in parallel or serial alignment. Damage to the membrane produced by arrays containing more than two bubbles can be understood as a combination of damage produced by all three alignments of two bubbles.

Local pressure changes in lipid bilayers due to adsorption of melittin and magainin-h2 antimicrobial peptides: results from computer simulations.

We performed a series of coarse-grained computer simulations in order to study how the placement of melittin and magainin-h2 antimicrobial peptides on the surface of the bilayer changes the local pressure profiles in the bilayer. The simulations were done using the NPT ensemble when the total stress on the bilayer was zero and also using the NP(z)AT ensemble, with a nonzero total stress. In the NPT ensemble, although the total stress was zero, each leaflet of the bilayer experienced a nonzero stress, and the stresses are equal by magnitude, but opposite in their direction. The observed stresses acting on the monolayers may cause the rupture of the monolayers to release the stress. Our simulations were done at different peptide to lipid ratio (P/L). When the P/L ratio was 1/50 there was no large difference in the local pressure profile for bilayers with melittin versus bilayers with magainin-h2. When simulations were performed in the NP(z)AT ensemble at P/L = 3/100 we observed a large difference in the pressure profiles in the bilayers with melittin peptides compared to the bilayer with magainin-h2. The observed in this case difference in stress may explain the difference in actions of melittin and magainin at high P/L.

Shock wave interaction with a phospholipid membrane: coarse-grained computer simulations.

We used MARTINI coarse-grained force field to study poration of a lipid bilayer by a shock wave induced nanobubble collapse. Different systems containing different sized nanobubbles that were exposed to shock waves propagating with different velocities were simulated. We observed creation of pores and damage to bilayers and also subsequent pore closing and the bilayer recovery after shock wave passed the bilayer. In all our systems where bilayers were damaged, they recovered; nevertheless we observed that a large amount of water crossed the pore that was temporarily created. We also observed that not every lipid molecule remained in the bilayer after recovery, some lipids moved out into water and created micelles.

Melittin creates transient pores in a lipid bilayer: results from computer simulations.

To study the interaction between melittin peptides and lipid bilayer, we performed coarse-grained simulations on systems containing melittin interacting with a bilayer containing zwitterionic dipalmitoylphosphatidylcholine (DPPC) and anionic palmitoyloleoylphosphatidylglycerol (POPG) phospholipids in a 7:3 ratio. Eight different systems were considered: four at low and four at high peptide to lipid (P/L) ratios. In case of low P/L ratio we did not observe any pore creation in the bilayer. In two out of four of the simulations with the high P/L ratio, appearance of transient pores in the bilayer was observed. These pores were created due to an assembly of 3-5 melittin peptides. Not all of the peptides in the pores were in a transmembrane conformation; many of them had their termini residues anchored to the same leaflet, and these peptides assumed bent, U-shaped, conformations. We propose that when an assembly of melittin peptides creates pores, such an assembly acts as a "wedge" that splits the bilayer. To get a more detailed description of melittin on the bilayer surface and in transient pores, we performed coarse-grained to united-atom scale transformations and after that performed 50 ns molecular dynamics simulations using the united atom description of the systems. While these simulations did not show much of the change in the pore structure during the 50 ns time interval, they clearly showed the presence of water in the transient pores. The appearance of transient pores together with the translocation of peptides across the membranes is consistent with the mechanism proposed to explain graded dye leakage from large vesicles in the presence of melittin.

Difference between magainin-2 and melittin assemblies in phosphatidylcholine bilayers: results from coarse-grained simulations.

We performed coarse-grained computer simulations using MARTINI force field to study the difference in the self-assembly and possible pore creation in DPPC phospholipid membranes by two different antimicrobial peptides: magainin-2 and melittin. Simulations showed that magainin-2 peptides create large sized disordered toroidal pores that allow easy water permeation across them. Melittin assemblies contain peptides in U-shaped conformations that, although creating holes in membranes, block effectively the passage of water. These observed structures are consistent with the dye efflux experiments performed on vesicles exposed to solutions containing antimicrobial peptides.

Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins.

Collective motions on ns-µs time scales are known to have a major impact on protein folding, stability, binding and enzymatic efficiency. It is also believed that these motions may have an important role in the early stages of prion protein misfolding and prion disease. In an effort to accurately characterize these motions and their potential influence on the misfolding and prion disease transmissibility we have conducted a combined analysis of molecular dynamic simulations and NMR-derived flexibility measurements over a diverse range of prion proteins. Using a recently developed numerical formalism, we have analyzed the essential collective dynamics (ECD) for prion proteins from 8 different species including human, cow, elk, cat, hamster, chicken, turtle and frog. We also compared the numerical results with flexibility profiles generated by the random coil index (RCI) from NMR chemical shifts. Prion protein backbone flexibility derived from experimental NMR data and from theoretical computations show strong agreement with each other, demonstrating that it is possible to predict the observed RCI profiles employing the numerical ECD formalism. Interestingly, flexibility differences in the loop between second beta strand (S2) and the second alpha helix (HB) appear to distinguish prion proteins from species that are susceptible to prion disease and those that are resistant. Our results show that the different levels of flexibility in the S2-HB loop in various species are predictable via the ECD method, indicating that ECD may be used to identify disease resistant variants of prion proteins, as well as the influence of prion proteins mutations on disease susceptibility or misfolding propensity.

Neutral-red reaction is related to virulence and cell wall methyl-branched lipids in Mycobacterium tuberculosis.

Searching for virulence marking tests for Mycobacterium tuberculosis, Dubos and Middlebrook reported in 1948 that in an alkaline aqueous solution of neutral-red, the cells of the virulent H37Rv M. tuberculosis strain fixed the dye and became red in color, whereas the cells of the avirulent H37Ra M. tuberculosis strain remained unstained. In the 1950 and 1960s, fresh isolates of M. tuberculosis were tested for this neutral-red cytochemical reaction and it was reported that they were neutral-red positive, whereas other mycobacteria of diverse environmental origins that were non-pathogenic for guinea pigs were neutral-red negative. However, neutral-red has not really been proven to be a virulence marker. To test if virulence is in fact correlated to neutral-red, we studied a clinical isolate of M. tuberculosis that was originally neutral-red positive but, after more than 1 year passing through culture mediums, turned neutral-red negative. We found that, in comparison to the original neutral-red positive strain, this neutral-red negative variant was attenuated in two murine models of experimental tuberculosis. Lipid analysis showed that this neutral-red negative natural mutant lost the capacity to synthesize pthiocerol dimycocerosates, a cell wall methyl-branched lipid that has been related to virulence in M. tuberculosis. We also studied the neutral-red of different gene-targeted M. tuberculosis mutants unable to produce pthiocerol dimycocerosates or other cell wall methyl-branched lipids such as sulfolipids, and polyacyltrehaloses. We found a negative neutral-red reaction in mutants that were deficient in more than one type of methyl-branched lipids. We conclude that neutral-red is indeed a marker of virulence and it indicates important perturbations in the external surface of M. tuberculosis cells.

Homoserine and asparagine are host signals that trigger in planta expression of a pathogenesis gene in Nectria haematococca.

Some pathogenesis-related genes are expressed in fungi only when the pathogen is in the host, but the host signals that trigger these gene expressions have not been identified. Virulent Nectria haematococca infects pea plants and requires either pelA, which is induced by pectin, or pelD, which is induced only in planta. However, the host signal(s) that trigger pelD expression was unknown. Here we report the isolation of the host signals and identify homoserine and asparagine, two free amino acids found in uniquely high levels in pea seedlings, as the pelD-inducing signals. N. haematococca has evolved a mechanism to sense the host tissue environment by using the high levels of two free amino acids in this plant, thereby triggering the expression of pelD to assist the pathogenic process.

G-protein-coupled receptor (GPCR) kinase phosphorylation and beta-arrestin recruitment regulate the constitutive signaling activity of the human cytomegalovirus US28 GPCR.

Phosphorylation of G-protein-coupled receptors (GPCRs) by GRKs and subsequent recruitment of beta-arrestins to agonist-occupied receptors serves to terminate or attenuate signaling by blocking G-proteins from further interaction with the receptors. Human cytomegalovirus encodes a GPCR termed US28 that is homologous to the human chemokine family of GPCRs but differs from the cellular receptors in that it maintains high constitutive activity in the absence of agonist. Although US28 is constitutively active, mechanisms that regulate this activity are unknown. We provide evidence that US28 is constitutively phosphorylated by GRKs in cells and that in consequence, beta-arrestin 2 is localized to the plasma membrane. Deletion of the carboxyl terminal 40 amino acids in US28 generates a receptor that is severely impaired in its ability to become phosphorylated and recruit beta-arrestin and accordingly demonstrates increased inositol phosphate signaling. This result indicates that the carboxyl terminus of US28 contains an important signaling regulatory region and mutational analysis deleting carboxyl terminal serines identified serine 323 as a critical residue within this region. In addition, overexpression of wild type GRK5 leads to hyperphosphorylation of US28 that results in a decrease of inositol phosphate accumulation. These results are consistent with the hypothesis that GRK phosphorylation and recruitment of beta-arrestin to the US28 viral GPCR attenuates signaling to the traditional Galphaq-stimulated inositol phosphate pathway. Finally, in contrast to the results with inositol phosphate signaling, we provide evidence that the US28 carboxyl-terminal phosphorylation sites and beta-arrestin-interacting domain are required for maximal activation of the p38 mitogen-activated protein kinase. Taken together, these results indicate that US28 interacts with these important regulatory proteins to control multiple aspects of signal transmission. Understanding the regulation of viral GPCRs by GRKs and beta-arrestins will provide important new insights into not only aspects of viral pathogenesis but also basic mechanisms of receptor signaling.