Aggregation of an Amyloidogenic Peptide on Gold Surfaces.

Solid surfaces have been shown to affect the aggregation and assembly of many biomolecular systems. One important example is the formation of protein fibrils, which can occur on a range of biological and synthetic surfaces. The rate of fibrillation depends on both the protein structure and the surface chemistry, with the different molecular and oligomer structures adopted by proteins on surfaces likely to be crucial. In this paper, the aggregation of the model amyloidogenic peptide, Aß(16-22), corresponding to a hydrophobic segment of the amyloid beta protein on a gold surface is studied using molecular dynamics simulation. Previous simulations of this peptide on gold surfaces have shown that it adopts conformations on surfaces that are quite different from those in bulk solution. These simulations show that this then leads to significant differences in the oligomer structures formed in solution and on gold surfaces. In particular, oligomers formed on the surface are low in beta-strands so are unlike the structures formed in bulk solution. When oligomers formed in solution adsorb onto gold surfaces they can then restructure themselves. This can then help explain the inhibition of Aß(16-22) fibrillation by gold surfaces and nanoparticles seen experimentally.

Effect of Surface Hydrophobicity on the Adsorption of a Pilus-Derived Adhesin-like Peptide.

Bacterial colonization of abiotic surfaces such as those of medical implants, membrane filters, and everyday household items is a process of tremendous importance for public health. Bacteria use adhesive cell surface structures called adhesins to establish contact with abiotic surfaces. Among them, protein filaments called type IV pili are particularly important and found in many Gram-negative pathogens such as Pseudomonas aeruginosa. Understanding the interaction of such adhesin proteins with different abiotic surfaces at the molecular level thus represents a fundamental prerequisite for impeding bacterial colonization and preventing the spread of infectious diseases. In this work, we investigate the interaction of a synthetic adhesin-like peptide, PAK128-144ox, derived from the type IV pilus of P. aeruginosa with hydrophilic and hydrophobic self-assembled monolayers (SAMs). Using a combination of molecular dynamics (MD) simulations, quartz crystal microbalance with dissipation monitoring (QCM-D), and spectroscopic investigations, we find that PAK128-144ox has a higher affinity for hydrophobic than for hydrophilic surfaces. Additionally, PAK128-144ox adsorption on the hydrophobic SAM is furthermore accompanied by a strong increase in α-helix content. Our results show a clear influence of surface hydrophobicity and further indicate that PAK128-144ox adsorption on the hydrophobic surface is enthalpically favored, while on the hydrophilic surface, entropic contributions are more significant. However, our spectroscopic investigations also suggest aggregation of the peptide under the employed experimental conditions, which is not considered in the MD simulations and should be addressed in more detail in future studies.

Effect of the air-water interface on the conformation of amyloid beta.

It has long been recognized that liquid interfaces, such as the air-water interface (AWI), can enhance the formation of protein fibrils. This makes liquid interfaces attractive templates for fibril formation but fully realizing this requires knowledge of protein behavior at interfaces, which is currently lacking. To address this, molecular dynamics simulation is used to investigate fragments of amyloid beta, a model fibril forming protein, at the air-water interface. At the air-water interface, the enrichment of aggregation-prone helical conformations provides a mechanism for the enhancement of fibrillation at interfaces. The conformational ensemble at the air-water interface was also considerably reduced compared to bulk solution due to the tendency of hydrophobic side chains partitioning into the air restricting the range of conformations. Little overlap between the conformational ensembles at the AWI and in the bulk solution was found, suggesting that AWI induces the formation of a different set of structures compared to bulk solution. The smaller Aß(16-22) and Aß(25-35) fragments show an increase in the propensity for an ordered secondary structure at the air-water interface but with a increased propensity for turn over other motifs, illustrating the importance of intra-protein interactions for stabilizing helical and extended conformations.

No-show rates to a sleep clinic: drivers and determinants.

STUDY OBJECTIVES: Attendance to sleep clinic appointments is imperative to diagnose sleep-related disorders and to offer appropriate treatment. As part of our quality assurance program, we assessed predictors of no-show rates at our sleep clinic. We hypothesize that no-show rates can be predicted by demographics, appointment type (new vs established) and timing, and insurance status. METHODS: We performed a 10-month, retrospective chart review of patients scheduled at Saint Louis University's SLUCare Sleep Disorders Center. Multivariable logistic regression was used to determine which factors were independently associated with no-show. RESULTS: A total of 2,532 clinical visits were reviewed, and the overall no-show rate was 21.2%. Factors associated with a higher incidence of no-show rates included younger age (17-40 years: 21.5%; 41-64 years: 23.5%; ≥65 years: 14.0%; P < .0001), appointment type (new: 30.5% vs established: 18.3%; P < .0001), and insurance status (no insurance: 24.6% vs public: 22.6% vs private: 15.9%; P < .0001). Multivariable logistic regression confirmed the independent association between no-show and age ≤ 40 years (adjusted odds ratio = 1.72; 95% confidence interval: 1.44, 2.20), new patient status (adjusted odds ratio = 1.78; 95% confidence interval: 1.44, 2.20), and absence of health insurance (adjusted odds ratio = 1.62; 95% confidence interval: 1.24, 2.11). Sex, appointment time, day of the week, and season did not significantly influence no-show rates. CONCLUSIONS: Independent predictors of no-show appointments included younger age, new patient status, and lack of health insurance. Our findings will aid future efforts to identify patients with high predictors of nonadherence. Further studies are needed to develop methods to decrease no-show rates once high-risk appointments have been identified.

Effect of surface chemistry on islet amyloid polypeptide conformation.

The formation of dense, linear arrays (fibrils) by biomolecules is the hallmark of a number of degenerative diseases, such as Alzheimer's and type-2 diabetes. Protein fibrils have also attracted interest as building blocks for new materials. It has long been recognized that surfaces can affect the fibrillation process. Recent work on the model fibril forming protein human islet amyloid polypeptide (hIAPP) has shown that while the protein concentration is highest at hydrophobic surfaces, the rate of fibril formation is lower than on other surfaces. To understand this, replica exchange molecular dynamics simulations were used to investigate the conformations that hIAPP adopts on surfaces of different hydrophobicities. The hydrophobic surface stabilizes α-helical structures which are significantly different to those found on the hydrophilic surface and in bulk solution. There is also a greatly reduced conformational ensemble on the hydrophobic surface due to long-lived contacts between hydrophobic residues on the protein and the surface. This new microscopic information will help us determine the mechanism of the enhancement of fibril formation on surfaces and provides new insight into the effect of nanointerfaces and protein conformation.

Measuring the Impact of PEGylation on a Protein-Polysaccharide Interaction.

PEGylation is the most widely used half-life extension strategy for protein therapeutics. While it imparts a range of attractive attributes PEGylation can impede protein binding and reduce efficacy. A model system to probe the effects of PEGylation on protein binding has practical applications. Here, we present a system based on complex formation between a hexavalent lectin (RSL) and the globular polysaccharide Ficoll PM70 (a type of glycocluster). Mutants of the lectin were used to generate conjugates with 3, 6, or 12 PEG (1 kDa) chains. Using NMR spectroscopy we monitored how the degree of PEGylation impacted the lectin-Ficoll interaction. The binding propensity was observed to decrease with increasing polymer density. Apparently, the extended PEG chains sterically impede the lectin-Ficoll binding. This deduction was supported by molecular dynamics simulations of the protein-polymer conjugates. The implications for protein-surface interactions are discussed.

Atomistic Study of Zwitterionic Peptoid Antifouling Brushes.

Using molecular dynamics (MD) simulations, we study the molecular behavior and hydration properties of a set of zwitterionic "peptoid" brushes, grafted on a rutile surface, that has been previously reported to exhibit excellent resistance against protein adsorption and cell attachment. Peptoids are novel poly( N-substituted glycine) peptide mimics with the side chains attached to amide nitrogens. They constitute a unique model polymer system because hundreds of side chains have been demonstrated, and the exact chain length and sequence order of the residues/monomers may be specified in experiments. In this report, we vary the brush grafting density as well as the side chain/polymer molecular volume. We include in our study polysarcosine as an uncharged comparison with a small polymer chain cross-section. Sarcosine is the simplest peptoid residue with only a nominally hydrophobic methyl group as side chain, but is also reported to exhibit high antifouling performance. Overall, we show in detail how molecular volume and hydration effects are intertwined in a zwitterionic polymer brush. For example, the zwitterionic design significantly promotes extended chain conformations and could actually lower the overall electrostatic potential. Some properties promoted by the balanced charges, such as chain flexibility and hydration, increase more prominently at "low" to "intermediate" chain densities. These and other observations should provide insight on the molecular behavior of peptoids and inform the design of zwitterionic antifouling polymer brushes.

Adsorption and conformations of lysozyme and α-lactalbumin at a water-octane interface.

As proteins contain both hydrophobic and hydrophilic amino acids, they will readily adsorb onto interfaces between water and hydrophobic fluids such as oil. This adsorption normally causes changes in the protein structure, which can result in loss of protein function and irreversible adsorption, leading to the formation of protein interfacial films. While this can be advantageous in some applications (e.g., food technology), in most cases it limits our ability to exploit protein functionality at interfaces. To understand and control protein interfacial adsorption and function, it is necessary to understand the microscopic conformation of proteins at liquid interfaces. In this paper, molecular dynamics simulations are used to investigate the adsorption and conformation of two similar proteins, lysozyme and α-lactalbumin, at a water-octane interface. While they both adsorb onto the interface, α-lactalbumin does so in a specific orientation, mediated by two amphipathic helices, while lysozyme adsorbs in a non-specific manner. Using replica exchange simulations, both proteins are found to possess a number of distinct interfacial conformations, with compact states similar to the solution conformation being most common for both proteins. Decomposing the different contributions to the protein energy at oil-water interfaces suggests that conformational change for α-lactalbumin, unlike lysozyme, is driven by favourable protein-oil interactions. Revealing these differences between the factors that govern the conformational change at interfaces in otherwise similar proteins can give insight into the control of protein interfacial adsorption, aggregation, and function.

Macroscopic chiral symmetry breaking in monolayers of achiral nonconvex platelets.

The fabrication of chiral structures using achiral building blocks is a fundamental problem that remains a challenge in materials science. In this work we present a molecular dynamics simulation study of nonconvex polygonal platelets, interacting via soft-repulsive interactions, that are confined in two-dimensional space. These particle models are designed to promote, even at moderate densities, a natural offset displacement between the edges of neighbouring particles. In particular we demonstrate that nonconvex platelets exhibit macroscopic chiral symmetry breaking when the symmetry of the particles equals (or is multiple of) the number of nearest neighbours in the condensed crystalline phase, corresponding to the situation of platelets with 4-, 6-, and 12-fold symmetries.

Adsorption of the natural protein surfactant Rsn-2 onto liquid interfaces.

To stabilize foams, droplets and films at liquid interfaces a range of protein biosurfactants have evolved in nature. Compared to synthetic surfactants, these combine surface activity with biocompatibility and low solution aggregation. One recently studied example is Rsn-2, a component of the foam nest of the frog Engystomops pustulosus, which has been predicted to undergo a clamshell-like opening transition at the air-water interface. Using atomistic molecular dynamics simulations and surface tension measurements we study the adsorption of Rsn-2 onto air-water and cyclohexane-water interfaces. The protein adsorbs readily at both interfaces, with adsorption mediated by the hydrophobic N-terminus. At the cyclohexane-water interface the clamshell opens, due to the favourable interaction between hydrophobic residues and cyclohexane molecules and the penetration of cyclohexane molecules into the protein core. Simulations of deletion mutants showed that removal of the N-terminus inhibits interfacial adsorption, which is consistent with the surface tension measurements. Deletion of the hydrophilic C-terminus also affects adsorption, suggesting that this plays a role in orienting the protein at the interface. The characterisation of the interfacial behaviour gives insight into the factors that control the interfacial adsorption of proteins, which may inform new applications of this and similar proteins in areas including drug delivery and food technology and may also be used in the design of synthetic molecules showing similar changes in conformation at interfaces.

Experimental and computational examination of anastellin (FnIII1c)-polymer interactions.

Using a combination of experimental and computational approaches, the interaction between anastellin, a recombinant fragment of fibronectin, and representative biomaterial surfaces has been examined. Anastellin and superfibronectin have been seen to exhibit antiangiogenic properties and other properties that may make it suitable for consideration for incorporation into biomaterials. The molecular interaction was directly quantified by atomic force microscope (AFM)-based force spectroscopy, complemented by adsorption measurements using quartz crystal microbalance (QCM). Using AFM, it was found that the anastellin molecule facilitates a stronger adhesion on polyurethane films (72.0 pN nm-1 ) than on poly (methyl methacrylate) films (68.6 pN nm-1 ). However, this is not consistent with the QCM adsorption measurements, which show no significant difference. Molecular dynamics simulations of the behavior of anastellin on polyurethane in aqueous solution were performed to rationalize the experimental data, and show that anastellin is capable of rapid adsorption to PU while its secondary structure is stable upon adsorption in water. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 737-745, 2017.

Phase behaviour of self-assembled monolayers controlled by tuning physisorbed and chemisorbed states: A lattice-model view.

The self-assembly of molecules on surfaces into 2D structures is important for the bottom-up fabrication of functional nanomaterials, and the self-assembled structure depends on the interplay between molecule-molecule interactions and molecule-surface interactions. Halogenated benzene derivatives on platinum have been shown to have two distinct adsorption states: a physisorbed state and a chemisorbed state, and the interplay between the two can be expected to have a profound effect on the self-assembly and phase behaviour of these systems. We developed a lattice model that explicitly includes both adsorption states, with representative interactions parameterised using density functional theory calculations. This model was used in Monte Carlo simulations to investigate pattern formation of hexahalogenated benzene molecules on the platinum surface. Molecules that prefer the physisorbed state were found to self-assemble with ease, depending on the interactions between physisorbed molecules. In contrast, molecules that preferentially chemisorb tend to get arrested in disordered phases. However, changing the interactions between chemisorbed and physisorbed molecules affects the phase behaviour. We propose functionalising molecules in order to tune their adsorption states, as an innovative way to control monolayer structure, leading to a promising avenue for directed assembly of novel 2D structures.

Conformations of Myoglobin-Derived Peptides at the Air-Water Interface.

The conformational change exhibited by proteins at liquid interfaces, such as the air-water and oil-water interfaces, has long been of interest both for understanding protein structure outside of native environments and for applications in areas including food technology and pharmaceuticals. Using molecular simulation, this article studies the conformations of two peptides derived from myoglobin, for which the emulsification behavior has been studied. Both peptides were found to readily adsorb onto the air-water interface, with one of these (experimentally, the more effective stabilizer) adopting a flat, extended conformation and the other peptide remaining close to its solution conformation.

Mechanochemical Tuning of the Binaphthyl Conformation at the Air-Water Interface.

Gradual and reversible tuning of the torsion angle of an amphiphilic chiral binaphthyl, from -90° to -80°, was achieved by application of a mechanical force to its molecular monolayer at the air-water interface. This 2D interface was an ideal location for mechanochemistry for molecular tuning and its experimental and theoretical analysis, since this lowered dimension enables high orientation of molecules and large variation in the area. A small mechanical energy (<1 kcal mol(-1) ) was applied to the monolayer, causing a large variation (>50 %) in the area of the monolayer and modification of binaphthyl conformation. Single-molecule simulations revealed that mechanical energy was converted proportionally to torsional energy. Molecular dynamics simulations of the monolayer indicated that the global average torsion angle of a monolayer was gradually shifted.

Scaling Behavior of Polymers at Liquid/Liquid Interfaces.

The dynamics of a polymer chain confined in a soft 2D slit formed by two immiscible liquids is studied by means of molecular dynamics simulations. We show that the scaling behavior of a polymer confined between two liquids does not follow that predicted for polymers adsorbed on solid or soft surfaces such as lipid bilayers. Indeed, our results show that in the diffusive regime the polymer behaves like in bulk solution, following the Zimm model, and with the hydrodynamic interactions dominating its dynamics. Although the presence of the interface does not affect the long-time diffusion properties, it has an influence on the dynamics at short time scale, where for low molecular weight polymers the subdiffusive regime almost disappears. Simulations carried out when the liquid interface is sandwiched between two solid walls show that, when the confinement is a few times larger than the blob size, the Rouse dynamics is recovered.

Thermodynamics of linear and star polymers at fluid interfaces.

Performing molecular dynamics simulations on model systems we study the structural changes and thermodynamic stability of polymers of varying topology (linear and star-shaped) at interface between two liquids. We find that homopolymers are attracted to the interface in both good and poor solvent conditions showing that they are surface active molecules even though not amphiphilic. In most cases changing polymer topology had only a minor effect on the desorption free energy. A noticeable dependence on polymer topology is only seen for relatively high molecular weight polymers at interface between two good solvents. Examining separately the enthalpic and entropic components of the desorption free energy suggests that its largest contribution is the decrease in the enthalpic part of interfacial free energy caused by the adsorption of the polymer at the interface. Finally we propose a simple method to qualitatively predict the trend of the interfacial free energy as a function of the polymer molecular weight.

Aggregation of nanoparticles on one and two-component bilayer membranes.

Using dissipative particle dynamics simulations the aggregation of nanoparticles on single and two-component bilayers is investigated. For a uniform bilayer the aggregation of nanoparticles depends strongly on the location of the particles in the bilayer; particles residing on the bilayer exterior cluster strongly under the influence of bilayer-mediated interactions, whereas the interaction between the particles in the bilayer interior is significantly weaker leading to more loosely bound, dynamic aggregates. The aggregation of nanoparticles on two-component bilayers composed of immiscible components changes due to competition between nanoparticle clustering and their adsorption on the boundary between the bilayer components. This reduces the size of the nanoparticle clusters formed on the bilayer exterior, with the clusters adhering onto the boundary between the bilayer components. Due to their weaker attraction nanoparticles in the interior of a mixed bilayer no longer aggregate and instead form strings along the boundary between the two bilayer components. Nanoparticles with an affinity to one bilayer component nucleate small domains of their favoured component around themselves. For asymmetric mixtures this leads to a notable change in the aggregation behaviour of the nanoparticles.

Conformations and effective interactions of polymer-coated nanoparticles at liquid interfaces.

We investigate conformations and effective interactions of polymer-coated nanoparticles adsorbed at a model liquid-liquid interface via molecular dynamics simulations. The polymer shells strongly deform at the interface, with the shape governed by a balance between maximizing the decrease in interfacial area between the two solvent components, minimizing unfavorable contact between polymer and solvent, and maximizing the conformational entropy of the polymers. Using potential of mean force calculations, we compute the effective interaction between the nanoparticles at the liquid-liquid interface. We find that it differs quantitatively from the bulk and is significantly affected by the length of the polymer chains and by the solvent quality. Under good solvent conditions, the effective interactions are always repulsive and soft for long chains. The repulsion range decreases as the solvent quality decreases. In particular, under poor solvent conditions, short chains may fail to induce steric repulsion, leading to a net attraction between the nanoparticles, whereas with long-enough chains the effective interaction potential may feature an additional repulsive shoulder at intermediate distances.

Molecular simulation of hydrophobin adsorption at an oil-water interface.

Hydrophobins are small, amphiphilic proteins expressed by strains of filamentous fungi. They fulfill a number of biological functions, often related to adsorption at hydrophobic interfaces, and have been investigated for a number of applications in materials science and biotechnology. In order to understand the biological function and applications of these proteins, a microscopic picture of the adsorption of these proteins at interfaces is needed. Using molecular dynamics simulations with a chemically detailed coarse-grained potential, the behavior of typical hydrophobins at the water-octane interface is studied. Calculation of the interfacial adsorption strengths indicates that the adsorption is essentially irreversible, with adsorption strengths of the order of 100 k(B)T (comparable to values determined for synthetic nanoparticles but significantly larger than small molecule surfactants and biomolecules). The protein structure at the interface is unchanged at the interface, which is consistent with the biological function of these proteins. Comparison of native proteins with pseudoproteins that consist of uniform particles shows that the surface structure of these proteins has a large effect on the interfacial adsorption strengths, as does the flexibility of the protein.

Structural variability and dynamics of the P3HT/PCBM interface and its effects on the electronic structure and the charge-transfer rates in solar cells.

Using a range of realistic interface geometries obtained from a molecular dynamics simulation we study the effects of different microscopic atomic arrangements on the electronic structure and charge transfer rates of the prototypical photovoltaic interface between P3HT (poly(3-hexylthiophene)) and PCBM ([6,6]-phenyl-C(61)-butyric acid methyl ester). The electronic structures of charge-transfer (CT) states belong to two groups that can be denoted as "charge-separated" and "charge-bridging" states. For the former group of structures, which may lead to fully separated charges, the ranges and the average values of internal reorganization energy, the electronic coupling and the charge separated states energy are evaluated. A range and distribution of absolute charge separation (CS) and recombination (CR) rates are computed using the Marcus-Levich-Jortner rate equation. Due to the variety of P3HT/PCBM interface structures, a very broad range of CS (7.7 × 10(9)-1.8 × 10(12) s(-1)) and CR (2.5 × 10(5)-1.1 × 10(10) s(-1)) "instantaneous" rates are computed. However, the energetic parameters affecting the rate evolve in time due to the dynamic nature of the interface with a characteristic timescale of about 10 ns. For this reason the slowest CR instantaneous rates are not observed and the minimum CR rate observed is determined by the rate of conformational rearrangement at the interface. The combination of these observations provides a more general framework for the interpretation of experimental spectroscopic data, suggesting that the analysis based on simple first order rates may be insufficient to describe charge transfer in organic solar cell interfaces.