Influence of silicon nanocone on cell membrane self-sealing capabilities for targeted drug delivery-Computer simulation study.

Efficient and non-invasive techniques of cargo delivery to biological cells are the focus of biomedical research because of their great potential importance for targeted drug therapy. Therefore, much effort is being made to study the characteristics of using nano-based biocompatible materials as systems that can facilitate this task while ensuring appropriate self-sealing of the cell membrane. Here, we study the effects of indentation and withdrawal of nanocone on phospholipid membrane by applying steered molecular dynamics (SMD) technique. Our results show that the withdrawal process directly depends on the initial position of the nanocone. The average force and work are considerably more significant in case of the withdrawal starting from a larger depth. This result is attributed to stronger hydrophobic interactions between the nanocone and lipid tails of the membrane molecules. Furthermore, when the indenter was started from the lower initial depth, the number of lipids removed from the membrane was several times smaller than the deeper indentation. The choice of the least invasive method for nanostructure-assisted drug delivery is crucial for possible applications in medicine. Therefore, the results presented in this work might be helpful in efficient and safe drug delivery with nanomaterials.

Collagen type II-hyaluronan interactions - the effect of proline hydroxylation: a molecular dynamics study.

Hyaluronan-collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents the results from molecular dynamics calculations of HA-collagen type II interactions with hyaluronan. The applied protocol employed docking and geometry optimization of complexes built using collagen structures with different numbers of hydroxyl groups attached to proline moieties. It was established that the hydroxyproline/proline ratio affects both structural and energetic features of the collagen-hyaluronan complex. Proline hydroxylation was found to significantly influence the number of all identified types of molecular forces, hydrophobic interactions, water bridges and hydrogen bonds, which can be formed between collagen and hyaluronan. Importantly, an increase in the hydroxyproline/proline ratio in the collagen chain increases the binding affinity for hyaluronan. This is illustrated by the linear correlation between the binding free energy and the hydroxylation degree. A comparison of the results obtained for 3 and 4 hydroxylation of proline indicates that the hydroxyl group attachment position plays a minor role in complex stabilization. However, a slightly stronger affinity was observed for 4 hydroxylation. In order to evaluate the effect of the aqueous environment on the collagen-hyaluronan complex stability, the enthalpic and entropic contributions to the free energy of solvation were analyzed.

New Materials Based on Molecular Interaction between Hyaluronic Acid and Bovine Albumin.

In this work, the interactions between hyaluronic acid and bovine serum albumin were investigated. The film-forming properties of the mixture were proven, and the mechanical and surface properties of the films were measured. The results showed the interactions between hyaluronic acid and albumin, mainly by hydrogen bonds. Molecular docking was used for the visualization of the interactions. The films obtained from the mixture of hyaluronic acid possessed different properties to films obtained from the single component. The addition of bovine serum albumin to hyaluronic acid led to a decrease in the mechanical properties, and to an increase in the surface roughness of the film. The new materials that have been obtained by blending can form a new group of materials for biomedicine and cosmetology.

Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface.

Albumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions on human serum albumin-hyaluronan/chondroitin-6-sulfate interactions examined using molecular docking followed by molecular dynamics simulations. We analyze chosen glycosaminoglycans binding by employing a conformational entropy approach. In addition, several protein-polymer complexes have been studied to check how the binding site and presence of ions influence affinity. The presence of divalent cations contributes to the decrease of conformational entropy near carboxyl and sulfate groups. This observation can indicate the higher affinity between glycosaminoglycans and albumin. Moreover, domains IIIA and IIIB of albumin have the highest affinity as those are two domains that show a positive net charge that allows for binding with negatively charged glycosaminoglycans. Finally, in discussion, we suggest some research path to find particular features that would carry information about the dynamics of the particular type of polymers or ions.

Effect of Chitosan Deacetylation on Its Affinity to Type III Collagen: A Molecular Dynamics Study.

The ability to form strong intermolecular interactions by linear glucosamine polysaccharides with collagen is strictly related to their nonlinear dynamic behavior and hence bio-lubricating features. Type III collagen plays a crucial role in tissue regeneration, and its presence in the articular cartilage affects its bio-technical features. In this study, the molecular dynamics methodology was applied to evaluate the effect of deacetylation degree on the chitosan affinity to type III collagen. The computational procedure employed docking and geometry optimizations of different chitosan structures characterized by randomly distributed deacetylated groups. The eight different degrees of deacetylation from 12.5% to 100% were taken into account. We found an increasing linear trend (R2 = 0.97) between deacetylation degree and the collagen-chitosan interaction energy. This can be explained by replacing weak hydrophobic contacts with more stable hydrogen bonds involving amino groups in N-deacetylated chitosan moieties. In this study, the properties of chitosan were compared with hyaluronic acid, which is a natural component of synovial fluid and cartilage. As we found, when the degree of deacetylation of chitosan was greater than 0.4, it exhibited a higher affinity for collagen than in the case of hyaluronic acid.

Collagen Type II-Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations.

Chitosan-collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence chitosan's affinity for collagen. One of the most important ones is the deacetylation degree (DD) in chitosan and the hydroxylation degree (HD) of proline (PRO) moieties in collagen. In this paper, combinations of both factors were analyzed using a very efficient molecular dynamics approach. It was found that DD and HD modifications significantly affect the structural features of the complex related to considered types of interactions, namely hydrogen bonds, hydrophobic, and ionic contacts. In the case of hydrogen bonds both direct and indirect (water bridges) contacts were examined. In case of the most collagen analogues, a very good correlation between binding free energy and DD was observed.

Steered Molecular Dynamics of Lipid Membrane Indentation by Carbon and Silicon-Carbide Nanotubes-The Impact of Indenting Angle Uncertainty.

Due to the semi-liquid nature and uneven morphologies of biological membranes, indentation may occur in a range of non-ideal conditions. These conditions are relatively unstudied and may alter the physical characteristics of the process. One of the basic challenges in the construction of nanoindenters is to appropriately align the nanotube tip and approach the membrane at a perpendicular angle. To investigate the impact of deviations from this ideal, we performed non-equilibrium steered molecular dynamics simulations of the indentation of phospholipid membranes by homogeneous CNT and non-homogeneous SiCNT indenters. We used various angles, rates, and modes of indentation, and the withdrawal of the relative indenter out of the membrane in corresponding conditions was simulated.

Albumin-Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics.

The lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin is one of the major components in synovial fluid. Its electrostatic properties, including the ability to form molecular complexes, are closely related to pH, solvation, and the presence of ions. In the context of synovial fluid, it is relevant to describe the possible interactions between albumin and hyaluronate, taking into account solution composition effects. In this study, the influence of Na+, Mg2+, and Ca2+ ions on human serum albumin-hyaluronan interactions were examined using molecular dynamics tools. It was established that the presence of divalent cations, and especially Ca2+, contributes mostly to the increase of the affinity between hyaluronan and albumin, which is associated with charge compensation in negatively charged hyaluronan and albumin. Furthermore, the most probable binding sites were structurally and energetically characterized. The indicated moieties exhibit a locally positive charge which enables hyaluronate binding (direct and water mediated).

Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations.

This work presents the analysis of the conformation of albumin in the temperature range of 300 K - 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory-De Gennes type exponent of 0 . 4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher's test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal-Wallis test, we also analyze differences between the root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306 K - 309 K are different than in another temperature. Using the Kullback-Leibler theory, we investigate differences between the distribution of the root mean square displacement for each temperature and time window.

Influence of the Molecular Weight and the Presence of Calcium Ions on the Molecular Interaction of Hyaluronan and DPPC.

Hyaluronan is an essential physiological bio macromolecule with different functions. One prominent area is the synovial fluid which exhibits remarkable lubrication properties. However, the synovial fluid is a multi-component system where different macromolecules interact in a synergetic fashion. Within this study we focus on the interaction of hyaluronan and phospholipids, which are thought to play a key role for lubrication. We investigate how the interactions and the association structures formed by hyaluronan (HA) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) are influenced by the molecular weight of the bio polymer and the ionic composition of the solution. We combine techniques allowing us to investigate the phase behavior of lipids (differential scanning calorimetry, zeta potential and electrophoretic mobility) with structural investigation (dynamic light scattering, small angle scattering) and theoretical simulations (molecular dynamics). The interaction of hyaluronan and phospholipids depends on the molecular weight, where hyaluronan with lower molecular weight has the strongest interaction. Furthermore, the interaction is increased by the presence of calcium ions. Our simulations show that calcium ions are located close to the carboxylate groups of HA and, by this, reduce the number of formed hydrogen bonds between HA and DPPC. The observed change in the DPPC phase behavior can be attributed to a local charge inversion by calcium ions binding to the carboxylate groups as the binding distribution of hyaluronan and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine is not changed.

Application of Graphene as a Nanoindenter Interacting with Phospholipid Membranes-Computer Simulation Study.

Synthesis of graphene (GN) in 2004 stimulated wide interest in potential applications of 2D materials in catalysis, optoelectronics, biotechnology, and construction of sensing devices. In the presented study, interactions between GN sheets and phospholipid bilayers are examined using steered molecular dynamics simulations. GN sheets of different sizes were inserted into a bilayer and subsequently withdrawn from it at two different rates (1 and 2 m/s). In some cases, nanoindentation led to substantial damage of the phospholipid bilayer; however, an effective self-sealing process occurred even after significant degradation. The average force and work, deflection of the membrane during indentation, withdrawal processes, and structural changes caused by moving sheets are discussed. These quantities are utilized to estimate the suitability of GN sheets for targeted drug delivery or other nanomedicine tools. The results are compared with those obtained for other nanostructures such as homogeneous and heterogeneous nanotubes.

Biolubrication synergy: Hyaluronan - Phospholipid interactions at interfaces.

The manner in which nature has solved lubrication issues has fascinated scientists for centuries, in particular when considering that lubrication is achieved in aqueous media. The most outstanding system in this respect is likely the synovial joint, where close to frictionless motion is realized under different loads and shear rates. This review article focuses on two components present in the synovial area, hyaluronan and phospholipids. We recapitulate what has been learned about their interactions at interfaces from recent experiments, with focus on results obtained using reflectivity techniques at large scale facilities. In parallel, modelling experiments have been carried out and from these efforts new detailed knowledge about how hyaluronan and phospholipids interact has been gained. In this review we combine findings from modelling and experiments to gain deeper insight. Finally, we summarize what has been learned of the lubrication performance of mixtures of phospholipids and hyaluronan.

Interactions of a short hyaluronan chain with a phospholipid membrane.

Hyaluronic acid and phospholipids are two components that are present in the synovial fluid, and both are implicated as important facilitators of joint lubrication. In this work we aim to clarify how hyaluronic acid interacts with a phospholipid bilayer through their molecular interactions at the bilayer surface. To this end we performed molecular dynamics simulations of one hyaluronic acid molecule at a phospholipid bilayer in aqueous solution. The simulations were carried out for two aqueous solutions of equal concentrations, containing either NaCl or CaCl2. We analyzed hydrogen bonds, hydrophobic contacts and cation mediated bridges to clarify how hyaluoronic acid binds to a phospholipid bilayer. The analysis shows that calcium ions promote longer lasting bonds between the species as they create calcium ion bridges between the carboxylate group of hyaluronic acid and the phosphate group of the phospholipid. This type of additional bonding does not significantly influence the total number of contact created, but rather stabilizes the contact. The presented results can facilitate understanding of the role of hyaluronic acid and phospholipid interactions in terms of lubrication of articular cartilage.

The Amphoteric and Hydrophilic Properties of Cartilage Surface in Mammalian Joints: Interfacial Tension and Molecular Dynamics Simulation Studies.

In this paper, we explain the amphoteric character of the cartilage surface by studying a lipid bilayer model built from phospholipids. We examined the interfacial tension values and molecular dynamics simulation in solutions of varying pH. The effects of negative and positive charge density (or fixed charges) on the (cartilage/cartilage) friction coefficient were investigated. In physiological (or synovial) fluid, after the isoelectric point (pI), the curve of interfacial tension decreases rapidly as it reaches pH 7.4 and then approaches a constant value at higher pH. It was shown that the curve of the interfacial tension curve exhibits a maximum value at the isoelectric point with a Gaussian shape feature. The phospholipid bilayers facilitate an almost frictionless contact in the joint. Moreover, the slippage of the bilayer and the short-range repulsion between the surfaces of the negatively charged cartilage surfaces are the main determinants of the low frictional properties of the joint.

Hydrogen and Water Bonding between Glycosaminoglycans and Phospholipids in the Synovial Fluid: Molecular Dynamics Study.

Synovial fluid is a lubricant of the synovial joint that shows remarkable tribological properties. These properties originate in the synergy between its components, with two of its major components, glycosaminoglycans (GAGs) and phospholipids (PLs), playing a major role in boundary and mixed lubrication regimes. All-atom molecular dynamic simulations were performed to investigate the way these components bond. Hyaluronic acid (HA) and chondroitin sulphate (CS) bonding with three types of lipids was tested. The results show that both glycosaminoglycans bind lipids at a similar rate, except for 1,2-d-ipalmitoyl-sn-glycero-3-phosphoethanolamine lipids, which bind to chondroitin at a much higher rate than to hyaluronan. The results suggest that different synovial fluid lipids may play a different role when binding to both hyaluronan and chondroitin sulphate. The presented results may help in understanding a process of lubrication of articular cartilage at a nanoscale level.

Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment.

Hyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and the small world network approach to investigate dynamic couplings using a distance map applied to oxygen atoms in a chain of hyaluronic acid in the presence of phospholipids and water. The distance characterizing the coupling can be defined in various ways to bring out the most evident differences between various scenarios of the polymer chain conformation We show herein a physical distance understood as H-bond length and classes of these distances which are defined in a coarse-grained picture of the molecule. Simulation results indicate that addition of phospholipids has little influence on hyaluronic acid crosslinking. However, longer chains and addition of lipids promote appreciably long lasting (resilient) networks that may be of importance in biological systems. Specific sites for hydrogen bonding of phospholipids to hyaluronic acid have also been identified.

Correction: Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment.

Correction for 'Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment' by Piotr Beldowski et al., Soft Matter, 2018, DOI: 10.1039/c8sm01388h.

The Anomalies of Hyaluronan Structures in Presence of Surface Active Phospholipids-Molecular Mass Dependence.

Interactions between hyaluronan (A-) and phospholipids play a key role in many systems in the human body. One example is the articular cartilage system, where the synergistic effect of such interactions supports nanoscale lubrication. A molecular dynamics simulation has been performed to understand the process of formation of hydrogen bonds inside the hyaluronan network, both in the presence and absence of phospholipids. Additionally, the effect of the molecular mass of (A-) was analyzed. The main finding of this work is a robust demonstration of the optimal parameters (H-bond energy, molecular mass) influencing the facilitated lubrication mechanism of the articular cartilage system. Simulation results show that the presence of phospholipids has the greatest influence on hyaluronan at low molecular mass. We also show the specific sites of H-bonding between chains. Simulation results can help to understand how hyaluronan and phospholipids interact at several levels of articular cartilage system functioning.

Hyaluronan-Chondroitin Sulfate Anomalous Crosslinking Due to Temperature Changes.

Glycosaminoglycans are a wide class of biopolymers showing great lubricating properties due to their structure and high affinity to water. Two of them, hyaluronic acid and chondroitin sulfate, play an important role in articular cartilage lubrication. In this work, we present results of the all-atom molecular dynamics simulations of both molecules placed in water-based solution. To mimic changes of the physiological conditions, especially temperature, of the synovial fluid in joints under successive load (e.g., walking, jogging, jumping), simulations have been performed at different physiological temperatures in the range of 300 to 320 Kelvin (normal intra-articular temperature is 305 K). The stability of the biopolymeric network at equilibrium (isothermal and isobaric) conditions has been studied. To understand the process of physical crosslinking, the dynamics of intra- and intermolecular hydrogen bonds forming and breaking have been studied. The results show that following addition of chondroitin sulfate, hyaluronan creates more intermolecular hydrogen bonds than when in homogeneous solution. The presence of chondroitin in a hyaluronan network is beneficial as it may increase its stability. Presented data show hyaluronic acid and chondroitin sulfate as viscosity modifiers related to their crosslinking properties in different physicochemical conditions.

Entropy Production Associated with Aggregation into Granules in a Subdiffusive Environment.

We study the entropy production that is associated with the growing or shrinking of a small granule in, for instance, a colloidal suspension or in an aggregating polymer chain. A granule will fluctuate in size when the energy of binding is comparable to k B T , which is the "quantum" of Brownian energy. Especially for polymers, the conformational energy landscape is often rough and has been commonly modeled as being self-similar in its structure. The subdiffusion that emerges in such a high-dimensional, fractal environment leads to a Fokker-Planck Equation with a fractional time derivative. We set up such a so-called fractional Fokker-Planck Equation for the aggregation into granules. From that Fokker-Planck Equation, we derive an expression for the entropy production of a growing granule.