Chain Flexibility in Self-Assembled Monolayers Affects Protein Adsorption and Surface Hydration: A Molecular Dynamics Study

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a β-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH₃, -CH₃, and -CF₃. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation. It was found that the adsorption free energy of the SCAs was linearly related to the surface hydrophobicity, which was computed as the free energy of cavity formation near the SAM-water interfaces. In addition, the hydrophobic -CH₃ and -CF₃ SAMs produced substantial conformational changes in HP7 because of the strong hydrophobic attractions to the nonpolar side chains. The hydrophilic surface terminated by -OH also promoted structural changes in HP7 resulting from the formation of hydrogen bonds between the hydrophilic tail and HP7. Consequently, the moderate amphiphilic surface terminated by -OCH₃ avoided the denaturation of HP7 most efficiently, thus improving the biocompatibility of the surface. In conclusion, these results provide a deep understanding of protein adsorption for a wide range of polymeric surfaces, and they can potentially aid the design of appropriate biocompatible coatings for medical applications.

Cell-membrane-inspired polymers for constructing biointerfaces with efficient molecular recognition

Fabrication of devices that accurately recognize, detect, and separate target molecules from mixtures is a crucial aspect of biotechnology for applications in medical, pharmaceutical, and food sciences. This technology has also been recently applied in solving environmental and energy-related problems. In molecular recognition, biomolecules are typically complexed with a substrate, and specific molecules from a mixture are recognized, captured, and reacted. To increase sensitivity and efficiency, the activity of the biomolecules used for capture should be maintained, and non-specific reactions on the surface should be prevented. This review summarizes polymeric materials that are used for constructing biointerfaces. Precise molecular recognition occurring at the surface of cell membranes is fundamental to sustaining life; therefore, materials that mimic the structure and properties of this particular surface are emphasized in this article. The requirements for biointerfaces to eliminate nonspecific interactions of biomolecules are described. In particular, the major issue of protein adsorption on biointerfaces is discussed by focusing on the structure of water near the interface from a thermodynamic viewpoint; moreover, the structure of polymer molecules that control the water structure is considered. Methodologies enabling stable formation of these interfaces on material surfaces are also presented.

Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins

Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.

Effects of Side-Chain Spacing and Length on Hydration States of Poly(2-methoxyethyl acrylate) Analogues: A Molecular Dynamics Study

Hydration states of polymers are known to directly influence the adsorption of biomolecules. Particularly, intermediate water (IW) has been found able to prevent protein adsorption. Experimental studies have examined the IW content and nonthrombogenicity of poly(2-methoxyethyl acrylate) analogues with different side-chain spacings and lengths, which are HPx (x is the number of backbone carbons in a monomer) and PMCyA (y is the number of carbons in-between ester and ether oxygens of the side-chain) series, respectively. HPx was reported to possess more IW content but lower nonthrombogenicity compared to PMCyA with analogous composition. To understand the reason for the conflict, molecular dynamics simulations were conducted to elucidate the difference in the properties between the HPx and PMCyA. Simulation results showed that the presence of more methylene groups in the side chain more effectively prohibits water penetration in the polymer than those in the polymer backbone, causing a lower IW content in the PMCyA. At a high water content, the methoxy oxygen in the shorter side chain of the HPx cannot effectively bind water compared to that in the PMCyA side chain. HPx side chains may have more room to contact with molecules other than water (e.g., proteins), causing experimentally less nonthrombogenicity of HPx than that of PMCyA. In summary, theoretical simulations successfully explained the difference in the effects of side-chain spacing and length in atomistic scale.

Effect of an ionic environment on membrane fouling: a molecular dynamics study

The effect of the ionic environment on membrane fouling was investigated for polyamide (PA) and graphene oxide (GO) membranes using equilibrium molecular dynamics (MD) simulations. For each of these membranes, bovine serum albumin (BSA) was considered as the model foulant. The effect of the foulant on the membranes is investigated at seawater concentration and also in a normal aqueous environment. We investigated the translational and rotational motion of the protein relative to the membrane, interaction energy between the protein and the membrane surface, structural changes in the protein, and ion distribution around the protein and the membrane surface for all the systems. We found that the effects of ions were very different on both the membranes. Specifically, with an increase in ionic strength, the repulsion between the protein and membrane was observed in the case of GO, while for PA, no significant changes were observed for the same. Also, the ion distribution around the protein and the membrane surface were found to be different. In particular, for GO, there were more number of chloride ions around the protein and the membrane than that of sodium ions, which was probably the reason for the repulsion in the case of GO. However, in the case of PA, the membrane surface did not exhibit any affinity towards a specific ion, and the protein in the case of PA was surrounded by more number of sodium ions than chloride ions.

Molecular Dynamics Study on the Water Mobility and Side-Chain Flexibility of Hydrated Poly(ω-methoxyalkyl acrylate)s

Intermediate water (IW) is known to play an important role in the antifouling property of biocompatible polymers. However, how IW prevents protein adsorption is still unclear. To understand the role of IW in the antifouling mechanism, molecular dynamics simulation was used to investigate the dynamic properties of water and side-chains for hydrated poly(ω-methoxyalkyl acrylate)s (PMCxA, where x indicates the number of methylene carbons) with x = 1-6 and poly(n-butyl acrylate) (PBA) in this study. Since the polymers uptake more water than their equilibrium water content (EWC) at the polymer/water interface, we analyzed the hydrated polymers at a water content higher than that of EWC. It was found that the water molecules interacting with one polymer oxygen atom (BW1), of which most are IW molecules, in PMC2A exhibit the lowest mobility, while those in PBA and PMC1A show a higher mobility. The result was consistent with the expectation that the biocompatible polymer with a long-resident hydration layer possesses good antifouling property. Through the detailed analysis of side-chain binding with three different types of BW1 molecules, we found that the amount of side-chains simultaneously interacting with two BW1 molecules, which exhibit the highest flexibility among the three kinds of side-chains, is the lowest for PMC1A. The high mobility of BW1 is thus suggested as the main factor for the poor protein adsorption resistance of PMC1A even though it possesses enough IW content and relatively flexible side-chains. Contrarily, a maximum amount of side-chains simultaneously interacting with two BW1 molecules was found in the hydrated PMC3A. The moderate side-chain length of PMC3A allows side-chains to simultaneously interact with two BW1 molecules and minimizes the hydrophobic part attractively interacting with a protein at the polymer/water interface. The unique structure of PMC3A may be the reason causing the best protein adsorption resistance among the PMCxAs.

Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. In this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

Comparison of Protein-Repellent Behavior of Linear versus Dendrimer-Structured Surface-Immobilized Polymers

For many biomedical applications, material surfaces should not only prevent unspecific protein adsorption and bacterial attachment as in many other applications in the food, health, or marine industry, but they should also promote the adhesion of tissue cells. In order to take a first step toward the challenging development of protein and bacteria-repelling and cell-adhesion-promoting materials, polyamine and poly(amido amine) surface coatings with terminal amine groups and varying structure (dendrimer, oligomer, polymer) were immobilized on model surfaces via silane chemistry. Physicochemical analysis showed that all modifications are hydrophilic (contact angles <60°) and possess similar surface free energies (SFEs, ∼46-54 mN/m), whereas their amine group densities and zeta potentials at physiological conditions (pH 7.4) varied greatly (-50 to +75 mV). In protein adsorption experiments with single proteins (human serum albumin (HSA) and lysozyme) as well as complex physiological fluids (fetal bovine serum (FBS) and human saliva), the amounts of adsorbed protein were found to correlate strongly with the zeta potential of the surface coatings. Both modifications based on linear polymers exhibited good protein repellency toward all proteins examined and are thus promising for testing in cell adhesion studies.

Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance

Non-specific protein adsorption represents a significant challenge for the design of efficient and safe nanoparticles for biomedical applications since it may prevent functional ligands to target the desired specific receptors which can limit the efficacy of novel drug delivery systems and biosensors. The biofilm formation initiated by protein adsorption on surfaces limits the lifetime and safety of medical implants and tissue regenerative scaffolds. The development of biofouling resistant surfaces is therefore a major goal for the widespread uptake of nanomedicine. Here, we provide a relatively simple computational screening method based on the rational physically grounded criteria that may suffice in selection of surface grafted ligands for protein rejection, and test whether these criteria can be extrapolated from a specific protein to generic protein-resistant surfaces. Using all-atom molecular dynamics simulations we characterise four types of ligand functionalised surfaces at aqueous interfaces in terms of the surface hydrophobicity and ligand dynamics. We demonstrate how our hypothesised interfacial design based on the select physical characteristics of the ligated surfaces can enable the rejection of a protein from the surface. The ligand screening procedure and the detailed atomistic characterisation of the protein rejection process presented suggest that minimizing the adsorption of surface active proteins requires specific surface topographies and ligand chemistries that are able to maximise the entropic penalty associated with the restriction of the ligand dynamics and trapping interfacial water by adsorbed proteins.

Molecular Insights into the Loading and Dynamics of Doxorubicin on PEGylated Graphene Oxide Nanocarriers

Molecular dynamics (MD) simulations were performed to investigate the loading and dynamics of doxorubicin (DOX) anticancer drug on graphene oxide (GO) and poly(ethylene glycol) (PEG) decorated GO (PEGGO) nanocarriers in an aqueous environment at human body temperature (310 K) and physiological pH level of 7.4. Mechanisms of DOX adsorption on PEGGO as a function of PEG chain length were revealed. While the total DOX-nanocarrier interaction energy was the same for the DOX/GO (control), DOX/Sh-PEGGO (short PEG chains consisting of 15 repeat units), and DOX/L-PEGGO (long PEG chains consisting of 30 repeat units) within the margin of error, the PEG-DOX interactions increased with an increase in the PEG chain length. At the same time, the PEG-DOX solvent-accessible contact area almost doubled going from the short to long PEG chains. PEGylation of the GO effectively causes an increase in the average water density around the nanocarrier, which can act as a barrier, leading to the DOX migration to the solvated PEG-free part of the GO surface. This effect is more pronounced for shorter PEG chains. The DOX-DOX solvent-accessible contact area is smaller in the DOX/GO system, which means the drug molecules are less aggregated in this system. However, the level of DOX aggregation is slightly higher for the PEGGO systems. The computational results in this work shed light on the fact that increasing the PEG chain length benefits DOX loading on the nanocarrier, revealing an observation that is difficult to acertain through experiments. Moreover, a detailed picture is provided for the DOX adsorption and retention in PEGGO drug delivery systems, which would enable the researchers to improve the drug's circulation time, as well as its delivery and targeting efficiency.

Resistance of Zwitterionic Peptide Monolayers to Biofouling

Self-assembled monolayers (SAMs) are widely used in science and engineering, and recent progress has demonstrated the utility of zwitterionic peptides with alternating lysine (K) and glutamic acid (E) residues for antifouling purposes. Aiming at developing a peptide-based fouling-resistant SAM suitable for presentation of surface-attached pheromones for barnacle larvae, we have investigated five different peptide SAMs, where four are based on the EK motif, and the fifth was designed based on general principles for fouling resistance. The SAMs were formed by self-assembly onto gold substrates via cysteine residues on the peptides, and formation of SAMs was verified via ellipsometry, wettability, infrared reflection-absorption spectroscopy and cyclic voltammetry. Settlement of cypris larvae of the barnacle Balanus (=Amphibalanus) amphitrite, the target of pheromone studies, was tested. SAMs were also subjected to fouling assays using protein solutions, blood serum, and the bacterium Mycobacterium marinum. The results confirm the favorable antifouling properties of EK-containing peptides in most of the assays, although this did not apply to the barnacle larvae settlement test, where settlement was low on only one of the peptide SAMs. The one peptide that had antifouling properties for barnacles did not contain a pheromone motif, and would not be susceptible to degredation by common serine proteases. We conclude that the otherwise broadly effective antifouling properties of EK-containing peptide SAMs is not directly applicable to barnacles, and that great care must be exercised in the design of peptide-based SAMs for presentation of barnacle-specific ligands.

Mixing Poly(ethylene glycol) and Poly(2-alkyl-2-oxazoline)s Enhances Hydration and Viscoelasticity of Polymer Brushes and Determines Their Nanotribological and Antifouling Properties

Poly(2-alkyl-2-oxazoline)s (PAOXAs) have progressively emerged as suitable alternatives for replacing poly(ethylene glycol) (PEG) in a variety of biomaterial-related applications, especially in the designing of polymer brush-based biointerfaces because of their stealth properties and chemical robustness. When equimolar mixtures of PEG and PAOXAs are assembled on surfaces to yield mixed polymer brushes, the interfacial physicochemical properties of the obtained films are significantly altered, in some cases, surpassing the biopassive and lubricious characteristics displayed by single-component PAOXA and PEG counterparts. With a combination of variable angle spectroscopic ellipsometry, quartz crystal microbalance with dissipation, and atomic force microscopy-based methods, we demonstrate that mixing of PEG brushes with equimolar amounts of PAOXA grafts determines an increment in film's hydration and viscoelasticity. In the case of mixtures of PEG and poly(2-methyl-2-oxazoline) or poly(2-ethyl-2-oxazoline), brushes displaying full inertness toward serum proteins and improved lubricity with respect to the corresponding single-component layers can be generated, while providing a multifunctional surface that substantially enlarges the applicability of the designed coatings.

In Situ Molecular-Level Observation of Methanol Catalysis at the Water-Graphite Interface

Methanol occupies a central role in chemical synthesis and is considered an ideal candidate for cleaner fuel storage and transportation. It can be catalyzed from water and volatile organic compounds, such as carbon dioxide, thereby offering an attractive solution for reducing carbon emissions. However, molecular-level experimental observations of the catalytic process are scarce, and most existing catalysts tend to rely on empirically optimized, expensive, and complex nanocomposite materials. This lack of molecular-level insights has precluded the development of simpler, more cost-effective alternatives. Here, we show that graphite immersed in ultrapure water is able to spontaneously catalyze methanol from volatile organic compounds in ambient conditions. Using single-molecule resolution atomic force microscopy (AFM) in liquid, we directly observe the formation and evolution of methanol-water nanostructures at the surface of graphite. These molecularly ordered structures nucleate near catalytically active surface features, such as atomic step edges, and grow progressively as further methanol is being catalyzed. Complementary nuclear magnetic resonance analysis of the liquid confirms the formation of methanol and quantifies its concentration. We also show that electric fields significantly enhance the catalysis rate, even when as small as that induced by the natural surface potential of the silicon AFM tip. These findings could have a significant impact on the development of organic catalysts and on the function of nanoscale carbon devices.

Lysozyme orientation and conformation on MoS2 surface: Insights from molecular simulations

Two-dimensional molybdenum disulfide (MoS₂) has attracted intense interest owing to its unique properties and promising biosensor applications. To develop effective biocompatible platforms, it is crucial to understand the interactions between MoS₂ and biological molecules such as proteins, but little knowledge exists on the orientation and conformation of proteins on the MoS₂ surface at the molecular level. In this work, the lysozyme adsorption on the MoS₂ surface was studied by molecular dynamics simulations, wherein six different orientations were selected based on the different faces of lysozyme. Simulation results showed that lysozyme tends to adsorb on the MoS₂ surface in an "end-on" orientation, indicating that orientations within this range are favorable for stable adsorption. The end-on orientation could be further categorized into "bottom end-on" and "top end-on" orientations. The driving forces responsible for the adsorption were dominated by van der Waals interactions and supplemented by electrostatic interactions. Further, the conformations of the lysozyme adsorbed on the MoS₂ surface were basically preserved. This simulation study promotes the fundamental understanding of interactions between MoS₂ and proteins and can guide the development of future biomedical applications of MoS₂.