Protein diffusion and long-term adsorption states at charged solid surfaces

Estimating Binding Energies of π-Stacked Aromatic Dimers Using Force Field-Driven Molecular Dynamics

π-π stacking are omnipresent interactions, crucial in many areas of chemistry, and often studied using quantum chemical methods. Here, we report a simple and computationally efficient method of estimating the binding energies of stacked polycyclic aromatic hydrocarbons based on steered molecular dynamics. This method leverages the force field parameters for accurate calculation. The presented results show good agreement with those obtained through DFT at the ωB97X-D3/cc-pVQZ level of theory. It is demonstrated that this force field-driven SMD method can be applied to other aromatic molecules, allowing insight into the complexity of the stacking interactions and, more importantly, reporting π-π stacking energy values with reasonable precision.

Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study

Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.

Chitin and Chitosan Binding to the α-Chitin Crystal: A Molecular Dynamics Study

Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito-oligomers to the (100) surface of an α-chitin crystal using molecular dynamics (MD), steered MD, and umbrella sampling. The convergence of the free energy was carefully considered and yielded a binding energies of -12.5 and -2 kcal mol^-1 for 6-monomer-long chitin and uncharged chitosan oligomers, respectively. We also found that the results for the umbrella sampling were consistent with the force profile from the steered MD and with classical MD simulations of the adsorption process. Our results give insight into the molecular-scale interactions, which can be helpful for the design of new chitin composite films. Furthermore, the free energy curves we present can be used to validate coarse-grained models for chitin and chitosan, which are necessary to study the self-assembly of chitin crystals due to the long time scale of the process.

Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study

Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.

Adsorption of lysozyme into a charged confining pore

Several applications arise from the confinement of proteins on surfaces because their stability and biological activity are enhanced. It is also known that the way in which a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white lysozyme, HEWL, into a negatively charged silica pore is examined by employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account via including the Debye-Hückel potentials into the Cα structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find that the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. Under these conditions, the pK_a shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of the pK_a shift for HEWL available in the literature and to some experimental data.

Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study

Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti₃C₂T_x (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti₃C₂T_x surfaces, and the order of interaction strength is Ti₃C₂O₂ > Ti₃C₂F₂ > Ti₃C₂(OH)₂. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti₃C₂O₂ and Ti₃C₂F₂ surfaces are more concentrated than that on the Ti₃C₂(OH)₂ surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti₃C₂T_x. Besides, the distribution of the interfacial water layer on the Ti₃C₂T_x surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti₃C₂T_x materials and may help us evaluate the engineering of their surfaces for future biorelated applications.

Cross-Plane and In-Plane Heat Conductions in Layer-by-Layer Membrane: Molecular Dynamics Study

A material with anisotropic heat conduction characteristics, which is determined by molecular scale structure, provides a way of controlling heat flow in nanoscale spaces. As such, here, we consider layer-by-layer (LbL) membranes, which are an electrostatic assembly of polyelectrolyte multilayers and are expected to have different heat conduction characteristics between cross-plane and in-plane directions. We constructed models of a poly(acrylic acid)/polyethylenimine (PAA/PEI) LbL membrane sandwiched by charged solid walls and investigated their anisotropic heat conduction using molecular dynamics simulations. In the cross-plane direction, the thermal boundary resistance between the solid wall and the LbL membrane and that between the constituent PAA and PEI layers decrease with increasing degree of ionization (solid surface charge density and the number of electric charges per PAA/PEI molecule). When the degree of ionization is low, the cross-plane thermal conductivity of a constituent layer is higher than that of the bulk state. As the degree of ionization increases, however, the cross-plane thermal conductivity of PAA, a linear polymer, decreases because of the increase in the number of in-plane oriented polymer chains. In the in-plane direction, we investigated the heat conduction of each layer and found the enhancement of effective in-plane thermal conductivity again due to the in-plane oriented chain alignment. The heat conduction in the LbL membrane is three-dimensionally enhanced compared to those in the bulk states of the constituent polymers because of the electrostatic interactions in the cross-plane direction and the molecular alignment in the in-plane direction.

Adsorption of Fibronectin Fragment on Surfaces Using Fully Atomistic Molecular Dynamics Simulations

The effect of surface chemistry on the adsorption characteristics of a fibronectin fragment (FNIII^8⁻10) was investigated using fully atomistic molecular dynamics simulations. Model surfaces were constructed to replicate self-assembled monolayers terminated with methyl, hydroxyl, amine, and carboxyl moieties. It was found that adsorption of FNIII^8⁻10 on charged surfaces is rapid, specific, and driven by electrostatic interactions, and that the anchoring residues are either polar uncharged or of opposing charge to that of the targeted surfaces. On charged surfaces the presence of a strongly bound layer of water molecules and ions hinders FNIII^8⁻10 adsorption. In contrast, adsorption kinetics on uncharged surfaces are slow and non-specific, as they are driven by van der Waals interactions, and the anchoring residues are polar uncharged. Due to existence of a positively charged area around its cell-binding region, FNIII^8⁻10 is available for subsequent cell binding when adsorbed on a positively charged surface, but not when adsorbed on a negatively charged surface. On uncharged surfaces, the availability of the fibronectin fragment's cell-binding region is not clearly distinguished because adsorption is much less specific.

Simulated and experimental force spectroscopy of lysozyme on silica

The force spectra of proteins detaching from oxide surfaces measured by atomic force microscopy (AFM) often present complex patterns of peaks, which are difficult to correlate with individual bond-breaking events at the atomic scale. In this work we rationalize experimental AFM force spectra of hen-egg-white lysozyme detaching from silica by means of all-atom steered molecular dynamics (SMD) simulations. In particular, we demonstrate that the native tertiary structure of lysozyme is preserved if, and only if, its four intramolecular disulfide bridges are intact. Otherwise, the protein pulled off the surface undergoes severe unfolding, which is well captured by SMD simulations in explicit solvent. Implicit solvent simulations, on the contrary, wrongly predict protein unfolding even in the presence of S-S bridges, due to the lack of additional structural stabilization provided by the water's hydrogen-bond network within and surrounding the protein. On the basis of our combined experimental and theoretical findings, we infer that the rugged force spectra characteristic of lysozyme/silica interfaces are not due to the successive breaking of internal disulfide bonds leading to partial unfolding events. Rather, they reflect the detachment of several molecules bound to the same AFM tip, each anchored to the surface via multiple hydrogen and ionic bonds.

Energy Landscape of Negatively Charged BSA Adsorbed on a Negatively Charged Silica Surface

We study the energy landscape of the negatively charged protein bovine serum albumin adsorbed on a negatively charged silica surface at pH 7. We use fully atomistic molecular dynamics (MD) and steered MD (SMD) to probe the energy of adsorption and the pathway for the surface diffusion of the protein and its associated activation energy. We find an adsorption energy ∼1.2 eV, which implies that adsorption is irreversible even on experimental time scales of hours. In contrast, the activation energy for surface diffusion is ∼0.4 eV so that it is observable on the MD simulation time scale of 100 ns. This analysis paves the way for a more detailed understanding of how a protein layer forms on biomaterial surfaces, even when the protein and surface share the same electrical polarity.

Bovine Serum Albumin Adsorption at a Silica Surface Explored by Simulation and Experiment

Molecular details of BSA adsorption on a silica surface are revealed by fully atomistic molecular dynamics (MD) simulations (with a 0.5 μs trajectory), supported by dynamic light scattering (DLS), zeta potential, multiparametric surface plasmon resonance (MP-SPR), and contact angle experiments. The experimental and theoretical methods complement one another and lead to a wider understanding of the mechanism of BSA adsorption across a range of pH 3-9. The MD results show how the negatively charged BSA at pH7 adsorbs to the negatively charged silica surface, and reveal a unique orientation with preserved secondary and tertiary structure. The experiments then show that the protein forms complete monolayers at ∼ pH6, just above the protein's isoelectric point (pH5.1). The surface contact angle is maximum when it is completely coated with protein, and the hydrophobicity of the surface is understood in terms of the simulated protein conformation. The adsorption behavior at higher pH > 6 is also consistently interpreted using the MD picture; both the contact angle and the adsorbed protein mass density decrease with increasing pH, in line with the increasing magnitude of negative charge on both the protein and the surface. At lower pH < 5 the protein starts to unfold, and the adsorbed mass dramatically decreases. The comprehensive picture that emerges for the formation of oriented protein films with preserved native conformation will help guide efforts to create functional films for new technologies.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

How Negatively Charged Proteins Adsorb to Negatively Charged Surfaces: A Molecular Dynamics Study of BSA Adsorption on Silica

How proteins adsorb to inorganic material surfaces is critically important for the development of new biotechnologies, since the orientation and structure of the adsorbed proteins impacts their functionality. While it is known that many negatively charged proteins readily adsorb to negatively charged oxide surfaces, a detailed understanding of how this process occurs is lacking. In this work we study the adsorption of BSA, an important transport protein that is negatively charged at physiological conditions, to a model silica surface that is also negatively charged. We use fully atomistic molecular dynamics to provide detailed understanding of the noncovalent interactions that bind the BSA to the silica surface. Our results provide new insight into the competing roles of long-range electrostatics and short-range forces, and the consequences this has for the orientation and structure of the adsorbed proteins.

Steering protein adsorption at charged surfaces: electric fields and ionic screening

Protein adsorption at charged surfaces is a common process in the development of functional technological devices.

Equilibration of complexes of DNA and H-NS proteins on charged surfaces: a coarse-grained model point of view

The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS proteins similar to those observed by AFM microscopy. They furthermore highlight the antagonistic effects of the interactions between DNA and the surface. Indeed, increasing these interactions slows down the equilibration of naked plasmids on the surface but, on the other hand, enables a faster equilibration of DNA/H-NS complexes. Based on the distribution of the lifetimes of H-NS bridges and the time evolution of the number of trans-binding protein dimers during equilibration of the complexes on the surface, it is argued that the decrease of the equilibration time of the complex upon increase of the interaction strength between DNA and the surface is ascribable to the associated decrease of the probability to form new bridges between DNA and the proteins.

Lysozyme adsorption at a silica surface using simulation and experiment: effects of pH on protein layer structure

Hen Egg White Lysozyme (HEWL) is a widely used exemplar to study protein adsorption on surfaces and interfaces. Here we use fully atomistic Molecular Dynamics (MD) simulations, Multi-Parametric Surface Plasmon Resonance (MP-SPR), contact angle and zeta potential measurements to study HEWL adsorption at a silica surface. The simulations provide a detailed description of the adsorption mechanism and indicate that at pH7 the main adsorption driving force is electrostatics, supplemented by weaker hydrophobic forces. Moreover, they reveal the preferred orientation of the adsorbed protein and show that its structure is only slightly altered at the interface with the surface. This provides the basis for interpreting the experimental results, which indicate the surface adsorbs a close-packed monolayer at about pH10 where the surface has a large negative zeta potential and the HEWL is positively charged. At higher pH, the adsorption amount of the protein layer is greatly reduced due to the loss of charge on the protein. At lower pH, the smaller zeta potential of the surface leads to lower HEWL adsorption. These interpretations are complemented by the contact angle measurements that show how the hydrophobicity of the surface is greatest when the surface coverage is highest. The simulations provide details of the hydrophobic residues exposed to solution by the adsorbed HEWL, completing the picture of the protein layer structure.

Adsorption and catalytic activity of glucose oxidase accumulated on OTCE upon the application of external potential

This article describes the adsorption of glucose oxidase (GOx) onto optically transparent carbon electrodes (OTCE) under the effect of applied potential and the analysis of the enzymatic activity of the resulting GOx/OTCE substrates. In order to avoid electrochemical interferences with the enzyme redox center, control electrochemical experiments were performed using flavin adenine dinucleotide (FAD) and GOx/OTCE substrates. Then, the enzyme adsorption experiments were carried out as a function of the potential applied (ranged from the open circuit potential to +950mV), the pH solution, the concentration of enzyme, and the ionic strength on the environment. The experimental results demonstrated that an increase in the adsorbed amount of GOx on the OTCE can be achieved when the potential was applied. Although the increase in the adsorbed amount was examined as a function of the potential, a maximum enzymatic activity was observed in the GOx/OTCE substrate achieved at +800mV. These experiments suggest that although an increase in the amount of enzyme adsorbed can be obtained by the application of an external potential to the electrode, the magnitude of such potential can produce detrimental effects in the conformation of the adsorbed protein and should be carefully considered. As such, the article describes a simple and rational approach to increase the amount of enzyme adsorbed on a surface and can be applied to improve the sensitivity of a variety of biosensors.

Spontaneous membrane-translocating peptide adsorption at silica surfaces: a molecular dynamics study

Spontaneous membrane-translocating peptides (SMTPs) have recently been shown to directly penetrate cell membranes. Adsorption of a SMTP, and some engineered extensions, at model silica surfaces is studied herein using fully atomistic molecular dynamics simulations in order to assess their potential to construct novel drug delivery systems. The simulations are designed to reproduce the electric fields above single, siloxide-rich charged surfaces, and the trajectories indicate that the main driving force for adsorption is electrostatic. An increase in the salt concentration slows down but does not prevent adsorption of the SMTP to the surface; it also does not result in peptide desorption, suggesting additional binding via hydrophobic forces. The results are used to design extensions to the peptide sequence which we find enhance adsorption but do not affect the adsorbed conformation. We also investigate the effect of surface hydroxylation on the peptide adsorption. In all cases, the final adsorbed conformations are with the peptide flattened to the surface with arginine residues, which are key to the peptide’s function, anchoring it to the surface so that they are not exposed to solution. This conformation could impact their role in membrane translocation and thus has important implications for the design of future drug delivery vehicles.