Paul A. Mulheran

Mechanism of hen egg white lysozyme adsorption on a charged solid surface

The mechanism of hen egg white lysozyme (HEWL) adsorption on a negatively charged, hydrophilic surface has been studied using atomistic molecular dynamics (MD) simulation. Sixteen 90 ns trajectories provide adequate data to allow a detailed description of the adsorption process to be formulated. Two distinct adsorption sites have been identified. The main one is located on the N,C-terminal protein face and comprises Arg128 (the crucial one), supplemented by Arg125, Arg5, and Lys1; the minor one is used accidentally and contains only Arg68. Adsorption of this protein is driven by electrostatics, where the orientation of the protein dipole moment defines the direction of protein movement. The diffusion range on the surface depends on protein side-chain penetration through the surface water layers. This is facilitated by the long-range electric field of the charged surface, which can align polar side chains to be perpendicular to the surface. A simulation of adsorption onto a neutral ionic surface shows no such surface water layer penetration. Therefore, protein flexibility is seen to be an important factor, and to adsorb the HEWL has to adjust its structure. Nevertheless, at a flat surface only a slight loss of α-helical content is required. The adsorbed HEWL molecule is oriented between side-on and end-on ways, where the angle between the protein long axis (which mostly approximates the dipole moment) and the surface varies between 45° and 90°. Simulations with targeted mutations confirm the picture that emerges from these studies. The active site is located on the opposite face to the main adsorption site; hence, the activity of the immobilized HEWL should not be affected by the surface interactions. Our results provide a detailed insight into the adsorption mechanism and protein mobility at the surface. This knowledge will aid the proper interpretation of experimental results and the design of new experiments and functional systems.

Molecular Dynamics Simulations of Hen Egg White Lysozyme Adsorption at a Charged Solid Surface

Hen egg white lysozyme (HEWL) adsorption on negatively charged, hydrophilic surfaces has been investigated using atomistic molecular dynamics. Analysis of six 20 ns trajectories performed at pH 7 and ionic strength 0.02 M (NaCl) reveals that conformational alterations are required for HEWL adsorption, and that upon adsorption the protein loses some alpha-helical content. Simulations for a few different initial orientations show that the HEWL protein adsorbs on a flat surface with an angle between the protein long axis and the surface of about 45 degrees . The main adsorption site is located on the N,C-terminal part of the HEWL surface; the major role is played by Lys1, Arg5, Arg14, and Arg128. Adsorption is not found with contrary orientations. Two additional 20 ns trajectories calculated with 0.5 M ionic strength suggest that the main force governing adsorption is electrostatic attraction between parts of the protein and the surface. A trajectory obtained for the protein situated inside a cubic box built from the charged surfaces shows that the adsorption pattern is different for flat and nonflat surfaces, and in particular, adsorption on the nonflat surface requires tertiary structure alterations and partial unfolding. The observed trends are consistent with both experimental and previous computational studies.

What governs protein adsorption and immobilization at a charged solid surface

The adsorption of hen egg white lysozyme at a model charged surface is studied using fully atomistic molecular dynamics simulations. The simulations are performed over a 90 ns time scale which is sufficient to observe rotational and translational steps in the adsorption process. Electrostatics is found to play a key role in guiding the protein to the favorable binding orientation with the N,C-terminal face against the substrate. However, full immobilization appears to only occur through the strong interaction of Arg128 with the surface, facilitated by the protein’s flexibility at the terminal face. Simulated mutation at this residue confirms its crucial role. This work demonstrates that electrostatics alone might not be sufficient to guide the development of material systems that exploit protein adsorption and immobilization.

Multiprotein Interactions during Surface Adsorption: a Molecular Dynamics Study of Lysozyme Aggregation at a Charged Solid Surface

Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein–protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein–protein and protein–surface), and gives an insight into processes to be considered in the development of new functionalized material systems.

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

The diffusion pathways of lysozyme adsorbed to a model charged ionic surface are studied using fully atomistic steered molecular dynamics simulation. The simulations start from existing protein adsorption trajectories, where it has been found that one particular residue, Arg128 at the N,C-terminal face, plays a crucial role in anchoring the lysozyme to the surface [Langmuir 2010 , 26 , 15954 - 15965]. We first investigate the desorption pathway for the protein by pulling the Arg128 side chain away from the surface in the normal direction, and its subsequent readsorption, before studying diffusion pathways by pulling the Arg128 side chain parallel to the surface. We find that the orientation of this side chain plays a decisive role in the diffusion process. Initially, it is oriented normal to the surface, aligning in the electrostatic field of the surface during the adsorption process, but after resorption it lies parallel to the surface, being unable to return to its original orientation due to geometric constraints arising from structured water layers at the surface. Diffusion from this alternative adsorption state has a lower energy barrier of ∼0.9 eV, associated with breaking hydrogen bonds along the pathway, in reasonable agreement with the barrier inferred from previous experimental observation of lysozyme surface clustering. These results show the importance of studying protein diffusion alongside adsorption to gain full insight into the formation of protein clusters and films, essential steps in the future development of functionalized surfaces.

Protein adsorption mechanisms on solid surfaces: lysozyme-on-mica

A methodology for discovering the mechanisms and dynamics of protein clustering on solid surfaces is reviewed and complemented by atomistic molecular dynamics (MD) simulations. In situ atomic force microscopy images of the early stages of protein film formation are quantitatively compared with Monte Carlo simulations, using cluster statistics to differentiate various growth models. We have studied lysozyme adsorption on mica as a model system, finding that all surface-supported clusters are mobile with diffusion constant inversely related to cluster size. Furthermore, our results suggest that protein monomers diffusing to the surface from solution only adhere to the bare surface with a finite probability. Fully atomistic MD simulations reveal that the lysozyme does indeed have a preferred orientation for binding to the surface, so that proteins with incorrect orientations move away from the surface rather than towards it. Agreement with experimental studies in the literature for the residues involved in the surface adsorption is found.

Surface and interstitial Ti diffusion at the rutile TiO2(110) surface

Diffusion of Ti through the TiO(2)(110) rutile surface plays a key role in the growth and reactivity of TiO(2). To understand the fundamental aspects of this important process, we present an analysis of the diffusion of Ti ad-species at the stoichiometric TiO(2)(110) surface using complementary computational methodologies of density functional theory corrected for on-site Coulomb interactions (DFT + U) and a charge equilibration (QEq) atomistic potential to identify minimum energy pathways. We find that diffusion of Ti from the surface to subsurface (and vice versa) follows an interstitialcy exchange mechanism, involving exchange of surface Ti with the 6-fold coordinated Ti below the bridging oxygen rows. Diffusion in the subsurface between layers also follows an interstitialcy mechanism. The diffusion of Ti is discussed in light of continued attempts to understand the re-oxidation of non-stoichiometric TiO(2)(110) surfaces.

Simulation of reconstructions of the polar ZnO(0001) surfaces

Surface reconstructions on the polar ZnO(0001) surface are investigated using empirical potential models. Several possible reconstructions based around triangular motifs are investigated. The quenching of the dipole moment in the material dominates the energetics of the surface patterns so that no one particular size of surface triangular island or pit is strongly favored. We employ Monte Carlo simulations to explore which patterns emerge from a high-temperature quench and during deposition of additional ZnO monolayers. The simulations show that a range of triangular islands and pits evolve in competition with one another. The surface patterns we discover are qualitatively similar to those observed experimentally.

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 proteins 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.

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.