Computer simulations and neutron reflectivity of proteins at interfaces

Applications of neutron reflectometry in biology

Over the last 10 years, neutron reflectometry (NR) has emerged as a powerful technique for the investigation of biologically relevant thin films. The great advantage of NR with respect to many other surface-sensitive techniques is its sub-nanometer resolution that enables structural characterizations at the molecular level. In the case of bio-relevant samples, NR is non-destructive and can be used to probe thin films at buried interfaces or enclosed in bulky sample environment equipment. Moreover, recent advances in biomolecular deutera-tion enabled new labeling strategies to highlight certain structural features and to resolve with better accuracy the location of chemically similar molecules within a thin film.

In this chapter I will describe some applications of NR to bio-relevant samples and discuss some of the data analysis approaches available for biological thin films. In particular, examples on the structural characterization of biomembranes, protein films and protein-lipid interactions will be described.

Understanding protein adsorption phenomena at solid surfaces

Protein adsorption at solid surfaces plays a key role in many natural processes and has therefore promoted a widespread interest in many research areas. Despite considerable progress in this field there are still widely differing and even contradictive opinions on how to explain the frequently observed phenomena such as structural rearrangements, cooperative adsorption, overshooting adsorption kinetics, or protein aggregation. In this review recent achievements and new perspectives on protein adsorption processes are comprehensively discussed. The main focus is put on commonly postulated mechanistic aspects and their translation into mathematical concepts and model descriptions. Relevant experimental and computational strategies to practically approach the field of protein adsorption mechanisms and their impact on current successes are outlined.

Detecting cryptic epitopes created by nanoparticles

As potential applications of nanotechnology and nanoparticles increase, so too does the likelihood of human exposure to nanoparticles. Because of their small size, nanoparticles are easily taken up into cells (by receptor-mediated endocytosis), whereupon they have essentially free access to all cellular compartments. Similarly to macroscopic biomaterial surfaces (that is, implants), nanoparticles become coated with a layer of adsorbed proteins immediately upon contact with physiological solutions (unless special efforts are taken to prevent this). The process of adsorption often results in conformational changes of the adsorbed protein, which may be affected by the larger curvature of nanoparticles compared with implant surfaces. Protein adsorption may result in the exposure at the surface of amino acid residues that are normally buried in the core of the native protein, which are recognized by the cells as "cryptic epitopes." These cryptic epitopes may trigger inappropriate cellular signaling events (as opposed to being rejected by the cells as foreign bodies). However, identification of such surface-exposed epitopes is nontrivial, and the molecular nature of the adsorbed proteins should be investigated using biological and physical science methods in parallel with systems biology studies of the induced alterations in cell signaling.

Effect of Cosolvents on the Adsorption of Peptides at the Solid−Liquid Interface

The adsorption of a peptide at solid surfaces is the result of a complex interplay of interactions between the peptide, solvent, and surface. In this work, Monte Carlo simulations were performed to evaluate the effect of the solvent hydrogen bonding ability on the adsorption of the peptide ASP(1)-ASP(2)-ILE(3)-ILE(4)-ASP(5)-ASP(6)-ILE(7)-ILE(8) at a charged surface consisting of CH(2) atoms with a fixed lattice arrangement. Various water-alcohol mixtures were used as solvent because alcohols are known to alter the dielectric constant, hydrophobicity, and hydrogen bonding capacity of water. Solvent-solvent, solvent-surface, solvent-peptide, and peptide-surface interactions were studied independently and correlated with the observed peptide behavior at the solvent-surface interface. We concluded that the behavior (and orientation) of the peptide at the surface is directly related to changes in water-water hydrogen bonding properties in water-alcohol mixtures. In the presence of increasing concentrations of methanol, the strength of solvent-peptide and solvent-surface interactions was reduced, and as a result, a stronger interaction between the peptide and the surface was observed. Stronger solvent-peptide and solvent-surface interactions were responsible for a weaker interaction of the peptide with the surface in the presence of increasing concentrations of glycerol. These results suggest that by changing solvent conditions it is possible to finely tune the orientation of a macromolecule at solid/liquid interfaces.

Adsorption of comb copolymers on weakly attractive solid surfaces

In this work continuum and lattice Monte Carlo simulation methods are used to study the adsorption of linear and comb polymers on flat surfaces. Selected polymer segments, located at the tips of the side chains in comb polymers or equally spaced along the linear polymers, are attracted to each other and to the surface via square-well potentials. The rest of the polymer segments are modeled as tangent hard spheres in the continuum model and as self-avoiding random walks in the lattice model. Results are presented in terms of segment-density profiles, distribution functions, and radii of gyration of the adsorbed polymers. At infinite dilution the presence of short side chains promotes the adsorption of polymers favoring both a decrease in the depletion-layer thickness and a spreading of the polymer molecule on the surface. The presence of long side chains favors the adsorption of polymers on the surface, but does not permit the spreading of the polymers. At finite concentration linear polymers and comb polymers with long side chains readily adsorb on the solid surface, while comb polymers with short side chains are unlikely to adsorb. The simple models of comb copolymers with short side chains used here show properties similar to those of associating polymers and of globular proteins in aqueous solutions, and can be used as a first approximation to investigate the mechanism of adsorption of proteins onto hydrophobic surfaces.

A Combined Atomic Force Microscopy and Molecular Dynamics Simulation Study on a Plastocyanin Mutant Chemisorbed on a Gold Surface

A mutant of copper plastocyanin, covalently bound to an Au (111) surface through an engineered disulfide bridge, was investigated in aqueous medium by atomic force microscopy (AFM) and molecular dynamics (MD) simulations. Tapping-mode AFM images revealed adsorption of single molecules which are homogeneously distributed over the substrate and strongly bound to gold and display uniform lateral size. A statistical analysis of the height of the macromolecules on the gold substrate evidenced a distribution around a mean value consistent with that expected from the crystallographic data and with a relatively large standard deviation. A 10-ns classical MD simulation of mutated plastocyanin, hydrated by a layer of water, covalently bound to a gold surface by one or two sulfur atoms, was performed. The simulations indicate that the bound protein retains, in both cases, its overall tertiary structure during the dynamic evolution. Moreover, the macro-molecule can assume different orientations with respect to the gold substrate, which give rise to a distribution of heights on the gold substrate. Experimental and MD simulation results are compared and discussed in connection with the topological and dynamical properties of the protein system.