Coarse-Grained Modelling of Protein Adsorption

The adsorption of proteins is a very common phenomenon, happening almost always when a protein solution comes into contact with a solid. However, it is far from always clear what the results of adsorption will be in terms of adsorbed amount, protein orientation, and protein conformation. In this work, the adsorption of two proteins – histatin 5 and fibrinogen – has been studied using coarse-grained Monte Carlo simulations and, in case of histatin 5, ellipsometry. Histatin 5 is a short (24 residues long), cationic protein present in the saliva of higher primates. Its main function is that it kills the fungus Candida albicans. Fibrinogen is a 340 kDa rod-like protein that is abundant in the blood of vertebrates. It has an important role in blood clotting. While histatin 5 is an intrinsically disordered protein, fibrinogen is mainly ordered with two ~400 amino acid residues long disordered appendages. This difference made us use two different models for the proteins– one for histatin 5 and the disordered fibrinogen fragments, and another for the main body of fibrinogen. Whereas the disordered proteins were modelled as beads on a necklace, the fibrinogen main body was modelled as a completely rigid body based on the crystal structure. The surface that the proteins were adsorbed on was a hydrophilic silica surface – modelled in the simulations as completely flat with (most of the time) a uniform, smeared charge.The main results for histatin 5 are the following: (i) the adsorbed amount of histatin 5 changes with ionic strength – but the trends are different depending on pH, (ii) the electrostatic interactions between charged groups are not enough to account for the experimentally observed adsorption of histatin 5 to silica surfaces, (iii) the coarse-grained model used in these studies cannot explain the experimentally observed pH-dependence of the adsorbed amount as a function of ionic strength, (iv) a library of only a few structures (with different weights) represent well the conformational ensemble of histatin 5, and (v) simulations suggest that the amount of secondary structure motifs of histatin 5 increases somewhat upon adsorption.The main results for fibrinogen are the following: (i) the disordered appendages make an important contribution to the adsorption free energy, (ii) the side of the end of the fibrinogen rod adsorbs in a similar manner regardless of surface curvature, meaning that the protein protrudes further into solution the higher the surface curvature, and (iii) we hypothesise that this difference in protrusion can account for the fact that adsorbed fibrinogen increases adhesion of the bacterium S. epidermidis on smooth surfaces while decreasing it on nanostructured surfaces

Adsorption of Fibrinogen on Silica Surfaces-The Effect of Attached Nanoparticles

When a biomaterial is inserted into the body, proteins rapidly adsorb onto its surface, creating a conditioning protein film that functions as a link between the implant and adhering cells. Depending on the nano-roughness of the surface, proteins will adsorb in different amounts, with different conformations and orientations, possibly affecting the subsequent attachment of cells to the surface. Thus, modifications of the surface nanotopography of an implant may prevent biomaterial-associated infections. Fibrinogen is of particular importance since it contains adhesion epitopes that are recognized by both eukaryotic and prokaryotic cells, and can therefore influence the adhesion of bacteria. The aim of this study was to model adsorption of fibrinogen to smooth or nanostructured silica surfaces in an attempt to further understand how surface nanotopography may affect the orientation of the adsorbed fibrinogen molecule. We used a coarse-grained model, where the main body of fibrinogen (visible in the crystal structure) was modeled as rigid and the flexible α C-chains (not visible in the crystal structure) were modeled as completely disordered. We found that the elongated fibrinogen molecule preferably adsorbs in such a way that it protrudes further into solution on a nanostructured surface compared to a flat one. This implicates that the orientation on the flat surface increases its bio-availability

Density fluctuations of hard-sphere fluids in narrow confinement

Spatial confinement induces microscopic ordering of fluids, which in turn alters many of their dynamic and thermodynamic properties. However, the isothermal compressibility has hitherto been largely overlooked in the literature, despite its obvious connection to the underlying microscopic structure and density fluctuations in confined geometries. Here, we address this issue by probing density profiles and structure factors of hard- sphere fluids in various narrow slits, using x-ray scattering from colloid-filled nanofluidic containers and integral-equation-based statistical mechanics at the level of pair distributions for inhomogeneous fluids. Most importantly, we demonstrate that density fluctuations and isothermal compressibilities in confined fluids can be obtained experimentally from the long-wavelength limit of the structure factor, providing a formally exact and experimentally accessible connection between microscopic structure and macroscopic, thermodynamic properties. Our approach will thus, for example, allow direct experimental verification of theoretically predicted enhanced density fluctuations in liquids near solvophobic interfaces

Making sense of adsorption : Attempting to explain the adsorption of histatin 5 with models, metaphors, and machines

This thesis summarises two studies in which the main purpose was to find out how and why the amount of the protein histatin 5 that adsorbs to negatively charged surfaces changes with pH and ionic strength. Histatin 5 is an intrinsically disordered saliva protein, and in the oral environment it adsorbs to tooth enamel. The approach here is to simplify the biological system by using an aqueous buffer solution instead of saliva, and a silica surface to represent the tooth enamel. Ellipsometry measurements were performed in order to answer the question of how the adsorbed amount changes with pH and ionic strength. Coarse-grained Monte Carlo simulations were used to investigate the molecular mechanisms behind the adsorption of histatin 5 and try to elucidate why the experiments give certain trends. The obtained results could have implications for the understanding of the role of histatin 5 in the oral environment, as well as for fundamental understanding of the adsorption of flexible proteins or polyelectrolytes.The main take-home messages are the following: (i) the adsorbed amount of histatin 5 changes with ionic strength – but the trends are different depending on the pH of the solution, (ii) the change in surface charge with pH and ionic strength can strongly affect the adsorbed amount, (iii) the electrostatic interactions between charged groups are not enough to account for the experimentally observed adsorption of histatin 5 to silica surfaces, and (iv) the coarse-grained model used in these studies cannot explain the experimentally observed pH-dependence of the adsorbed amount as a function of ionic strength. However, the simulations cast light on the balance between the electrostatic attraction between the protein and the surface and the electrostatic repulsion between adsorbed proteins, the deficiencies of the Langmuir isotherm, and the implications of protein charge regulation for adsorption

Adsorption of polyelectrolyte-like proteins to silica surfaces and the impact of pH on the response to ionic strength. A Monte Carlo simulation and ellipsometry study

Hypothesis The adsorbed amount of the polyelectrolyte-like protein histatin 5 on a silica surface depends on the pH and the ionic strength of the solution. Interestingly, an increase in ionic strength affects the adsorbed amount differently depending on the pH of the solution, as shown by ellipsometry measurements (Hyltegren, 2016). We have tested the hypothesis that the same (qualitative) trends can be found also from a coarse-grained model that takes all charge–charge interactions into account within the frameworks of Gouy–Chapman and Debye–Hückel theories. Experiments Using the same coarse-grained model as in our previous Monte Carlo study of single protein adsorption (Hyltegren, 2016), simulations of systems with many histatin 5 molecules were performed and then compared with ellipsometry measurements. The strength of the short-ranged attractive interaction between the protein and the surface was varied. Findings The coarse-grained model does not qualitatively reproduce the pH-dependence of the experimentally observed trends in adsorbed amount as a function of ionic strength. However, the simulations cast light on the balance between electrostatic attraction between protein and surface and electrostatic repulsion between adsorbed proteins, the deficiencies of the Langmuir isotherm, and the implications of protein charge regulation in concentrated systems

Adsorption of the intrinsically disordered saliva protein histatin 5 to silica surfaces. A Monte Carlo simulation and ellipsometry study.

The adsorption of histatin 5 to hydrophilic silica surfaces is governed by electrostatic attractive forces between the positive protein and the negative surface. Hence pH and ionic strength control the adsorbed amount, which can be described by coarse-grained Monte Carlo simulations accounting for electrostatic forces and charge regulation of the protein

Integrating All-Atom and Coarse-Grained Simulations - Toward Understanding of IDPs at Surfaces

We present a scheme for transferring conformational degrees of freedom from all-atom (AA) simulations of an intrinsically disordered protein (IDP) to coarse-grained (CG) Monte Carlo (MC) simulations using conformational swap moves. AA simulations of a single histatin 5 peptide in water were used to obtain a structural ensemble, which is reweighted in a CGMC simulation in the presence of a negatively charged surface. For efficient sampling, the AA trajectory was condensed using two approaches: RMSD clustering (based on the root-mean-square difference in atom positions) and a "nalve" truncation, where only every 100th frame of the trajectory was included in the library. The results show that even libraries with few structures well reproduce the radius of gyration and interaction free energy as functions of the distance from the surface. We further observe that the surface slightly promotes the secondary structure of histatin 5 and more so if using explicit surface charges rather than smeared charges