Marie Skepö

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014, 10, 5113 - 5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment.

Adsorption of Unstructured Protein beta-Casein to Hydrophobic and Charged Surfaces

In this Monte Carlo simulation study we use mesoscopic modeling to show that β-casein, an unstructured milk protein, adsorbs to surfaces not only due to direct electrostatic and hydrophobic interactions but also due to structural rearrangement and charge regulation due to proton uptake and release. β-casein acts as an amphiphilic chameleon, changing properties according to the chemical environment, and binding is observed to both positively and negatively charged surfaces. The binding mechanisms, however, are fundamentally different. A detailed, per-residue-level analysis shows that the adsorption process is controlled by a few very specific regions of the protein and that these change dramatically with pH. Caseins, being the most abundant proteins in milk, are crucial for the properties of fermented dairy products, such as nutrition, texture, and viscosity, but may also influence adhesion to packaging materials. The latter leads to product losses of about 10%, leading to economical and environmental problems.

Structure of polyelectrolytes in 3 : 1 salt solutions

Polyion conformation and the distribution of small ions near the polyion have been investigated using Monte Carlo simulations. The systems of interest contained one polyion and its monovalent counterions, and variable amount of a 3:1 salt. With monovalent counterions only, the polyion is strongly extended. As salt is added, the polyion folds, and the most compact and spherical-like structure appears at a three-fold excess of the trivalent counterions. The polyion exerts a strong influence on the nearest-neighbor distance among the trivalent ions, an effect being relevant for energy transfer reactions.

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models

Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [ Henriques et al. J. Chem. Theory Comput. 2015 , 11 , 3420 - 3431 ], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.

Role of histidine for charge regulation of unstructured peptides at interfaces and in bulk

Histidine‐rich, unstructured peptides adsorb to charged interfaces such as mineral surfaces and microbial cell membranes. At a molecular level, we investigate the adsorption mechanism as a function of pH, salt, and multivalent ions showing that (1) proton charge fluctuations are—in contrast to the majority of proteins—optimal at neutral pH, promoting electrostatic interactions with anionic surfaces through charge regulation and (2) specific zinc(II)‐histidine binding competes with protons and ensures an unusually constant charge distribution over a broad pH interval. In turn, this further enhances surface adsorption. Our analysis is based on atomistic molecular dynamics simulations, coarse grained Metropolis Monte Carlo, and classical polymer density functional theory. This multiscale modeling provides a consistent picture in good agreement with experimental data on Histatin 5, an antimicrobial salivary peptide. Biological function is discussed and we suggest that charge regulation is a significant driving force for the remarkably robust activity of histidine‐rich antimicrobial peptides. Proteins 2014; 82:657–667.

Model simulations of the adsorption of statherin to solid surfaces: Effects of surface charge and hydrophobicity

The structural properties of the salivary protein statherin upon adsorption have been examined using a coarse-grained model and Monte Carlo simulation. A simple model system with focus on electrostatic interactions and short-ranged attractions among the uncharged amino acids has been used. To mimic hydrophobically modified surfaces, an extra short-ranged interaction was implemented between the amino acids and the surface. It has been shown that the adsorption and the thickness of the adsorbed layer are determined by (i) the affinity for the surface, i.e., denser layer with an extrashort-ranged potential, and (ii) the distribution of the charges along the chain. If all the amino acids have a high affinity for the surface, the protein adsorbs in a train conformation, if the surface is negatively charged the protein adsorbs in a tail-train conformation, whereas if the surface is positively charged the protein adsorbs in a loop conformation. The latter gives rise to a more confined adsorbed layer.

Coarse-grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS

Monte Carlo simulations and coarse‐grained modeling have been used to analyze Histatin 5, an unstructured short cationic salivary peptide known to have anticandidical properties. The calculated scattering functions have been compared with intensity curves and the distance distribution function P(r) obtained from small angle X‐ray scattering (SAXS), at both high and low salt concentrations. The aim was to achieve a molecular understanding and a physico‐chemical insight of the obtained SAXS results and to gain information of the conformational changes of Histatin 5 due to altering salt content, charge distribution, and net charge. From a modeling perspective, the accuracy of the electrostatic interactions are of special interest. The used coarse‐grained model was based on the primitive model in which charged hard spheres differing in charge and in size represent the ionic particles, and the solvent only enters the model through its relative permittivity. The Hamiltonian of the model comprises three different contributions: (i) excluded volumes, (ii) electrostatic, and (iii) van der Waals interactions. Even though the model can be considered as gross omitting all atomistic details, a great correspondence is obtained with the experimental results. Proteins 2016; 84:777–791.

Adsorption of the Flexible Salivary Proteins Statherin and PRP-1 to Negatively Charged Surfaces – A Monte Carlo Simulation and Ellipsometric Study

The structural properties of the salivary proteins, acidic proline rich PRP-1 and statherin, adsorbed onto negatively charged surfaces have been studied by Monte Carlo simulations and ellipsometry. It is shown that both proteins adsorb to negatively charged surfaces, although their net charges are negative. Experimentally, an initial fast mass-controlled film build-up was detected for both proteins, and plateaus were reached within 10 min. The isotherm shape and the adsorbed amounts were similar for PRP-1 to hydrophilic and hydrophobic surfaces, while statherin adsorbs to a greater extent to the hydrophobic surface. These results could be explained from the simulation results by considering the proteins as diblock polyampholytes. It has also been shown that the adsorption of PRP-1 to a negatively charged surface may be purely electrostatically driven, while pure electrostatic interaction is not sufficient to drive adsorption of statherin, i.e., an extra short-ranged attractive interaction is necessary to account for the experimental observations.

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

HYPOTHESIS 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. EXPERIMENTS The amount of histatin 5 adsorbed to hydrophilic silica surfaces at different pH and ionic strengths was measured using null ellipsometry. The results were compared with coarse-grained Monte Carlo simulations of a single histatin 5 molecule and a surface with a fixed, smeared charge set according to experimental values for silica. The Langmuir isotherm was used to calculate the surface coverage from the simulation results. The effect of charge regulation of the protein was investigated. FINDINGS Even though electrostatic attractive forces are important for the investigated system, a non-electrostatic short-ranged attraction with a strength of about 2.9kBT per amino acid was needed in the simulations to get surface coverages close to experimental values. The importance of electrostatics increases with increasing pH. Charge regulation of the protein affected the results from the simulations only at high surface charge and low ionic strength.

Confined polyelectrolytes: The complexity of a simple system.

The interaction between polyelectrolytes and counterions in confined situations and the mutual relationship between chain conformation and ion condensation is an important issue in several areas. In the biological field, it assumes particular relevance in the understanding of the packaging of nucleic acids, which is crucial in the design of gene delivery systems. In this work, a simple coarse‐grained model is used to assess the cooperativity between conformational change and ion condensation in spherically confined backbones, with capsides permeable to the counterions. It is seen that the variation on the degree of condensation depends on counterion valence. For monovalent counterions, the degree of condensation passes through a minimum before increasing as the confining space diminishes. In contrast, for trivalent ions, the overall tendency is to decrease the degree of condensation as the confinement space also decreases. Most of the particles reside close to the spherical wall, even for systems in which the density is higher closer to the cavity center. This effect is more pronounced, when monovalent counterions are present. Additionally, there are clear variations in the charge along the concentric layers that cannot be totally ascribed to polyelectrolyte behavior, as shown by decoupling the chain into monomers. If both chain and counterions are confined, the formation of a counterion rich region immediately before the wall is observed. Spool and doughnut‐like structures are formed for stiff chains, within a nontrivial evolution with increasing confinement.