Anisotropic Protein Interactions in Salt Solutions and at Interfaces: Coarse Grained Modeling

Anisotropic protein interactions have a strong orientation dependence resulting from an uneven distribution of charged and hydrophobic residues on the protein surface. They play an important role in protein behaviors such as protein association, surface adsorption and phase separation. In this thesis, we have studied the effect of anisotropic interactions on the behavior of various proteins mainly by focusing on electrostatic interactions. We have developed coarse grained models, specific to each system by considering their essential details and used Metropolis Monte Carlo method to simulate protein behaviors in salt solutions and at charged interfaces. We show that anisotropic dipolar interactions may overcome the net charge repulsion between similarly charged proteins and favor the protein association. The strong directionality of these interactions may reinforce specific protein orientations, required for protein activity. Note that hydrophobic anisotropy can also compete with the directionality of the dipolar interactions and may force the proteins into less favorable dipole orientations. We also show that the charge regulation effects and the specific Hofmeister ion binding can significantly alter the charge distribution of proteins, and thus they should not be overlooked in the studies of protein electrostatics. Our results indicate that to gain a comprehensive understanding of protein electrostatics, one needs to consider: (i) the higher order multipole interactions; (ii) the hydrophobic patchiness that can compete with the multipole interactions; (iii) the charge regulation effects; as well as (iv) the specific ion binding. The extent of these factors can roughly be estimated by examining the dipole moment, the locations of hydrophobic patches, the number of residues with acid dissociation constants around solution pH as well as the concentration of binding ions and the exposed area of their binding sites

Solution electrostatics beyond pH: a coarse grained approach to ion specific interactions between macromolecules

Oblivious to ion specificity, pH has been a key parameter for macromolecular solutions for little more than a century. We here widen the concept by describing the ionization of macromolecules not only via pH, but also pX where X are other binding species. Using binding constants, measured by NMR, of chloride and thiocyanate to amino acid motifs on g-crystallin, we calculate i) titration curves as a function of pH and pX and ii) estimate second virial coefficients using both approximate theory and computer simulations. In agreement with experiment, a Hofmeister reversal for protein-protein interactions is observed when crossing iso-electric conditions. Thiocyanate binding further leads to large charge fluctuations that may trigger intermolecular charge regulation interactions

Dimerization of Terminal Domains in Spiders Silk Proteins Is Controlled by Electrostatic Anisotropy and Modulated by Hydrophobic Patches

The well-tuned spinning technology from spiders has attracted many researchers with the promise of producing high-performance, biocompatible, and yet biodegradable fibers. So far, the intricate chemistry and rheology of spinning have eluded us. A breakthrough was achieved recently, when the 3D structures of the N and C terminal domains of spider dragline silk were resolved and their pH-induced dimerization was revealed. To understand the terminal domains' dimerization mechanisms, we developed a protein model based on the experimental structures that reproduces charge and hydrophobic anisotropy of the complex protein surfaces. Monte Carlo simulations were used to study the thermodynamic dimerization of the N-terminal domain as a function of pH and ionic strength. We show that the hydrophobic and electrostatic anisotropies of the N-terminal domain cooperate constructively in the association process. The dipolar attractions at pH 6 lead to weakly bound dimers by forcing an antiparallel monomer orientation, stabilized by hydrophobic locking at close separations. Elevated salt concentrations reduce the thermodynamic dimerization constant due to screened electrostatic dipolar attraction. Moreover, the mutations on ionizable residues reveal a free energy of binding, proportional to the dipole moment of the mutants. It has previously been shown that dimers, formed at pH 6, completely dissociate at pH 7, which is thought to be due to altered protein charges. In contrast, our study indicates that the pH increase has no influence on the charge distribution of the N-terminal domain. Instead, the pH-induced dissociation is due to an adapted, loose conformation at pH 7, which significantly hampers both electrostatic and hydrophobic attractive interactions

Adsorption of beta-casein to hydrophilic silica surfaces. Effect of pH and electrolyte

Adsorption of beta-casein to hydrophilic silica surfaces has been studied as an effect of pH and electrolyte, in the latter concentration, valency, and specificity (calcium or magnesium) have been considered. The used protein concentration has been an order of magnitude below the critical aggregation concentration, which implies that the protein is in monomeric form. By varying the salt concentration, the pH, and the concentration of divalent ions as calcium and magnesium, it is clearly shown that electrostatic interactions are of importance for adsorption of beta-casein to silica surfaces and tunes the adsorbed amount and saturation of the surface. Our results show that there is counterbalance between: (i) electrostatic repulsion between the surface and the protein, (ii) electrostatic attraction between positively charged amino acids in the protein and the surface, and (iii) electrostatic repulsion and excluded volumes between adsorbed proteins at the surface, and that the positively charged amino acids serve as anchoring points. (C) 2013 Elsevier Ltd. All rights reserved

Anisotropic Interactions in Protein Mixtures,: Self Assembly and Phase Behavior in Aqueous Solution

Recent experimental studies show that oppositely charged proteins can self-assemble to form seemingly stable microspheres in aqueous salt solutions. We here use parallel tempering Monte Carlo simulations to study protein phase separation of lysozyme/alpha-lactalbumin mixtures and show that anisotropic electrostatic interactions are important for driving protein self-assembly. In both dilute and concentrated protein phases, the proteins strongly align according to their charge distribution. While this alignment can be greatly diminished by a single point mutation, phase separation is completely suppressed when neglecting electrostatic anisotropy. The results highlight the importance of subtle electrostatic interactions even in crowded biomolecular environments where other short-ranged forces are often thought to dominate

Faunus - a flexible framework for Monte Carlo simulation

Faunus is a set of building blocks or statistical mechanical Lego' for constructing molecular simulation programs to study complex solutions, including proteins, polymers, salts, phospholipid membranes, surfaces and/or rigid macro-molecules. Current focus is on Metropolis Monte Carlo (MC) algorithms with support for anisotropic particles (multipolar, polarisable and sphero-cylindrical) and a flexible Hamiltonian. The design is inherently modular and it is trivial to extend functionality to cover new interaction potentials, geometries or moves. In this study, we present basic features, C++ design principles and review- selected applications. The latter includes splined pair potentials, two-dimensional parallel tempering of protein mixtures and MC swap moves for modelling ion-specific effects without ions

High Expression of Midkine in the Airways of Patients with Cystic Fibrosis.

Mutations in the CFTR gene result in impaired host defense during cystic fibrosis (CF), where Pseudomonas aeruginosa becomes a key pathogen. We investigated the expression pattern of the antibacterial growth factor midkine in CF and possible interference with its activity by the altered airway microenvironment. High midkine expression was found in CF lung tissue compared with controls, involving epithelium of the large and small airways, alveoli, and cells of the submucosa (i.e. neutrophils and mast cells). In CF sputum, midkine was present at 100-fold higher levels but was also subject to increased degradation, compared with midkine in sputum from healthy controls. Midkine had a bactericidal effect on P. aeruginosa but increasing salt concentrations and low pH impaired the activity. Molecular modeling suggested that the effects of salt and pH were due to electrostatic screening and a charge-neutralization of the membrane, respectively. Both neutrophil elastase and elastase of P. aeruginosa cleaved midkine to smaller fragments, resulting in impaired bactericidal activity. Thus, midkine is highly expressed in CF but its bactericidal properties may be impaired by the altered microenvironment as reflected by the in vitro conditions used in this study