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.

High expression of midkine in the airways of patients with cystic fibrosis.

Mutations in the cystic fibrosis transmembrane conductance regulator (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 (MK) in CF and the possible interference with its activity by the altered airway microenvironment. High MK expression was found in CF lung tissue compared with control samples, involving epithelia of the large and small airways, alveoli, and cells of the submucosa (i.e., neutrophils and mast cells). In CF sputum, MK was present at 100-fold higher levels, but was also subject to increased degradation, compared with MK in sputum from healthy control subjects. MK exerted a bactericidal effect on P. aeruginosa, but increasing salt concentrations and low pH impaired this activity. Molecular modeling suggested that the effects of salt and pH were attributable to electrostatic screening and a charge-neutralization of the membrane, respectively. Both the neutrophil elastase and elastase of P. aeruginosa cleaved MK to smaller fragments, resulting in impaired bactericidal activity. Thus, MK 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.

Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo.

Hybrid simulation procedures which combine molecular dynamics with Monte Carlo are attracting increasing attention as tools for improving the sampling efficiency in molecular simulations. In particular, encouraging results have been reported for nonequilibrium candidate protocols, in which a Monte Carlo move is applied gradually, and interleaved with a process that equilibrates the remaining degrees of freedom. Although initial studies have uncovered a substantial potential of the method, its practical applicability for sampling structural transitions in macromolecules remains incompletely understood. Here, we address this issue by systematically investigating the efficiency of the nonequilibrium candidate Monte Carlo on the sampling of rotameric distributions of two peptide systems at atomistic resolution both in vacuum and explicit solvent. The studied systems allow us to directly probe the efficiency with which a single or a few slow degrees of freedom can be driven between well-separated free-energy minima and to explore the sensitivity of the method toward the involved free parameters. In line with results on other systems, our study suggests that order-of-magnitude gains can be obtained in certain scenarios but also identifies challenges that arise when applying the procedure in explicit solvent.

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.

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 y-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.

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/α-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.