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Molecular-level computer simulations of peptide aggregation, translocation, and protonation at and in biomembranes are impeded by the large time and length scales involved. We present a computationally efficient, coarse-grained, and solvent-free model for the interaction between lipid bilayers and peptides. The model combines an accurate description of mechanical membrane properties with a new granular representation of the dielectric mismatch between lipids and the aqueous phase. All-atom force fields can be easily mapped onto the coarse-grained model, and parameters for coarse-grained monopeptides accurately extrapolate to membrane permeation free energies for the corresponding dipeptides and tripeptides. Acid-base equilibria of titratable amino acid residues are further studied using a constant-pH ensemble, capturing protonation state changes upon membrane translocation. Important differences between histidine, lysine, and arginine are observed, which are in good agreement with experimental observations.

Poly(vinyl alcohol) (PVA) is an amphiphilic macromolecule with surfactant activity. The peculiar behavior of this polymer at the water-air interface is at the basis of its use as material for hydrated microdevices, films, and nanofibers. This work aims to investigate the behavior of PVA and water within the surface domain of highly diluted aqueous solutions by means of atomistic molecular dynamics simulations. Monodisperse atactic oligomers of 30 residues were distributed within water slabs in a vacuum box and allowed to diffuse toward the surface. After equilibration, structural features and dynamical properties of polymer chains and water in the interfacial domains were analyzed as a function of PVA surface concentration at 293 K. Surface pressure values obtained from simulations are in agreement with experimental values at corresponding polymer specific surface areas. In the explored concentration range of 6-34 μmol of residues/m(2), the chains display a transition between two states. At lower surface concentrations, elongated, quite rigid structures are adsorbed on the surface, whereas partially submerged globular aggregates, locally covered by thin water layers, are formed at higher surface concentrations. At PVA concentrations higher than about 20 μmol of residues/m(2), the percolation of chain aggregates over the interface plane produces a surface-confined polymer network with stable pores filled by water molecules. A substantial slowing of polymer and water dynamics in the interfacial domains is highlighted by the mean squared displacement time behavior of terminal residues and the interaction time of PVA-water hydrogen bonding. The diffusion coefficient of water and lifetime of hydrogen bonds between solvent molecules are halved and doubled, respectively, at the interface with the highest polymer concentration. The attenuation of water and polymer mobility concur to stabilize PVA hydrated networks in contact with air.

Molecular dynamics (MD) simulations of a poly(vinyl alcohol), PVA, oligomer in very diluted aqueous solution have been carried out, at the 2-fold aim to investigate structural and dynamical features of this system and to comparatively test the robustness of G45A3 and G45A4 GROMOS force fields in modeling PVA in aqueous environment. An atactic PVA chain of 30 repeating units in water at concentration of 3% (w/w) has been simulated at 293, 303, and 323 K. The trajectory analysis has focused on the temperature influence on chain size, conformational properties and intramolecular hydrogen bonding of PVA. The PVA-water interaction and the polymer induced modifications of water properties have been also investigated. Simulation results have been compared with available experimental data on PVA aqueous solutions, in order to evaluate the reliability of these force fields in the MD simulation of PVA-based systems in aqueous environment. Findings obtained from the simulations with the G45A4 force field have shown a better agreement with experimental results and have highlighted peculiar structural and dynamical characteristics of PVA in dilute aqueous solution. In particular, the simulation has shown a heterogeneity in the overall chain structure, not affected by temperature, and the absence of intrachain hydrogen bonds between nonadjacent residues. The trajectory analysis has revealed that the polymer influence on water structure and dynamics involves about six water molecules per PVA residue.