Diffusion of water and sodium counter-ions in nanopores of aβ-lactoglobulin crystal: a molecular dynamics study

Abstract

The dynamics of water and sodium counter-ions(Na+)in a C2221 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. Theeffect of the fluctuation of the protein atoms on the motion of water and sodium ions isstudied by comparing simulations in a rigid and in a flexible lattice. The electrostaticinteractions of sodium ions with the positively charged LYS residues inside the crystalchannels significantly influence the ionic motion. According to our results, water moleculesclose to the protein surface undergo an anomalous diffusive motion. On the other hand, themotion of water molecules further away from the protein surface is normal diffusive.Protein fluctuations affect the diffusion constant of water, which increases from0.646 ± 0.108 to0.887 ± 0.41 nm2 ns−1, when protein fluctuations are taken into account. The pore size (0.63–1.05 nm) and thewater diffusivities are in good agreement with previous experimental results. The dynamicsof sodium ions is disordered. LYS residues inside the pore are the main obstacles to themotion of sodium ions. However, the simulation time is still too short for providing aprecise description of anomalous diffusion of sodium ions. The results are not only ofinterest for studying ion and water transport through biological nanopores, butmay also elucidate water–protein and ion–protein interactions in protein crystals.