The effect of hydration and dynamics on the mass density of single proteins

Abstract

The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses molecular dynamics simulations to quantify the volume of solvent excluded by a protein. Applied to a dataset of 260 soluble proteins, this yields an average density of 1.296 ± 0.001 g cm−3, notably lower than the widely cited value of 1.35 g cm−3. Contrary to previous suggestions, we find no correlation between protein density and molecular weight. We instead find correlations with residue composition, particularly with hydrophobic amino acid content. Using these correlations, we train a regressor capable of accurately predicting protein density from sequence-derived features alone. Examining the effect of incorporating water molecules on the measured density, we find that water molecules buried in internal cavities have a negligible effect, whereas those at the surface have a profound impact. Furthermore, by calculating the density of a titin domain and of the Bovine Pancreatic Trypsin over molecular dynamics trajectories, we show that individual proteins can occupy states with close but distinguishable densities. Finally, we analyze the density of water in the vicinity of proteins, showing that the first two hydration shells exhibit higher density than bulk water. When included in cumulative density calculations, these hydration layers contribute to a net increase in local solvent density. Overall, we find that proteins are less dense than previously reported, which is offset by their ability to induce a higher density of water in their vicinity.