Effect of unfolding on the thickness of the hydration layer of a protein

Abstract

Properties of water in the hydration layer around a protein is intimately correlated with its function. A knowledge of the thickness of the hydration layer is important to understand its role in guiding the foldingunfolding of the protein. We have performed atomistic molecular dynamics simulations of the folded native and a partially unfolded molten globule structure of the villin headpiece subdomain or HP-36 in aqueous solution to estimate the effect of unfolding on the thickness of hydration layer around different segments of the protein. In particular, several dynamic properties of water around different segments of the folded native and the unfolded structure have been calculated by varying the thickness of the hydration layers. It is found that unfolding of a segment of the protein is correlated with the dynamics of water around it, i.e., within the first hydration layer. The effect of unfolding on water properties has been found to diminish when water molecules present beyond the first hydration layer were included in the calculations.

Importance of Protein Conformational Motions and Electrostatic Anchoring Sites on the Dynamics and Hydrogen Bond Properties of Hydration Water

“…The calculations are carried out by considering those water molecules that are present within a distance of 5 Å from the surface of different segments of barstar (α-helices, β-sheet, and the interconnecting loops). This is consistent with earlier reports , where it is shown that the effects of a protein on water dynamical properties are primarily restricted to those that are present in its first hydration layer (within ∼5 Å). The results reported are based on calculations over the equilibrated trajectories as obtained from simulations S1, S2, and S3.…”