Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations

Abstract

We have analyzed a set of molecular dynamics (MD) trajectories of maltose in vacuum and water for solute imposed structuring on the solvent. To do this, we used a novel technique to calculate water probability densities to locate the areas in which the solvent is most populated in the maltose solution. We found that only the layer of water within the first maltose hydration shell has a probability density 50% and greater than that of bulk water. On investigating this water layer using Voronoi polyhedra (VP) analysis it was seen that only the waters adjacent to the hydrophobic (CH and CH2) groups are more structured than bulk water. We found that in a maltose solution of approximately 1.0 g/cm3 the solute does not disrupt the structure of the surrounding water beyond the first hydration shell. Next we performed a 700-ps MD simulation of a maltohexaose strand in a box of 4096 SPC/E waters. The water probability density calculations and the VP analysis of the maltohexaose solution show that the larger amylose repeat unit decreases the solvent configurational entropy of the water beyond the first hydration shell. Analysis of this trajectory reveals that the helical conformation of the maltohexaose strand is preserved via bridging intermolecular water hydrogen bonds, indicating that a single amylose helical turn in water is preserved by hydrophilic and not hydrophobic interactions. Using VP analysis we present a method to accurately determine the number of water molecules in the first hydration shell of dissolved solutes. In the case of maltose, there are 40 water molecules in this shell, while for maltohexaose the number is 98. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 445–456, 2001