Hydrophilicity of proteins and DNA

Abstract

A computational method (PROBIS) is described which can be used to quantify and visualise the hydrophilicity of biomacromolecules. Analysis of oligopeptides shows that an isolated betastrand is nearly six times more hydrophilic than an alpha-helix. For globular proteins only about 40% of the surface can hydrogen bond to solvent water. The substrate binding sites of protease active sites are found to be very hydrophilic, providing a continuous hydrogen bonded channel for substrate binding and transport. A study of DNA shows the A-conformer to be more hydrophilic than the B-form and that GC base pairs are more hydrophilic than AT base pairs. Poly(dA)·poly(dT) in the B-form shows a hydrophilic ribbon running the length of the minor groove. Poly(dG)·poly(dC) in B-DNA shows an additional hydrophilic ribbon in the major groove which may play a role in inducing the B to A transition. The minor groove of B- and the major groove of A-DNA are shown to be able to hydrogen bond strongly to water along the length of the molecule. © 1990.