Structural characteristics of hydration sites in lysozyme

A new method is presented for determining the hydration site of proteins, where the effect of structural fluctuations in both protein and hydration water is explicitly considered by using molecular dynamics simulation (MDS). The whole hydration sites (HS) of lysozyme are composed of 195 single HSs and 38 clustered ones (CHS), and divided into 231 external HSs (EHS) and 2 internal ones (IHS). The largest CHSs, 'Hg' and 'Lβ', are the IHSs having 2.54 and 1.35 mean internal hydration waters respectively. The largest EHS, 'Clft', is located in the cleft region. The real hydration structure of a CHS is an ensemble of multiple structures. The transition between two structures occurs through recombinations of some H-bonds. The number of the experimental X-ray crystal waters is nearly the same as that of the estimated MDS hydration waters for 70% of the HSs, but significantly different for the rest of HSs.

Graphical AbstractResearch Highlights► A new method is presented for defining and analyzing hydration sites of lysozyme. ► Effects of fluctuations in protein and hydration water are explicitly considered. ► Structural characteristics of major hydration sites are described based on MDS data. ► Diverse H-bond recombination between protein and water plays an essential role. ► Hydration waters from MDS and crystal waters from X-ray analysis are compared.