Hydration of amino acid residues in proteins: what can we learn from data mining?

Lada Biedermannová, Jiří Černý, Bohdan Schneider

Inst. of Biotechnology, Laboratory of Biomolecular Recognition,
Vídeňská 1083, 142 20 Prague, Czech Republic
tel: (+420) 241 06 36 24; email: lada.biedermannova@ibt.cas.cz

It is nowadays accepted that water is not only a passive medium, but a key determinant of protein structure, dynamics and function, and that protein-water interactions govern various processes, including protein folding, enzymatic catalysis, and molecular recognition. Water does not simply fill up the available space around proteins, but occupies specific sites and forms localized clusters, determined by its hydrogen-bonding capabilities. Distribution of water around amino acid residues in proteins has been the subject of several studies, but only on a small number of crystal structures [1], or without consideration of the amino acid conformation, i.e. secondary structure and side-chain rotameric state [2].

We therefore decided to study the hydration patterns for all twenty standard amino acids in their main conformational states (rotamers), using large number of high-resolution protein crystal structures. Specifically, we used a set of 2,818 PDB structures of monomeric proteins with resolution better than 1.8 Å, maximum R-factor value of 0.22 and mutual sequence identity of the protein chains of 50% or less. The contacts of each amino acid residue with waters within 3.2 Å were detected. Residue conformations were clustered separately in each class defined by residue type, secondary structure (alpha helix/beta sheet) and chi1 rotameric state (as gauche+, gauche-, or trans) using quality threshold algorithm. Clusters of residues with the associated water molecules were then subjected to the method of density representation [3] in order to identify the preferred location of hydration sites. Briefly, atom positions of water oxygens were transformed using a Fourier transform technique to the corresponding electron densities. Density peaks of water molecules were then detected and positions of hydration sites, their occupancies, and B-factors refined using standard crystallographic procedures.

The result of our study is a detailed atlas of the structure of protein hydration, containing the hydration sites, i.e. most populated positions of waters around each amino acid residue type in each of its main conformational states. Analysis of these hydration sites revealed frequent occurrence of positions where water interacts simultaneously with the side-chain and main-chain of the amino acid residue. By comparing the hydration of various conformers we also observed strong dependence of the positions of hydration sites on the amino acid conformation. Thus, our analysis revealed the spatial distribution of the preferred water positions in the first hydration layer of proteins. The hydrated amino acid rotamers obtained from our study can be used in many areas of structural biology, from molecular replacement and crystallographic refinement, to the improvement of accuracy of ab initio protein structure prediction methods.

The study was conducted at the Institute of Biotechnology AS CR (RVO:86652036) and was supported by project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF and by the Czech Science Foundation (GA CR) grant no. P205/12/P729.

1.         N. Thanki, J. M. Thornton, J. M. Goodfellow, J. Mol. Biol. 1988, 202, 637.

2.         D. Matsuoka and M. Nakasako, J. Phys. Chem. B 2009, 113, 11274.

3.         B. Schneider, H. M. Berman, Biophys. J. 1995, 69, 2661.