Proteins and nucleic acids evolved in the aqueous environment, and water
is therefore deeply interrelated with both biomolecular structure and function.
The first layer of water molecules around the biomolecular surface - the
hydration shell - has properties different from the bulk water [1]. The
dynamics of these water molecules is significantly reduced, and the shell
mostly consists of ordered (localized) water molecules. However, the first
shell water molecules do not have an ice-like structural properties. These
ordered water molecules play significant role in recognition and binding of
ligands.
In our work, we utilize crystallographic data to compile the average hydration
patterns around biomolecules. Firstly, we investigated hydration of DNA
building blocks [2, 3], and later hydration of amino acids in proteins as a
function of their rotameric state and the secondary structure [4, 5]. Recently,
we analyzed hydration of DNA dinucleotides as a function of their conformation
and sequence [6]. Here, we present the overview of these results as well as the
methodology we used to obtain the data and the potential application of the
results.
[1] Biedermannová L. & Schneider B.: Hydration of
proteins and nucleic acids: Advances in experiment and theory. A review.
Biochimica et Biophysica Acta - General Subjects 1860: 1821-1835 (2016).
[2] Schneider B. & Berman H.M.: Hydration of the DNA Bases Is Local.
Biophysical J. 69: 2661-2669 (1995).
[3] Schneider B., Patel K. & Berman H.M.: Hydration of the Phosphate Group
in Double-Helical DNA. Biophysical J. 75: 2422-2434 (1998).
[4] Biedermannová L. & Schneider B.: Structure of the ordered hydration of
amino acids in proteins: analysis of crystal structures.
Acta Crystallographica D71: 2192-2202 (2015).
[5] Černý J., Schneider B. & Biedermannová L.: WatAA: Atlas of Protein
Hydration. Exploring synergies between data mining and ab initio calculations.
Phys. Chem. Chem. Phys. 19, 17094 (2017).
[6] Biedermannová L. et al., to be published (2020).