Statistical survey of the buried waters in the Protein Data Bank

Amino Acids
Oliviero Carugo

Abstract

The structures of buried water molecules were studied in an ensemble of high-quality and non-redundant protein crystal structures. Buried water molecules were clustered and classified in lake-like clusters, which are completely isolated from the bulk solvent, and bay-like clusters, which are in contact with the bulk solvent through a surface water molecule. Buried water molecules are extremely common: lake-like clusters are found in 89 % of the protein crystal structures and bay-like clusters in 93 %. Clusters with only one water molecule are much more common than larger clusters. Both cluster types incline to be surrounded by loop residues, and to a minor extent by residues in extended secondary structure. Helical residues on the contrary do not tend to surround clusters of buried water molecules. One buried water molecule is found every 30-50 amino acid residues, depending on the secondary structures that are more abundant in the protein. Both main- and side-chain atoms are in contact with buried waters; they form four hydrogen bonds with the first water and 1-1.5 additional hydrogen bond for each additional water in the cluster. Consequently, buried water molecules appear to be firmly packed and rigid like the protein atoms....Continue Reading

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Citations

Apr 27, 2016·International Journal of Biological Macromolecules·Oliviero Carugo
Jan 18, 2017·Protein Science : a Publication of the Protein Society·Juliana Sakamoto YonedaB A Wallace
Aug 29, 2019·Journal of Molecular Recognition : JMR·Manuela Maurer, Chris Oostenbrink
Dec 12, 2017·Protein Engineering, Design & Selection : PEDS·Oliviero Carugo
Jun 17, 2020·Protein Science : a Publication of the Protein Society·Michael Blaber
Oct 19, 2017·Scientific Reports·Oliviero CarugoDavide M Proserpio
May 12, 2021·Nature Chemistry·Alistair J ScottDerek N Woolfson
Jun 30, 2021·Chemical Society Reviews·Marley L SamwaysJonathan W Essex
May 6, 2017·Journal of Medicinal Chemistry·Francesca SpyrakisGlen E Kellogg
Oct 6, 2018·Journal of Chemical Information and Modeling·Matthew R MastersMarkus A Lill
Sep 30, 2021·BMC Bioinformatics·Oliviero Carugo

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