Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.

TitleRevisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.
Publication TypeJournal Article
Year of Publication2016
Authorsvan Bergen, L. A. H., M. Alonso, A. Palló, L. Nilsson, F. De Proft, and J. Messens
JournalSci Rep
Volume6
Pagination30369
Date Published2016 Jul 29
ISSN2045-2322
Abstract

In many established methods, identification of hydrogen bonds (H-bonds) is primarily based on pairwise comparison of distances between atoms. These methods often give rise to systematic errors when sulfur is involved. A more accurate method is the non-covalent interaction index, which determines the strength of the H-bonds based on the associated electron density and its gradient. We applied the NCI index on the active site of a single-cysteine peroxiredoxin. We found a different sulfur hydrogen-bonding network to that typically found by established methods, and we propose a more accurate equation for determining sulfur H-bonds based on geometrical criteria. This new algorithm will be implemented in the next release of the widely-used CHARMM program (version 41b), and will be particularly useful for analyzing water molecule-mediated H-bonds involving different atom types. Furthermore, based on the identification of the weakest sulfur-water H-bond, the location of hydrogen peroxide for the nucleophilic attack by the cysteine sulfur can be predicted. In general, current methods to determine H-bonds will need to be reevaluated, thereby leading to better understanding of the catalytic mechanisms in which sulfur chemistry is involved.

DOI10.1038/srep30369
Alternate JournalSci Rep
PubMed ID27468924
PubMed Central IDPMC4965862
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