Title | Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE. |
Publication Type | Journal Article |
Year of Publication | 2016 |
Authors | van Bergen, L. A. H., M. Alonso, A. Palló, L. Nilsson, F. De Proft, and J. Messens |
Journal | Sci Rep |
Volume | 6 |
Pagination | 30369 |
Date Published | 2016 Jul 29 |
ISSN | 2045-2322 |
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. |
DOI | 10.1038/srep30369 |
Alternate Journal | Sci Rep |
PubMed ID | 27468924 |
PubMed Central ID | PMC4965862 |
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