Download MendeleyRevisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.
van Bergen, L.A., Alonso, M., Pallo, A., Nilsson, L., De Proft, F., Messens, J.(2016) Sci Rep 6: 30369-30369
- PubMed: 27468924
- DOI: https://doi.org/10.1038/srep30369
- Primary Citation of Related Structures:
4X0X, 4X1U - PubMed 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.
Organizational Affiliation:
Research Group of General Chemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
