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Unconventional interactions between water and heterocyclic nitrogens in protein structures
Author(s) -
Stollar Elliott J.,
Gelpí Jose Luis,
Velankar Sameer,
Golovin Adel,
Orozco Modesto,
Luisi Ben F.
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20216
Subject(s) - indole test , side chain , tryptophan , histidine , imidazole , chemistry , hydrogen bond , folding (dsp implementation) , quenching (fluorescence) , crystallography , molecule , stereochemistry , fluorescence , biochemistry , amino acid , organic chemistry , physics , engineering , polymer , quantum mechanics , electrical engineering
We report an unusual interaction in which a water molecule approaches the heterocyclic nitrogen of tryptophan and histidine along an axis that is roughly perpendicular to the aromatic plane of the side chain. The interaction is distinct from the well‐known conventional aromatic hydrogen‐bond, and it occurs at roughly the same frequency in protein structures. Calculations indicate that the water–indole interaction is favorable energetically, and we find several cases in which such contacts are conserved among structural orthologs. The indole–water interaction links side chains and peptide backbone in turn regions, connects the side chains in β‐sheets, and bridges secondary elements from different domains. We suggest that the water–indole interaction can be indirectly responsible for the quenching of tryptophan fluorescence that is observed in the folding of homeodomains and, possibly, many other proteins. We also observe a similar interaction between water and the imidazole nitrogens of the histidine side chain. Taken together, these observations suggest that the unconventional water–indole and water–imidazole interactions provide a small but favorable contribution to protein structures. Proteins 2004. © 2004 Wiley‐Liss, Inc.