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Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions
Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
* Author to whom correspondence should be addressed.
Received: 21 May 2012; in revised form: 6 June 2012 / Accepted: 8 June 2012 / Published: 13 June 2012
Abstract: In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., πO → σS* versus nO → σS* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (πO) rather than in the plane (nO). S···X interactions in four model proteins, phospholipase A2 (PLA2), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.
Keywords: Protein Data Bank; chalcogen bonds; σ-hole bonds; molecular assembly; protein engineering; drug design
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Iwaoka, M.; Isozumi, N. Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions. Molecules 2012, 17, 7266-7283.
Iwaoka M, Isozumi N. Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions. Molecules. 2012; 17(6):7266-7283.
Iwaoka, Michio; Isozumi, Noriyoshi. 2012. "Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions." Molecules 17, no. 6: 7266-7283.