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Possible roles of S · · · O and S · · · N interactions in the functions and evolution of phospholipase A 2

View Article: PubMed Central - PubMed

ABSTRACT

To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A2 (PLA2) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA2 domain group (PLA2-DG), while an additional three S···O interactions were found for the snake PLA2 domain group (sPLA2-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA2-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA2 were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA2 family.

No MeSH data available.


Formation and structural features of the S···X interaction. (A) The divalent S atom adopts the coordination from a heteroatom X, changing the valence state from a tetrahedral to a hypervalent trigonal bipyramidal state. (B) The most frequently observed S···O interactions in proteins. The S atom of a disulfide bond (SSC type) approaches a main-chain amide O atom in a direction vertical to the peptide plane maintaining the linearity of the three S–S···O atoms.
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f1-2_23: Formation and structural features of the S···X interaction. (A) The divalent S atom adopts the coordination from a heteroatom X, changing the valence state from a tetrahedral to a hypervalent trigonal bipyramidal state. (B) The most frequently observed S···O interactions in proteins. The S atom of a disulfide bond (SSC type) approaches a main-chain amide O atom in a direction vertical to the peptide plane maintaining the linearity of the three S–S···O atoms.

Mentions: Weak nonbonded interactions are important physicochemical forces that control the structure and function of proteins1. Ionic interactions, hydrogen bonds, and van der Waals forces are mainly considered part of this class of interactions, but some novel interaction patterns, such as C–H···O hydrogen bonds2–4, cation-π interactions5–7, and CH/π interactions8,9, were recently characterized in folded protein structures and were claimed to be important for stability and function. The S···X interactions (Fig. 1)10–12 that form between a cysteine (Cys) or methionine (Met) side chain and the nearby heteroatom X (X=O, N, S) belong to such non-conventional weak interactions that stabilize protein structures to some extent.


Possible roles of S · · · O and S · · · N interactions in the functions and evolution of phospholipase A 2
Formation and structural features of the S···X interaction. (A) The divalent S atom adopts the coordination from a heteroatom X, changing the valence state from a tetrahedral to a hypervalent trigonal bipyramidal state. (B) The most frequently observed S···O interactions in proteins. The S atom of a disulfide bond (SSC type) approaches a main-chain amide O atom in a direction vertical to the peptide plane maintaining the linearity of the three S–S···O atoms.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036642&req=5

f1-2_23: Formation and structural features of the S···X interaction. (A) The divalent S atom adopts the coordination from a heteroatom X, changing the valence state from a tetrahedral to a hypervalent trigonal bipyramidal state. (B) The most frequently observed S···O interactions in proteins. The S atom of a disulfide bond (SSC type) approaches a main-chain amide O atom in a direction vertical to the peptide plane maintaining the linearity of the three S–S···O atoms.
Mentions: Weak nonbonded interactions are important physicochemical forces that control the structure and function of proteins1. Ionic interactions, hydrogen bonds, and van der Waals forces are mainly considered part of this class of interactions, but some novel interaction patterns, such as C–H···O hydrogen bonds2–4, cation-π interactions5–7, and CH/π interactions8,9, were recently characterized in folded protein structures and were claimed to be important for stability and function. The S···X interactions (Fig. 1)10–12 that form between a cysteine (Cys) or methionine (Met) side chain and the nearby heteroatom X (X=O, N, S) belong to such non-conventional weak interactions that stabilize protein structures to some extent.

View Article: PubMed Central - PubMed

ABSTRACT

To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A2 (PLA2) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA2 domain group (PLA2-DG), while an additional three S···O interactions were found for the snake PLA2 domain group (sPLA2-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA2-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA2 were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA2 family.

No MeSH data available.