Limits...
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.


The dendrogram of snake PLA2 (sPLA2-DG). The eight commonly observed S···X interactions (see Table 2) are mapped on the figure by color circles, the number of which indicates the strength of the corresponding interaction; one circle for 0.1<d≤0.2 Å, two circles for 0.0<d≤0.1 Å, and three circles for d≤0.0 Å. As for Russell’s viper (r. viper), the smallest value of d was used for each interaction to determine the number of circles.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC5036642&req=5

f4-2_23: The dendrogram of snake PLA2 (sPLA2-DG). The eight commonly observed S···X interactions (see Table 2) are mapped on the figure by color circles, the number of which indicates the strength of the corresponding interaction; one circle for 0.1<d≤0.2 Å, two circles for 0.0<d≤0.1 Å, and three circles for d≤0.0 Å. As for Russell’s viper (r. viper), the smallest value of d was used for each interaction to determine the number of circles.

Mentions: The evolution of snake PLA2 was subsequently analyzed. Fig. 4 shows a dendrogram of snake PLA2 mapping the seven common S···O interactions and one common S···N.


Possible roles of S · · · O and S · · · N interactions in the functions and evolution of phospholipase A 2
The dendrogram of snake PLA2 (sPLA2-DG). The eight commonly observed S···X interactions (see Table 2) are mapped on the figure by color circles, the number of which indicates the strength of the corresponding interaction; one circle for 0.1<d≤0.2 Å, two circles for 0.0<d≤0.1 Å, and three circles for d≤0.0 Å. As for Russell’s viper (r. viper), the smallest value of d was used for each interaction to determine the number of circles.
© Copyright Policy
Related In: Results  -  Collection

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

f4-2_23: The dendrogram of snake PLA2 (sPLA2-DG). The eight commonly observed S···X interactions (see Table 2) are mapped on the figure by color circles, the number of which indicates the strength of the corresponding interaction; one circle for 0.1<d≤0.2 Å, two circles for 0.0<d≤0.1 Å, and three circles for d≤0.0 Å. As for Russell’s viper (r. viper), the smallest value of d was used for each interaction to determine the number of circles.
Mentions: The evolution of snake PLA2 was subsequently analyzed. Fig. 4 shows a dendrogram of snake PLA2 mapping the seven common S···O interactions and one common S···N.

View Article: PubMed Central - PubMed

ABSTRACT

To investigate possible roles of S&middot;&middot;&middot;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&middot;&middot;&middot;X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S&middot;&middot;&middot;O interactions and one common S&middot;&middot;&middot;N interaction for the PLA2 domain group (PLA2-DG), while an additional three S&middot;&middot;&middot;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&middot;&middot;&middot;O and S&middot;&middot;&middot;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&middot;&middot;&middot;X interactions play some role in the functions and evolution of the PLA2 family.

No MeSH data available.