Influence of cation-pi interactions to the structural stability of prokaryotic and eukaryotic translation elongation factors.
We have investigated the role of cation-pi interactions on translation elongation factors. In our investigation, an average of four significant cation-pi interactions were found, that is, an average of one cation-pi interaction per 44 residues in the ten elongation factors were observed. The analysis on the influence of short (< + or - 4), medium (> + or - 4 to < + or - 20) and long (>20) range contacts showed that cation-pi interactions are mainly formed by medium and long-range contacts. Arg-Tyr pair was found largest in number but energetic contribution of Arg-Trp pair was found most. Preferred secondary structural conformation analysis of the residues involved in cation-pi interaction indicates that the cationic Arg prefers to be in helix and Lys having equal probability for helix and strand, whereas the aromatic Phe and Trp were found mostly in helix while Tyr in strand regions. The cation-pi interaction residues involved in these proteins were found highly conserved with 48.86% residues having conservation score of > or = 6. Analysis of secondary structure preference of the energetically significant cation-pi residues in different solvent accessible range indicates that most of the pi residues are found buried or partially buried whereas cationic residues were found mostly at the protein surface. The results presented in this study will be useful for structural stability studies in translation elongation factors.
Anbarasu
Anand
A
School of Biotechnology, Chemical Engineering and Biomedical Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India. vibhuranjanprasad2006@vit.ac.in
Prasad
Vibhu Ranjan
VR
Sathpathy
Shankha
S
Sethumadhavan
Rao
R
D000596:Amino Acids / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry; D002412:Cations / Q000737:chemistry*; D006801:Humans; D010445:Peptide Elongation Factors / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry
D000596:Amino Acids; D001426:Bacterial Proteins; D002412:Cations; D010445:Peptide Elongation Factors; D016601:RNA-Binding Proteins