In-silico approaches for studying cross-talk of different kinases associated in diverse biological processes with their interacting substrates partners

Abstract

The Signal transduction pathway uses docking interaction with kinases which may also be regulated by phosphorylation. Regulation of these docking interactions by phosphorylation allows an additional level of control over the diverse biological processes including Crosstalk induction of defense. Amino acid sequences surrounding the phosphorylation motif have been extensively studied. However, the present study, attempts have been made to identify the presence of important determinants/motifs for substrate specificity of Mitogen activated protein kinase (MAPK), CaM kinase II, Protein kinase C, Receptor tyrosine kinase in the 54 identified MAPK 3 and MAPK 6 substrates of Arabidopsis thaliana. All identified substrates do not possess the known (p) S/ (p) T-P phosphorylation sites. Out of 54 substrates, 47 have S/T-P site and 7 are lacking such sites for interaction. Likewise 8 shows XXRRX(p)S pattern, 28 shows HYDXRXX(p)SXX pattern, 35 shows HYDXXRXX(p)S pattern, 12 shows R/K(1-3)X(p) S/T(HYD)R/K(1-3) pattern and 17 shows Na(1-3)-X-(p)Y-XX-HYD pattern. In order to ascertain the role of surrounding hydrophobic amino acids in the interaction, the other conserved pattern/Motif were also identified in the MAPK substrates which include XXRRX(p)S, HYDXRXX(p)SXX, HYDXXRXX(p)S, R/K(1-3)X(p)S/T(HYD)R/K(1-3) Na((1-3)-X- (p)Y-XX-HYD (Na-Hydrophilic; HYD- Hydrophobic; X- Any amino acid) pattern. These conserved patterns show activation sites for other kinases viz. MAPK Activated Protein kinase-1, MAPK Activated Protein kinase -2, CaM Kinase II, Protein kinase C, Tyrosine protein kinase respectively. Identification of interacting partners based on the surrounding amino acids of phosphorylation sites could be useful in the understanding of such complex hierarchical networks involved in controlling the defense signaling pathways. © 2011 Taj G, et al.