Effect of Activation Loop Phosphorylation on Lemur Tyrosine Kinase 3 (LMTK3) activity: A Molecular Dynamics Simulation Study

Author: Himakshi Sarma and Venkata Satish Kumar Mattaparthi

Journal Name:

Download PDF

Abstract

Protein kinases catalyze the phosphorylation reaction, and they themselves become catalytically activated through phosphorylation of their activation loop. LMTK3 is an oncogenic kinase, reported in various types of cancer. Recent study highlights LMTK3 phosphorylation by CDK5 results in breast cancer tumourogenesis. We determined the probable activation loop in LMTK3 and carried out in silico phosphorylation at probable phosphorylation site (Thr189) in activation loop and studied the effects of phosphorylation on conformational dynamics. We substituted Glu for phosphorylated Thr189 and noticed Glu does not mimic the effect of phosphorylation. From Molecular dynamics analysis, phosphorylated, unphosphorylated and mutated LMTK3 found to be stable. But phosphorylated loop region shows much fluctuation. Thereby ATP binding mode was observed to be different in phosphorylated as compared to unphosphorylated LMTK3. Phosphorylation mediated conformational change in the ATP binding site of LMTK

Keywords

Breast cancer tumourogenesis; Phosphorylation sites; Molecular docking; Activation segment; Conformational dynamics.

Conclusion

In this computational study we determinedthe probable activation segment in LMTK3. Then we studied the dynamics of LMTK3 upon phosphorylation and compared its dynamics with unphosphorylated and mutated LMTK3 structures. RMSD and potential energy analysis reveal that phosphorylated, unphosphorylated and mutated LMTK3 structures are stable during the MD simulation. Despite the stability of the structures we see mainly the phosphorylated activation segment undergoes much conformational changes as compared to unphosphorylated and mutated one. We also inferred that Glu(189) Thr mutationin phosphorylated LMTK3 does not mimic the effect of phosphorylation. The conformational change in the phosphorylated activation segment of LMTK3 was found to have significant impact on the ATP binding site. As a result the binding mode of ATP found to be different in phosphorylated LMTK3 as compared to unphosphorylated LMTK3. The conformational change in ATP binding site may facilitate the catalysis of phos

References

Eukaryotic protein kinases are the largest gene family that regulates several important cellular processes, such as cell growth and differentiation (Ban et. al., 2011; Waldrop, 2014). Protein kinases share a conserved core consisting of two lobes, the N-terminal (small N-lobe) and C-terminal (large C-lobe). These two lobes form a deep pocket that accommodates an ATP molecule (Kornev et. al., 2010). The N-lobe consists of five β-strands and an α-helix (called αC-helix). The C-lobe contains α-helices and includes the activation segment which is 20-35 residues stretch located between a conserved DFG motif and APE motif that is conformationaly very flexible and its conformation can influence both substrate binding and catalytic efficiency (Huse et. al., 2002; Nolen et. al., 2004). Phosphorylation is the commonest posttranslational modification of proteins in eukaryotic cells (Olsen et. al., 2013). Eukaryotic protein kinases (EPKs) are the family of enzymes that catalyse the phosphoryl

How to cite this article

Himakshi Sarma and Venkata Satish Kumar Mattaparthi (2017). Effect of Activation Loop Phosphorylation on Lemur Tyrosine Kinase 3 (LMTK3) activity: A Molecular Dynamics Simulation Study. Biological Forum – An International Journal 9(1): 194-206.