An In silico analysis on the phosphorylation dependent structural and thermal stability of thermophilic proteins

In the present study the effect of phosphorylation on the structural stability and energy transfer in two structurally homologous thermophilic proteins, 1QMP and 1DZ3 were investigated. In 1QMP one of the residues (Asp55) phosphorylated while 1DZ3 this modification is not observed. This modification has provided an ideal model to explore the influence of phosphorylation on thermostability of the protein. Molecular dynamics (MD) simulations were performed to assess the structural stability and flexibility of both proteins following the analyses of root-mean-square deviation and root-mean-square fluctuation (RMSF). Subsequent, vibrational energy transfer calculations were followed to characterize pathways of intramolecular energy propagation and also to evaluate the effect of phosphorylation via residue level communication within the protein matrix. The key residues and interaction networks involved in energy transport were visualized through communication maps, provided insights into influence of phosphorylation on intramolecular energy flow and also on the overall structural stability. Furthermore, steered molecular dynamics simulation were carried out to reveal the unfolding mechanism and thermal resistance of the proteins under the influence of applied force. The results have revealed that the 1QMP possess higher structural rigidity, enhanced energy transport efficiency, and greater resistance to unfolding as compared to 1DZ3. Overall, phosphorylation at Asp55 strengthens vibrational energy transfer pathways and contributes to the enhanced thermostability of thermophilic proteins.