Exploring conformation changes of Janus kinase 2 pseudokinase mediated by mutations through Gaussian accelerated molecular dynamics and principal component analysis

Abstract

The pseudokinase domain (JH2) of the protein tyrosine kinase (Janus kinase 2, JAK2) regulates the activity of a tyrosine kinase domain (JH1) in JAK2, which is further affected by mutations in the JH2. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by construction of free energy landscapes (FELs) and principal component analysis (PCA) were performed to study effect of two mutations V617F and V617F/E596A on the conformations of the ATP-bound JH2. The dynamic analyses reveal that mutations affect the structural flexibility and correlated motions of the JH2, meanwhile also change the dynamics behavior of the P-loop and αC-helix of the JH2. The information from FELs unveils that mutations induce less energy states than the free JH2 and the WT one. The analyses of interaction networks uncover that mutations affect the salt bridge interactions of ATP with K581, K677 and R715 and alter hydrogen bonding interactions (HBIs) of ATP with the JH2. The changes in conformations of the JH2 and ATP-JH2 interaction networks caused by mutations in turn generate effect on the activity regulations of the JH2 on the JH1. This work is expected to provide significant theoretical helps for deeply understanding the function of the JH2 and drug design toward JAK2.

Communicated by Ramaswamy H. Sarma

Keywords:

• Protein tyrosine kinase
• pseudokinase domain
• GaMD simulations
• free energy landscape
• principal component analysis

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by high-caliber talent of Tuojiang scholar from Shandong Jiaotong University (No.TJXZ202204) and Natural Science Foundation of Shandong Province Grant (ZR2019MA040, ZR2021MA069 and ZR2020ME231).