Structural and molecular dynamics simulation studies of CBL-interacting protein kinase CIPK and its complexes related to plant salinity stress.
Prabir Kumar DasTanya BhatnagarSanhita BanikSambit MajumdarDebajyoti DuttaPublished in: Journal of molecular modeling (2024)
Computational methods are used to model the entire Arabidopsis thaliana CIPK24 protein structure in its autoinhibited and open-activated states. Arabidopsis thaliana CIPK24-CBL4 complex is predicted based on the protein-protein docking methods. The available structural and functional data support the CIPK24 and the CIPK24-CBL4 complex models. Models are energy-minimized and subjected to molecular dynamics (MD) simulations. MD simulations for 500 ns and 300 ns enabled us to predict the importance of conserved residues of the proteins. Finally, the work is extended to predict the CIPK24-CBL4 complex with the upstream kinase GRIK2. MD simulation for 300 ns on the ternary complex structure enabled us to identify the critical CIPK24-GRIK2 interactions. Together, these data could be used to engineer the CBL-CIPK interaction network for developing salt tolerance in crops.
Keyphrases
- molecular dynamics
- arabidopsis thaliana
- protein protein
- molecular dynamics simulations
- density functional theory
- protein kinase
- small molecule
- dengue virus
- electronic health record
- molecular docking
- transcription factor
- big data
- minimally invasive
- artificial intelligence
- binding protein
- deep learning
- tyrosine kinase
- amino acid
- network analysis
- cell wall
- case control