Research paper In silico prediction and characterization of three-dimensional structure of Actin-1 of Arabidopsis thaliana

Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana. Thisprotein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the im-portance of this protein, very little information is availa ble regarding its structure and function in plants. In thisstudy, analysis of the protein sequence was done an d comparative model of Actin-1 was constructed (UNIPROTID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID:1NLV-A) as template employing Modelle r version 9.9. The stable structure was generated by 5 nanosecond mole-cular dynamics simulation steps usin g GROMOS43A1 96 force field that characterized its structural and dynamicfeature. The biochemical function of the final simulated structure was also investigated using PROFUNC. Themolecular simulation study suggested that the modeled Acti n-1 protein retain its stable conformation in aqueoussolution. The predicted binding sites in the modeled Actin- 1 protein are very informative for further protein-ligandinteraction study.