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 . This

protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance

of this protein, very little information is available regarding its structure and function in plants. In this

study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT

ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID:

1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular

dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic

feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The

molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous

solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand

interaction study.