REVIEW PAPER
In silico prediction and characterization of three-dimensional
structure of Actin-1 of Arabidopsis thaliana
Publication date: 2014-10-23
BioTechnologia 2013;94(4):432-443
KEYWORDS
ABSTRACT
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.
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.
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