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

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.

Role of Actin Dynamics and GhACTIN1 Gene in Cotton Fiber Development: A Prototypical Cell for Study

“…The actin exists in two forms: un-polymerized molecules as G-Actin and polymerized filaments as F-Actin [ 58 ]. The genome of Arabidopsis thaliana contains a total of 10 actin genes, excluding 2 pseudogenes [ 45 ]; another 8 actin genes fall into 2 classes—encoding vegetative and reproductive protein isovariants [ 73 ]. The vegetative isovariants predominate in the stems, roots, leaves, and petals, whereas reproductive isovariants are found in pollen, ovules, and embryonic parts [ 74 , 75 ].…”

“…A three-dimensional (3D) model of the ACTIN-1 protein of A. thaliana indicates that it possesses four subdomains, similar to the sub-domains observed in mammalian actin. However, in subdomain 2, the DNase-I loop presents most of the variable parts [ 73 ]. The monomeric actin (G-actin) molecule has four domains that bind ATP in their centers, thereby triggering polymerization.…”