In silico prediction of 3D structure of Opaque-2 protein in maize

摘要

Opaque-2 (o2) protein is a transcription factor regulating the expression of genes involved in controlling the amount of limiting amino acids in maize kernels. Quality protein maize (QPM) is the maize with enhanced level of lysine and tryptophan along with normal kernel phenotype developed so as to minimize the nutritional problems pertaining to protein energy malnutrition (PEM) in countries where maize is the stable food. This protein, however, has showed anomalous behaviour in some of the QPM lines developed so far to usual that is enhanced essential amino acids. In the event to understand the functioning of the o2 protein, its tertiary structure needs to be understood. Due to the technical limitation to uphold the native state of o2 protein after crystallization process during X ray crystallography projects the need for predicting the protein structure computationally using in silico tools. Hence, the current research aimed at predicting in silico tertiary structure of o2 protein using Phyre2 and so, on-line analytical tools. From a total of 120 templates aligned, 16 templates showed more than 95% confidence with the query input and gave a 3D model. The results showed presence of a helices and coils in o2 protein with absence of p pleated sheet structure. Presence of many coils provided the reason for variable behaviour of this protein. The best probable structure predicted by Phyre2 software showed the presence of residues of which 27% were modelled at >90% confidence, while 79% were predicted disordered/coiled. Structure was validated using SELECT pro web tool with Global Relative Model Confidence Score of 0.009. This information may play a key role in unveiling the behaviour in terms of quantitative profile of lysine and tryptophan of QPM lines having o2 protein.