Sequence to Structure Analysis of DOPA Protein from Mucuna pruriens: A Computational Biology Approach
Journal Title: International journal of Emerging Trends in Science and Technology - Year 2015, Vol 2, Issue 8
Abstract
L-DOPA, (L-3, 4-dihydroxyphenylalanine), an anti-nutritional compound is an important intermediate of secondary metabolism in higher plants and is known as a precursor of alkaloids, betalain, melanine, and others. We analyzed the amino acid sequence of DOPA protein from M. pruriens by using computational methods. The DOPA protein M. pruriens was subjected to sequence, structural and functional annotation. Functional domain prediction through Conserved Domain Database (CDD) suggested that DOPA proteins of M. pruriens contain Aspartate aminotransferase (AAT) superfamily associated with various cellular activities. The analysis of predicted secondary structure by PsiPred and SOPMA has shown that high percentage of helices in the protein structure makes DOPA more flexible for folding processes. Sub-cellular localization predictions suggested it to be a cytoplasmic `protein. Homology modeling method was used to deduce the three-dimensional (3D) structure of selected DOPA proteins from M. pruriens. From template search results it has been identified that all the hypothetical proteins share more than 50% sequence identity with crystal structure of Sus scrofa, indicating proteins are evolutionary conserved. Several quality assessment and validation parameters computed indicated that predicted homology models are in accordance with literature. Current study will help researchers to better understanding of the predicted models and refinement.
Authors and Affiliations
Laxman Nagar
Keywords
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