In silico structural modeling and analysis of physicochemical properties of curcumin synthase (CURS1, CURS2, and CURS3) proteins of Curcuma longa

R Santhoshkumar,A Yusuf

doi:10.1186/s43141-020-00041-x

R Santhoshkumar, A Yusuf

Open Access

https://doi.org/10.1186/s43141-020-00041-x

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Abstract

BackgroundPharmaceutically important curcuminoid synthesis in C. longa is controlled by CURS1, CURS2, and CURS3 genes. The present study detected the physicochemical properties and structural characteristics including the secondary and 3D structure of CURS proteins. The primary, secondary, and tertiary structure of the CURS proteins were modeled and characterized using multiple bioinformatics tools such as ExPasy ProtParam tools, self-optimized prediction method with alignment (SOPMA), PSIPRED, and SWISS-MODEL. The predicted secondary structure of curcumin synthase provided an α-helix and random coil as the major components. The reliability of the modeled structure was confirmed using PROCHECK and QMEAN programs. ResultsThe molecular weight of CURS1 is 21093.19 Da, theoretical pI as 4.93, and an aliphatic index of 99.19. Molecular weight of CURS2 and CURS3 proteins are 20266.13 Da and 20629.52 Da, theoretical pI as 5.28 and 4.96, and an aliphatic index of 89.30 and 86.37, respectively. In the predicted secondary structure of CURS proteins, alpha helices and random coils of CURS1, CUR2, and CURS3 were 42.72, 41.38, and 44.74% and 24.87, 31.03, and 17.89, respectively. The extended strands were 16.24, 19.40, and 17.89. QMEAN Z-score is − 0.83, − 0.89, and − 1.09 for CURS1, CURS2, and CURS3, respectively. ConclusionPrediction of the 3D model of a protein by in silico analysis is a highly challenging aspect to confirm the NMR or X-ray crystallographic data. This report can contribute to the understanding of the structure, physicochemical properties, structural motifs, and protein-protein interaction of CURS1, CUR2, and CURS3.

Highlights

Important curcuminoid synthesis in C. longa is controlled by CURS1, CURS2, and CURS3 genes
A viable alternative approach developed to predict the in silico 3D structure of proteins based on homology modeling using an unknown protein sequence with more than 35% of similarity [12] serves the purpose with better validation
The Open Reading Frame (ORF) finder demarcated a putative 588 bp, 675 bp, and 570 bp ORF for the three cloned CURS nucleotide sequences translated to CURS proteins with 195, 224, and 190 amino acid residues for CURS1, CURS2, and CURS3 with ATG as the initiation codon

Summary

Introduction

Important curcuminoid synthesis in C. longa is controlled by CURS1, CURS2, and CURS3 genes. The primary, secondary, and tertiary structure of the CURS proteins were modeled and characterized using multiple bioinformatics tools such as ExPasy ProtParam tools, selfoptimized prediction method with alignment (SOPMA), PSIPRED, and SWISS-MODEL. The predicted secondary structure of curcumin synthase provided an α-helix and random coil as the major components. Curcuminoids have anti-inflammatory, antimutagenic, anti-diabetic, anti-bacterial, and hepatoprotective activities [3]. It is known for its free-radical scavenging antioxidant activity [4], healing of the dermal. Type III polyketide synthases (PKSs) consists of structurally simple homodimers of ketosynthase that are involved in the biosynthesis of most of the plant polyketides [10]. A viable alternative approach developed to predict the in silico 3D structure of proteins based on homology modeling using an unknown protein sequence with more than 35% of similarity [12] serves the purpose with better validation

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