In silico analysis and homology modeling of strictosidine synthase involved in alkaloid biosynthesis in catharanthus roseus

Abstract

Abstract Background In this study, strictosidine synthase (STR) from Catharanthus roseus that plays an important role in alkaloid biosynthesis was selected. The purpose of this work was to perform in silico analysis and to predict the three-dimensional structure of this protein that is not available. Results Physicochemical characterization was performed by Expasy’s Protparam server. The computed theoretical isoelectric point (pI) found to be less than 7 indicates the acidic nature of this protein. The aliphatic index 73.04 indicates the thermal stability of the protein. Grand average hydropathy (GRAVY) was predicted to be − 285; this lower value of GRAVY shows the possibility of better interaction of this protein with water. Functional analysis of these proteins was performed by SOSUI server which predicted the transmembrane helix. Secondary structure analysis was carried out by SOPMA that revealed that Alpha helix dominated among secondary structure elements followed by random coil, extended strand, and beta turns. The modeling of the three-dimensional structure of the STR was performed by Swiss model. The model was validated using protein structure checking tools PROCHECK and PROVE. Conclusions This study reveals in silico analysis by Expasy Protparam server, SOPMA, and SOSUI server. Homology modeling of STR was performed by Swiss model.

Keywords

• Catharanthus roseus
• STR
• SOSUI
• PROCHECK
• PROVE