Abstract
BackgroundIn 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. ResultsPhysicochemical 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. ConclusionsThis study reveals in silico analysis by Expasy Protparam server, SOPMA, and SOSUI server. Homology modeling of STR was performed by Swiss model.
Highlights
In this study, strictosidine synthase (STR) from Catharanthus roseus that plays an important role in alkaloid biosynthesis was selected
In this study, Strictosidine synthase (STR) involved in the first step of alkaloid biosynthesis present in C. roseus was selected
SOSUI is a functional analysis tool which distinguishes between membrane and soluble proteins from amino acid sequences and predicts the transmembrane helices
Summary
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. Catharanthus roseus (C. roseus) is an important medicinal plant used to treat various diseases. The plant is distributed throughout the world. It is known to produce modern chemotherapeutic agent for pain-relieving properties [1]. One of the important types of alkaloid is the vinblastine produced from C. roseus which was reported due to its antitumor activity and has wide pharmaceutical use [2]. It has been reported that accumulation of free radicals can cause pathological conditions such as ischemia, asthma, arthritis, inflammation, neurodegeneration, Parkinson’s diseases, mongolism, aging process, and perhaps dementia [3].
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