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Insilico Analysis of Proteins of Curcuma Caesia Roxb

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Insilico Analysis of Proteins of Curcuma Caesia Roxb Academic Sciences International Journal of Pharmacy and Pharmaceutical Sciences ISSN- 0975-1491 Vol 6, Issue 2, 2014 Research Article INSILICO ANALYSIS OF PROTEINS OF CURCUMA CAESIA ROXB S. VIJAYA BHARATHI Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, India. Email: [email protected] Received: 09 Jan 2014, Revised and Accepted: 24 Feb 2014 ABSTRACT Objective: In this present study, 10 proteins of Curcuma caesia were analysed using bioinformatics tools. Methods: Structural prediction and functional characterization of proteins of Curcuma caesia were done using Expasy Protparm server, SOPMA, TMHMM and SOSUI tools. Chalcone synthase of Curcuma caesia was submitted to Blastp. Plants of different family showing identity 80% and above were selected and its sequences retrieved, aligned using Clustal Omega. Using NJ plot, phylogenetic tree was constructed for the aligned sequence. Results: Structure prediction showed that α – helix, random coil, β – turn and extended strand predominates. Transmembrane region was found in AtpF protein. Phylogenetic analysis of chalcone synthase of Curcuma caesia reveals that the plants of Costaceae, Liliaceae, and Musaceae family are closely related. Conclusion: Curcuma caesia an endangered medicinal plant has to be analysed further for identifying its various medicinal properties. Keywords: Curcuma caesia, Computational tools, Chalcone synthase, Phylogeny. INTRODUCTION arhythmic, anti-hypertensive, and anti-inflammatory activities [10]. Flavonoids are synthesized via the phenylpropanoid and Medicinal plants have played a significant role in ancient polyketide pathway, which starts with the condensation of one traditional systems of medication in many countries. They are rich molecule of CoA-ester of cinnamic acid or derivatives such as source of bioactive compounds and thus serve as important raw coumaric or ferulic acid, and three molecules of malonyl-CoA, materials for drug production [1]. Infectious diseases are the yielding a naringenin chalcone as major product. This reaction is world's leading cause of premature deaths [2]. Therefore, there is carried out by the enzyme chalcone synthase (CHS). The chalcone a continuous and urgent need to discover new antimicrobial is isomerised to a flavanone by the enzyme chalcone flavanone compounds with diverse chemical structures and novel isomerase (CHI). From these central intermediates, the pathway mechanisms of action [3]. In recent years, secondary plant diverges into several branches, each resulting in a different class metabolites (phytochemical) have been extensively investigated as of flavonoids. Flavanone 3-hydroxylase (F3H) catalyzes the a source of medicinal agents [4]. Contrary to the synthetic drugs, stereospecific 3ß-hydroxylation of (2S)-flavanones to antimicrobials of plant origin are not associated with side effects. dihydroflavonols. For the biosynthesis of anthocyanins, They are also cheap, easily available and affordable [5]. Curcuma dihydroflavonol reductase (DFR) catalyzes the reduction of Linn. is a large genus belonging to the family Zingiberaceae, dihydroflavonols to flavan-3, 4-diols (leucoanthocyanins), which comprises about 80 species of rhizomatous herbs. Curcuma plants are converted to anthocyanidins by anthocyanidin synthase (ANS). (rhizomes and leaves) have a camphoraceous aroma and contain The formation of glycosides is catalyzed by UDP glucose-falconoid many functional compounds such as phenolics, flavonoids and 3-O-glucosyl transferees (UFGT), which stabilizes the different antioxidant enzymes. Curcuma caesia is commonly anthocyanidins by 3-O-glucosylation [11]. Chalcone known as black turmeric (Kali haldi) which is a perennial herb synthase or naringenin-chalcone synthase (CHS) (CHS, EC found throughout the Himalayan region, North-east and central 2.3.1.74) is an enzyme ubiquitous to higher plants and belongs to a India. The paste of rhizome is used traditionally for the treatment family of polyketide synthase enzymes (PKS) known as type III of leucoderma, asthma, tumor, piles etc. Curcuma caesia has PKS. Type III PKSs are associated with the production medicinal value due to its bioactive compound viz alkaloids, of chalcones, a class of organic compounds found mainly in plants steroids, phenolics, and tannins. Essential oil of C. caesia has been as natural defense mechanisms and as synthetic intermediates. known for its antifungal activity [6]. The rhizome oil of C. caesia CHS was the first type III PKS to be discovered. It is the first contains 76.6% δ -camphor; 1,8-cineole (9.06%), ocimene (15.66%), 1- ar -curcumene (14.84%), δ – camphor (18.88%), δ - committed enzyme in flavonoid biosynthesis. CHS is believed to linalool (20.42%), δ -borneol (8.7%) and zingiberol act as a central hub for the enzymes involved in the flavonoid (12.60%)[7].Curcuma caesia has scientifically studied for various pathway [12].CHS gene expression is influenced by many stresses therapeutical activities like antioxidant, antibacterial, antipyretic, and environmental factors. These include light and UV radiation, larvicidal, insecticidal, antimicrobial, wound healing and anti- wound and pathogen attack, as well as plant-microbe interactions. hyperglycemic [8]. Flavonoids are low molecular weight, Several groups of defense-related genes have also been identified polyphenolic compounds available in all-dietary plants [9].Over with respect to insect and microbial pathogens and include 4000 structurally unique flavonoids have been identified in plants. protease inhibitors, chitinase, phenylalanine ammonia lyase and The common feature of these compounds is phenyl benzopyrone chalcone synthase, all of which accumulate systemically[13]. The skeleton (C6-C3-C6). They are mainly classified into flavonol, major drawbacks of experimental methods that have been used to flavanols, flavanonols, flavanones, flavones, and isoflavones on the characterize the proteins of various organisms are the time frame basis of saturation level and opening of the central ring. involved, high cost and the fact that these methods are not Flavonoids are important plant secondary metabolites that serve amenable to high throughput techniques. In silico approaches various functions in higher plants. These include pigmentation, UV provide a viable solution to these problems [14]. protection, fertility, antifungal defense and the recruitment of MATERIALS AND METHODS nitrogen-fixing bacteria. Sequence Retrieval Flavonoids possess wide spectrum of biological activities that might be able to influence processes that are dys- regulated during The FASTA sequence of the proteins [TABLE: 1] were retrieved from cardiovascular diseases. These include free radical scavenging, Genbank database hosted by the NCBI antioxidant, anti-thrombotic, antiapoptotic, anti ischemic, anti- (http://www.ncbi.nlm.nih.gov) [12]. Bharathi et al. Int J Pharm Pharm Sci, Vol 6, Issue 2, 216-220 Table 1: Proteins of Curcuma caesia S. No. Accession number Protein Length 1 AEF58786.1 Chalcone synthase (CHS2) 189 2 AEF58785.1 Chalcone synthase (CHS1) 189 3 AET36763.1 RNA polymerase C 173 4 AET36755.1 RNA polymerase B 123 5 AET36747.1 Ribulose-1,5-bisphosphate carboxylase/oxygenase 187 6 AET36733.1 Maturase K 265 7 AET36725.1 AtpF 44 8 AET36717.1 Acetyl-CoA carboxylase-D 127 9 AET36740.1 PsbK 8 10 AGL98016.1 PsbA 18 Table 2: Parameters computed using Expasy’s ProtParam tool. Protein Accession Length Mol.wt pI - + Ec II AI GRAVY Number R R Chalcone synthase AEF58786.1 189 20153.9 4.75 28 17 17990 33.8 99.68 -0.015 Chalcone synthase AEF58785.1 189 20355.2 4.93 22 14 22125 32.02 90.85 0.127 RNA polymerase C AET36763.1 173 19257.4 8.89 18 21 8605 36.70 110.98 -0.0009 RNA polymerase B AET36755.1 123 13371.2 5.89 14 12 13075 25.16 92.76 -0.156 Ribulose-1,5-bisphosphate carboxylase/ AET36747.1 187 20663.5 7.58 21 22 30495 22.81 80.32 -0.271 oxygenase Maturase K AET36733.1 265 32118.8 9.72 15 36 70165 31.72 98.53 -0.014 AtpF AET36725.1 44 4907.7 5.19 2 1 9970 15.54 117.27 0.755 Acetyl-CoA carboxylase-D AET36717.1 127 13748.9 5.39 12 11 7450 36.99 101.42 0.193 PsbK AET36740.1 8 964 9.75 0 1 5500 8.75 61.25 0.113 Psb A AGL98016.1 18 1842.0 4.35 2 0 * 14.23 92.22 0.150 Mol. Wt – molecular weight(Daltons), pI – Isoelectric point, -R - Number of negative residues, +R – Number of Positive residues, EC – Extinction Coefficient at 280 nm, II – Instability Index, AI – Aliphatic Index, GRAVY – Grand Average Hydropathicity, * - No Trp, Tyr or Cys residue (should not be visible by UV spectrophotometry ). Table 3: Secondary structure results of proteins of curcuma caesia. Secondary AEF58 AEF5878 AET3676 AET3675 AET3674 AET3673 AET3672 AET3671 AET3674 AGL9801 structure 786.1 5.1 3.1 5.1 7.1 3.1 5.1 7.1 0.1 6.1 Alpha helix 40.74% 43.39% 37.57% 13.82% 33.69% 44.15% 29.55% 45.67% 0.00% 0.00% 310 helix 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% Pi helix 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% Beta bridge 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% Extended 18.52% 16.40% 15.03% 34.15% 22.99% 23.02% 36.36% 18.90% 0.00% 33.33% strand Beta turn 9.52% 7.94% 7.51% 12.20% 5.35% 4.15% 0.00% 7.87% 0.00% 5.56% Bend 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% region Random 31.22% 32.28% 39.88% 39.84% 37.97% 28.68% 34.09% 27.56% 100.00% 61.11% coil Ambigous 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% states Other 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% states Table 4: Transmembrane region predicted by SOSUI server Protein Accession Number Transmembrane region Length Type AtpF AET36725.1 ILATNPINLSVVLGVLIYF 19 PRIMARY Primary Structure Prediction:- For Physio-chemical Functional characterization characterization, theoretical Isoelectric Point (pI), molecular weight, total number of positive and negative residues, extinction SOSUI and TMHMM v.2.0 tools were used to characterize whether the protein is soluble or transmembrane in nature.
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