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Three Dimensional Structure Modeling and Ramachandran Plot Analysis of Autographa Californica Nucleopolyhdro Viral Protein

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Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Three dimensional structure modeling and ramachandran plot analysis of autographa californica nucleopolyhdro viral protein S.T. Gopukumar1*, Sreeya G. Nair2, R. Radha2, N.V. Sugathan3, Anooj E. S4, Lekshmi Gangadhar4 1Department of Medical Research, Sarada Krishna Homoeopathic Medical College, Kulasekharam. TN, India 2Department of Zoology, Sree Ayyappa College for Women, Chunkankadai, Nagercoil, TN, India 3Department of Practice of Medicine, Sarada Krishna Homoeopathic Medical College, Kulasekharam. TN, India 4Xcellogen Biotech India Pvt Ltd, Nagercoil, Tamilnadu, India *Corresponding Author E-mail: [email protected] (Gopukuma) ABSTRACT: Background: Autographa Californica’s nucleopolyhedro is a viral protein found in baciloviridae. It is made of double stranded DNA genome. They viral protein easily infects this insect and affects the expression system. Method: The main aim of this work is to predict various viral proteins (Autographa Californica nucleopolyhedro). FASTA sequences are retrived from NCBI (National Center for Biotechnology Information) database. Then Basic Local Alignment Search Tool (BLAST) used to find regions of similarity in different sequences. The homology modeling was done in swiss model. The template model also constructed. Results: Comparative modeling of this program to predict the protein sequence identity is 46.83%.The template protein e value is 110 and they chain A having identify 100% similarity maximum score 320.Further the protein structure was validated in Ramachandran plot. Conclusion: From Ramachandran plot analysis it was found that the portions of residues falling into the favored regions was 98%.The predicted 3D model further characterized and analyzed using other techniques. Key words: Basic Local Alignment, Ramachandran Plot, Model, Proteins How to cite this article: Gopukumar ST, Nair SG, et al (2020): Three dimensional structure modelling and ramachandran plot analysis of autograph californica nucleopolyhdro viral protein, Ann Trop Med & Public Health; 23(S6):773-780. DOI: http://doi.org/10.36295/ASRO.2020.23626 INTRODUCTION: Autographa Californica is a one of the type of moth flies widely present in plants. It is the family of Noctuidae. It is mainly found from Southern British Columbia, New Mexico, and colored [1]. The wing span is 36-42 nm. It is mainly present in the location July to October. Nucleopolyhedro virus (NPV) affecting insects, butter flies and moths [2]. This virus family is baciloviridae.It has the main purposed to use as a pesticide [3]. It has a double stranded DNA structure.Autographa Californica has some commercial use and applications in the pharmaceutical industries. This virus affects the whole expression system and destroys the function of insect [4]. The NCBI (National Center for Biotechnology Information) is a major resource for bioinformatics tools and services. This database containing DNA, RNA and protein sequences are retrived and updated daily. Basic Local Alignment Search Tool (BLAST) is a tools performed to compare the amino acid and nucleotide sequences [5]. Heuristic algorithm used to calculating the optimal alignment of different sequences. This tool available on the web of NCBI.BLAST can be used for identifying species or find homologous species. These results are given in a graphical format showing the hits found a table showing sequence identifier scoring related BLAST score for these [6]. 773 Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Homology modeling is a technique in structural biology significantly contributing known protein structure and experimentally determined structure [7]. This homology modeling contains various steps for template modeling, side chain modeling, model optimization and validation [8]. This procedure generate the unknown and target known structures are identified. Swiss model is a server used to build the protein structure automatically and anootated.It is a main purpose for used to make protein model in life science and research worldwide [9, 10, 11]. Ramachandran plot is used to the protein structure and conformations are validated in RAMPAGE server [12]. It is used to visualize energetically allowed regions for backbone dihedral angles and amino acid residues in protein structure [13]. This graph denoted three different regions favored allowed and outlier. and the protein was structurally validated [14]. The present study focuses on Three Dimensional Structure modeling and analysis of Autographa Californica nucleopolyhedro viral protein modeled from Swissmodell server and the structure was validated in Ramachandran plot analysis. MATERIALS AND METHODS: Sequence retrieval Autographa Californica nucleopolyhedro viral nucleotide sequences FASTA formats are retrived from National Center for Biotechnology Information (NCBI) database. Basic Local Alignment Search Tool (BLAST) Search BLASTn suit page and uploaded the query sequence files (Autographa Californica nucleopolyhedro viral nucleotide sequences) FASTA file was uploaded. The job title was entered then the protein selection for highly similar sequences in mega blast. Run the BLAST button. Homology modeling in swiss model BLAST and HHbits are the two hits are used for swiss model template alignment. Target sequences are searched in BLAST and 173 similar templates are identified in this NCBI BLAST server. These files are generated in SMTL format. The templates are selected and they further analyzed for model building.PROMOD3 is a server used to the protein model was constructed. The protein side chain is reconstructed then insertion and deletion in the fragments. Final resulting model was constructing certain force fields are applied. The protein scoring function was calculated by QMEAN. Further the ligand was selected for the target and template based. Oligomeric state conservation is a techniques are used to the Quartnery structure of protein was modeled. Various algorithm are used to the final structure was build (supervised machine learning algorithm Support Vector Machines (SVM) which combines interface conservation).GMQE it is the one of score value highly calculated the protein model. Structure validation in Ramachandran plot analysis of RAMPAGE The Structure was modeled then the PDB coordinate file was uploaded in the RAMPAGE server. The server plot the graphical representation of protein 3D structure was confirmed by the maximum favored regions. The regions are denoted in different colors and the protein model was verified. 774 Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Autographa Californica Sequence retrived NCBI BLAST similarity search Homology modeling Swiss model 775 Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Structure validation –RAMPAGE Over all flow chat of Methodolog RESULTS: Sequence retrieval from NCBI Fig 1: Autographa Californica nucleopolyhedro viral nucleotide sequences FASTA formats Retrived from NCBI Sequence similarity search 776 Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Fig 2: Basic Local Alignment Search Tool BLAST similarity Autographa Californica nucleopolyhedro viral nucleotide sequences Protein structure prediction Fig 3: The protein structure was predicted swiss model sequence identity 46.83% 777 Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Fig 4: The SWISS MODEL template library was searched with BLAST for evolutionary related structures matching the target sequence Fig 5: Autographa Californica nucleopolyhedro viral templates 778 Gopukumar et al (2020): Analysis of nucleopolyhedro viral protein March 2020 Vol. 23 Issue S6 Fig 6: The Autographa Californica nucleopolyhedro viral protein viewed in Pymol Ramachandran plot analysis for structure validation Fig 7: Use of Ramachandran plot to predict the quality of protein structure. A good quality Ramachandran plot contains most torsional angles in followed region 98%. Fig 1, 2, 3 shows that Protein retrived and sequence alignments. Fig 4, 5, 6 shows that the protein modeled Fig 7 shows that the protein validation in Ramachandran plot CONCLUSION: Autographa Californica nucleopolyhedro viral nucleotide sequences FASTA formats Retrived from NCBI.BLAST server used to the sequence are identity is 46.83%.The template protein e value is 110 and they chain A having identify 100% similarity maximum score 320.The swiss model used to predict the protein structure and the top fifty templates are identified A further 1,025 templates were found which were considered to be less suitable for modeling than the filtered list.(2hii.2.B,2ijx.1.A,3ugt.1.B,3v75.1.A,3a1j.1.A,3a1j.1.B,3a1j.1.C,3d1e.1.B, 3mle.1.A, 3bni.1.A, 2ijx.3.A, 4o1i.1.A, 4o1i.1.B, 4tns.2.A, 2joi.1.A, 6i3g.1.A, 4qiv.1.A, 2zvm.1.E,)The protein properties understand experimental structural biology and computational structure modeling. The protein 3D models are predicted in Insilco and comparative modeling methods X-ray crystallography and NMR then Cryo-EM methods are used to the protein structure was validated in Ramachandran plot.Torsinal angles denoted the protein favored regions are identified in the structure. Different and experimental methods are used to the protein structure was modeled in abinitio and homology modeling in routinely analyzed and verified Ramachandran plot. ACKNOWLEDGEMENT:
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