Abstract
Computational approach was done in protein molecules of the Rose leaf curl virus and its betasatellite component isolated from Rose plants. Moreover in-depth study was done using in silico approach such as restriction map, GC profile and prediction of binding sites for ligand molecule analysis. Hence, an approach has been taken into consideration to unearth a treatment against geminiviruses, resulting in huge yield loss across the globe. This study provides a great deal of novel knowledge and will be employed for the selection of inhibitors in opposition to geminivirus proteins focusing on begomovirus and paves a way for developing antiviral agents in the near future.
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References
Aloy P, Russell RB (2004) Ten thousand interactions for the molecular biologist. Nat Biotechnol 22:1317–1321
Bairoch A (2000) The ENZYME database in (2000). Nucleic Acids Res 28:304–305
Balakrishnan M, Srivastava RC, Pokhriyal M (2010) Homology modeling and docking studies between HIV-1 protease and carbamic acid. Indian J Biotechnol 9:96–100
Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A (2016) CryptoSite: expanding the druggable proteome by characterization and prediction of cryptic binding sites. J Mol Biol 428:709–719
Gao F, Zhang C (2006) GC-profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res 34:W686–W691
Groisman EA, Ochman H (1996) Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87:791–794
Hacker J, Carniel E (2001) Ecological fitness, genomic islands and bacterial pathogenicity: a Darwinian view of the evolution of microbes. EMBO Rep 2:376–381
Hannum G et al (2009) Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet 5:e1000782
Heinrichs A (2008) Proteomics: solving a 3D jigsaw puzzle. Nat Rev Mol Cell Biol 9:3–3
Hentschel U, Hacker J (2001) Pathogenicity islands: the tip of the iceberg. Microbes Infect 3:545–548
Ilyas M, Nawaz K, Shafiq M, Haider MS, Shahid AA (2013) Complete nucleotide sequences of two begomoviruses infecting Madagascar periwinkle (Catharanthus roseus) from Pakistan. Arch Virol 158:505–510
Ivashchenko A, Pyrkova A, Niyazova R, Alybayeva A, Baskakov K (2016) Prediction of miRNA binding sites in mRNA. Bioinformation 12(4):237–240
Källberg M, Wang H, Wang S, Peng J, Wang Z, Lu H, Xu J (2012) Template-based protein structure modeling using the RaptorX web server. Nat Protoc 7:1511–1522
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709–742
Lima AT, Sobrinho RR, González-Aguilera J, Rocha CS, Silva SJ, Xavier CA, Silva FN, Duffy S, Zerbini FM (2013) Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts. J Gen Virol 94:418–431
Mansoor S, Briddon RW, Zafar Y, Stanley J (2003) Geminivirus disease complexes: an emerging threat. Trends Plant Sci 8:128–134
Marwal A, Sahu AK, Choudhary DK, Gaur RK (2013a) Complete nucleotide sequence of a begomovirus associated with satellites molecules infecting a new host Tagetes patula in India. Virus Genes 47(1):194–198
Marwal A, Sahu A, Sharma P, Gaur RK (2013b) Molecular characterizations of two Begomoviruses infecting Vinca rosea and Raphanus sativus in India. Virol Sin 28(1):053–056
Marwal A, Sahu A, Gaur RK (2013c) First report of airborne begomovirus infection in Melia azedarach (Pride of India), an ornamental tree in India. Aerobiologia. doi:10.1007/s10453-013-9319-x
Marwal A, Sahu A, Gaur RK (2013d) Molecular characterization of begomoviruses and DNA satellites associated with a new host Spanish Flag (Lantana camara) in India. ISRN Virol. doi:10.5402/2013/915703
Perez A, Morrone JA, Simmerling C, Dill KA (2016) Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol 36:25–31
Pingoud A, Jeltsch A (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res 29:3705–3727
Qin W, Zhao G, Carson M, Jia C, Lu H (2016) Knowledge-based three-body potential for transcription factor binding site prediction. IET Syst Biol 10(1):23–29
Raj SK, Khan MS, Snehi SK, Kumar S, Khan AA (2007) Natural occurrence of a Begomovirus on Dimorphotheca sinuate in India. Aust Plant Dis Notes 2:25–26
Roberts RJ, Vincze T, Posfai J, Macelis (2003) REBASE—restriction enzymes and methyltransferases. Nucleic Acids Res 31:418–420
Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A (2004) A structural perspective on protein-protein interactions. Curr Opin Struct Biol 14:313–324
Salwinski L, Eisenberg D (2003) Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol 13:377–382
Shin WH, Bures MG, Kihara D (2016) PatchSurfers: two methods for local molecular property-based binding ligand prediction. Methods 93:41–50
Szilagyi A, Grimm V, Arakaki AK, Skolnick J (2005) Prediction of physical protein-protein interactions. Phys Biol 2:S1–16
Taherzadeh G, Yang Y, Zhang LAWC, Zhou Y (2016) Sequence-based prediction of protein–peptide binding sites using support vector machine. J Comput Chem. doi:10.1002/jcc.24314
Urbino C, Gutiérrez S, Antolik A, Bouazza N, Doumayrou J, Granier M, Martin DP, Peterschmitt M (2013) Within-host dynamics of the emergence of tomato yellow leaf curl virus recombinants. PLoS One 8:e58375. doi:10.1371/journal.pone.0058375
Vincze T, Posfai J, Roberts RJ (2003) NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31:3688–3691
Wass MN, Kelley LA, Sternberg MJE (2010) 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res 38:W469–W473
Acknowledgements
The authors are thankful to Science and Engineering Research Board – Department of Science and Technology, New Delhi, India, for the financial assistance (File No. YSS/2015/000265) and also to University Grant Commission, New Delhi for providing financial assistantship under Research Award for Teacher (F.30-1/2014/RA-2014-16-GE-RAJ-4696 (SA-II).
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Marwal, A., Mishra, M., Sekhsaria, C., Gaur, R.K. (2017). Computational Analysis and Predicting Ligand Binding Site in the Rose leaf curl virus and Its Betasatellite Proteins: A Step Forward for Antiviral Agent Designing. In: Saxena, S., Tiwari, A. (eds) Begomoviruses: Occurrence and Management in Asia and Africa. Springer, Singapore. https://doi.org/10.1007/978-981-10-5984-1_9
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