Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement

References

• Altschul, S. F. , Gish, W. , Miller, W. , Myers, E. & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology , 215 , 403–410.10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Bernauer, J. , Bahadur, R. P. , Rodier, F. , Janin, J. , & Poupon, A. (2008). DiMoVo: A Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions. Bioinformatics , 24 , 652–658.10.1093/bioinformatics/btn022
   PubMed Web of Science ®Google Scholar
• Bowers, J. , Boursiquot, J. M. , This, P. , Chu, K. , Johansson, H. & Meredith, C. (1999). Historical genetics: The parentage of chardonnay, gamay, and other wine grapes of Northeastern France. Science , 285 , 1562–1565.10.1126/science.285.5433.1562
   PubMed Web of Science ®Google Scholar
• Chapus, C. , Rovery, M. , Sarda, L. , & Verger, R. (1988). Minireview on pancreatic lipase and colipase. Biochimie , 70 , 1223–1234.10.1016/0300-9084(88)90188-5
   PubMed Web of Science ®Google Scholar
• Colovos, C. , & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science , 2 , 1511–1519.10.1002/pro.v2:9
   PubMed Web of Science ®Google Scholar
• Darden, T. , York, D. , & Pedersen, L. (1993). Particle mesh Ewald: An W log(N) method for Ewald sums in large systems. Journal of Chemical Physics , 98 , 10089–10092.
   Web of Science ®Google Scholar
• Falk, A. , Feys, B. J. , Frost, L. N. , Jones, J. D. , Daniels, M. J. , & Parker, J. E. (1999). EDS1, an essential component of R gene-mediated disease resistance in Arabidopsis has homology to eukaryotic lipases. Proceedings of the National Academy of Sciences , 96 , 3292–3297.10.1073/pnas.96.6.3292
   PubMed Web of Science ®Google Scholar
• Ferris, H. , Zheng, L. , & Walker, M. A. (2013). Soil temperature effects on the interaction of grape rootstocks and plant-parasitic nematodes. Journal of Nematology , 45 , 49–57.
   PubMed Web of Science ®Google Scholar
• Feys, B. J. , Moisan, L. J. , Newman, M. A. , & Parker, J. E. (2001). Direct interaction between the Arabidopsis disease resistance signaling proteins, EDS1 and PAD4. EMBO Journal , 20 , 5400–5411.10.1093/emboj/20.19.5400
   PubMed Web of Science ®Google Scholar
• Fu, Z. Q. , & Dong, X. (2013). Systemic acquired resistance: Turning local infection into global defense. Annual Review of Plant Biology , 64 , 839–863.10.1146/annurev-arplant-042811-105606
   PubMed Web of Science ®Google Scholar
• Gao, F. , Shu, X. , Ali, M. B. , Howard, S. , Li, N. , Winterhagen, P. , ... Gassmann, W. (2010). A functional EDS1 ortholog is differentially regulated in powdery mildew resistant and susceptible grapevines and complements an Arabidopsis eds1 mutant. Planta , 231 , 1037–1047.10.1007/s00425-010-1107-z
   PubMed Web of Science ®Google Scholar
• Garcia, A. V , Blanvillain-Baufumé, S. , Huibers, R. P. , Wiermer, M. , Li, G. , Gobbato, E. , … Parker, J. E. (2010). Balanced nuclear and cytoplasmic activities of EDS1 are required for a complete plant innate immune response. EDS1. PLoS Pathogen , 6 , e1000970. Retrieved from http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000970
   Web of Science ®Google Scholar
• Goodstein, D. M. , Shu, S. , Howson, R. , Neupane, R. , Hayes, R. D. , Fazo, J. , ... Rokhsar, D. S. (2012). Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research , 40 , D1178–D1186.10.1093/nar/gkr944
   PubMed Web of Science ®Google Scholar
• Guex, N. , & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. Electrophoresis , 18 , 2714–2723.10.1002/(ISSN)1522-2683
   PubMed Web of Science ®Google Scholar
• Hess, B. , Bekker, H. , Berendsen, H. J. C. , & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry , 18 , 1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Hooft, R. W. W. , Vriend, G. , Sander, C. , & Abola, E. E. (1996). Errors in protein structures. Nature , 381 , 272–272.10.1038/381272a0
   PubMed Web of Science ®Google Scholar
• Jain, S. , Mohan, R. , Singh, Y. , Rai, R. , Sharma, V. , & Mehrotra, S. (2014). Medicinal value of grape seed extracts: A review. World Journal of Pharmaceutical Research , 3 , 3036–3043.
   Google Scholar
• Kahn, K. , & Bruice, T. C. (2001). Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides. Journal of Computational Chemistry , 23 , 977–996.
   Web of Science ®Google Scholar
• Khanna, S. , Venojarvi, M. , Roy, S. , Sharma, N. , Trikha, P. , Bagchi, D. , ... Sen, C. K. (2002). Dermal wound healing properties of redox-active grape seed proantho cyanidins. Free Radical Biology & Medicine , 33 , 1089–1096.
   PubMed Web of Science ®Google Scholar
• Kotchoni, S. O. , & Gachomo, E. W. (2006). The reactive oxygen species network pathways: An essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants. Journal of Biosciences , 31 , 389–404.10.1007/BF02704112
   PubMed Web of Science ®Google Scholar
• Kunkel, B. N. , & Brooks, D. M. (2002). Cross talk between signaling pathways in pathogen defense. Current Opinion in Plant Biology , 5 , 325–331.10.1016/S1369-5266(02)00275-3
   PubMed Web of Science ®Google Scholar
• Laskoswki, R. A. , MacArthur, M. W. , Moss, D. S. & Thorton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Applied Crystallography , 26, 283–291.10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Maiorov, V. N. , & Crippen, G. M. (1994). Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. Journal of Molecular Biology , 235 , 625–634.10.1006/jmbi.1994.1017
   PubMed Web of Science ®Google Scholar
• Marchler-Bauer, A. , Panchenko, A. R. , Shoemaker, B. A. , Thiessen, P. A. , Geer, L. Y. , & Bryant, S. H. (2002). CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Research , 30 , 281–283.10.1093/nar/30.1.281
   PubMed Web of Science ®Google Scholar
• McEntyre, J. & Ostell, J. (2002). The NCBI handbook . Bethesda, MD : National Center for Biotechnology Information.
   Google Scholar
• Pearson, R. C. , & Goheen, A. C. (1988). Compendium of grape diseases . United Kingdom: CABI Publisher.
   Google Scholar
• Pontius, J. , Richelle, J. , & Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology , 264 , 121–136.10.1006/jmbi.1996.0628
   PubMed Web of Science ®Google Scholar
• Pronk, S. , Páll, S. , Schulz, R. , Larsson, P. , Bjelkmar, P. , Apostolov, R. , … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics , 29 , 845–854.10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Rietz, S. , Stamm, A. , Malonek, S. , Wagner, S. , Becker, D. , Medina-Escobar, N. , ... Parker, J. E. (2011). Different roles of Enhanced Disease Susceptibility1 (EDS1) bound to and dissociated from Phytoalexin Deficient4 (PAD4) in Arabidopsis immunity. New Phytologist , 191 , 107–119.10.1111/j.1469-8137.2011.03675.x
   PubMed Web of Science ®Google Scholar
• Shikhamany, S. D. (2001). Grape production in India (2001/2007) . Thailand: RAP Publication.
   Google Scholar
• Shrikhande, A. J. (2000). Wine by-products with health benefits. Food Research International , 33 , 469–474.10.1016/S0963-9969(00)00071-5
   Web of Science ®Google Scholar
• Singh, I. , & Shah, K. (2012). In silico study of interaction between rice proteins Enhanced Disease Susceptibility 1 and phytoalexin deficient 4, theregulators of salicylic acid signalling pathway. Journal of Biosciences , 37 , 563–571.10.1007/s12038-012-9208-4
   PubMed Web of Science ®Google Scholar
• Sinha, P. , Prajneshu & Varma, A. (2004). Statistical modelling and forecasting of powdery mildews affecting agricultural crops: An overview. Journal of the Indian Society of Agricultural Statistics , 57 , 257–270.
   Google Scholar
• Stintzi, A. , Heitz, T. , Prasad, V. , Wiedemann-Merdinoglu, S. , Kauffmann, S. , Geoffroy, P. , ... Fritig, B. (1993). Plant ‘pathogenesis-related’ proteins and their role in defense against pathogens. Biochimie , 75 , 687–706.10.1016/0300-9084(93)90100-7
   PubMed Web of Science ®Google Scholar
• Vaguine, A. A. , Richelle, J. , & Wodak, S. J. (1999). SFCHECK: A unified set of procedure for evaluating the quality of macromolecular structure-factor data and their agreement with atomic model. Acta Crystallographica , D55 , 191–205.
   Google Scholar
• Venugopal, S. C. , Jeong, R. D. , Mandal, M. K. , Zhu, S. , Chandra-Shekara, A. C. , Xia, Y. , ... Kachroo, P. (2009). Enhanced Disease Susceptibility 1 and salicylic acid act redundantly to regulate resistance gene-mediated signaling. PLoS Genetics , 5 , e1000545.10.1371/journal.pgen.1000545
   PubMed Web of Science ®Google Scholar
• Volt, A. C. , Dempsey, D. A. , & Klessing, D. F. (2009). Salicylic acid, amultifaceted hormone to combat disease. Annual Review of Phytopathology , 47 , 177–206.10.1146/annurev.phyto.050908.135202
   PubMed Web of Science ®Google Scholar
• Weng, X. , Hamel, L. , Martin, L. M. & Peckham, J. (2005). A genetic algorithm for energy minimization in bio-molecular systems. Evolutionary Computation, The 2005 IEEE Congress , 1 , 49–56.
   Google Scholar
• Wiel, A. V. D. , Golde, P. H. M. V. , & Hart, H. C. (2001). Blessings of the grape. European Journal of Internal Medicine , 12 , 484–489.10.1016/S0953-6205(01)00170-4
   PubMedGoogle Scholar
• Wong, H. , & Schotz, M. C. (2002). The lipase gene family. The Journal of Lipid Research , 43 , 993–999.10.1194/jlr.R200007-JLR200
   PubMed Web of Science ®Google Scholar
• Xu, D. , & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal , 101 , 2525–2534.10.1016/j.bpj.2011.10.024
   PubMed Web of Science ®Google Scholar
• Yadav, M. , Jain, S. , Bhardwaj, A. , Nagpal, R. , Puniya, M. , Tomar, R. , ... Yadav, H. (2009). Biological and medicinal properties of grapes and their bioactive constituents: An update. Journal of Medicinal Food , 12 , 473–484.10.1089/jmf.2008.0096
   PubMed Web of Science ®Google Scholar
• Zhang, J. , Liang, Y. , & Zhang, Y. (2011). Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure , 19 , 1784–1795.10.1016/j.str.2011.09.022
   PubMed Web of Science ®Google Scholar
• Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics , 9 , 40.10.1186/1471-2105-9-40
   PubMed Web of Science ®Google Scholar