Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach

Abé, 2011, Monomeric and dimeric conformation of the vinculin tail five-helix bundle in solution determined by EPR-spectroscopy, Biophys. J., 101, 1772, 10.1016/j.bpj.2011.08.048 Agarwal, 2010, Overexpression of PgDREB2A transcription factor enhances abiotic stress tolerance and activates downstream stress-responsive genes, Mol. Biol. Rep., 37, 1125, 10.1007/s11033-009-9885-8 Allagulova, 2003, The plant dehydrins. Structure putative functions, Biochemistry, 68, 945 Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Anbazhagan, 2015, DREB1A overexpression in transgenic chickpea alters key traits influencing plant water budget across water regimes, Plant Cell Rep., 34, 199, 10.1007/s00299-014-1699-z Schrödinger Release 2014-4, Desmond MD System, version 4.0, D.E. Shaw Research, 2014. New York, NY. Arnold, 2006, The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling, Bioinformatics, 22, 195, 10.1093/bioinformatics/bti770 Bachmair, 1986, In vivo half-life of a protein is a function of its amino-terminal residue, Science, 234, 179, 10.1126/science.3018930 Bartels, 2005, Drought and salt tolerance in plants, Crit. Rev. Plant Sci., 24, 23, 10.1080/07352680590910410 Bhattacharya, 2007, Evaluating proteins structures determined by structural genomics consortia, Proteins, 66, 778, 10.1002/prot.21165 Biasini, 2014, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Res., 42, W252, 10.1093/nar/gku340 Bolser, 2015, Triticeae resources in ensembl plants, Plant Cell Physiol., 56, e3, 10.1093/pcp/pcu183 Budak, 2013, Drought tolerance in modern and wild wheat, Sci. World J., 2013, 548246, 10.1155/2013/548246 Castrignano, 2006, The PMDB protein model database, Nucleic Acids Res., 34, D306, 10.1093/nar/gkj105 Cunningham, 2015, Ensembl 2015, Nucleic Acids Res., 43, D662, 10.1093/nar/gku1010 Danyluk, 1998, Accumulation of an acidic dehydrin in the vicinity of the plasma membrane during cold acclimation of wheat, Plant Cell, 10, 623, 10.1105/tpc.10.4.623 Darden, 1993, Particle mesh Ewald: an N log (N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397 Dash, 2012, PLEXdb: gene expression resources for plants and plant pathogens, Nucleic Acids Res., 40, D1194, 10.1093/nar/gkr938 Essman, 1995, A smooth particle mesh Ewald method, J. Chem. Phys., 103, 8577, 10.1063/1.470117 Franca, 2014, Homology modeling: an important tool for the drug discovery, J. Biomol. Struct. Dyn., 6, 1 Gajula, 2013, How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy, BMC Genom., 14, S4, 10.1186/1471-2164-14-S2-S4 Gajula, 2013, Molecular interaction studies of shrimp antiviral protein PmAV with WSSV RING finger domain in-silico, J. Appl. Bioinform. Comput. Biol., 2, 10, 10.4172/2329-9533.1000103 Gasteiger, 2005, Protein identification and analysis tools on the ExPASy server, 571 Geourjon, 1995, SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments, Comput. Appl. Biosci., 11, 681 Gill, 1998, Calculation of protein extinction coefficients from amino acid sequence data, Anal. Biochem., 182, 319, 10.1016/0003-2697(89)90602-7 Guex, 1997, SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling, Electrophoresis, 18, 2714, 10.1002/elps.1150181505 Guo, 2010, Probing the α-helical structural stability of stapled p53 peptides: MD simulations and analysis, Chem. Biol. Drug Des., 75, 348, 10.1111/j.1747-0285.2010.00951.x Gupta, 2008, Wheat genomics: present status and future prospects, Int. J. Plant Genom., 2008, 896451 Guruprasad, 1990, Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence, Protein Eng., 4, 155, 10.1093/protein/4.2.155 Hammada, 2014, Physiological and biochemical studies on drought tolerance of wheat plants by application of amino acids and yeast extract, Ann. Agric. Sci., 59, 133, 10.1016/j.aoas.2014.06.018 Hassan, 2015, Roles of dehydrin genes in wheat tolerance to drought stress, J. Adv. Res., 6, 179, 10.1016/j.jare.2013.11.004 Ikai, 1980, Thermostability and aliphatic index of globular proteins, J. Biochem., 88, 1895 Jorgensen, 1996, Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc., 118, 11225, 10.1021/ja9621760 Kasuga, 1999, Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor, Nat. Biotechnol., 17, 287, 10.1038/7036 Kumar, 2013, In silico analysis of protein- protein interaction between resistance and virulence protein during leaf rust disease in wheat (Triticum aestivum L.), World Res. J. Pept. Protein, 2, 52 Kyte, 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol., 157, 105, 10.1016/0022-2836(82)90515-0 Laskowski, 1993, Main-chain bond lengths and bond angles in protein structures, J. Mol. Biol., 20, 1049, 10.1006/jmbi.1993.1351 Laskowski, 2005, ProFunc: a server for predicting protein function from 3D structure, Nucleic Acids Res., 33, W89, 10.1093/nar/gki414 Lata, 2011, Role of DREBs in regulation of abiotic stress responses in plants, J. Exp. Bot., 62, 4731, 10.1093/jxb/err210 Lawlor, 2002, Photosynthetic carbon assimilation and associated metabolism in relation to water deficits in higher plants, Plant Cell Environ., 25, 275, 10.1046/j.0016-8025.2001.00814.x Lee, 2010, DREB2C interacts with ABF2, a bZIP protein regulating abscisic acid-responsive gene expression, and its over expression affects abscisic acid sensitivity, Plant Physiol., 153, 716, 10.1104/pp.110.154617 Li, 2005, Very fast empirical prediction and rationalization of protein pKa values, Proteins, 61, 704, 10.1002/prot.20660 Lindahl, 2008, 3 Liu, 1998, Two transcription factors DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis, Plant Cell, 10, 391, 10.1105/tpc.10.8.1391 Lopes, 2014, Integration of phenotyping and genetic platforms for a better understanding of wheat performance under drought, J. Exp. Bot., 65, 6167, 10.1093/jxb/eru384 Marchler-Bauer, 2011, CDD: a Conserved Domain Database for the functional annotation of proteins, Nucleic Acids Res., 39, D225, 10.1093/nar/gkq1189 McGuffin, 2000, The PSIPRED protein structure prediction server, Bioinformatics, 16, 404, 10.1093/bioinformatics/16.4.404 Mickelbart, 2015, Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability, Nat. Rev. Genet., 16, 237, 10.1038/nrg3901 Nakashima, 2014, The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat, Front. Plant Sci., 5, 170, 10.3389/fpls.2014.00170 Nezhadahmadi, 2013, Drought tolerance in wheat, Sci. World J., 2013, 610721, 10.1155/2013/610721 Notredame, 2008, T-coffee: a novel method for fast and accurate multiple sequence alignment, J. Mol. Biol., 302, 205, 10.1006/jmbi.2000.4042 Pandey, 2014, Isolation and characterization of dehydration-responsive element-binding factor 2 (DREB2) from Indian wheat (T. aestivum L.) cultivars, Aust. J. Crop Sci., 8, 44 Pettersen, 2004, UCSF Chimera visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Rahaie, 2010, A MYB gene from wheat (Triticum aestivum L.) is up-regulated during salt and drought stresses and differentially regulated between salt-tolerant and sensitive genotypes, Plant Cell Rep., 29, 835, 10.1007/s00299-010-0868-y Rorat, 2006, Plant dehydrins-tissue location, structure and function, Cell Mol. Biol. Lett., 11, 536, 10.2478/s11658-006-0044-0 Ryckaert, 2016, Numerical integration of the Cartesian equations of motion of a system with constraints: MD of n-alkanes, J. Comput. Phys., 197, 327 Sali, 1993, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol., 234, 779, 10.1006/jmbi.1993.1626 Shivakumar, 2010, Prediction of absolute solvation free energies using MD free energy perturbation and the OPLS force field, J. Chem. Theory Comput., 6, 1509, 10.1021/ct900587b Sillitoe, 2015, CATH: comprehensive structural and functional annotations for genome sequences, Nucleic Acids Res., 43, D376, 10.1093/nar/gku947 Singh, 2002, Transcription factors in plant defense and stress responses, Curr. Opin. Plant Biol., 5, 430, 10.1016/S1369-5266(02)00289-3 Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Vriend, 1990, WHAT IF: a molecular modeling and drug design program, J. Mol. Graph., 8, 52, 10.1016/0263-7855(90)80070-V Wahid, 2007, Expression of dehydrins under heat stress and their relationship with water relations of sugarcane leaves, Biol. Plant., 51, 104, 10.1007/s10535-007-0021-0 Warde-Farley, 2010, The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function, Nucleic Acids Res., 38, W214, 10.1093/nar/gkq537 Xiong, 2014, 3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces, Methods Mol. Biol., 1137, 105, 10.1007/978-1-4939-0366-5_8 Yamaguchi-Shinozaki, 1993, The plant hormone abscisic acid mediates the drought-induced expression but not the seed-specific expression of rd22, a gene responsive to dehydration-stress in Arabidopsis thaliana, Mol. Gen. Genet., 238, 17, 10.1007/BF00279525 Zhang, 2012, A wheat R2R3-MYB gene TaMYB30-B Improves drought stress tolerance in transgenic Arabidopsis, J. Exp. Bot., 63, 5873, 10.1093/jxb/ers237