Structural modeling and molecular simulation analysis of HvAP2/EREBP from barley

References

• Allen, M. D., Yamasaki, K., Ohme-Takagi, M., Tateno, M., & Suzuki, M. (1998). A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. The EMBO Journal, 17, 5484–5496.10.1093/emboj/17.18.5484
   PubMed Web of Science ®Google Scholar
• Angarica, V. E., Pérez, A. G., Vasconcelos, A. T., Collado-Vides, J., & Contreras-Moreira, B. (2008). Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9, 436–453.10.1186/1471-2105-9-436
   PubMed Web of Science ®Google Scholar
• Beckstein, O., Fourrier, A., & Iorga, B. I. (2014). Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. Journal of Computer-Aided Molecular Design, 28, 265–276.10.1007/s10822-014-9727-1
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular-dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690.10.1063/1.448118
   Web of Science ®Google Scholar
• Blake, T., Blake, V., Bowman, J., & Abdel-Haleem, H. (2011). In S. E. Ullrich (Ed.), Barley: Production, Improvement and Uses (pp. 522–531). Wiley-Blackwell.
   Google Scholar
• Blumwald, E. (2000). Sodium transport and salt tolerance in plants. Current Opinion in Cell Biology, 12, 431–434.
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., … Sacerdoti F. D. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. In SC 2006 Conference, Proc ACM/IEEE (pp. 43–43). Tampa, FL: IEEE.
   Google Scholar
• Bray, E. A. J., Bailey, S. E., & Weretilnyk, E. (2000). Responses to abiotic stresses. In W. Buchanan & G. R. Jones (Eds.), Biochemistry and Molecular Biology of Plants (pp. 1158–1176). UK: Wiley-Blackwell.
   Google Scholar
• Choi, H. I., Hong, J. H., Ha, J. O., Kang, J. Y., & Kim, S. Y. (2000). ABFs, a family of ABA-responsive element binding factors. Journal of Biological Chemistry, 275, 1723–1730.10.1074/jbc.275.3.1723
   PubMed Web of Science ®Google Scholar
• Coulocheri, S. A., Pigis, D. G., Papavassilliou, K. A., & Papavassillou, A. G. (2007). Hydrogen bonds in protein-DNA complexes: Where geometry meets plasticity. Biochimie, 89, 1291–1303.
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• De Boer, K., Tilleman, S., Pauwels, L., Vanden Bossche, R., De Sutter, V., Vanderhaeghen, R., … Goossens, A. (2011). APETALA2/ETHYLENE RESPONSE FACTOR and basic helix-loop-helix tobacco transcription factors cooperatively mediate jasmonate-elicited nicotine biosynthesis. The Plant Journal, 66, 1053–1065.10.1111/tpj.2011.66.issue-6
   PubMed Web of Science ®Google Scholar
• de Vries, S. J., van Dijk, M., & Bonvin, A. M. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883–897.10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Eden, E., Lipson, D., Yogev, S., & Yakhini, Z. (2007). Discovering motifs in ranked lists of DNA sequences. PLoS Computational Biology, 3, e39.
   PubMed Web of Science ®Google Scholar
• Filiz, E., & Tombuloğlu, H. (2014). In silico analysis of DREB transcription factor genesand proteins in grasses. Applied Biochemistry and Biotechnology, 174, 1272–1285.
   PubMed Web of Science ®Google Scholar
• Gill, S. C., & von Hippel, P. H. (1989). Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry, 182, 319–326.10.1016/0003-2697(89)90602-7
   PubMed Web of Science ®Google Scholar
• Greertz, M., & Maerk, S. J. (2010). Experimental strategies for studying transcription factor-DNA binding specificities. Briefings in Functional Genomics, 9, 362–373.
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing drug ability. Journal of Chemical Information and Modeling, 49, 377–389.10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Hao, D., Yamasaki, K., Sarai, A., & Ohme-Takagi, M. (2002). Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry, 41, 4202–4208.10.1021/bi015979v
   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
• Hess, B., Kutzner, C., Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.
   PubMed Web of Science ®Google Scholar
• Idicula-Thomas, S., & Balaji, P. V. (2005). Understanding the relationship between the primary structure of proteins and its propensity to be soluble on overexpression in Escherichia coli. Protein Science, 14, 582–592.10.1110/ps.041009005
   PubMed Web of Science ®Google Scholar
• Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry, 88, 1895–1898.
   PubMed Web of Science ®Google Scholar
• Jaiswal, S. K., Pandey, S. P., Sharma, S., Prasad, R., Prasad, L. C., Verma, R. P., & Joshi, A. K. (2010). Diversity in Indian barley (Hordeumvulgare) cultivars and identification of genotype-specific fingerprints using microsatellite markers. Journal of Genetics, 89, e46–54.
   Google Scholar
• Kagaya, Y., Ohmiya, K., & Hattori, T. (1999). RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Research, 27, 470–478.10.1093/nar/27.2.470
   PubMed Web of Science ®Google Scholar
• Kauffman, C., & Karypic, G. (2008). An analysis of information content present in protein–DNA interactions. Pacific Symposium on Biocomputing, 2008, 477–488.
   Google Scholar
• Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157, 105–132.10.1016/0022-2836(82)90515-0
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., & Thornton, J. M. (2001). PROCHECK: Validation of protein structure coordinates, in International Tables of Crystallography, Volume F. In M. G. Rossmann & E. Arnold (Eds.), Crystallography of Biological Macromolecules (pp. 722–725). Dordrecht: Kluwer Academic Publishers.
   Google Scholar
• Lata, C., Bhutty, S., Bahadur, R. P., Majee, M., & Prasad, M. (2011). Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setariaitalica (L.)]. Journal of Experimental Botany, 62, 3387–3401.10.1093/jxb/err016
   PubMed Web of Science ®Google Scholar
• Laurie, A. T. R., & Jackson, R. M. (2005). Q-SiteFinder: An energy-based method for the prediction of protein–ligand binding sites. Bioinformatics, 21, 1908–1916.10.1093/bioinformatics/bti315
   PubMed Web of Science ®Google Scholar
• Licausi, F., Giorgi, F. M., Zenoni, S., Osti, F., Pezzotti, M., & Perata, P. (2010). Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genomics, 11, 719–733.10.1186/1471-2164-11-719
   PubMed Web of Science ®Google Scholar
• Licausi, F., Ohme-Takagi, M., & Perata, P. (2013). APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: Mediators of stress responses and developmental programs. New Phytologist, 199, 639–649.10.1111/nph.12291
   PubMed Web of Science ®Google Scholar
• Luscombe, N. M., Laskowski, R. A., & Thornton, J. M. (2001). Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Research, 29, 2860–2874.10.1093/nar/29.13.2860
   PubMed Web of Science ®Google Scholar
• Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83–85.10.1038/356083a0
   PubMed Web of Science ®Google Scholar
• MacIsaac, K., & Fraenkel, E. (2006). Practical strategies for discovering regulatory DNA sequence motifs. PLoS Computational Biology, 2, 201–210.
   Web of Science ®Google Scholar
• Marfori, M., Mynott, A., Ellis, J. J., Mehdi, A. M., Saunders, N. F., Curmi, P. M., … Kobe, B. (2011). Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochimica et Biophysica Acta, 1813, 1562–1577.
   PubMed Web of Science ®Google Scholar
• Mayer, K. F., Waugh, R., Brown, J. W., Schulman, A., Langridge, P., Platzer, M., … Stein, N. (2012). A physical, genetic and functional sequence assembly of the barley genome. The International Barley Genome Sequencing Consortium. Nature, 491, 711–716.
   PubMed Web of Science ®Google Scholar
• Mizoi, J., Ohori, T., Moriwaki, T., Kidokoro, S., Todaka, D., Maruyama, K., … Yamaguchi-Shinozaki, K. (2013). GmDREB2A;2, a canonical dehydration-responsive element-binding protein 2-type transcription factor in soybean, is post-translationally regulated and mediates dehydration-responsive element-dependent gene expression. Plant Physiology, 161, 346–361.10.1104/pp.112.204875
   PubMed Web of Science ®Google Scholar
• Muhammad, N., Naeem, I., Sobia, I., & Ihsan, U. (2014). DREB1A from Oryza sativa var. IR6: Homology modelling and molecular docking. Turkish Journal of Botany, 38, 1095–1102.
   Web of Science ®Google Scholar
• Nevo, E., Fu, Y. B., Pavlicek, T., Khalifa, S., Tavasi, M., & Beiles, A. (2012). Evolution of wild cereals during 28 years of global warming in Israel. Proceedings of the National Academy of Sciences, 109, 3412–3415.10.1073/pnas.1121411109
   PubMed Web of Science ®Google Scholar
• Pandey, B., Sharma, P., Saini, M., Pandey, D. M., & Sharma, I. (2014). Isolation and characterization of dehydration-responsive element-binding factor 2 (DREB2) from Indian wheat (Triticum aestivum L.) cultivars. Australian Journal of Crop Science, 8, 44–54.
   Google Scholar
• Pandey, D. M., & Kumar, A. (2013). 3D structure prediction and protein–DNA interaction of CCCH-type zinc finger transcription factor gene in Rice (Oryza sativa L.). International Journal of Computational Bioinformatics and In Silico Modeling, 2, 94–103.
   Google Scholar
• Poulain, P., Saladin, A., Hartmann, B., & Prévost, C. (2008). Insights on protein-DNA recognition by coarse grain modelling. Journal of Computational Chemistry, 29, 2582–2592.10.1002/jcc.v29:15
   PubMed Web of Science ®Google Scholar
• Prajapati, G. K., Kashyap, N., Kumar, A., & Pandey, D. M. (2013). Identification of GCC Box in the promoter region of ubiquinol cytochrome C chaperone gene using molecular beacon probe and it’s in silico protein-DNA interaction study in rice (Oryza sativa L.). International Journal of Computational Bioinformatics and In Silico Modeling, 2, 213–222.
   Google Scholar
• Prescher, J. A., & Bertozzi, C. R. (2005). Chemistry in living systems. Nature Chemical Biology, 1, 13–21.
   PubMed Web of Science ®Google Scholar
• Qamarunnisa, S., Hussain, M. Q., Jabeen, N. T., Raza, S., Rafiq, M. K., Abid, A., … Naqvi, H. M. (2012). Insilicostudies on structure-function of DNA GCC-BOX binding domain of Brassica napus DREB1 protein. Pakistan Journal of Botony, 44, 493–500.
   Web of Science ®Google Scholar
• Sakuma, Y., Liu, Q., Dubouzet, J. G., Abe, H., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2002). DNA-binding specificity of the ERF/AP2 domain of arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochemical and Biophysical Research Communications, 290, 998–1009.10.1006/bbrc.2001.6299
   PubMed Web of Science ®Google Scholar
• Sharma, P., Saini, M., Tyagi, B. S., & Sharma, I. (2013). Molecular characterization of dimeric alpha-amylase inhibitor genes from Indian wheat genotypes. Indian Journal of Biotechnology, 12, 153–160.
   Web of Science ®Google Scholar
• Sharoni, A. M., Nuruzzaman, M., Satoh, K., Shimizu, T., Kondoh, H., Sasaya, T., … Kikuchi, S. (2011). Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant and Cell Physiology, 52, 344–360.10.1093/pcp/pcq196
   PubMed Web of Science ®Google Scholar
• Shinozaki, K., & Yamaguchi-Shinozaki, K. (2000). Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Current Opinion in Plant Biology, 3, 217–222.
   PubMed Web of Science ®Google Scholar
• Si, J., Zhang, Z., Lin, B., Schroeder, M., & Huang, B. (2011). Meta DB site: A meta approach to improve protein DNAbinding sites prediction. BMC Systems Biology, 5, S7–S14.10.1186/1752-0509-5-S1-S7
   Google Scholar
• Singh, B. P., Jayaswal, P. K., Singh, B., Singh, P. K., Kumar, V., Mishra, S., … Singh, N. K. (2015). Natural allelic diversity in OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance. Plant Cell Reports, 34, 993–1004.10.1007/s00299-015-1760-6
   PubMed Web of Science ®Google Scholar
• Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8, 127–134.10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Wang, J. M., Cieplak, P., & Kollman, P. A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry, 21, 1049–1074.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Wang, X., Chen, X., Liu, Y., Gao, H., Wang, Z., & Sun, G. (2011). CkDREB gene in Caragana korshinskii is involved in the regulation of stress response to multiple abiotic stresses as an AP2/EREBP transcription factor. Molecular Biology Reports, 38, 2801–2811.
   PubMed Web of Science ®Google Scholar
• Wu, Y., Tepper, H. L., & Voth, G. A. (2006). Flexible simple point-charge water model with improved liquid-state properties. The Journal of Chemical Physics, 124, 024503.10.1063/1.2136877
   PubMed Web of Science ®Google Scholar
• Xianjun, P., Xingyong, M., Weihong, F., Man, S., Liqin, C., Alam, I., … Gongshe, L. (2011). Improved drought and salt tolerance of Arabidopsis thaliana by transgenic expression of a novel DREB gene from Leymus chinensis. Plant Cell Reports, 30, 1493–1502.10.1007/s00299-011-1058-2
   PubMed Web of Science ®Google Scholar
• Xu, W., Li, F., Ling, L., & Liu, A. (2013). Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.). BMC Genomics, 14, 785–799.10.1186/1471-2164-14-785
   PubMed Web of Science ®Google Scholar
• Yan, H. W., Hong, L., Zhou, Y. Q., Jiang, H. Y., Zhu, S. W., Fan, J., & Cheng, B. J. (2013). A genome-wide analysis of the ERF gene family in sorghum. Genetics and Molecular Research, 12, 2038–2055.10.4238/2013.May.13.1
   PubMed Web of Science ®Google Scholar
• Zhang, Y. (2009). I-TASSER: Fully automated protein structure prediction in CASP8. Proteins: Structure, Function, and Bioinformatics, 77, 100–113.10.1002/prot.v77.9s
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Zhou, Q., Yang, Z., & Jiang, J. (2013). Discovery AP2/ERF family genes in silico in Medicagotruncatula. African Journal of Biotechnology, 12, 3636–3642.
   Google Scholar
• Zhuang, J., Anyia, A., Vidmar, J., Xiong, A. S., & Zhang, J. (2011). Discovery and expression assessment of the AP2-like genes in Hordeum vulgare. Acta Physiologiae Plantarum, 33, 1639–1649.10.1007/s11738-010-0700-x
   Web of Science ®Google Scholar
• Zhuang, J., Deng, D. X., Yao, Q. H., Zhang, J., Xiong, F., Chen, J. M., & Xiong, A. S. (2010a). Discovery, phylogeny and expression patterns of AP2-like genes in maize. Plant Growth Regulation, 62, 51–58.10.1007/s10725-010-9484-7
   Web of Science ®Google Scholar
• Zhuang, J., Xiong, A. S., Peng, R. H., Gao, F., Zhu, B., Zhang, J., … Yao, Q. H. (2010b). Analysis of Brassica rapa ESTs: Gene discovery and expression patterns of AP2/ERF family genes. Molecular Biology Reports, 37, 2485–2492.
   PubMed Web of Science ®Google Scholar