Homology modeling and molecular docking studies of Purple acid Phosphatase from Setaria italica (Foxtail millet)
Keywords:
PAPs, Homology modeling, Molecular docking, organophosphate, starvationAbstract
Purple acid Phosphatases (PAPs) hydrolyze insoluble organophosphate compounds to soluble Phosphorous which can be directly acquired by plants from the soil. PAPs have major functions in plant phosphorous nutrition and various studies have been carried out on expression and activity induced by phosphorous starvation. In the present study, the three-dimensional structure of PAPs of Setaria italica (Foxtail millet) was generated by homology modeling and was scrutinized by assessment analysis to confirm the suitability and reliability of the predicted model. Further, a molecular docking analysis was carried out using organophosphate compounds such as Diphosphate and Zoledronic acid to study the binding ability. The docked complexes showed the binding affinity of PAPs with the given organophosphate compounds (Diphosphate and Zoledronic acid) possessing energy values of -6.85 and -3.74 Kcal/mol respectively.
References
D. Zohary, M. Hopf and E. Weiss “Domestication of Plants in the Old World: The origin and spread of domesticated plants in Southwest Asia, Europe, and the Mediterranean Basin” Oxford University Press on Demand, 2012
J. L. Bennetzen, J. Schmutz, H. Wang, R. Percifield, J. Hawkins, A. C. Pontaroli, M. Estep, L. Feng, J. N. Vaughn and J. Grimwood “Reference genome sequence of the model plant Setaria” Nature biotechnology 30: 555-561, 2012
G. Zhang, X. Liu, Z. Quan, S. Cheng, X. Xu, S. Pan, M. Xie, P. Zeng, Z. Yue and W. Wang “Genome sequence of foxtail millet (Setariaitalica) provides insights into grass evolution and biofuel potential” Nature biotechnology 30: 549-554, 2012
K. M. Devos and M. D. Gale “Comparative genetics in the grasses” Plant molecular biology 35: 3-15, 1997
D. Xianmin, J. SCHNABLE, J. L. BENNETZEN and L. Jiayang “Initiation of Setaria as a model plant”. Frontiers of Agricultural Science and Engineering 1: 16-20, 2014
M. Muthamilarasan and M. Prasad “Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses” Theoretical and applied genetics 128: 1-14, 2015
H. Yuan and D. Liu “Signaling components involved in plant responses to phosphate starvation” Journal of Integrative Plant Biology 50: 849-859, 2008
H. Lambers and W. C. Plaxton “Phosphorus: back to the roots” Annual Plant Reviews 48: 3-22, 2015
J. Shen, L. Yuan, J. Zhang, H. Li, Z. Bai, X. Chen, W. Zhang and F. Zhang “Phosphorus dynamics: from soil to plant” Plant physiology 156: 997-1005, 2011
M. I. Stutter, C. A. Shand, T. S. George, M. S. Blackwell, R. Bol, R. L. MacKay, A. E. Richardson, L. M. Condron, B. L. Turner and P. M. Haygarth “Recovering phosphorus from soil: a root solution?” ACS Publications, 2012
H. Marschner “Function of mineral nutrients: micronutrient” In Mineral Nutrition of Higher Plants (ed. H Marschner), pp. 379–396. Academic Press, London, UK 1995
C. P. Vance, C. Uhde-Stone and D. L. Allan “Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource” New phytologist 157: 423-447, 2003
D. L. López-Arredondo, M. A. Leyva-González, S. I. González-Morales, J. López-Bucio and L. Herrera-Estrella “Phosphate nutrition: improving low-phosphate tolerance in crops” Annual review of plant biology 65: 95-123, 2014
B. Péret, T. Desnos, R. Jost, S. Kanno, O. Berkowitz and L. Nussaume “Root architecture responses: in search of phosphate” Plant physiology 166: 1713-1723, 2014
B. Zambelli, F. Musiani, S. Benini and S. Ciurli “Chemistry of Ni2+ in urease: sensing, trafficking, and catalysis” Accounts of chemical research 44: 520-530, 2011
G. Schenk, N. Mitić, G. R. Hanson and P. Comba “Purple acid phosphatase: A journey into the function and mechanism of a colorful enzyme” Coordination Chemistry Reviews 257: 473-482, 2013
Y. J. Hur, B. R. Jin, J. Nam, Y. S. Chung, J. H. Lee, H. K. Choi, D. J. Yun, G. Yi, Y. H. Kim and D. H Kim “Molecular characterization of OsPAP2: transgenic expression of a purple acid phosphatase up-regulated in phosphate-deprived rice suspension cells” Biotechnology letters 32: 163, 2010
H. T. Tran, W. Qian, B. A. Hurley, Y. M. SHE, D. Wang and W. C. Plaxton “Biochemical and molecular characterization of AtPAP12 and AtPAP26: the predominant purple acid phosphatase isozymes secreted by phosphate-starved Arabidopsis thaliana” Plant, cell & environment 33: 1789-1803, 2010
Y. Kong, X. Li, J. Ma, W. Li, G. Yan and C. Zhang “GmPAP4, a novel purple acid phosphatase gene isolated from soybean (Glycine max), enhanced extracellular phytate utilization in Arabidopsis thaliana” Plant cell reports 33: 655-667, 2014
L. Wang, Z. Li, W. Qian, W. Guo, X. Gao, L. Huang, H. Wang, H. Zhu, J. W. Wu and D. Wang “The Arabidopsis purple acid phosphatase AtPAP10 is predominantly associated with the root surface and plays an important role in plant tolerance to phosphate limitation” Plant Physiology 157: 1283-1299, 2011
B. A. Hurley, H. T. Tran, N. J. Marty, J. Park, W. A. Snedden, R. T. Mullen and W. C. Plaxton “The dual-targeted purple acid phosphatase isozyme AtPAP26 is essential for efficient acclimation of Arabidopsis to nutritional phosphate deprivation” Plant physiology 153: 1112-1122, 2010
J. Tian and H. Liao “The role of intracellular and secreted purple acid phosphatases in plant phosphorus scavenging and recycling” Annual Plant Reviews, Phosphorus Metabolism in Plants 48: 265, 2015
A. Durmus, C. Eicken, F. Spener and B. Krebs “Cloning and comparative protein modeling of two purple acid phosphatase isozymes from sweet potatoes (Ipomoea batatas)” Biochimica et BiophysicaActa (BBA)-Protein Structure and Molecular Enzymology 1434: 202-209, 1999
G. Schenk, L. Guddat, Y. Ge, L. Carrington, D. Hume, S. Hamilton and De J. Jersey “Identification of mammalian-like purple acid phosphatases in a wide range of plants” Gene 250: 117-125, 2000
D. Li, H. Zhu, K. Liu, X. Liu, G. Leggewie, M. Udvardi and D. Wang “Purple acid phosphatases of Arabidopsis thaliana comparative analysis and differential regulation by phosphate deprivation” Journal of Biological Chemistry 277: 27772-27781, 2002
C. Li, S. Gui, T. Yang, T. Walk, X. Wang X and H. Liao “Identification of soybean purple acid phosphatase genes and their expression responses to phosphorus availability and symbiosis” Annals of botany 109: 275-285, 2012
C. Liang, J. Wang, J. Zhao, J. Tian and H. Liao “Control of phosphate homeostasis through gene regulation in crops” Current opinion in plant biology 21: 59-66, 2014
E. González-Muñoz, A. O. Avendaño-Vázquez, R. A. C. Montes, S. de Folter, L. Andrés-Hernández, C. Abreu-Goodger and R. J. Sawers “The maize (Zea mays ssp. mays var. B73) genome encodes 33 members of the purple acid phosphatase family”. Frontiers in plant science 6, 2015
E. Gasteiger, C. Hoogland, A. Gattiker, Duvaud Se, M. R. Wilkins, R. D. Appel and A. Bairoch “Protein identification and analysis tools on the ExPASy server”. Springer
D. T. Jones “Protein secondary structure prediction based on position-specific scoring matrices” Journal of Molecular Biology 292: 195-202, 1999
Webb B and A Sali “Protein structure modeling with MODELLER” Protein Structure Prediction: 1-15, 2014
N. Guex, M. C. Peitsch “SWISS-MODEL and the Swiss-PDB Viewer: an environment for comparative protein modeling” Electrophoresis 18: 2714-2723, 1997
S. C. Lovell, I. W. Davis, W. B. Arendall III, P. I. W. de Bakker, J. M. Word, M. G. Prisant, J. S. Richardson and D. C. Richardson “Structure validation by Calpha geometry: phi,psi and Cbeta deviation” Proteins: Structure, Function & Genetics 50: 437-450, 2002
Noel M O`Boyle, Michael Banck, Craig A James, Chris Morley,TimVandermeersch and Geoffrey R Hutchison“Open Babel: An open chemical toolbox” Journal of Cheminformatics 3:33, 2011
G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, and A. J. Olson“Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility” J. Computational Chemistry 2009, 16: 2785-91, 2009
S. Rogers, R. Wells and M. Rechsteiner “Amino acid sequences common to rapidly degrade proteins: the PEST hypothesis” Science 234: 364-369, 1986
K. Guruprasad, B. B. Reddy and M. W. Pandit “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 engineering 4: 155-161, 1990
A. Ikai “Thermostability and aliphatic index of globular proteins”. The Journal of Biochemistry 88: 1895-1898, 1980
J. Kyte and R. F. Doolittle “A simple method for displaying the hydropathic character of a protein” Journal of molecular biology 157: 105-132, 1982
P. Zimmermann, B. Regierer, J. Kossmann, E. Frossard, N. Amrhein and M. Bucher “Differential expression of three purple acid phosphatases from potato”. Plant Biology 6: 519-528, 2004
H. Zhu, W. Qian, X. Lu, D. Li, X. Liu, K. Liu and D. Wang “Expression patterns of purple acid phosphatase genes in Arabidopsis organs and functional analysis of AtPAP23 predominantly transcribed in flower” Plant molecular biology 59: 581-594
G. G. Bozzo, K. G. Raghothama and W. C. Plaxton “Purification and characterization of two secreted purple acid phosphatase isozymes from phosphate starved tomato (Lycopersiconesculentum) cell cultures” European Journal of Biochemistry 269: 6278-6286, 2002
H. Kaija, S. L. Alatalo, J. M. Halleen, Y. Lindqvist, G. Schneider, H. K. Väänänen and P. Vihko “Phosphatase and oxygen radical-generating activities of mammalian purple acid phosphatase are functionally independent” Biochemical and biophysical research communications 292: 128-132, 2002
W. Y. Lin, S. I. Lin, T. J. Chiou “Molecular regulators of phosphate homeostasis in plants” Journal of experimental botany: ern303, 2009
E. Vanninen, M. Uusitupa, O. Siitonen, J. Laitinen, E. Länsimies and K. Pyöralä “Effect of diet therapy on maximum aerobic power in obese, hyperglycaemic men with recently diagnosed type 2 diabetes” Scandinavian journal of clinical and laboratory investigation 51: 289-297, 1991
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