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BioMed Research International
Volume 2014, Article ID 583606, 20 pages
http://dx.doi.org/10.1155/2014/583606
Research Article

Structural Comparison, Substrate Specificity, and Inhibitor Binding of AGPase Small Subunit from Monocot and Dicot: Present Insight and Future Potential

1Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013, India
2Department of Life Science & Bioinformatics, Assam University, Silchar, Assam 788011, India

Received 28 February 2014; Revised 8 April 2014; Accepted 21 April 2014; Published 2 September 2014

Academic Editor: Rituraj Purohit

Copyright © 2014 Kishore Sarma et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. R. Salamone, T. W. Greene, I. H. Kavakli, and T. W. Okita, “Isolation and characterization of a higher plant ADP-glucose pyrophosphorylase small subunit homotetramer,” FEBS Letters, vol. 482, no. 1-2, pp. 113–118, 2000. View at Publisher · View at Google Scholar · View at Scopus
  2. C. Martin and A. M. Smith, “Starch biosynthesis,” Plant Cell, vol. 7, no. 7, pp. 971–985, 1995. View at Publisher · View at Google Scholar · View at Scopus
  3. J. Preiss, “Biology and molecular biology of starch synthesis and its regulation,” Plant Molecular and Cellular Biology, vol. 7, pp. 59–114, 1991. View at Google Scholar
  4. J. Preiss, “Bacterial glycogen synthesis and its regulation,” Annual Review of Microbiology, vol. 38, pp. 419–458, 1984. View at Publisher · View at Google Scholar · View at Scopus
  5. C. J. Slattery, I. H. Kavakli, and T. W. Okita, “Engineering starch for increased quantity and quality,” Trends in Plant Science, vol. 5, no. 7, pp. 291–298, 2000. View at Publisher · View at Google Scholar · View at Scopus
  6. M. A. Ballicora, A. A. Iglesias, and J. Preiss, “ADP-glucose pyrophosphorylase: a regulatory enzyme for plant starch synthesis,” Photosynthesis Research, vol. 79, no. 1, pp. 1–24, 2004. View at Publisher · View at Google Scholar · View at Scopus
  7. L. A. Kleczkowski, “Is leaf ADP-glucose pyrophosphorylase an allosteric enzyme?” Biochimica et Biophysica Acta, vol. 1476, no. 1, pp. 103–108, 2000. View at Publisher · View at Google Scholar · View at Scopus
  8. A. Tiessen, J. H. M. Hendriks, M. Stitt et al., “Starch synthesis in potato tubers is regulated by post-translational redox modification of ADP-glucose pyrophosphorylase: a novel regulatory mechanism linking starch synthesis to the sucrose supply,” The Plant Cell, vol. 14, no. 9, pp. 2191–2213, 2002. View at Publisher · View at Google Scholar · View at Scopus
  9. C. Y. Tsai and O. E. Nelson, “Starch-deficient maize mutant lacking adenosine diphosphate glucose pyrophosphorylase activity,” Science, vol. 151, no. 3708, pp. 341–343, 1966. View at Publisher · View at Google Scholar · View at Scopus
  10. L. C. Hannah and O. E. Nelson Jr., “Characterization of ADP glucose pyrophosphorylase from shrunken 2 and brittle 2 mutants of maize,” Biochemical Genetics, vol. 14, no. 7-8, pp. 547–560, 1976. View at Publisher · View at Google Scholar · View at Scopus
  11. T. P. Lin, T. Casper, C. R. Sommerville, and J. Preiss, “A starch-deficient mutant of Arabidopsis thaliana with low ADP-glucose pyrophosphorylase activity lacks one of the two subunits of the enzyme,” Plant Physiology, vol. 88, pp. 1175–1181, 1988. View at Google Scholar
  12. B. Muller-Rober, U. Sonnewald, and L. Willmitzer, “Inhibition of the ADP-glucose pyrophosphorylase in transgenic potatoes leads to sugar-storing tubers and influences tuber formation and expression of tuber storage protein genes,” The EMBO Journal, vol. 11, no. 4, pp. 1229–1238, 1992. View at Google Scholar · View at Scopus
  13. D. M. Stark, K. P. Timmerman, G. I. Barry, J. Preiss, and G. M. Kishore, “Regulation of the amount of starch in plant tissues by ADP glucose pyrophosphorylase,” Science, vol. 258, no. 5080, pp. 287–292, 1992. View at Publisher · View at Google Scholar · View at Scopus
  14. A. A. Iglesias, G. F. Barry, C. Meyer et al., “Expression of the potato tuber ADP-glucose pyrophosphorylase in Escherichia coli,” The Journal of Biological Chemistry, vol. 268, no. 2, pp. 1081–1086, 1993. View at Google Scholar · View at Scopus
  15. T. H. Haugen, A. Ishaque, and J. Preiss, “Biosynthesis of bacterial glycogen. Characterization of the subunit structure of Escherichia coli B glucose 1 phosphate adenyltransferase (EC 2.7.7.27),” The Journal of Biological Chemistry, vol. 251, no. 24, pp. 7880–7885, 1976. View at Google Scholar · View at Scopus
  16. T. W. Okita, P. A. Nakata, J. M. Anderson, J. Sowokinos, M. Morell, and J. Preiss, “The subunit structure of potato tuber ADPglucose pyrophosphorylase,” Plant Physiology, vol. 93, no. 2, pp. 785–790, 1990. View at Publisher · View at Google Scholar · View at Scopus
  17. M. A. Ballicora, A. A. Iglesias, and J. Preiss, “ADP-glucose pyrophosphorylase, a regulatory enzyme for bacterial glycogen synthesis,” Microbiology and Molecular Biology Reviews, vol. 67, no. 2, pp. 213–225, 2003. View at Publisher · View at Google Scholar · View at Scopus
  18. B. J. Smith-White and J. Preiss, “Comparison of proteins of ADP-glucose pyrophosphorylase from diverse sources,” Journal of Molecular Evolution, vol. 34, no. 5, pp. 449–464, 1992. View at Publisher · View at Google Scholar · View at Scopus
  19. K. Ball and J. Preiss, “Allosteric sites of the large subunit of the spinach leaf ADPglucose pyrophosphorylase,” Journal of Biological Chemistry, vol. 269, no. 40, pp. 24706–24711, 1994. View at Google Scholar · View at Scopus
  20. M. A. Ballicora, M. J. Laughlin, Y. Fu, T. W. Okita, G. F. Barry, and J. Preiss, “Adenosine 5′-diphosphate-glucose pyrophosphorylase from potato tuber: significance of the N terminus of the small subunit for catalytic properties and heat stability,” Plant Physiology, vol. 109, no. 1, pp. 245–251, 1995. View at Publisher · View at Google Scholar · View at Scopus
  21. T. W. Greene, S. E. Chantler, M. L. Kahn, G. F. Barry, J. Preiss, and T. W. Okita, “Mutagenesis of the potato ADPglucose pyrophosphorylase and characterization of an allosteric mutant defective in 3-phosphoglycerate activation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 4, pp. 1509–1513, 1996. View at Publisher · View at Google Scholar · View at Scopus
  22. M. A. Ballicora, Y. Fu, N. M. Nesbitt, and J. Preiss, “ADP-glucose pyrophosphorylase from potato tubers. Site-directed mutagenesis studies of the regulatory sites,” Plant Physiology, vol. 118, no. 1, pp. 265–274, 1998. View at Publisher · View at Google Scholar · View at Scopus
  23. M. J. Laughlin, J. W. Payne, and T. W. Okita, “Substrate binding mutants of the higher plant ADP-glucose pyrophosphorylase,” Phytochemistry, vol. 47, no. 4, pp. 621–629, 1998. View at Publisher · View at Google Scholar · View at Scopus
  24. I. H. Kavakli, J. S. Park, C. J. Slattery, P. R. Salamone, J. Frohlick, and T. W. Okita, “Analysis of allosteric effector binding sites of potato ADP-glucose pyrophosphorylase through reverse genetics,” The Journal of Biological Chemistry, vol. 276, no. 44, pp. 40834–40840, 2001. View at Publisher · View at Google Scholar · View at Scopus
  25. P. R. Salamone, I. H. Kavakli, C. J. Slattery, and T. W. Okita, “Directed molecular evolution of ADP-glucose pyrophosphorylase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 2, pp. 1070–1075, 2002. View at Publisher · View at Google Scholar · View at Scopus
  26. I. H. Kavakli, T. W. Greene, P. R. Salamone, S. Choi, and T. W. Okita, “Investigation of subunit function in ADP-glucose pyrophosphorylase,” Biochemical and Biophysical Research Communications, vol. 281, no. 3, pp. 783–787, 2001. View at Publisher · View at Google Scholar · View at Scopus
  27. S. K. Hwang, S. Hamada, and T. W. Okita, “ATP binding site in the plant ADP-glucose pyrophosphorylase large subunit,” FEBS Letters, vol. 580, no. 28-29, pp. 6741–6748, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. S. K. Hwang, Y. Nagai, D. Kim, and T. W. Okita, “Direct appraisal of the potato tuber ADP-glucose pyrophosphorylase large subunit in enzyme function by study of a novel mutant form,” The Journal of Biological Chemistry, vol. 283, no. 11, pp. 6640–6647, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. J. M. Cross, M. Clancy, J. R. Shaw et al., “A polymorphic motif in the small subunit of ADP-glucose pyrophosphorylase modulates interactions between the small and large subunits,” The Plant Journal, vol. 41, no. 4, pp. 501–511, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. X. S. Jin, M. A. Ballicora, J. Preies, and J. H. Geiger, “Crystal structure of potato tuber ADP-glucose pyrophosphorylase,” The EMBO Journal, vol. 24, no. 4, pp. 694–704, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. F. Melo and E. Feytmans, “Assessing protein structures with a non-local atomic interaction energy,” Journal of Molecular Biology, vol. 277, no. 5, pp. 1141–1152, 1998. View at Publisher · View at Google Scholar · View at Scopus
  32. R. G. Bodade, S. D. Beedkar, A. V. Manwar, and C. N. Khobragade, “Homology modeling and docking study of xanthine oxidase of Arthrobacter sp. XL26,” International Journal of Biological Macromolecules, vol. 47, no. 2, pp. 298–303, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. S. Witz, P. Panwar, M. Schober et al., “Structure-function relationship of a plant NCS1 member—homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from arabidopsis,” PLoS ONE, vol. 9, Article ID e91343, 2014. View at Google Scholar
  34. B. Kamaraj and R. Purohit, “In-silico analysis of Betaine Aldehyde Dehydrogenase2 of Oryza sativa and significant mutations responsible for fragrance,” Journal of Plant Interactions, vol. 8, pp. 321–333, 2013. View at Publisher · View at Google Scholar · View at Scopus
  35. R. Xu, S. Zhang, J. Huang, and C. Zheng, “Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with arabidopsis and Oryza sativa,” PLoS ONE, vol. 8, Article ID e78982, 2013. View at Google Scholar
  36. M. Lakshmanan, B. Mohanty, and D. Y. Lee, “Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis,” Rice, vol. 6, pp. 1–5, 2013. View at Google Scholar
  37. R. Kolodny and M. Kosloff, “From protein structure to function via computational tools and approaches,” Israel Journal of Chemistry, vol. 53, no. 3-4, pp. 147–156, 2013. View at Publisher · View at Google Scholar · View at Scopus
  38. F. H. Wallrapp, J. J. Pan, G. Ramamoorthy et al., “Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 13, pp. E1196–E1202, 2013. View at Publisher · View at Google Scholar · View at Scopus
  39. G. L. Gac, C. Ka, R. Joubrel et al., “Structure-function analysis of the human ferroportin iron exporter (SLC40A1): effect of hemochromatosis type 4 disease mutations and identification of critical residues,” Human Mutation, vol. 34, pp. 1371–1380, 2013. View at Google Scholar
  40. N. Chaturvedi, V. K. Singh, and P. N. Pandey, “Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate,” Journal of Structural and Functional Genomics, vol. 14, no. 2, pp. 37–45, 2013. View at Publisher · View at Google Scholar · View at Scopus
  41. S. Kashyap, “In Silico modeling and functional interpretations of Cry1Ab15 toxin from Bacillus thuringiensis BtB-Hm-16,” BioMed Research International, vol. 2013, Article ID 471636, 10 pages, 2013. View at Publisher · View at Google Scholar
  42. K. Sarma, B. Dehury, J. Sahu et al., “A comparative proteomic approach to analyse structure, function and evolution of rice chitinases: a step towards increasing plant fungal resistance,” Journal of Molecular Modeling, vol. 18, no. 11, pp. 4761–4780, 2012. View at Publisher · View at Google Scholar · View at Scopus
  43. D. K. Rai and E. Rieder, “Homology modeling and analysis of structure predictions of the bovine rhinitis B virus RNA dependent RNA polymerase (RdRp),” International Journal of Molecular Sciences, vol. 13, no. 7, pp. 8998–9013, 2012. View at Publisher · View at Google Scholar · View at Scopus
  44. B. Ganguly and S. Prasad, “Homology modeling and functional annotation of bubaline pregnancy associated glycoprotein 2,” Journal of Animal Science and Biotechnology, vol. 3, article 13, 2012. View at Publisher · View at Google Scholar
  45. A. G. Thorsell, W. H. Lee, C. Persson et al., “Comparative structural analysis of lipid binding START domains,” PLoS ONE, vol. 6, no. 6, Article ID e19521, 2011. View at Publisher · View at Google Scholar · View at Scopus
  46. J. R. Manning, M. A. Bailey, D. C. Soares, D. R. Dunbar, and J. J. Mullins, “In silico structure-function analysis of pathological variation in the HSD11B2 gene sequence,” Physiological Genomics, vol. 42, no. 3, pp. 319–330, 2010. View at Publisher · View at Google Scholar · View at Scopus
  47. S. W. Chen and J. L. Pellequer, “Identification of functionally important residues in proteins using comparative models,” Current Medicinal Chemistry, vol. 11, no. 5, pp. 595–605, 2004. View at Publisher · View at Google Scholar · View at Scopus
  48. J. A. Peterson and S. E. Graham, “A close family resemblance: the importance of structure in understanding cytochromes P450,” Structure, vol. 6, no. 9, pp. 1079–1085, 1998. View at Publisher · View at Google Scholar · View at Scopus
  49. C. Dawar, S. Jain, and S. Kumar, “Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativa L.),” Journal of Molecular Modeling, vol. 19, no. 8, pp. 3351–3367, 2013. View at Publisher · View at Google Scholar · View at Scopus
  50. W. Wang and J. Messing, “Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed),” BMC Plant Biology, vol. 12, article 5, 2012. View at Publisher · View at Google Scholar · View at Scopus
  51. M. Petreikov, M. Eisenstein, Y. Yeselson, J. Preiss, and A. A. Schaffer, “Characterization of the AGPase large subunit isoforms from tomato indicates that the recombinant L3 subunit is active as a monomer,” Biochemical Journal, vol. 428, no. 2, pp. 201–212, 2010. View at Publisher · View at Google Scholar · View at Scopus
  52. I. Baris, A. Tuncel, N. Ozber, O. Keskin, and I. H. Kavakli, “Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase,” PLoS Computational Biology, vol. 5, no. 10, Article ID e1000546, 2009. View at Publisher · View at Google Scholar · View at Scopus
  53. N. Georgelis, J. R. Shaw, and L. C. Hannah, “Phylogenetic analysis of ADP-glucose pyrophosphorylase subunits reveals a role of subunit interfaces in the allosteric properties of the enzyme,” Plant Physiology, vol. 151, no. 1, pp. 67–77, 2009. View at Publisher · View at Google Scholar · View at Scopus
  54. A. Tuncel, I. H. Kavakli, and O. Keskin, “Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase,” Biophysical Journal, vol. 95, no. 8, pp. 3628–3639, 2008. View at Publisher · View at Google Scholar · View at Scopus
  55. N. Georgelis and L. C. Hannah, “Isolation of a heat-stable maize endosperm ADP-glucose pyrophosphorylase variant,” Plant Science, vol. 175, no. 3, pp. 247–254, 2008. View at Publisher · View at Google Scholar · View at Scopus
  56. D. Kim, S. K. Hwang, and T. W. Okita, “Subunit interactions specify the allosteric regulatory properties of the potato tuber ADP-glucose pyrophosphorylase,” Biochemical and Biophysical Research Communications, vol. 362, no. 2, pp. 301–306, 2007. View at Publisher · View at Google Scholar · View at Scopus
  57. M. A. Ballicora, E. D. Erben, T. Yazaki et al., “Identification of regions critically affecting kinetics and allosteric regulation of the Escherichia coli ADP-glucose pyrophosphorylase by modeling and pentapeptide-scanning mutagenesis,” Journal of Bacteriology, vol. 189, no. 14, pp. 5325–5333, 2007. View at Publisher · View at Google Scholar · View at Scopus
  58. C. M. Bejar, X. Jin, M. A. Ballicora, and J. Preiss, “Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases,” The Journal of Biological Chemistry, vol. 281, no. 52, pp. 40473–40484, 2006. View at Publisher · View at Google Scholar · View at Scopus
  59. E. Gasteiger, C. Hoogl, A. Gattiker et al., “Protein identification and analysis tools on the ExPASy server,” in The Proteomics Protocols Handbook, J. M. Walker, Ed., pp. 571–607, Humana Press, New Jersey, NJ, USA, 2005. View at Google Scholar
  60. Y. Wei, J. Thompson, and C. A. Floudas, “CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization,” Proceedings of the Royal Society A, vol. 468, no. 2139, pp. 831–850, 2012. View at Publisher · View at Google Scholar · View at MathSciNet · View at Scopus
  61. T. Ishida and K. Kinoshita, “Prediction of disordered regions in proteins based on the meta approach,” Bioinformatics, vol. 24, no. 11, pp. 1344–1348, 2008. View at Publisher · View at Google Scholar · View at Scopus
  62. L. Kong and S. Ranganathan, “Delineation of modular proteins: domain boundary prediction from sequence information,” Briefings in bioinformatics, vol. 5, no. 2, pp. 179–192, 2004. View at Publisher · View at Google Scholar · View at Scopus
  63. E. Quevillon, V. Silventoinen, S. Pillai et al., “InterProScan: protein domains identifier,” Nucleic Acids Research, vol. 33, no. 2, pp. W116–W120, 2005. View at Publisher · View at Google Scholar · View at Scopus
  64. M. Punta, P. C. Coggill, R. Y. Eberhardt et al., “The Pfam protein families database,” Nucleic Acids Research, vol. 40, no. 1, pp. D290–D301, 2012. View at Publisher · View at Google Scholar · View at Scopus
  65. A. Marchler-Bauer, C. Zheng, F. Chitsaz et al., “CDD: conserved domains and protein three-dimensional structure,” Nucleic Acids Research, vol. 41, no. 1, pp. D348–D352, 2013. View at Publisher · View at Google Scholar · View at Scopus
  66. I. Letunic, T. Doerks, and P. Bork, “SMART 7: recent updates to the protein domain annotation resource,” Nucleic Acids Research, vol. 40, no. 1, pp. D302–D305, 2012. View at Publisher · View at Google Scholar · View at Scopus
  67. J. C. Wootton, “Non-globular domains in protein sequences: automated segmentation using complexity measures,” Computers and Chemistry, vol. 18, no. 3, pp. 269–285, 1994. View at Publisher · View at Google Scholar · View at Scopus
  68. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Publisher · View at Google Scholar · View at Scopus
  69. P. Gouet, E. Courcelle, D. I. Stuart, and F. Métoz, “ESPript: analysis of multiple sequence alignments in PostScript,” Bioinformatics, vol. 15, no. 4, pp. 305–308, 1999. View at Publisher · View at Google Scholar · View at Scopus
  70. W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.,” Biopolymers, vol. 22, no. 12, pp. 2577–2637, 1983. View at Publisher · View at Google Scholar · View at Scopus
  71. M. A. Kurowski and J. M. Bujnicki, “GeneSilico protein structure prediction meta-server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3305–3307, 2003. View at Publisher · View at Google Scholar · View at Scopus
  72. D. Xu and Y. Zhang, “Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization,” Biophysical Journal, vol. 101, no. 10, pp. 2525–2534, 2011. View at Publisher · View at Google Scholar · View at Scopus
  73. V. Z. Spassov, P. K. Flook, and L. Yan, “LOOPER: a molecular mechanics-based algorithm for protein loop prediction,” Protein Engineering, Design and Selection, vol. 21, no. 2, pp. 91–100, 2008. View at Publisher · View at Google Scholar · View at Scopus
  74. V. Z. Spassov, L. Yan, and P. K. Flook, “The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions,” Protein Science, vol. 16, no. 3, pp. 494–506, 2007. View at Publisher · View at Google Scholar · View at Scopus
  75. B. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, “CHARMM: a program for macromolecular energy, minimization, and dynamics calculations,” Journal of Computational Chemistry, vol. 4, pp. 187–217, 1983. View at Google Scholar
  76. R. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, “PROCHECK-a program to check the stereochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993. View at Google Scholar
  77. C. Colovos and T. O. Yeates, “Verification of protein structures: patterns of nonbonded atomic interactions,” Protein Science, vol. 2, no. 9, pp. 1511–1519, 1993. View at Publisher · View at Google Scholar · View at Scopus
  78. R. Luthy, J. U. Bowie, and D. Eisenberg, “Assesment of protein models with three-dimensional profiles,” Nature, vol. 356, no. 6364, pp. 83–85, 1992. View at Publisher · View at Google Scholar · View at Scopus
  79. M. Pawlowski, M. J. Gajda, R. Matlak, and J. M. Bujnicki, “MetaMQAP: a meta-server for the quality assessment of protein models,” BMC Bioinformatics, vol. 9, article 403, 2008. View at Publisher · View at Google Scholar · View at Scopus
  80. D. Frishman and P. Argos, “Knowledge-based protein secondary structure assignment,” Proteins: Structure, Function and Genetics, vol. 23, no. 4, pp. 566–579, 1995. View at Publisher · View at Google Scholar · View at Scopus
  81. K. G. Tina, R. Bhadra, and N. Srinivasan, “PIC: protein interactions calculator,” Nucleic Acids Research, vol. 35, no. 2, pp. W473–W476, 2007. View at Publisher · View at Google Scholar · View at Scopus
  82. C. M. Venkatachalam, X. Jiang, T. Oldfield, and M. Waldman, “LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites,” Journal of Molecular Graphics and Modelling, vol. 21, no. 4, pp. 289–307, 2003. View at Publisher · View at Google Scholar · View at Scopus
  83. Z. Zhang, Y. Li, B. Lin, M. Schroeder, and B. Huang, “Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction,” Bioinformatics, vol. 27, no. 15, Article ID btr331, pp. 2083–2088, 2011. View at Publisher · View at Google Scholar · View at Scopus
  84. S. K. Boehlein, J. R. Shaw, L. C. Hannah, and J. D. Stewart, “Probing allosteric binding sites of the maize endosperm ADP-glucose pyrophosphorylase,” Plant Physiology, vol. 152, no. 1, pp. 85–95, 2010. View at Publisher · View at Google Scholar · View at Scopus
  85. G. Wu, D. H. Robertson, C. L. Brooks, and M. Vieth, “Detailed analysis of grid-based molecular docking: a case study of CDOCKER—a CHARMm-based MD docking algorithm,” Journal of Computational Chemistry, vol. 24, no. 13, pp. 1549–1562, 2003. View at Publisher · View at Google Scholar · View at Scopus
  86. K. Guruprasad, B. V. 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, vol. 4, no. 2, pp. 155–161, 1990. View at Publisher · View at Google Scholar · View at Scopus
  87. H. J. Dyson and P. E. Wright, “Intrinsically unstructured proteins and their functions,” Nature Reviews Molecular Cell Biology, vol. 6, no. 3, pp. 197–208, 2005. View at Publisher · View at Google Scholar · View at Scopus
  88. V. N. Uversky, C. J. Oldfield, and A. K. Dunker, “Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling,” Journal of Molecular Recognition, vol. 18, no. 5, pp. 343–384, 2005. View at Publisher · View at Google Scholar · View at Scopus
  89. A. K. Dunker, J. D. Lawson, C. J. Brown et al., “Intrinsically disordered protein,” Journal of Molecular Graphics and Modelling, vol. 19, no. 1, pp. 26–59, 2001. View at Publisher · View at Google Scholar · View at Scopus
  90. J. Kyte and R. F. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of Molecular Biology, vol. 157, no. 1, pp. 105–132, 1982. View at Publisher · View at Google Scholar · View at Scopus
  91. J. Sivaraman, V. Sauvé, A. Matte, and M. Cygler, “Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+,” The Journal of Biological Chemistry, vol. 277, no. 46, pp. 44214–44219, 2002. View at Publisher · View at Google Scholar · View at Scopus
  92. A. A. Iglesias and J. Preiss, “Bacterial glycogen and plant starch biosynthesis,” Biochemical Education, vol. 20, no. 4, pp. 196–203, 1992. View at Publisher · View at Google Scholar · View at Scopus
  93. N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon, “Electrostatics of nanosystems: application to microtubules and the ribosome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 18, pp. 10037–10041, 2001. View at Publisher · View at Google Scholar · View at Scopus
  94. C. Hylton and A. M. Smith, “The rb mutation of peas causes structural and regulatory changes in ADP glucose pyrophosphorylase from developing embryos,” Plant Physiology, vol. 99, no. 4, pp. 1626–1634, 1992. View at Publisher · View at Google Scholar · View at Scopus
  95. M. Olive, R. J. Ellis, and W. W. Schuch, “Isolation and nucleotide sequences of cDNA clones encoding ADP-glucose pyrophosphorylase polypeptides from wheat leaf and endosperm,” Plant Molecular Biology, vol. 12, no. 5, pp. 525–538, 1989. View at Publisher · View at Google Scholar · View at Scopus
  96. H. Weber, U. Heim, L. Borisjuk, and U. Wobus, “Cell-type specific, coordinate expression of two ADP-glucose pyrophosphorylase genes in relation to starch biosynthesis during seed development of Vicia faba L.,” Planta, vol. 195, no. 3, pp. 352–361, 1995. View at Publisher · View at Google Scholar · View at Scopus
  97. D. N. P. Doan, H. Rudi, and O. A. Olsen, “The allosterically unregulated isoform of ADP-glucose pyrophosphorylase from barley endosperm is the most likely source of ADP-glucose incorporated into endosperm starch,” Plant Physiology, vol. 121, no. 3, pp. 965–975, 1999. View at Publisher · View at Google Scholar · View at Scopus