Insights into Molecular Assembly of ACCase Heteromeric Complex in Chlorella variabilis—A Homology Modelling, Docking and Molecular Dynamic Simulation Study

详细信息    查看全文

• 作者：Namrata Misra (1) (2)
  Prasanna Kumar Panda (1) (2)
  Mahesh Chandra Patra (3)
  Sukanta Kumar Pradhan (3)
  Barada Kanta Mishra (1)
  
• 关键词：Acetyl ; CoA carboxylase ; Chlorella variabilis ; Homology modelling ; Docking ; Molecular dynamic simulations ; Principal component analysis ; Microalgae ; Biofuel
• 刊名：Applied Biochemistry and Biotechnology
• 出版年：2013
• 出版时间：July 2013
• 年：2013
• 卷：170
• 期：6
• 页码：1437-1457
• 全文大小：1180KB
• 参考文献：1. Podkowinski, J., & Tworak, A. (2011). BioTechnologia - Journal of Biotechnology, / Computational Biology and Bionanotechnology, 92, 321-35.
  2. Klaus, D., Ohlrogge, J. B., Neuhaus, H. E., & Dormann, P. (2004). / Planta, 219, 389-96. ss="external" href="http://dx.doi.org/10.1007/s00425-004-1236-3">CrossRef
  3. Roesler, K., Shintani, D., Savage, L., Boddupalli, S., & Ohlrogge, J. (1997). / Plant Physiology, 113, 75-1. ss="external" href="http://dx.doi.org/10.1104/pp.113.1.75">CrossRef
  4. Wan, M., Liu, P., Xia, J., Rosenberg, J. N., Oyler, G. A., Betenbaugh, M. J., et al. (2011). / Applied Microbiology and Biotechnology, 91, 835-44. ss="external" href="http://dx.doi.org/10.1007/s00253-011-3399-8">CrossRef
  5. Huerlimann, R., & Heimann, K. (2012). / Critical Reviews in Biotechnology, 1-7.
  6. Zhu, X. L., Yang, W. C., Yu, N. X., Yang, S. G., & Yang, G. F. (2011). / Journal of Molecular Modeling, 17, 495-03. ss="external" href="http://dx.doi.org/10.1007/s00894-010-0742-4">CrossRef
  7. Zhu, X. L., & Yang, G. F. (2012). / Current Computer-Aided Drug Design, 8, 62-9. ss="external" href="http://dx.doi.org/10.2174/157340912799218480">CrossRef
  8. Zhu, X. L., Zhang, L., Chen, Q., Wan, J., & Yang, G. F. (2006). / Journal of Chemical Information and Modeling, 46, 1819-826. ss="external" href="http://dx.doi.org/10.1021/ci0600307">CrossRef
  9. Zhu, X. L., Fei, H. G., Zhan, C. G., & Yang, G. F. (2009). / Journal of Chemical Information and Modeling, 49, 1936-943. ss="external" href="http://dx.doi.org/10.1021/ci900174d">CrossRef
  10. Tong, L. (2005). / Cellular and Molecular Life Sciences, 62, 1784-803. ss="external" href="http://dx.doi.org/10.1007/s00018-005-5121-4">CrossRef
  11. Diacovich, L., Mitchell, D. L., Pham, H., Gago, G., Melgar, M. M., Khosla, C., et al. (2004). / Biochemistry, 43, 14027-4036. ss="external" href="http://dx.doi.org/10.1021/bi049065v">CrossRef
  12. Athappilly, F. K., & Hendrickson, W. A. (1995). / Structure, 3, 1407-419. ss="external" href="http://dx.doi.org/10.1016/S0969-2126(01)00277-5">CrossRef
  13. Waldrop, G. L., Rayment, I., & Holden, H. M. (1994). / Biochemistry, 33, 10249-0256. ss="external" href="http://dx.doi.org/10.1021/bi00200a004">CrossRef
  14. Cho, C. Y., Yu, L. P., & Tong, L. (2009). / Journal of Biological Chemistry, 284, 11690-1697. ss="external" href="http://dx.doi.org/10.1074/jbc.M805783200">CrossRef
  15. Bilder, P., Lightle, S., Bainbridge, G., Ohren, J., Finzel, B., Sun, F., et al. (2006). / Biochemistry, 45, 1712-722. ss="external" href="http://dx.doi.org/10.1021/bi0520479">CrossRef
  16. Mochalkin, I., Miller, J. R., Evdokimov, A., Lightle, S., Yan, C., Stover, C. K., et al. (2008). / Protein Science, 17, 1706-718. ss="external" href="http://dx.doi.org/10.1110/ps.035584.108">CrossRef
  17. Polyak, S. W., Abell, A. D., Wilce, M. C. J., Zhang, L., & Booker, G. W. (2012). / Applied Microbiology and Biotechnology, 93, 983-92. ss="external" href="http://dx.doi.org/10.1007/s00253-011-3796-z">CrossRef
  18. Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F., & Sali, A. (2012). / Annual Reviews of Biophysics and Biomolecular Structures, 29, 291-25. ss="external" href="http://dx.doi.org/10.1146/annurev.biophys.29.1.291">CrossRef
  19. Smith, G. R., & Sternberg, M. J. E. (2002). / Current Opinion in Structural Biology, 12, 28-5. ss="external" href="http://dx.doi.org/10.1016/S0959-440X(02)00285-3">CrossRef
  20. Lietzan, A. D., Menefee, A. L., Zeczycki, T. N., Kumar, S., Attwood, P. V., Wallace, J. C., et al. (2011). / Biochemistry, 50, 9708-723. ss="external" href="http://dx.doi.org/10.1021/bi201277j">CrossRef
  21. Jitrapakdee, S., & Wallace, J. C. (2003). / Current Protein & Peptide Science, 4, 217-29. ss="external" href="http://dx.doi.org/10.2174/1389203033487199">CrossRef
  22. Misra, N., & Panda, P. K. (2013). / OMICS: A Journal of Integrative Biology, 17, 173-86. ss="external" href="http://dx.doi.org/10.1089/omi.2012.0094">CrossRef
  23. Baral, M., Misra, N., Panda, P. K., & Thirunavoukkarasu, M. (2012). / Biotechnology and Biotechnological Equipment, 26, 2794-800. ss="external" href="http://dx.doi.org/10.5504/bbeq.2011.0155">CrossRef
  24. Misra, N., Patra, M. C., Panda, P. K., Sukla, L. B., & Mishra, B. K. (2013). / Journal of Biomolecular Structure and Dynamics, 31, 241-57. ss="external" href="http://dx.doi.org/10.1080/07391102.2012.698247">CrossRef
  25. Blatti, J. L., Beld, J., Behnke, C. A., Mendez, M., Mayfield, S. P., & Burkart, M. D. (2012). / PLoS One, 7, 1-2. ss="external" href="http://dx.doi.org/10.1371/journal.pone.0042949">CrossRef
  26. Radakovits, R., Jinkerson, R. E., Darzins, A., & Posewitz, M. C. (2010). / Eukaryotic Cell, 9, 486-01. ss="external" href="http://dx.doi.org/10.1128/EC.00364-09">CrossRef
  27. Yu, W. L., Ansari, W., Schoepp, N. G., Hannon, M. J., Mayfield, S. P., & Burkart, M. D. (2011). / Microbial Cell Factories, 10, 91-02. ss="external" href="http://dx.doi.org/10.1186/1475-2859-10-91">CrossRef
  28. Sali, A., & Blundell, T. L. (1993). / Journal of Molecular Biology, 234, 779-15. ss="external" href="http://dx.doi.org/10.1006/jmbi.1993.1626">CrossRef
  29. Katoh, K., Kuma, K., Toh, H., & Miyata, T. (2005). / Nucleic Acids Research, 33, 511-18. ss="external" href="http://dx.doi.org/10.1093/nar/gki198">CrossRef
  30. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). / Molecular Biology and Evolution, 28, 2731-739. ss="external" href="http://dx.doi.org/10.1093/molbev/msr121">CrossRef
  31. Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., et al. (1998). / Journal of Computational Chemistry, 19, 1639-662. ss="external" href="http://dx.doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B">CrossRef
  32. Wang, Y., Bolton, E., Dracheva, S., Karapetyan, K., Shoemaker, B. A., Suzek, T. O., et al. (2010). / Nucleic Acids Research, 38, D255–D266. ss="external" href="http://dx.doi.org/10.1093/nar/gkp965">CrossRef
  33. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). / Nucleic Acids Research, 33, 363-67. ss="external" href="http://dx.doi.org/10.1093/nar/gki481">CrossRef
  34. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). / Journal of Computational Chemistry, 26, 1701-718. ss="external" href="http://dx.doi.org/10.1002/jcc.20291">CrossRef
  35. Oostenbrink, C., Villa, A., Mark, A. E., & van Gunsteren, W. F. (2004). / Journal of Computational Chemistry, 25, 1656-676. ss="external" href="http://dx.doi.org/10.1002/jcc.20090">CrossRef
  36. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). / Journal of Chemical Physics, 81, 3684-690. ss="external" href="http://dx.doi.org/10.1063/1.448118">CrossRef
  37. Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). / Journal of Computational Chemistry, 18, 1463-472. ss="external" href="http://dx.doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H">CrossRef
  38. Darden, T., York, D., & Pedersen, L. (1993). / Journal of Chemical Physics, 98, 10089-0092. ss="external" href="http://dx.doi.org/10.1063/1.464397">CrossRef
  39. Schuttelkopf, A. W., & van Aalten, D. M. (2004). / Acta Crystallographica Section D: Biological Crystallography, 60, 1355-363. ss="external" href="http://dx.doi.org/10.1107/S0907444904011679">CrossRef
  40. Humphrey, W., Dalke, A., & Schulten, K. (1996). / Journal of Molecular Graphics, 14, 33-8. ss="external" href="http://dx.doi.org/10.1016/0263-7855(96)00018-5">CrossRef
  41. Yang, L. W., Eyal, E., Bahar, I., & Kitao, A. (2009). / Bioinformatics, 25, 606-14. ss="external" href="http://dx.doi.org/10.1093/bioinformatics/btp023">CrossRef
  42. Lauria, A., Ippolito, M., & Almerico, A. M. (2009). / Computational Biology and Chemistry, 33, 386-90. ss="external" href="http://dx.doi.org/10.1016/j.compbiolchem.2009.07.010">CrossRef
  43. Laskowiski, R. A., Mac Arthur, M. W., Moss, D. S., & Thornton, J. M. (1993). / Journal of Applied Crystallography, 26, 283-91. ss="external" href="http://dx.doi.org/10.1107/S0021889892009944">CrossRef
  44. Benkert, P., Kunzli, M., & Schwede, T. (2009). / Nucleic Acids Research, 37, W510–W514. ss="external" href="http://dx.doi.org/10.1093/nar/gkp322">CrossRef
  45. Wiederstein, M., & Sippl, M. J. (2007). / Nucleic Acids Research, 35, W407–W410. ss="external" href="http://dx.doi.org/10.1093/nar/gkm290">CrossRef
  46. Eisenberg, D., Luthy, R., & Bowle, J. U. (1997). / Methods in Enzymology, 277, 396-04. ss="external" href="http://dx.doi.org/10.1016/S0076-6879(97)77022-8">CrossRef
  47. Colovos, C., & Yeates, T. O. (1993). / Protein Science, 2, 1511-519. ss="external" href="http://dx.doi.org/10.1002/pro.5560020916">CrossRef
  48. Benkert, P., Tosatto, S. C., & Schomburg, D. (2008). / Proteins, 71, 261-77. ss="external" href="http://dx.doi.org/10.1002/prot.21715">CrossRef
  49. Galperin, M. Y., & Koonin, E. V. (1997). / Protein Science, 6, 2639-643. ss="external" href="http://dx.doi.org/10.1002/pro.5560061218">CrossRef
  50. Climent, I., & Rubio, V. (1986). / Archives of Biochemistry and Biophysics, 251, 465-70. ss="external" href="http://dx.doi.org/10.1016/0003-9861(86)90353-X">CrossRef
  51. Fan, C., Moews, P. C., Walsh, C. T., & Knox, J. R. (1994). / Science, 266, 439-43. ss="external" href="http://dx.doi.org/10.1126/science.7939684">CrossRef
  52. Hara, T., Kato, H., Katsube, Y., & Oda, J. (1996). / Biochemistry, 35, 11967-1974. ss="external" href="http://dx.doi.org/10.1021/bi9605245">CrossRef
  53. Thoden, J. B., Wesenberg, G., Raushel, F. M., & Holden, H. M. (1999). / Biochemistry, 38, 2347-357. ss="external" href="http://dx.doi.org/10.1021/bi982517h">CrossRef
  54. Thoden, J. B., Firestine, S., Nixon, A., Benkovic, S., & Holden, H. M. (2000). / Biochemistry, 39, 8791-802. ss="external" href="http://dx.doi.org/10.1021/bi000926j">CrossRef
  55. Thoden, J. B., Blanchard, C. Z., Holden, H. M., & Waldrop, G. L. (2000). / Journal of Biological Chemistry, 275, 16183-6190. ss="external" href="http://dx.doi.org/10.1074/jbc.275.21.16183">CrossRef
  56. Kondo, S., Nakajima, Y., Sugio, S., Yong-Biao, J., Sueda, S., & Kondo, H. (2004). / Acta Crystallographica, D60, 486-92.
  57. Post, L. E., Post, D. J., & Raushel, F. M. (1990). / Journal of Biological Chemistry, 265, 7742-747.
  58. Reinstein, J., Brune, M., & Wittenghofer, A. (1988). / Biochemistry, 27, 4712-720. ss="external" href="http://dx.doi.org/10.1021/bi00413a020">CrossRef
  59. Saraste, M., Sibbald, P. R., & Wittinghofer, A. (1990). / Trends in Biochemical Sciences, 15, 430-34. ss="external" href="http://dx.doi.org/10.1016/0968-0004(90)90281-F">CrossRef
  60. Cronan, J. E., & Waldrop, G. L. (2002). / Progress in Lipid Research, 41, 407-35. ss="external" href="http://dx.doi.org/10.1016/S0163-7827(02)00007-3">CrossRef
  61. Samols, D., Thornton, C. G., Murtif, V. L., Kumar, G. K., Haase, F. C., & Wood, H. G. (1988). / Journal of Biological Chemistry, 263, 6461-464.
  62. Toh, H., Kondo, H., & Tanabe, T. (1993). / European Journal of Biochemistry, 215, 687-96. ss="external" href="http://dx.doi.org/10.1111/j.1432-1033.1993.tb18080.x">CrossRef
  63. Pal, D., & Chakrabati, P. (2002). / Biopolymers, 63, 195-06. ss="external" href="http://dx.doi.org/10.1002/bip.10051">CrossRef
  64. Gunasekaran, K., Ramakrishnan, C., & Balaram, P. (1996). / Journal of Molecular Biology, 264, 191-98. ss="external" href="http://dx.doi.org/10.1006/jmbi.1996.0633">CrossRef
  65. Thelen, J. J., Mekhedov, S., & Ohlrogge, J. B. (2001). / Plant Physiology, 125, 2016-028. ss="external" href="http://dx.doi.org/10.1104/pp.125.4.2016">CrossRef
  66. Fall, R. R., Glaser, M., & Vagelos, P. R. (1976). / Journal of Biological Chemistry, 251, 2063-069.
  67. Holden, H. M., Benning, M. M., Haller, T., & Gerlt, J. A. (2001). / Accounts of Chemical Research, 34, 145-57. ss="external" href="http://dx.doi.org/10.1021/ar000053l">CrossRef
  68. Kozaki, A., Mayumi, K., & Sasaki, Y. (2001). / Journal of Biological Chemistry, 276, 39919-9925. ss="external" href="http://dx.doi.org/10.1074/jbc.M103525200">CrossRef
  69. Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). / Proteins: Structure Function, and Bioinformatics, 17, 412-25. ss="external" href="http://dx.doi.org/10.1002/prot.340170408">CrossRef
  70. Garcia, A. E. (1992). / Physical Review Letters, 68, 2696-699. ss="external" href="http://dx.doi.org/10.1103/PhysRevLett.68.2696">CrossRef
  
• 作者单位：Namrata Misra (1) (2)
  Prasanna Kumar Panda (1) (2)
  Mahesh Chandra Patra (3)
  Sukanta Kumar Pradhan (3)
  Barada Kanta Mishra (1)
  
  1. Academy of Scientific and Innovative Research, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, 751 013, Odisha, India
  2. Bioresources Engineering Department, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, 751 013, Odisha, India
  3. Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, 751 003, Odisha, India
  

文摘

Acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that catalyses the first committed step of fatty acid biosynthesis, is considered as a potential target for improving lipid accumulation in oleaginous feedstocks, including microalgae. ACCase is composed of three distinct conserved domains, and understanding the structural details of each catalytic domain assumes great significance to gain insights into the molecular basis of the complex formation and mechanism of biotin transport. In the absence of a crystal structure for any single heteromeric ACCase till date, here we report the first heteromeric association model of ACCase from an oleaginous green microalga, Chlorella variabilis, using a combination of homology modelling, docking and molecular dynamic simulations. The binding site of the docked biotin carboxylase (BC) and carboxyltransferase (CT) were predicted to be contiguous but distinct in biotin carboxyl carrier protein (BCCP) molecule. Simulation studies revealed considerable flexibility for the BC and CT domains in the BCCP-bound forms, thus indicating the adaptive behaviour of BCCP. Further, principal component analysis revealed that in the presence of BCCP, the BC and CT domains exhibited an open-state conformation via the outward clockwise rotation of the binding helices. These conformational changes might be responsible for binding of BCCP domain and its translocation to the respective active sites. Various rearrangements of inter-domain hydrogen bonds (H-bonds) contributed to conformational changes in the structures. H-bond interactions between the interacting residue pairs involving Glu201BCCP/Arg255BC and Asp224BCCP/Gln228CT were found to be essential for the intermolecular assembly. The present findings are consistent with previous biochemical studies.