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Research Article

Computational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding

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Pages 4374-4383 | Received 13 Jul 2018, Accepted 08 Nov 2018, Published online: 28 Jan 2019

References

  • Andersen, H. C. (1983). Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52(1),24–34. doi:10.1016/0021-9991(83)90014-1
  • Bayly, C. I., Cieplak, P., Cornell, W., & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. The Journal of Physical Chemistry, 97(40),10269–10280. doi:10.1021/j100142a004
  • Burg, J. S., & Espenshade, P. J. (2011). Regulation of HMG-CoA reductase in mammals and yeast. Progress in Lipid Research, 50(4),403–410. doi:10.1016/j.plipres.2011.07.002
  • Burg, J. S., Powell, D. W., Chai, R., Hughes, A. L., Link, A. J., & Espenshade, P. J. (2008). Insig regulates HMG-CoA reductase by controlling enzyme phosphorylation in fission yeast. Cell Metabolism, 8(6),522–531. https://doi:10.1016/j.cmet.2008.09.004
  • Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16),1668–1688. doi:10.1002/jcc.20290
  • Cerqueira, N. M. F. S. A., Oliveira, E. F., Gesto, D. S., Santos-Martins, D., Moreira, C., Moorthy, H. N., … Fernandes, P. A. (2016). Cholesterol biosynthesis: A mechanistic overview. Biochemistry, 55(39),5483–5506. doi:10.1021/acs.biochem.6b00342
  • Clarke, P. R., & Hardie, D. G. (1990). Regulation of HMG-CoA reductase: Identification of the site phosphorylated by the AMP-activated protein kinase in vitro and in intact rat liver. The EMBO Journal, 9(8),2439–2446. doi:10.1002/j.1460-2075.1990.tb07420.x
  • Friesen, J. A., & Rodwell, V. W. (2004). The 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductases. Genome Biology, 5(11),248. doi:10.1186/gb-2004-5-11-248
  • Frisch, M. J.,Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2009). Gaussian 09. Gaussian, Inc. Wallingford CT. Wallingford CT: Gaussian Inc.
  • Haines, B. E., Steussy, C. N., Stauffacher, C. V., & Wiest, O. (2012). Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase. Biochemistry, 51(40),7983–7995. doi: 10.1021/bi3008593
  • Hardie, D. G., Hawley, S. A., & Scott, J. W. (2006). AMP-activated protein kinase – development of the energy sensor concept. The Journal of Physiology, 574(1),7–15. doi:10.1113/jphysiol.2006.108944
  • Hestenes, M. R., & Stiefel, E. (1952). Methods of conjugate gradients for solving linear systems. Journal of Research of the National Bureau of Standards, 49(6),409. doi:10.6028/jres.049.044
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3),712–725. doi:10.1002/prot.21123
  • Huff, M. W., & Telford, D. E. (2005). Lord of the rings – The mechanism for oxidosqualene:lanosterol cyclase becomes crystal clear. Trends in Pharmacological Sciences, 26(7),335–340. doi:10.1016/j.tips.2005.05.004
  • Istvan, E. S. (2001). Bacterial and mammalian HMG-CoA reductases: Related enzymes with distinct architectures. Current Opinion in Structural Biology, 11(6),746–751. doi:10.1016/S0959-440X(01)00276-7
  • Istvan, E. S., & Deisenhofer, J. (2000). The structure of the catalytic portion of human HMG-CoA reductase. Biochimica et Biophysica Acta – Molecular and Cell Biology of Lipids, 1529(1–3),9–18. doi:10.1016/S1388-1981(00)00134-7
  • Istvan, E. S., Palnitkar, M., Buchanan, S. K., & Deisenhofer, J. (2000). Crystal structure of the catalytic portion of human HMG-CoA reductase: Insights into regulation of activity and catalysis. The EMBO Journal, 19(5),819–830. doi:10.1093/emboj/19.5.819
  • Jawaid, S., Gertz, M., Corsino, C., Cheung, J., Seidle, H., & Couch, R. D. (2010). Human hydroxymethylglutaryl-coenzyme a reductase (HMGCR) and statin sensitivity. Indian Journal of Biochemistry and Biophysics, 47(6),331–339.
  • Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45),11225–11236. doi:10.1021/ja9621760
  • Lichtenstein, A. H. (1990). Intestinal cholesterol metabolism. Annals of Medicine, 22(1),49–52. doi:10.3109/07853899009147241
  • Lima, A. H., dos Santos, A. M., Alves, C. N., & Lameira, J. (2017). Computed insight into a peptide inhibitor preventing the induced fit mechanism of MurA enzyme from Pseudomonas aeruginosa. Chemical Biology & Drug Design, 89(4),599–607. doi:10.1111/cbdd.12882
  • Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., … Richardson, D. C. (2003). Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Structure, Function, and Bioinformatics, 50(3),437–450. doi:10.1002/prot.10286
  • Melo, F., & Feytmans, E. (1998). Assessing protein structures with a non-local atomic interaction energy. Journal of Molecular Biology, 277(5),1141–1152. doi:10.1006/jmbi.1998.1665
  • Miller, B. R., & Kung, Y. (2018). Structural features and domain movements controlling substrate binding and cofactor specificity in Class II HMG-CoA reductase. Biochemistry, 57(5),654–662. doi:10.1021/acs.biochem.7b00999
  • Minkara, M. S., Ucisik, M. N., Weaver, M. N., & Merz, K. M. (2014). Molecular dynamics study of Helicobacter pylori urease. Journal of Chemical Theory and Computation, 10(5),1852–1862. doi:10.1021/ct5000023
  • Omkumar, R. V., & Rodwell, V. W. (1994). Phosphorylation of ser871 impairs the function of His865 of syrian hamster 3-hydroxy-3-methylglutaryl-CoA reductase. The Journal of Biological Chemistry, 269(24),16862–16866. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8207009
  • Semighini, E. P., Resende, J. A., De Andrade, P., Morais, P. A. B., Carvalho, I., Taft, C. A., & Silva, C. H. T. P. (2011). Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes. Journal of Biomolecular Structure and Dynamics, 28(5),787–796. doi:10.1080/07391102.2011.10508606
  • Tabernero, L., Bochar, D. A., Rodwell, V. W., & Stauffacher, C. V. (1999). Substrate-induced closure of the flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase. Proceedings of the National Academy of Sciences of the United States of America, 96(13),7167–7171.
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9),1157–1174. doi:10.1002/jcc.20035
  • Warshel, A. (2014). Multiscale modeling of biological functions: From enzymes to molecular machines (Nobel Lecture). Angewandte Chemie International Edition, 53(38),10020–10031. doi:10.1002/anie.201403689
  • World Health Organization (2017). World Health Organization. The top 10 causes of death. Fact Sheet N°310. Retrieved from http://www.who.int/mediacentre/factsheets/fs310/en/
  • Yang, Z., Cao, Y., Hao, D., Yuan, X., Zhang, L., & Zhang, S. (2017). Binding profiles of cholesterol ester transfer protein with current inhibitors: A look at mechanism and drawback. Journal of Biomolecular Structure and Dynamics, 1,14. doi:10.1080/07391102.2017.1363661
  • Zhang, Y. (2009). I-TASSER: Fully automated protein structure prediction in CASP8. Proteins: Structure, Function, and Bioinformatics, 77(S9),100–113. doi:10.1002/prot.22588

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