In silico thermodynamics stability change analysis involved in BH₄ responsive mutations in phenylalanine hydroxylase: QM/MM and MD simulations analysis

References

• Ania, C. M. (2002). Tetrahydrobipetrin as an alternative treatment for mild phenylketonuria. The New England Journal of Medicine, 347, 2122–2132. doi:10.1056/NEJMoa021654
   PubMed Web of Science ®Google Scholar
• Baldwin, J. E., & Bradley, M. (1990). Isopenicillin N synthase: Mechanistic studies. Chemical Reviews, 90, 1079–1088. doi:10.1021/cr00105a00110.1021/cr00105a001
   Web of Science ®Google Scholar
• Batie, C. J., LaHaie, E., & Ballou, D. P. (1987). Purification and characterization of phthalate oxygenase and phthalate oxygenase reductase from Pseudomonas cepacia. Journal of Biological Chemistry, 262, 1510–1518. Retrieved from http://www.jbc.org/content/262/4/1510.long
   PubMed Web of Science ®Google Scholar
• Blau, N., & Erlandsen, H. (2004). The metabolic and molecular bases of tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency. Molecular Genetics and Metabolism, 82, 101–111. Retrieved from http://dx.doi.org/10.1016/j.ymgme.2004.03.00610.1016/j.ymgme.2004.03.006
   PubMed Web of Science ®Google Scholar
• Costas, M., Mehn, M. P., Jensen, M. P., & Que, L. (2004). Dioxygen activation at mononuclear nonheme iron active sites: Enzymes, models, and intermediates. Chemical Reviews, 104, 939–986. doi:10.1021/cr020628n10.1021/cr020628n
   PubMed Web of Science ®Google Scholar
• Dehouck, Y., Grosfils, A., Folch, B., Gilis, D., Bogaerts, P., & Rooman, M. (2009). Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics, 25, 2537–2543. doi:10.1093/bioinformatics/btp44510.1093/bioinformatics/btp445
   PubMed Web of Science ®Google Scholar
• Dehouck, Y., Kwasigroch, J. M., Gilis, D., & Rooman, M. (2011). PoPMuSiC 2.1: A web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC Bioinformatics, 12, 151. Retrieved from http://www.biomedcentral.com/1471-2105/12/15110.1186/1471-2105-12-151
   PubMed Web of Science ®Google Scholar
• Duch, D. S., Bowers, S. W., Woolf, J. H., & Nichol, C. A. (1984). Biopterin cofactor biosynthesis: GTP cyclohydrolase, neopterin and biopterin in tissues and body fluids of mammalian species. Life Sciences, 35, 1895–1901. Retrieved from http://dx.doi.org/10.1016/0024-3205(84)90541-110.1016/0024-3205(84)90541-1
   PubMed Web of Science ®Google Scholar
• Erlandsen, H., Bjørgo, E., Flatmark, T., & Stevens, R. C. (2000). Crystal structure and site-specific mutagenesis of pterin-bound human phenylalanine hydroxylase. Biochemistry, 39, 2208–2217.10.1021/bi992531+
   PubMed Web of Science ®Google Scholar
• Erlandsen, H., Pey, A. L., Gamez, A., Perez, B., Desviat, L. R., Aguado, C., … Stevens, R. C. (2004). From the cover: Correction of kinetic and stability defects by tetrahydrobiopterin in phenylketonuria patients with certain phenylalanine hydroxylase mutations. Proceedings of the National Academy of Sciences, 101, 16903–16908. doi:10.1073/pnas.040725610110.1073/pnas.0407256101
   PubMed Web of Science ®Google Scholar
• Feig, A. L., & Lippard, S. J. (1994). Reactions of non-heme iron (II) centers with dioxygen in biology and chemistry. Chemical Reviews, 94, 759–805. doi:10.1021/cr00027a01110.1021/cr00027a011
   Web of Science ®Google Scholar
• Field, M. J., Bash, P. A., & Karplus, M. (1990). A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. Journal of Computational Chemistry, 11, 700–733. doi:10.1002/jcc.54011060510.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Fitzpatrick, P. F. (2003). Mechanism of aromatic amino acid hydroxylation. Biochemistry, 42, 14083–14091. doi:10.1021/bi035656u10.1021/bi035656u
   PubMed Web of Science ®Google Scholar
• Francisco, W. A., Tian, G. C., Fitzpatrick, P. F., & Klinman, J. P. (1998). Oxygen-18 kinetic isotope effect studies of the tyrosine hydroxylase reaction: Evidence of rate limiting oxygen activation. Journal of the American Chemical Society, 120, 4057–4062.10.1021/ja973543q
   Web of Science ®Google Scholar
• Grahame-Smith, D. G. (1964). Tryptophan hydroxylation in brain. Biochemical and Biophysical Research Communications, 16, 586–592. doi:10.1016/0006-291X(64)90197-410.1016/0006-291X(64)90197-4
   PubMed Web of Science ®Google Scholar
• Haavik, J., & Toska, K. (1998). Tyrosine hydroxylase and Parkinson’s disease. Molecular Neurobiology, 16, 285–309. doi:10.1007/BF0274138710.1007/BF02741387
   PubMed Web of Science ®Google Scholar
• Jain, A.. (2013) Structure and ligand based drug designing of amino acid hydroxylase enzymes involved in neurodegeneration. Retrieved from http://dspace.dce.edu/handle/repository/14256
   Google Scholar
• Kappock, T. J., & Caradonna, J. P. (1996). Pterin-dependent amino acid hydroxylases. Chemical Reviews, 96, 2659–2756. doi:10.1021/cr940203410.1021/cr9402034
   PubMed Web of Science ®Google Scholar
• Kaufman, S., (1958). A new co-factor required for the enzymatic conversion of phenylalanine to tyrosine. Journal of Biological Chemistry, 230, 931–939. http://www.jbc.org/content/230/2/931
   PubMed Web of Science ®Google Scholar
• Kaufman, S. (1993). New tetrahydrobiopterin-dependent systems. Annual Review of Nutrition, 13, 261–286. doi:10.1146/annurev.nu.13.070193.00140110.1146/annurev.nu.13.070193.001401
   PubMed Web of Science ®Google Scholar
• Kaufman, S. (1995). Tyrosine hydroxylases. Advances in Enzymology and Related Areas of Molecular Biology, 70, 103–220. doi:10.1002/9780470123164.ch3
   PubMedGoogle Scholar
• Kaufman, S., Holtzman, N. A., Milstein, S., Butler, I. J., & Krumholz, A. (1975). Phenylketonuria due to deficiency of dihydrobiopetrin reductase. The New England Journal of Medicine, 293, 785–790. doi:10.1056/NEJM197510162931601
   PubMed Web of Science ®Google Scholar
• Kemsley, J. N., Mitić, N., Zaleski, K. L., Caradonna, J. P., & Solomon, E. I. (1999). Circular dichroism and magnetic circular dichroism spectroscopy of the catalytically competent ferrous active site of phenylalanine hydroxylase and its interaction with pterin cofactor. Journal of the American Chemical Society, 121, 1528–1536. doi:10.1021/ja9833063.10.1021/ja9833063
   Web of Science ®Google Scholar
• Khandelwal, A., Lukacova, V., Comez, D., Kroll, D. M., Raha, S., & Balaz, S. (2005). A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. Journal of Medicinal Chemistry, 48, 5437–5447.10.1021/jm049050v
   PubMed Web of Science ®Google Scholar
• Kollman, P. (1993). Free energy calculations: Applications to chemical and biochemical phenomena. Chemical Reviews, 93, 2395–2417. doi:10.1021/cr00023a00410.1021/cr00023a004
   Web of Science ®Google Scholar
• Lange, S. J., & Que, Jr. L. (1998). Oxygen activating nonheme iron enzymes. Current Opinion in Chemical Biology, 2, 159–172 Retrieved from http://dx.doi.org/10.1016/S1367-5931(98)80057-410.1016/S1367-5931(98)80057-4
   PubMed Web of Science ®Google Scholar
• Martinez, A., Knappskog, P., & Haavik, J. A. (2001). A structural approach into human tryptophan hydroxylase and its implications for the regulation of serotonin biosynthesis. Current Medicinal Chemistry, 8, 1077–1091. doi:10.2174/092986701337261610.2174/0929867013372616
   PubMed Web of Science ®Google Scholar
• Matsuura, S., Sugimoto, T., Murata, S., Sugawara, Y., & Iwasaki, H. (1985). Stereochemistry of biopterin co-factor and facile methods for the determination of the stereochemistry of a biologically active 5, 6, 7, 8-tetrahydropterin. Journal of Biochemistry, 98, 1341–1348. Retrieved from http://jb.oxfordjournals.org/content/98/5/1341.full.pdf+html
   PubMed Web of Science ®Google Scholar
• Muntau, A. C., & Gersting, S. W. (2010). Phenylketonuria as a model for protein misfolding diseases and for the development of next generation orphan drugs for patients with inborn errors of metabolism. Journal of Inherited Metabolic Disease, 33, 649–658. doi:10.1007/s10545-010-9185-410.1007/s10545-010-9185-4
   PubMed Web of Science ®Google Scholar
• Nichol, C. A., Smith, G. K., & Duch, D. S. (1985). Biosynthesis and metabolism of tetrahydrobiopterin and molybdopterin. Annual Review of Biochemistry, 54, 729–764. doi:10.1146/annurev.bi.54.070185.00350110.1146/annurev.bi.54.070185.003501
   PubMed Web of Science ®Google Scholar
• Niederwieser, A., Blau, N., Wang, M., Joller, P., Atares, M., & Cardesa-Garcia, J. (1984). GTP cyclohydrolase I deficiency, a new enzyme defect causing hyperphenylalaninemia with neopterin, biopterin, dopamine, and serotonin deficiencies and muscular hypotonia. European Journal of Pediatrics, 141, 208–214.10.1007/BF00572762
   PubMed Web of Science ®Google Scholar
• Niederwieser, A., Leimbacher, W., Curtius, H. Ch, Ponzone, A., Rey, F., & Leupold, D. (1985). Atypical phenylketonuria with “dihydrobiopterin synthetase” deficiency: Absence of phosphate-eliminating enzyme activity demonstrated in liver. European Journal of Pediatrics, 144, 13.10.1007/BF00491917
   PubMed Web of Science ®Google Scholar
• Pavon, J. A., Eser, B., Huynh, M. T., & Fitzpatrick, P. F. (2010). Single turnover kinetics of tryptophan hydroxylase: Evidence for a new intermediate in the reaction of the aromatic amino acid hydroxylases. Biochemistry, 49, 7563–7571. doi:10.1021/bi100744r10.1021/bi100744r
   PubMed Web of Science ®Google Scholar
• Que, Jr., L., & Ho, R. Y. N. (1996). Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chemical Reviews, 96, 2607–2624. doi:10.1021/cr960039f10.1021/cr960039f
   PubMed Web of Science ®Google Scholar
• Salowe, S. P., Marsh, E. N., & Townsend, C. A. (1990). Purification and characterization of clavaminate synthase from Streptomyces clavuligerus: An unusual oxidative enzyme in natural product biosynthesis. Biochemistry, 29, 6499–6508. doi:10.1021/bi00222a03410.1021/bi00479a023
   PubMed Web of Science ®Google Scholar
• Samuelsson, B., Dahlén, S.-E.; Lindgren, J.; Rouzer, C. A., & Serhan, C. N. (1987). Leukotrienes and lipoxins: Structures, biosynthesis and biological effects. Science, 237, 1171–1176. doi:10.1126/science.2820055. Retrieved from http://www.jbc.org/content/257/21/12746
   PubMed Web of Science ®Google Scholar
• Schrödinger, LLC, New York, NY. (2013). Protein prepwizard, Ligprep version 2.6, Glide version 5.8, QSite, version 5.0.
   Google Scholar
• Stoddard, B. L., Howell, P. L., Ringe, D., & Petsko, G. A. (1990). The 2.1 .ANG. Resolution structure of iron superoxide dismutase from Pseudomonas ovalis. Biochemistry, 29, 8885–8893. doi:10.1021/bi00490a00210.1021/bi00490a002
   PubMed Web of Science ®Google Scholar
• Van der Kamp, M. W., & Mulholland, A. J. (2013). Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry, 52, 2708–2728. Retrieved from http://dx.doi.org/10.1021/bi400215w10.1021/bi400215w
   PubMed Web of Science ®Google Scholar