The Quest for Accurate Theoretical Models of Metalloenzymes …
461
87. Loch JM, Potter J, Bachmann KA (1995) The influence of anesthetic agents on rat hepatic
cytochromes P450 in vivo. Pharmacology 50:146–153
88. Rettie AE, Rettenmeier AW, Howald WN, Baillie TA (1987) Cytochrome P-450–catalyzed
formation of delta 4-VPA, a toxic metabolite of valproic acid. Science (80-) 235:890–893
89. Sadeque AJM, Fisher MB, Korzekwa KR et al (1997) Human CYP2C9 and CYP2A6 mediate
formation of the hepatotoxin 4-ene-valproic acid. J Pharmacol Exp Ther 283:698–703
90. Wen X, Wang JS, Kivisto KT et al (2001) In vitro evaluation of valproic acid as an
inhibitor of human cytochrome P450 isoforms: preferential inhibition of cytochrome P450
2C9 (CYP2C9). Br J Clin Pharmacol Engl 547–553
91. Groves JT, McClusky GA (1976) Aliphatic hydroxylation via oxygen rebound. Oxygen transfer catalyzed by iron. J Am Chem Soc 98:859–861
92. Rude MA, Baron TS, Brubaker S et al (2011) Terminal olefin (1-alkene) biosynthesis by a
novel P450 fatty acid decarboxylase from Jeotgalicoccus species. Appl Environ Microbiol
77:1718–1727
93. Belcher J, McLean KJ, Matthews S et al (2014) Structure and biochemical properties of the
alkene producing cytochrome P450 OleTJE (CYP152L1) from the Jeotgalicoccus sp. 8456
bacterium. J Biol Chem 289:6535–6550
94. Porro CS, Sutcliffe MJ, de Visser SP (2009) Quantum mechanics/molecular mechanics studies
on the sulfoxidation of dimethyl sulfide by compound i and compound 0 of cytochrome P450:
which is the better oxidant?âe. J Phys Chem A 113:11635–11642. https://doi.org/10.1021/
jp9023926
95. Postils V, Saint-André M, Timmins A et al (2018) Quantum mechanics/molecular mechanics
studies on the relative reactivities of compound I and II in cytochrome P450 enzymes. Int J
Mol Sci 19. https://doi.org/10.3390/ijms19071974
96. Kumar D, Thiel W, de Visser SP (2011) Theoretical study on the mechanism of the oxygen
activation process in cysteine dioxygenase enzymes. J Am Chem Soc 133:3869–3882. https://
doi.org/10.1021/ja107514f
97. Fu Y, Dai Q, Zhang W et al (2010) The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-Methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chemie
122:9069–9072
98. Giri NC, Sun H, Chen H et al (2011) X-ray absorption spectroscopy structural investigation
of early intermediates in the mechanism of DNA repair by human ABH2. Biochemistry
50:5067–5076
99. Li D, Delaney JC, Page CM et al (2012) Exocyclic carbons adjacent to the N 6 of adenine are
targets for oxidation by the escherichia coli adaptive response protein AlkB. J Am Chem Soc
134:8896–8901
100. Yu B, Hunt JF (2009) Enzymological and structural studies of the mechanism of
promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB. Proc
Natl Acad Sci USA 106:14315–14320. DOI: https://doi.org/0812938106 [pii]. DOI:
https://doi.org/10.1073/pnas.0812938106
101. Falnes PO, Johansen RF, Seeberg E (2002) AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419:178–182. DOI:
https://doi.org/10.1038/nature01048 [pii]
102. Trewick SC, Henshaw TF, Hausinger RP et al (2002) Oxidative demethylation by Escherichia
coli AlkB directly reverts DNA base damage. Nature 419:174–178. https://doi.org/10.1038/
nature00908
103. Yi C, Yang CG, He C (2009) A non-heme iron-mediated chemical demethylation in DNA
and RNA. Acc Chem Res 42:519–529. DOI: https://doi.org/10.1021/ar800178j [pii]. DOI:
https://doi.org/10.1021/ar800178j
104. Ladwein KI, Jung M (2011) Oxidized cytosine metabolites offer a fresh perspective for active
DNA demethylation. Angew Chemie Int Ed 50:12143–12145
105. Mishina Y, Duguid EM, He C (2006) Direct reversal of DNA alkylation damage. Chem Rev
106:215–232. https://doi.org/10.1021/cr0404702
461
87. Loch JM, Potter J, Bachmann KA (1995) The influence of anesthetic agents on rat hepatic
cytochromes P450 in vivo. Pharmacology 50:146–153
88. Rettie AE, Rettenmeier AW, Howald WN, Baillie TA (1987) Cytochrome P-450–catalyzed
formation of delta 4-VPA, a toxic metabolite of valproic acid. Science (80-) 235:890–893
89. Sadeque AJM, Fisher MB, Korzekwa KR et al (1997) Human CYP2C9 and CYP2A6 mediate
formation of the hepatotoxin 4-ene-valproic acid. J Pharmacol Exp Ther 283:698–703
90. Wen X, Wang JS, Kivisto KT et al (2001) In vitro evaluation of valproic acid as an
inhibitor of human cytochrome P450 isoforms: preferential inhibition of cytochrome P450
2C9 (CYP2C9). Br J Clin Pharmacol Engl 547–553
91. Groves JT, McClusky GA (1976) Aliphatic hydroxylation via oxygen rebound. Oxygen transfer catalyzed by iron. J Am Chem Soc 98:859–861
92. Rude MA, Baron TS, Brubaker S et al (2011) Terminal olefin (1-alkene) biosynthesis by a
novel P450 fatty acid decarboxylase from Jeotgalicoccus species. Appl Environ Microbiol
77:1718–1727
93. Belcher J, McLean KJ, Matthews S et al (2014) Structure and biochemical properties of the
alkene producing cytochrome P450 OleTJE (CYP152L1) from the Jeotgalicoccus sp. 8456
bacterium. J Biol Chem 289:6535–6550
94. Porro CS, Sutcliffe MJ, de Visser SP (2009) Quantum mechanics/molecular mechanics studies
on the sulfoxidation of dimethyl sulfide by compound i and compound 0 of cytochrome P450:
which is the better oxidant?âe. J Phys Chem A 113:11635–11642. https://doi.org/10.1021/
jp9023926
95. Postils V, Saint-André M, Timmins A et al (2018) Quantum mechanics/molecular mechanics
studies on the relative reactivities of compound I and II in cytochrome P450 enzymes. Int J
Mol Sci 19. https://doi.org/10.3390/ijms19071974
96. Kumar D, Thiel W, de Visser SP (2011) Theoretical study on the mechanism of the oxygen
activation process in cysteine dioxygenase enzymes. J Am Chem Soc 133:3869–3882. https://
doi.org/10.1021/ja107514f
97. Fu Y, Dai Q, Zhang W et al (2010) The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-Methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chemie
122:9069–9072
98. Giri NC, Sun H, Chen H et al (2011) X-ray absorption spectroscopy structural investigation
of early intermediates in the mechanism of DNA repair by human ABH2. Biochemistry
50:5067–5076
99. Li D, Delaney JC, Page CM et al (2012) Exocyclic carbons adjacent to the N 6 of adenine are
targets for oxidation by the escherichia coli adaptive response protein AlkB. J Am Chem Soc
134:8896–8901
100. Yu B, Hunt JF (2009) Enzymological and structural studies of the mechanism of
promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB. Proc
Natl Acad Sci USA 106:14315–14320. DOI: https://doi.org/0812938106 [pii]. DOI:
https://doi.org/10.1073/pnas.0812938106
101. Falnes PO, Johansen RF, Seeberg E (2002) AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419:178–182. DOI:
https://doi.org/10.1038/nature01048 [pii]
102. Trewick SC, Henshaw TF, Hausinger RP et al (2002) Oxidative demethylation by Escherichia
coli AlkB directly reverts DNA base damage. Nature 419:174–178. https://doi.org/10.1038/
nature00908
103. Yi C, Yang CG, He C (2009) A non-heme iron-mediated chemical demethylation in DNA
and RNA. Acc Chem Res 42:519–529. DOI: https://doi.org/10.1021/ar800178j [pii]. DOI:
https://doi.org/10.1021/ar800178j
104. Ladwein KI, Jung M (2011) Oxidized cytosine metabolites offer a fresh perspective for active
DNA demethylation. Angew Chemie Int Ed 50:12143–12145
105. Mishina Y, Duguid EM, He C (2006) Direct reversal of DNA alkylation damage. Chem Rev
106:215–232. https://doi.org/10.1021/cr0404702