458
M. G. Quesne and S. P. de Visser
26. Cramer CJ, Truhlar DG (1992) AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution. J Comput Aided Mol Des 6:629–666. https://doi.
org/10.1007/BF00126219
27. Faponle AS, Quesne MG, de Visser SP (2016) Origin of the regioselective fatty-acid hydroxylation versus decarboxylation by a cytochrome P450 peroxygenase: what drives the reaction
to Biofuel production? Chemistry 22:5478–5483. https://doi.org/10.1002/chem.201600739
28. Quesne MG, Latifi R, Gonzalez-Ovalle LE et al (2014) Quantum mechanics/molecular
mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair
enzymes. Chem—A Eur J 20:435–446. https://doi.org/10.1002/chem.201303282
29. Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank nucleic acids research.
Nucl Acids Res 28:235–242
30. Dolinsky TJ, Czodrowski P, Li H et al (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucl Acids Res
35:W522–W525
31. Wang J, Wolf RM, Caldwell JW et al (2004) Development and testing of a general amber
force field. J Comput Chem 25:1157–1174. https://doi.org/10.1002/jcc.20035
32. Brooks BR, Brooks CL 3rd, Mackerell ADJ et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614. https://doi.org/10.1002/jcc.21287
33. Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) A biomolecular force field
based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter
sets 53A5 and 53A6. J Comput Chem 25:1656–1676
34. Maseras F, Morokuma K (1995) Imomm: A new ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J Comp Chem
16:1170–1179
35. Hu L, Söderhjelm P, Ryde U (2011) On the convergence of QM/MM energies. J Chem Theory
Comput 7:761–777
36. Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision B.01. Gaussian 09,
Revis. B.01, Gaussian, Inc, Wallingford CT
37. Sherwood P, de Vries AH, Guest MF et al (2003) QUASI: a general purpose implementation of
the QM/MM approach and its application to problems in catalysis. J Mol Struct THEOCHEM
632:1–28
38. Cao L, Ryde U (2018) On the difference between additive and subtractive QM/MM calculations. Front Chem 6:89. https://doi.org/10.3389/fchem.2018.00089
39. Solomon EI, Brunold TC, Davis MI et al (2005) Oxygenases: mechanisms and structural
motifs for O-2 activation. Chem Rev 105:550–555. https://doi.org/10.1021/cr040653o
40. Bugg TDH, Ramaswamy S (2008) Non-heme iron-dependent dioxygenases: unravelling catalytic mechanisms for complex enzymatic oxidations. Curr Opin Chem Biol 12:134–140.
https://doi.org/10.1016/j.cbpa.2007.12.007
41. Quesne MG, Faponle AS, Goldberg DP, Visser SPD (2015) Catalytic function and mechanism
of heme and nonheme iron(IV)-Oxo complexes in nature
42. de Visser SP (2018) Mechanistic insight on the activity and substrate selectivity of nonheme
iron dioxygenases. Chem Rec. https://doi.org/10.1002/tcr.201800033
43. Fetzner S, Steiner RA (2010) Cofactor-independent oxidases and oxygenases. Appl Microbiol
Biotechnol 86:791–804. https://doi.org/10.1007/s00253-010-2455-0
44. Bauer I, Max N, Fetzner S, Lingens F (1996) 2,4-dioxygenases catalyzing n-heterocyclicring cleavage and formation of carbon monoxide. purification and some properties of 1H3-hydroxy-4-oxoquinaldine 2,4-dioxygenase from arthrobacter sp. Ru61a and comparison
with 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase from pseudomonas putida 33/1. Eur J
Biochem 240:576–583. https://doi.org/10.1111/j.1432-1033.1996.0576h.x
45. Hernández-Ortega A, Quesne MG, Bui S et al (2014) Origin of the proton-transfer step in
the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase: effect of the basicity of
an active site His residue. J Biol Chem 289:8620–8632. https://doi.org/10.1074/jbc.M113.
543033
M. G. Quesne and S. P. de Visser
26. Cramer CJ, Truhlar DG (1992) AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution. J Comput Aided Mol Des 6:629–666. https://doi.
org/10.1007/BF00126219
27. Faponle AS, Quesne MG, de Visser SP (2016) Origin of the regioselective fatty-acid hydroxylation versus decarboxylation by a cytochrome P450 peroxygenase: what drives the reaction
to Biofuel production? Chemistry 22:5478–5483. https://doi.org/10.1002/chem.201600739
28. Quesne MG, Latifi R, Gonzalez-Ovalle LE et al (2014) Quantum mechanics/molecular
mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair
enzymes. Chem—A Eur J 20:435–446. https://doi.org/10.1002/chem.201303282
29. Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank nucleic acids research.
Nucl Acids Res 28:235–242
30. Dolinsky TJ, Czodrowski P, Li H et al (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucl Acids Res
35:W522–W525
31. Wang J, Wolf RM, Caldwell JW et al (2004) Development and testing of a general amber
force field. J Comput Chem 25:1157–1174. https://doi.org/10.1002/jcc.20035
32. Brooks BR, Brooks CL 3rd, Mackerell ADJ et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614. https://doi.org/10.1002/jcc.21287
33. Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) A biomolecular force field
based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter
sets 53A5 and 53A6. J Comput Chem 25:1656–1676
34. Maseras F, Morokuma K (1995) Imomm: A new ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J Comp Chem
16:1170–1179
35. Hu L, Söderhjelm P, Ryde U (2011) On the convergence of QM/MM energies. J Chem Theory
Comput 7:761–777
36. Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision B.01. Gaussian 09,
Revis. B.01, Gaussian, Inc, Wallingford CT
37. Sherwood P, de Vries AH, Guest MF et al (2003) QUASI: a general purpose implementation of
the QM/MM approach and its application to problems in catalysis. J Mol Struct THEOCHEM
632:1–28
38. Cao L, Ryde U (2018) On the difference between additive and subtractive QM/MM calculations. Front Chem 6:89. https://doi.org/10.3389/fchem.2018.00089
39. Solomon EI, Brunold TC, Davis MI et al (2005) Oxygenases: mechanisms and structural
motifs for O-2 activation. Chem Rev 105:550–555. https://doi.org/10.1021/cr040653o
40. Bugg TDH, Ramaswamy S (2008) Non-heme iron-dependent dioxygenases: unravelling catalytic mechanisms for complex enzymatic oxidations. Curr Opin Chem Biol 12:134–140.
https://doi.org/10.1016/j.cbpa.2007.12.007
41. Quesne MG, Faponle AS, Goldberg DP, Visser SPD (2015) Catalytic function and mechanism
of heme and nonheme iron(IV)-Oxo complexes in nature
42. de Visser SP (2018) Mechanistic insight on the activity and substrate selectivity of nonheme
iron dioxygenases. Chem Rec. https://doi.org/10.1002/tcr.201800033
43. Fetzner S, Steiner RA (2010) Cofactor-independent oxidases and oxygenases. Appl Microbiol
Biotechnol 86:791–804. https://doi.org/10.1007/s00253-010-2455-0
44. Bauer I, Max N, Fetzner S, Lingens F (1996) 2,4-dioxygenases catalyzing n-heterocyclicring cleavage and formation of carbon monoxide. purification and some properties of 1H3-hydroxy-4-oxoquinaldine 2,4-dioxygenase from arthrobacter sp. Ru61a and comparison
with 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase from pseudomonas putida 33/1. Eur J
Biochem 240:576–583. https://doi.org/10.1111/j.1432-1033.1996.0576h.x
45. Hernández-Ortega A, Quesne MG, Bui S et al (2014) Origin of the proton-transfer step in
the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase: effect of the basicity of
an active site His residue. J Biol Chem 289:8620–8632. https://doi.org/10.1074/jbc.M113.
543033