메뉴 건너뛰기




Volumn 120, Issue 6, 2013, Pages 937-945

Computational modeling of the direct hydride transfer mechanism for the MAO catalyzed oxidation of phenethylamine and benzylamine: ONIOM (QM/QM) calculations

Author keywords

Dispersion corrected DFT; Enzyme mechanism; Enzyme modeling; Flavoenzymes; Hydride transfer

Indexed keywords

AMINE OXIDASE (FLAVIN CONTAINING) ISOENZYME A; AMINE OXIDASE (FLAVIN CONTAINING) ISOENZYME B; BENZYLAMINE; PHENETHYLAMINE;

EID: 84878728510     PISSN: 03009564     EISSN: 14351463     Source Type: Journal    
DOI: 10.1007/s00702-013-1027-8     Document Type: Article
Times cited : (54)

References (38)
  • 1
    • 34250862303 scopus 로고    scopus 로고
    • The aromatic cage in the active site of monoamine oxidase B: Effect on the structural and electronic properties of bound benzylamine and p-nitrobenzylamine
    • 17401536 10.1007/s00702-007-0670-3
    • Akyüz MA, Erdem SS, Edmondson DE (2007) The aromatic cage in the active site of monoamine oxidase B: effect on the structural and electronic properties of bound benzylamine and p-nitrobenzylamine. J Neural Transm 114:693-698
    • (2007) J Neural Transm , vol.114 , pp. 693-698
    • Akyüz, M.A.1    Erdem, S.S.2    Edmondson, D.E.3
  • 2
    • 34250817103 scopus 로고
    • A new mixing of Hartree-Fock and local density-functional theories
    • 10.1063/1.464304
    • Becke AD (1993) A new mixing of Hartree-Fock and local density-functional theories. J Chem Phys 98-2:1372-1377
    • (1993) J Chem Phys , vol.98 , Issue.2 , pp. 1372-1377
    • Becke, A.D.1
  • 3
    • 0042693016 scopus 로고    scopus 로고
    • Insights into the mode of inhibition of human mitochondrial monoamine oxidase B from high-resolution crystal structures
    • 12913124 10.1073/pnas.1633804100 1:CAS:528:DC%2BD3sXmvVejt7c%3D
    • Binda C, Li M, Hubálek F, Restelli N, Edmondson DE, Mattevi A (2003) Insights into the mode of inhibition of human mitochondrial monoamine oxidase B from high-resolution crystal structures. Proc Natl Acad Sci 100:9750-9755
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 9750-9755
    • Binda, C.1    Li, M.2    Hubálek, F.3    Restelli, N.4    Edmondson, D.E.5    Mattevi, A.6
  • 4
    • 55849117399 scopus 로고    scopus 로고
    • Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections
    • 18989472 10.1039/b810189b 1:CAS:528:DC%2BD1cXhtlCksbfO
    • Chai JD, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem Chem Phys 10:6615-6620
    • (2008) Phys Chem Chem Phys , vol.10 , pp. 6615-6620
    • Chai, J.D.1    Head-Gordon, M.2
  • 5
    • 24644437716 scopus 로고    scopus 로고
    • Three-dimensional structure of human monoamine oxidase A (MAO A): Relation to the structures of rat MAO A and human MAO B
    • 16129825 10.1073/pnas.0505975102
    • Colibus LD, Binda C, Lustig A, Edmondson DE, Mattevi A (2005) Three-dimensional structure of human monoamine oxidase A (MAO A): relation to the structures of rat MAO A and human MAO B. Proc Natl Acad Sci 102:12684-12689
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 12684-12689
    • Colibus, L.D.1    Binda, C.2    Lustig, A.3    Edmondson, D.E.4    Mattevi, A.5
  • 6
    • 0033515394 scopus 로고    scopus 로고
    • A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives
    • 10.1016/S0166-1280(98)00475-8
    • Dapprich S, Komaromi I, Byun KS, Morokuma K, Frisch MJ (1999) A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives. J Mol Struct (Theochem) 461-462:1-21
    • (1999) J Mol Struct (Theochem) , vol.461-462 , pp. 1-21
    • Dapprich, S.1    Komaromi, I.2    Byun, K.S.3    Morokuma, K.4    Frisch, M.J.5
  • 7
    • 77953428396 scopus 로고    scopus 로고
    • Tyrosyl radical formation and propagation in flavin dependent monoamine oxidases
    • 20480485 10.1002/cbic.201000184 1:CAS:528:DC%2BC3cXnsVWnsbs%3D
    • Dunn RV, Munro AW, Turner NJ, Rigby SE, Scrutton NS (2010) Tyrosyl radical formation and propagation in flavin dependent monoamine oxidases. Chem Bio Chem 11:1228-1231
    • (2010) Chem Bio Chem , vol.11 , pp. 1228-1231
    • Dunn, R.V.1    Munro, A.W.2    Turner, N.J.3    Rigby, S.E.4    Scrutton, N.S.5
  • 8
    • 3242781888 scopus 로고    scopus 로고
    • Structure and mechanism of monoamine oxidase
    • 15279562 10.2174/0929867043364784 1:CAS:528:DC%2BD2cXlslWmu7s%3D
    • Edmondson DE, Mattevi A, Binda C, Li M, Hubálek F (2004) Structure and mechanism of monoamine oxidase. Curr Med Chem 11:1983-1993
    • (2004) Curr Med Chem , vol.11 , pp. 1983-1993
    • Edmondson, D.E.1    Mattevi, A.2    Binda, C.3    Li, M.4    Hubálek, F.5
  • 9
    • 80051667006 scopus 로고    scopus 로고
    • Computational investigation on the structure-activity relationship of the biradical mechanism for monoamine oxidase
    • 21476070 10.1007/s00702-011-0635-4 1:CAS:528:DC%2BC3MXnslOns7Y%3D
    • Erdem SS, Büyükmenekşe B (2011) Computational investigation on the structure-activity relationship of the biradical mechanism for monoamine oxidase. J Neural Transm 118:1021-1029
    • (2011) J Neural Transm , vol.118 , pp. 1021-1029
    • Erdem, S.S.1    Büyükmenekşe, B.2
  • 10
    • 0035903856 scopus 로고    scopus 로고
    • Computer modeling of oxygen containing heptylamines as monoamine oxidase inactivators
    • 10.1016/S0166-1280(01)00587-5 1:CAS:528:DC%2BD3MXmt12hu7Y%3D
    • Erdem SS, Yelekçi K (2001) Computer modeling of oxygen containing heptylamines as monoamine oxidase inactivators. J Mol Struct (Theochem) 572:97-106
    • (2001) J Mol Struct (Theochem) , vol.572 , pp. 97-106
    • Erdem, S.S.1    Yelekçi, K.2
  • 11
    • 32544432876 scopus 로고    scopus 로고
    • A computational study on the amine-oxidation mechanism of monoamine oxidase: Insight into the polar nucleophilic mechanism
    • 16467939 10.1039/b511350d 1:CAS:528:DC%2BD28Xht1Wrtbw%3D
    • Erdem SS, Karahan Ö, YIldIz I, Yelekçi K (2006) A computational study on the amine-oxidation mechanism of monoamine oxidase: insight into the polar nucleophilic mechanism. Org Biomol Chem 4:646-658
    • (2006) Org Biomol Chem , vol.4 , pp. 646-658
    • Erdem, S.S.1    Karahan, Ö.2    Yildiz, I.3    Yelekçi, K.4
  • 12
    • 84878714279 scopus 로고    scopus 로고
    • Quantum chemical modeling of the inhibition mechanism of monoamine oxidase by oxazolidinone and analogous heterocyclic compounds
    • 10.3109/14756366.2012.753882 23323992
    • Erdem SS, AltInbaş GÖ, Boz U (2013) Quantum chemical modeling of the inhibition mechanism of monoamine oxidase by oxazolidinone and analogous heterocyclic compounds. J Enzyme Inhib Med Chem. doi: 10.3109/14756366.2012. 753882
    • (2013) J Enzyme Inhib Med Chem
    • Erdem, S.S.1    Altinbaş, G.2    Boz, U.3
  • 13
    • 84862643577 scopus 로고    scopus 로고
    • N-O bond cleavage mechanism(s) in nitrous oxide reductase
    • 22434248 10.1007/s00775-012-0888-x 1:CAS:528:DC%2BC38XktFCkt7o%3D
    • Ertem MZ, Cramer CJ, Himo F, Siegbahn PEM (2012) N-O bond cleavage mechanism(s) in nitrous oxide reductase. J Biol Inorg Chem 17:687-698
    • (2012) J Biol Inorg Chem , vol.17 , pp. 687-698
    • Ertem, M.Z.1    Cramer, C.J.2    Himo, F.3    Siegbahn, P.E.M.4
  • 14
    • 72049099611 scopus 로고    scopus 로고
    • Oxidation of amines by flavoproteins
    • 19651103 10.1016/j.abb.2009.07.019 1:CAS:528:DC%2BD1MXhsFyitbjI
    • Fitzpatrick PF (2010) Oxidation of amines by flavoproteins. Arch Biochem Biophys 493:13-25
    • (2010) Arch Biochem Biophys , vol.493 , pp. 13-25
    • Fitzpatrick, P.F.1
  • 16
    • 0028601412 scopus 로고
    • Hydrogen tunneling in the flavoenzyme monoamine oxidase B
    • 7993913 10.1021/bi00253a026 1:CAS:528:DyaK2cXmvFGrtr8%3D
    • Jonsson T, Edmondson DE, Klinman JP (1994) Hydrogen tunneling in the flavoenzyme monoamine oxidase B. Biochemistry 33:14871-14878
    • (1994) Biochemistry , vol.33 , pp. 14871-14878
    • Jonsson, T.1    Edmondson, D.E.2    Klinman, J.P.3
  • 17
    • 33645716728 scopus 로고
    • Comparison of density functional and MP2 calculations on the water monomer and dimer
    • 10.1021/j100091a024 1:CAS:528:DyaK2cXmtFemsr4%3D
    • Kim K, Jordan KD (1994) Comparison of density functional and MP2 calculations on the water monomer and dimer. J Phys Chem 98:10089-10094
    • (1994) J Phys Chem , vol.98 , pp. 10089-10094
    • Kim, K.1    Jordan, K.D.2
  • 19
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • 10.1103/PhysRevB.37.785
    • Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37-2:785-789
    • (1988) Phys Rev B , vol.37 , Issue.2 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 20
    • 79955878968 scopus 로고    scopus 로고
    • Quantum chemical modeling of enzymatic reactions: The case of decarboxylation
    • 10.1021/ct200031t 1:CAS:528:DC%2BC3MXjvFejsr4%3D
    • Liao R-Z, Yu J-G, Himo F (2011) Quantum chemical modeling of enzymatic reactions: the case of decarboxylation. J Chem Theory Comput 7:1494-1501
    • (2011) J Chem Theory Comput , vol.7 , pp. 1494-1501
    • Liao, R.-Z.1    Yu, J.-G.2    Himo, F.3
  • 21
    • 34547691533 scopus 로고    scopus 로고
    • Irreversible inactivation of mitochondrial monoamine oxidase
    • S. Chapman R. Perham N. Scrutton (eds) Rudolf Weber Agency for Scientific Publications Berlin
    • Lu X, Rodrigez M, Silverman RB, Vintem APB, Ramsay RR (2002) Irreversible inactivation of mitochondrial monoamine oxidase. In: Chapman S, Perham R, Scrutton N (eds) Flavins and flavoproteins. Rudolf Weber Agency for Scientific Publications, Berlin, p 817
    • (2002) Flavins and Flavoproteins , pp. 817
    • Lu, X.1    Rodrigez, M.2    Silverman, R.B.3    Vintem, A.P.B.4    Ramsay, R.R.5
  • 22
    • 80051596304 scopus 로고    scopus 로고
    • Nitrogen kinetic isotope effects for the monoamine oxidase B-catalyzed oxidation of benzylamine and (1,1-2H2) benzylamine: Nitrogen rehybridization and CH bond cleavage are not concerted
    • 21786798 10.1021/ja205629b 1:CAS:528:DC%2BC3MXpsFSksr8%3D
    • MacMillar S, Edmondson DE, Matsson O (2011) Nitrogen kinetic isotope effects for the monoamine oxidase B-catalyzed oxidation of benzylamine and (1,1-2H2) benzylamine: nitrogen rehybridization and CH bond cleavage are not concerted. J Am Chem Soc 133:12319-12321
    • (2011) J Am Chem Soc , vol.133 , pp. 12319-12321
    • Macmillar, S.1    Edmondson, D.E.2    Matsson, O.3
  • 23
    • 0033550070 scopus 로고    scopus 로고
    • Structure-activity relationships in the oxidation of para-substituted benzylamine analogues by recombinant human liver monoamine oxidase A
    • 10521274 10.1021/bi990920y 1:CAS:528:DyaK1MXmtVOnt7c%3D
    • Miller JR, Edmondson DE (1999) Structure-activity relationships in the oxidation of para-substituted benzylamine analogues by recombinant human liver monoamine oxidase A. Biochemistry 38:13670-13683
    • (1999) Biochemistry , vol.38 , pp. 13670-13683
    • Miller, J.R.1    Edmondson, D.E.2
  • 24
    • 0034642217 scopus 로고    scopus 로고
    • Structure-activity relations in the oxidation of phenethylamine analogues by recombinant human liver monoamine oxidase A
    • 11106506 10.1021/bi001957h 1:CAS:528:DC%2BD3cXotVaktr4%3D
    • Nandigama RK, Edmondson DE (2000) Structure-activity relations in the oxidation of phenethylamine analogues by recombinant human liver monoamine oxidase A. Biochemistry 39:15258-15265
    • (2000) Biochemistry , vol.39 , pp. 15258-15265
    • Nandigama, R.K.1    Edmondson, D.E.2
  • 25
    • 33746344685 scopus 로고    scopus 로고
    • Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study
    • 16821888 10.1021/jp0619181 1:CAS:528:DC%2BD28XlvVWlsbw%3D
    • Prabhakar R, Vreven T, Frisch MJ, Morokuma K, Musaev DG (2006) Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study. J Phys Chem B 110:13608-13613
    • (2006) J Phys Chem B , vol.110 , pp. 13608-13613
    • Prabhakar, R.1    Vreven, T.2    Frisch, M.J.3    Morokuma, K.4    Musaev, D.G.5
  • 26
    • 34250852848 scopus 로고    scopus 로고
    • Insight into the mechanism of flavoprotein-catalyzed amine oxidation from nitrogen isotope effect on the reaction of N-methyltryptophan oxidase
    • 17542620 10.1021/bi700482h 1:CAS:528:DC%2BD2sXlvFKjt7k%3D
    • Ralph EC, Hirschi JS, Anderson MA, Cleland WW, Singleton DA, Fitzpatrick PF (2007) Insight into the mechanism of flavoprotein-catalyzed amine oxidation from nitrogen isotope effect on the reaction of N-methyltryptophan oxidase. Biochemistry 46:7655-7664
    • (2007) Biochemistry , vol.46 , pp. 7655-7664
    • Ralph, E.C.1    Hirschi, J.S.2    Anderson, M.A.3    Cleland, W.W.4    Singleton, D.A.5    Fitzpatrick, P.F.6
  • 27
    • 67849101722 scopus 로고    scopus 로고
    • Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of noncovalent complexes
    • 10.1021/ct9000922 1:CAS:528:DC%2BD1MXmtl2msLc%3D
    • Rezac J, Fanfrlik J, Salahub D, Hobza P (2009) Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of noncovalent complexes. J Chem Theory Comput 5:1749-1760
    • (2009) J Chem Theory Comput , vol.5 , pp. 1749-1760
    • Rezac, J.1    Fanfrlik, J.2    Salahub, D.3    Hobza, P.4
  • 28
    • 0000480438 scopus 로고
    • Electron transfer chemistry of monoamine oxidase
    • S. Mariano (eds) 2 JAI Press Inc Greenwich
    • Silverman RB (1992) Electron transfer chemistry of monoamine oxidase. In: Mariano PS (ed) Advances in electron transfer chemistry, vol 2. JAI Press Inc,. Greenwich, pp 177-213
    • (1992) Advances in Electron Transfer Chemistry , pp. 177-213
    • Silverman, R.B.1
  • 29
    • 44449117421 scopus 로고    scopus 로고
    • Structure of human monoamine oxidase A at 2.2-Å resolution: The control of opening the entry for substrates/inhibitors
    • 18391214 10.1073/pnas.0710626105 1:CAS:528:DC%2BD1cXltFShsLo%3D
    • Son SY, Ma J, Kondou Y, Yoshimura M, Yamashita E, Tsukihara T (2008) Structure of human monoamine oxidase A at 2.2-Å resolution: the control of opening the entry for substrates/inhibitors. Proc Natl Acad Sci 105:5739-5744
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 5739-5744
    • Son, S.Y.1    Ma, J.2    Kondou, Y.3    Yoshimura, M.4    Yamashita, E.5    Tsukihara, T.6
  • 30
    • 35748980308 scopus 로고    scopus 로고
    • General performance of density functionals
    • 17718548 10.1021/jp0734474 1:CAS:528:DC%2BD2sXpsFSmsLs%3D
    • Sousa SF, Fernandes PA, Ramos MJ (2007) General performance of density functionals. J Phys Chem A 111:10439-10452
    • (2007) J Phys Chem A , vol.111 , pp. 10439-10452
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 31
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of parameters for semiempirical methods. V. Modification of NDDO approximations and application to 70 elements
    • 17828561 10.1007/s00894-007-0233-4 1:CAS:528:DC%2BD2sXhtlequr7N
    • Stewart JJP (2007) Optimization of parameters for semiempirical methods. V. Modification of NDDO approximations and application to 70 elements. J Mol Model 13:1173-1213
    • (2007) J Mol Model , vol.13 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 32
    • 0037016014 scopus 로고    scopus 로고
    • First-principles molecular dynamics investigation of the d-amino acid oxidative half-reaction catalyzed by the flavoenzyme d-amino acid oxidase
    • 12450374 10.1021/bi020309q 1:CAS:528:DC%2BD38XosVCitrg%3D
    • Tilocca A, Gamba A, Vanoni MA, Fois E (2002) First-principles molecular dynamics investigation of the d-amino acid oxidative half-reaction catalyzed by the flavoenzyme d-amino acid oxidase. Biochemistry 41:14111-14121
    • (2002) Biochemistry , vol.41 , pp. 14111-14121
    • Tilocca, A.1    Gamba, A.2    Vanoni, M.A.3    Fois, E.4
  • 33
    • 84870616612 scopus 로고    scopus 로고
    • How are biogenic amines metabolized by monoamine oxidases?
    • Vianello R, Repic M, Mavri J (2012) How are biogenic amines metabolized by monoamine oxidases? Eur J Org Chem 7057-7065
    • (2012) Eur J Org Chem , pp. 7057-7065
    • Vianello, R.1    Repic, M.2    Mavri, J.3
  • 34
    • 34250873549 scopus 로고    scopus 로고
    • Do monomeric vs dimeric forms of MAO-A make a difference? A direct comparison of the catalytic properties of rat and human MAO-A's
    • 17401534 10.1007/s00702-007-0678-8 1:CAS:528:DC%2BD2sXls1Sgtrk%3D
    • Wang J, Edmondson DE (2007) Do monomeric vs dimeric forms of MAO-A make a difference? A direct comparison of the catalytic properties of rat and human MAO-A's. J Neural Transm 114:721-724
    • (2007) J Neural Transm , vol.114 , pp. 721-724
    • Wang, J.1    Edmondson, D.E.2
  • 35
    • 80052245133 scopus 로고    scopus 로고
    • 2H Kinetic isotope effects and pH dependence of catalysis as mechanistic probes of rat monoamine oxidase A: Comparisons with the human enzyme
    • 21819071 10.1021/bi200951z 1:CAS:528:DC%2BC3MXhtVWkurjP
    • Wang J, Edmondson DE (2011) 2H Kinetic isotope effects and pH dependence of catalysis as mechanistic probes of rat monoamine oxidase A: comparisons with the human enzyme. Biochemistry 50:7710-7717
    • (2011) Biochemistry , vol.50 , pp. 7710-7717
    • Wang, J.1    Edmondson, D.E.2
  • 36
    • 3142771297 scopus 로고    scopus 로고
    • New hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
    • 10.1016/j.cplett.2004.06.011 1:CAS:528:DC%2BD2cXlsFKgtbs%3D
    • Yanai T, Tew D, Handy NA (2004) New hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem Phys Lett 393:51-57
    • (2004) Chem Phys Lett , vol.393 , pp. 51-57
    • Yanai, T.1    Tew, D.2    Handy, N.A.3
  • 37
    • 84870586357 scopus 로고    scopus 로고
    • Appropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methods
    • 10.1002/jcc.23112
    • Yuan L, Jijun Z, Fengyu L, Zhongfang C (2013) Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods. J Comput Chem 34:121-131
    • (2013) J Comput Chem , vol.34 , pp. 121-131
    • Yuan, L.1    Jijun, Z.2    Fengyu, L.3    Zhongfang, C.4
  • 38
    • 43049141516 scopus 로고    scopus 로고
    • The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functional
    • 10.1007/s00214-007-0310-x 1:CAS:528:DC%2BD1cXltFyltbY%3D
    • Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functional. Theor Chem Acc 120:215-241
    • (2008) Theor Chem Acc , vol.120 , pp. 215-241
    • Zhao, Y.1    Truhlar, D.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.