메뉴 건너뛰기




Volumn 27, Issue 4, 2013, Pages 295-304

Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase

Author keywords

Bioelectrochemistry; Enzyme promiscuity; Flavoproteins; GROMOS; Protein ligand interactions; Reaction mechanism

Indexed keywords

AMINO ACIDS; BIOCHEMISTRY; BIODEGRADATION; FUNGI; GLUCOSE; HYDROGEN BONDS; MOLECULAR DYNAMICS; REACTION INTERMEDIATES; REACTION KINETICS; VAN DER WAALS FORCES;

EID: 84878503057     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-013-9645-7     Document Type: Article
Times cited : (27)

References (29)
  • 1
    • 37549014470 scopus 로고    scopus 로고
    • Characterization of pyranose dehydrogenase from Agaricus meleagris and its application in the C-2 specific conversion of d-galactose
    • 10.1016/j.jbiotec.2007.10.013 1:CAS:528:DC%2BD1cXhtlegtA%3D%3D
    • Sygmund C, Kittl R, Volc J, Halada P, Kubátová E, Haltrich D, Peterbauer CK (2008) Characterization of pyranose dehydrogenase from Agaricus meleagris and its application in the C-2 specific conversion of d-galactose. J Biotechnol 133:334-342
    • (2008) J Biotechnol , vol.133 , pp. 334-342
    • Sygmund, C.1    Kittl, R.2    Volc, J.3    Halada, P.4    Kubátová, E.5    Haltrich, D.6    Peterbauer, C.K.7
  • 2
    • 0030979941 scopus 로고    scopus 로고
    • Pyranose 2-dehydrogenase, a novel sugar oxidoreductase from the basidiomycete fungus Agaricus bisporus
    • 10.1007/s002030050424 1:CAS:528:DyaK2sXhvFOqu78%3D
    • Volc J, Kubátová E, Wood DA, Daniel G (1997) Pyranose 2-dehydrogenase, a novel sugar oxidoreductase from the basidiomycete fungus Agaricus bisporus. Arch Microbiol 167:119-125
    • (1997) Arch Microbiol , vol.167 , pp. 119-125
    • Volc, J.1    Kubátová, E.2    Wood, D.A.3    Daniel, G.4
  • 3
    • 0034890010 scopus 로고    scopus 로고
    • Screening of basidiomycete fungi for the quinone-dependent sugar C-2/C-3 oxidoreductase, pyranose dehydrogenase, and properties of the enzyme from Macrolepiota rhacodes
    • 10.1007/s002030100308 1:CAS:528:DC%2BD3MXns1Wgt78%3D
    • Volc J, Kubátová E, Daniel G, Sedmera P, Haltrich D (2001) Screening of basidiomycete fungi for the quinone-dependent sugar C-2/C-3 oxidoreductase, pyranose dehydrogenase, and properties of the enzyme from Macrolepiota rhacodes. Arch Microbiol 176:178-186
    • (2001) Arch Microbiol , vol.176 , pp. 178-186
    • Volc, J.1    Kubátová, E.2    Daniel, G.3    Sedmera, P.4    Haltrich, D.5
  • 4
    • 33846425319 scopus 로고    scopus 로고
    • Properties of pyranose dehydrogenase purified from the litter-degrading fungus Agaricus xanthoderma
    • 10.1111/j.1742-4658.2007.05634.x 1:CAS:528:DC%2BD2sXitVOhur0%3D
    • Kujawa M, Volc J, Halada P, Sedmera P, Divne C, Sygmund C, Leitner C, Peterbauer CK, Haltrich D (2007) Properties of pyranose dehydrogenase purified from the litter-degrading fungus Agaricus xanthoderma. FEBS J 274:879-894
    • (2007) FEBS J , vol.274 , pp. 879-894
    • Kujawa, M.1    Volc, J.2    Halada, P.3    Sedmera, P.4    Divne, C.5    Sygmund, C.6    Leitner, C.7    Peterbauer, C.K.8    Haltrich, D.9
  • 5
    • 76649136470 scopus 로고    scopus 로고
    • Pyranose dehydrogenases: Biochemical features and perspectives of technological applications
    • 10.1007/s00253-009-2226-y 1:CAS:528:DC%2BC3cXjslWqug%3D%3D
    • Peterbauer CK, Volc J (2010) Pyranose dehydrogenases: biochemical features and perspectives of technological applications. Appl Microbiol Biotechnol 85:837-848
    • (2010) Appl Microbiol Biotechnol , vol.85 , pp. 837-848
    • Peterbauer, C.K.1    Volc, J.2
  • 7
    • 0035430520 scopus 로고    scopus 로고
    • Purification and characterization of pyranose oxidase from the white rot fungus Trametes multicolor
    • 10.1128/AEM.67.8.3636-3644.2001 1:CAS:528:DC%2BD3MXlvFSksrw%3D
    • Leitner C, Volc J, Haltrich D (2001) Purification and characterization of pyranose oxidase from the white rot fungus Trametes multicolor. Appl Environ Microbiol 67:3636-3644
    • (2001) Appl Environ Microbiol , vol.67 , pp. 3636-3644
    • Leitner, C.1    Volc, J.2    Haltrich, D.3
  • 9
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • 10.1073/pnas.0408930102 1:CAS:528:DC%2BD2MXksVKgt7k%3D
    • Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102:6679-6685
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 11
    • 77956915511 scopus 로고    scopus 로고
    • H-bonding and positive charge at the N(5)/O(4) locus are critical for covalent flavin attachment in Trametes pyranose 2-oxidase
    • 10.1016/j.jmb.2010.08.011 1:CAS:528:DC%2BC3cXht1SqtrbE
    • Tan T-C, Pitsawong W, Wongnate T, Spadiut O, Haltrich O, Chaiyen P, Divne C (2010) H-bonding and positive charge at the N(5)/O(4) locus are critical for covalent flavin attachment in Trametes pyranose 2-oxidase. J Mol Biol 402:578-594
    • (2010) J Mol Biol , vol.402 , pp. 578-594
    • Tan, T.-C.1    Pitsawong, W.2    Wongnate, T.3    Spadiut, O.4    Haltrich, O.5    Chaiyen, P.6    Divne, C.7
  • 12
    • 79957747146 scopus 로고    scopus 로고
    • Regioselective control of β-d-glucose oxidation by pyranose 2-oxidase is intimately coupled to conformational degeneracy
    • 10.1016/j.jmb.2011.04.019 1:CAS:528:DC%2BC3MXmslyht78%3D
    • Tan T-C, Haltrich D, Divne C (2011) Regioselective control of β-d-glucose oxidation by pyranose 2-oxidase is intimately coupled to conformational degeneracy. J Mol Biol 409:588-600
    • (2011) J Mol Biol , vol.409 , pp. 588-600
    • Tan, T.-C.1    Haltrich, D.2    Divne, C.3
  • 13
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    • 10.1002/pmic.200300771 1:CAS:528:DC%2BD2cXkvFGitLg%3D
    • Blom N, Sicheritz-Pontén T, Gupta R, Gammeltoft S, Brunak S (2004) Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4:1633-1649
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1    Sicheritz-Pontén, T.2    Gupta, R.3    Gammeltoft, S.4    Brunak, S.5
  • 14
    • 84856215641 scopus 로고    scopus 로고
    • Architecture, implementation and parallelization of the GROMOS software for biomolecular simulation
    • 10.1016/j.cpc.2011.12.014 1:CAS:528:DC%2BC38XhsFKiurc%3D
    • Schmid N, Christ CD, Christen M, Eichenberger AP, van Gunsteren WF (2012) Architecture, implementation and parallelization of the GROMOS software for biomolecular simulation. Comp Phys Commun 183:890-903
    • (2012) Comp Phys Commun , vol.183 , pp. 890-903
    • Schmid, N.1    Christ, C.D.2    Christen, M.3    Eichenberger, A.P.4    Van Gunsteren, W.F.5
  • 15
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • 10.1002/jcc.20090 1:CAS:528:DC%2BD2cXmvVOhtr4%3D
    • 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
    • (2004) J Comput Chem , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 17
    • 0002178685 scopus 로고    scopus 로고
    • Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency
    • 10.1063/1.480557 1:CAS:528:DC%2BD3cXit12gtQ%3D%3D
    • Amadei A, Chillemi G, Ceruso MA, Grottesi A, Di Nola A (2000) Molecular dynamics simulations with constrained roto-translational motions: theoretical basis and statistical mechanical consistency. J Chem Phys 112:9-23
    • (2000) J Chem Phys , vol.112 , pp. 9-23
    • Amadei, A.1    Chillemi, G.2    Ceruso, M.A.3    Grottesi, A.4    Di Nola, A.5
  • 19
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • 10.1016/0021-9991(77)90098-5 1:CAS:528:DyaE2sXktVGhsL4%3D
    • Ryckaert J-P, Ciccotti G, Berendsen HJ (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 23:327-341
    • (1977) J Comp Phys , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.3
  • 20
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • 10.1063/1.469273 1:CAS:528:DyaK2MXkslOmsLg%3D
    • Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451-5459
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 21
    • 0035878765 scopus 로고    scopus 로고
    • Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
    • 10.1063/1.1379764 1:CAS:528:DC%2BD3MXltFCmurg%3D
    • Heinz TN, van Gunsteren WF, Hünenberger PH (2001) Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. J Chem Phys 115:1125-1136
    • (2001) J Chem Phys , vol.115 , pp. 1125-1136
    • Heinz, T.N.1    Van Gunsteren, W.F.2    Hünenberger, P.H.3
  • 22
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • 10.1016/0009-2614(93)89366-P 1:CAS:528:DyaK2cXhtVOksb8%3D
    • Schlitter J (1993) Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem Phys Lett 215:617-621
    • (1993) Chem Phys Lett , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • 10.1002/bip.360221211 1:CAS:528:DyaL2cXkslegtQ%3D%3D
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 24
    • 77954889093 scopus 로고    scopus 로고
    • Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations
    • 10.1124/dmd.110.032946 1:CAS:528:DC%2BC3cXhtVWktrjE
    • Vasanthanathan P, Olsen L, Jørgensen FS, Vermeulen NPE, Oostenbrink C (2010) Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations. Drug Metab Dispos 38:1347-1354
    • (2010) Drug Metab Dispos , vol.38 , pp. 1347-1354
    • Vasanthanathan, P.1    Olsen, L.2    Jørgensen, F.S.3    Vermeulen, N.P.E.4    Oostenbrink, C.5
  • 25
    • 84862884578 scopus 로고    scopus 로고
    • Cytochrome P450 3A4 inhibition by ketoconazole: Tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations
    • 10.1021/ci300118x 1:CAS:528:DC%2BC38XmvFWqt70%3D
    • Bren U, Oostenbrink C (2012) Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations. J Chem Inf Model 52:1573-1582
    • (2012) J Chem Inf Model , vol.52 , pp. 1573-1582
    • Bren, U.1    Oostenbrink, C.2
  • 26
    • 81555196346 scopus 로고    scopus 로고
    • Identification of a catalytic base for sugar oxidation in the pyranose 2-oxidase reaction
    • 10.1002/cbic.201100564 1:CAS:528:DC%2BC3MXhtlejurbF
    • Wongnate T, Sucharitakul J, Chaiyen P (2011) Identification of a catalytic base for sugar oxidation in the pyranose 2-oxidase reaction. ChemBioChem 12:2577-2586
    • (2011) ChemBioChem , vol.12 , pp. 2577-2586
    • Wongnate, T.1    Sucharitakul, J.2    Chaiyen, P.3
  • 27
    • 0037171621 scopus 로고    scopus 로고
    • C-3 oxidation of non-reducing sugars by a fungal pyranose dehydrogenase: Spectral characterization
    • 10.1016/S1381-1177(02)00014-0 1:CAS:528:DC%2BD38Xis1ent7Y%3D
    • Volc J, Sedmera P, Halada P, Daniel G, Přikrylová V, Haltrich D (2002) C-3 oxidation of non-reducing sugars by a fungal pyranose dehydrogenase: spectral characterization. Mol Cat B 17:91-100
    • (2002) Mol Cat B , vol.17 , pp. 91-100
    • Volc, J.1    Sedmera, P.2    Halada, P.3    Daniel, G.4    Přikrylová, V.5    Haltrich, D.6
  • 29
    • 84865428476 scopus 로고    scopus 로고
    • Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle
    • 10.1021/bi300505z
    • Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT (2012) Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle. Biochemistry 51:6595-6608
    • (2012) Biochemistry , vol.51 , pp. 6595-6608
    • Hernández-Ortega, A.1    Lucas, F.2    Ferreira, P.3    Medina, M.4    Guallar, V.5    Martínez, A.T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.