메뉴 건너뛰기




Volumn 1824, Issue 5, 2012, Pages 750-758

QM/MM investigation on the catalytic mechanism of Bacteroides thetaiotaomicron α-glucosidase BtGH97a

Author keywords

BtGH97a; pNP Glc; QM MM; Reaction mechanism

Indexed keywords

ALPHA GLUCOSIDASE;

EID: 84859411812     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2012.03.005     Document Type: Article
Times cited : (6)

References (38)
  • 1
    • 33846015876 scopus 로고    scopus 로고
    • Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period
    • J.I. Gordon, M.K. Bjursell, and E.C. Martens Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period J. Biol. Chem. 281 2006 36269 36279
    • (2006) J. Biol. Chem. , vol.281 , pp. 36269-36279
    • Gordon, J.I.1    Bjursell, M.K.2    Martens, E.C.3
  • 4
    • 0029929874 scopus 로고    scopus 로고
    • Updating the sequence-based classification of glycosyl hydrolases
    • B. Henrissat, and A. Bairoch Updating the sequence-based classification of glycosyl hydrolases Biochem. J. 316 1996 695 696
    • (1996) Biochem. J. , vol.316 , pp. 695-696
    • Henrissat, B.1    Bairoch, A.2
  • 5
    • 0141644339 scopus 로고    scopus 로고
    • Bacteroiades thetaiotaomicron: A dynamic, niche-adapted human symbiont
    • L.E. Comstock, and M.J. Coyne Bacteroiades thetaiotaomicron: a dynamic, niche-adapted human symbiont Bioessays 25 2003 926 929
    • (2003) Bioessays , vol.25 , pp. 926-929
    • Comstock, L.E.1    Coyne, M.J.2
  • 7
    • 25444464874 scopus 로고    scopus 로고
    • GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily
    • D.G. Naumoff GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily BMC Genomics 6 2005 112 123
    • (2005) BMC Genomics , vol.6 , pp. 112-123
    • Naumoff, D.G.1
  • 8
    • 79959695560 scopus 로고    scopus 로고
    • GH97 is a new family of alpha-glucosidases
    • D.G. Naumoff GH97 is a new family of alpha-glucosidases FEBS J. 272 2005 94 95
    • (2005) FEBS J. , vol.272 , pp. 94-95
    • Naumoff, D.G.1
  • 9
  • 10
    • 54949157712 scopus 로고    scopus 로고
    • Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora
    • T.M. Gloster, J.P. Turkenburg, J.R. Potts, B. Henrissat, and G.J. Davies Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora Chem. Biol. 15 2008 1058 1067
    • (2008) Chem. Biol. , vol.15 , pp. 1058-1067
    • Gloster, T.M.1    Turkenburg, J.P.2    Potts, J.R.3    Henrissat, B.4    Davies, G.J.5
  • 11
    • 0025827916 scopus 로고
    • Characterization of a neopullulanase and an alpha-glucosidase from Bacteroides thetaiotaomicron 95-1
    • K.A. Smith, and A.A. Salyers Characterization of a neopullulanase and an alpha-glucosidase from Bacteroides thetaiotaomicron 95-1 J. Bacteriol. 173 1991 2962 2968
    • (1991) J. Bacteriol. , vol.173 , pp. 2962-2968
    • Smith, K.A.1    Salyers, A.A.2
  • 12
    • 78649580944 scopus 로고    scopus 로고
    • Glycosidic-bond hydrolysis mechanism catalyzed by cellulase Cel7A from Trichoderma reesei: A comprehensive theoretical study by performing MD, QM, and QM/MM calculations
    • J.H. Li, L.K. Du, and L.S. Wang Glycosidic-bond hydrolysis mechanism catalyzed by cellulase Cel7A from Trichoderma reesei: a comprehensive theoretical study by performing MD, QM, and QM/MM calculations J. Phys. Chem. B 114 2010 15261 15268
    • (2010) J. Phys. Chem. B , vol.114 , pp. 15261-15268
    • Li, J.H.1    Du, L.K.2    Wang, L.S.3
  • 13
    • 77950130195 scopus 로고    scopus 로고
    • QM/MM studies on the beta-galactosidase catalytic mechanism: Hydrolysis and transglycosylation reactions
    • N.F. Bras, P.A. Fernandes, and M.J. Ramos QM/MM studies on the beta-galactosidase catalytic mechanism: hydrolysis and transglycosylation reactions J. Chem. Theory Comput. 6 2010 421 433
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 421-433
    • Bras, N.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 14
    • 76249117092 scopus 로고    scopus 로고
    • QM/MM study on the catalytic mechanism of cellulose hydrolysis catalyzed by cellulase Cel5A from Acidothermus cellulolyticus
    • J.L. Liu, X.M. Wang, and D.G. Xu QM/MM study on the catalytic mechanism of cellulose hydrolysis catalyzed by cellulase Cel5A from Acidothermus cellulolyticus J. Phys. Chem. B 114 2010 1462 1470
    • (2010) J. Phys. Chem. B , vol.114 , pp. 1462-1470
    • Liu, J.L.1    Wang, X.M.2    Xu, D.G.3
  • 15
    • 77956075525 scopus 로고    scopus 로고
    • Redox mechanism of glycosidic bond hydrolysis catalyzed by 6-phospho-alpha-glucosidase: A DFT study
    • W.J. Huang, J. Llano, and J.W. Gauld Redox mechanism of glycosidic bond hydrolysis catalyzed by 6-phospho-alpha-glucosidase: a DFT study J. Phys. Chem. B 114 2010 11196 11206
    • (2010) J. Phys. Chem. B , vol.114 , pp. 11196-11206
    • Huang, W.J.1    Llano, J.2    Gauld, J.W.3
  • 16
    • 84855310108 scopus 로고    scopus 로고
    • QM/MM studies on the glycosylation mechanism of rice BGlu1 beta-glucosidase
    • J.H. Wang, Q.Q. Hou, L.H. Dong, Y.J. Liu, and C.B. Liu QM/MM studies on the glycosylation mechanism of rice BGlu1 beta-glucosidase J. Mol. Graph. Model. 30 2011 148 152
    • (2011) J. Mol. Graph. Model. , vol.30 , pp. 148-152
    • Wang, J.H.1    Hou, Q.Q.2    Dong, L.H.3    Liu, Y.J.4    Liu, C.B.5
  • 17
    • 17044377101 scopus 로고
    • Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization
    • A. Warshel, and M. Karplus Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization J. Am. Chem. Soc. 94 1972 5612 5625
    • (1972) J. Am. Chem. Soc. , vol.94 , pp. 5612-5625
    • Warshel, A.1    Karplus, M.2
  • 18
    • 0017100947 scopus 로고
    • Theoretical studies of enzymatic reactions: Dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
    • A. Warshel, and M. Levitt Theoretical studies of enzymatic reactions: dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 103 1976 227 249
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 19
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • M.J. Field, P.A. Bash, and M. Karplus A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 11 1990 700 733
    • (1990) J. Comput. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 20
    • 0036025446 scopus 로고    scopus 로고
    • Quantum mechanical methods for enzyme kinetics
    • J.L. Gao, and D.G. Truhlar Quantum mechanical methods for enzyme kinetics Annu. Rev. Phys. Chem. 53 2002 467 505
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 467-505
    • Gao, J.L.1    Truhlar, D.G.2
  • 21
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM methods for biomolecular systems
    • H.M. Senn, and W. Thiel QM/MM methods for biomolecular systems Angew. Chem. Int. Ed. 48 2009 1198 1229
    • (2009) Angew. Chem. Int. Ed. , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 24
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges
    • J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 25
    • 0037827688 scopus 로고    scopus 로고
    • Crystal structure of rice alpha-galactosidase complexed with d-galactose
    • Z. Fujimoto, S. Kaneko, M. Momma, H. Kobayashi, and H. Mizuno Crystal structure of rice alpha-galactosidase complexed with d-galactose J. Biol. Chem. 278 2003 20313 20318
    • (2003) J. Biol. Chem. , vol.278 , pp. 20313-20318
    • Fujimoto, Z.1    Kaneko, S.2    Momma, M.3    Kobayashi, H.4    Mizuno, H.5
  • 29
    • 4243539377 scopus 로고
    • Electronic structure calculations on workstation computers: The program system TURBOMOLE
    • R. Ahlrichs, M. Bar, M. Haser, H. Horn, and C. Kolmel Electronic structure calculations on workstation computers: the program system TURBOMOLE Chem. Phys. Lett. 162 1989 165 169
    • (1989) Chem. Phys. Lett. , vol.162 , pp. 165-169
    • Ahlrichs, R.1    Bar, M.2    Haser, M.3    Horn, H.4    Kolmel, C.5
  • 30
    • 0030175155 scopus 로고    scopus 로고
    • DL-POLY-2.0: A general-purpose parallel molecular dynamics simulation package
    • W. Smith, and T.R. Forester DL-POLY-2.0: a general-purpose parallel molecular dynamics simulation package J. Mol. Graph. Model. 14 1996 136 141
    • (1996) J. Mol. Graph. Model. , vol.14 , pp. 136-141
    • Smith, W.1    Forester, T.R.2
  • 31
    • 0345713551 scopus 로고    scopus 로고
    • Hybrid models for combined quantum mechanical and molecular mechanical approaches
    • D. Bakowies, and W. Thiel Hybrid models for combined quantum mechanical and molecular mechanical approaches J. Phys. Chem. 100 1996 10580 10594
    • (1996) J. Phys. Chem. , vol.100 , pp. 10580-10594
    • Bakowies, D.1    Thiel, W.2
  • 34
    • 0034658025 scopus 로고    scopus 로고
    • Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
    • S.R. Billeter, A.J. Turner, and W. Thiel Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates Phys. Chem. Chem. Phys. 2 2000 2177 2186
    • (2000) Phys. Chem. Chem. Phys. , vol.2 , pp. 2177-2186
    • Billeter, S.R.1    Turner, A.J.2    Thiel, W.3
  • 35
    • 84966262179 scopus 로고
    • Updating quasi-Newton matrices with limited storage
    • J. Nocedal Updating quasi-Newton matrices with limited storage Math. Comput. 35 1980 773 782
    • (1980) Math. Comput. , vol.35 , pp. 773-782
    • Nocedal, J.1
  • 36
    • 33646887390 scopus 로고
    • On the limited memory BFGS method for large scale optimization
    • D.C. Liu, and J. Nocedal On the limited memory BFGS method for large scale optimization Math. Program. 45 1989 503 528
    • (1989) Math. Program. , vol.45 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 38
    • 84988122931 scopus 로고
    • An algorithm for the location of transition states
    • J. Baker An algorithm for the location of transition states J. Comput. Chem. 7 1986 385 395
    • (1986) J. Comput. Chem. , vol.7 , pp. 385-395
    • Baker, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.