메뉴 건너뛰기




Volumn 18, Issue 1, 2012, Pages 145-150

Brønsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory

Author keywords

BEP relationship; Density functional theory; Enzyme catalysis

Indexed keywords

OXOACID; THIAMINE;

EID: 84856278114     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1062-z     Document Type: Article
Times cited : (5)

References (33)
  • 2
    • 33947672445 scopus 로고    scopus 로고
    • Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity
    • DOI 10.1529/biophysj.106.096016
    • Fazelinia H, Cirino PC, Maranas CD (2007) Extending iterative protein redesign and optimization (IPRO) in protein library design for ligand specificity. Biophys J 92:2120-2130 (Pubitemid 46495273)
    • (2007) Biophysical Journal , vol.92 , Issue.6 , pp. 2120-2130
    • Fazelinia, H.1    Cirino, P.C.2    Maranas, C.D.3
  • 3
    • 51849142353 scopus 로고    scopus 로고
    • Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
    • 10.1002/bit.22010 1:CAS:528:DC%2BD1cXhsVWktLbN
    • Senger RS, Papoutsakis ET (2008) Genome-scale model for Clostridium acetobutylicum: part I. Metabolic network resolution and analysis. Biotechnol Bioeng 101:1036-1052
    • (2008) Biotechnol Bioeng , vol.101 , pp. 1036-1052
    • Senger, R.S.1    Papoutsakis, E.T.2
  • 4
    • 51849157931 scopus 로고    scopus 로고
    • Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems
    • 10.1002/bit.22009 1:CAS:528:DC%2BD1cXhsVWktLbO
    • Senger RS, Papoutsakis ET (2008) Genome-scale model for Clostridium acetobutylicum: part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol Bioeng 101:1053-1071
    • (2008) Biotechnol Bioeng , vol.101 , pp. 1053-1071
    • Senger, R.S.1    Papoutsakis, E.T.2
  • 5
    • 51849115840 scopus 로고    scopus 로고
    • Genome-scale reconstruction and in silico analysis of the clostridium acetobutylicum ATCC 824 metabolic network
    • 10.1007/s00253-008-1654-4 1:CAS:528:DC%2BD1cXhtFWls7jO
    • Lee J, Yun H, Feist AM, Palsson BO, Lee SY (2008) Genome-scale reconstruction and in silico analysis of the clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 80:849-862
    • (2008) Appl Microbiol Biotechnol , vol.80 , pp. 849-862
    • Lee, J.1    Yun, H.2    Feist, A.M.3    Palsson, B.O.4    Lee, S.Y.5
  • 7
    • 34547809313 scopus 로고    scopus 로고
    • A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data
    • DOI 10.1186/1471-2105-8-228
    • Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET (2007) A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinform 8:228-236 (Pubitemid 47225393)
    • (2007) BMC Bioinformatics , vol.8 , pp. 228
    • Thomas, R.1    Paredes, C.J.2    Mehrotra, S.3    Hatzimanikatis, V.4    Papoutsakis, E.T.5
  • 8
    • 58149476770 scopus 로고    scopus 로고
    • OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold
    • 1:CAS:528:DC%2BD1MXmslCiu7w%3D
    • Fazelinia H, Cirino PC, Maranas CD (2009) OptGraft: a computational procedure for transferring a binding site onto an existing protein scaffold. Prot Sci 18:180-195
    • (2009) Prot Sci , vol.18 , pp. 180-195
    • Fazelinia, H.1    Cirino, P.C.2    Maranas, C.D.3
  • 9
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox
    • DOI 10.1038/nprot.2007.99, PII NPROT.2007.99
    • Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nat Protoc 2:727-738 (Pubitemid 47040034)
    • (2007) Nature Protocols , vol.2 , Issue.3 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.O.5    Herrgard, M.J.6
  • 12
    • 33645752331 scopus 로고    scopus 로고
    • Genome-scale thermodynamic analysis of Escherichia coli metabolism
    • 10.1529/biophysj.105.071720 1:CAS:528:DC%2BD28Xhslarsb8%3D
    • Henry CS, Jankowski MD, Broadbelt LJ, Hatzimanikatis V (2006) Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J 90:1453-1461
    • (2006) Biophys J , vol.90 , pp. 1453-1461
    • Henry, C.S.1    Jankowski, M.D.2    Broadbelt, L.J.3    Hatzimanikatis, V.4
  • 13
    • 65549153067 scopus 로고    scopus 로고
    • Thermodynamic analysis of biodegradation pathways
    • 10.1002/bit.22285 1:CAS:528:DC%2BD1MXmtlGqu7w%3D
    • Finley SD, Broadbelt LJ, Hatzimanikatis V (2009) Thermodynamic analysis of biodegradation pathways. Biotechnol Bioeng 103:532-541
    • (2009) Biotechnol Bioeng , vol.103 , pp. 532-541
    • Finley, S.D.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 14
    • 0028727474 scopus 로고
    • Computer generated reaction networks: On-the-fly calculation of species properties using computational quantum chemistry
    • 10.1016/0009-2509(94)00326-2 1:CAS:528:DyaK2MXksFWgu7c%3D
    • Broadbelt LJ, Stark SM, Klein MT (1994) Computer generated reaction networks: on-the-fly calculation of species properties using computational quantum chemistry. Chem Eng Sci 49:4991-5010
    • (1994) Chem Eng Sci , vol.49 , pp. 4991-5010
    • Broadbelt, L.J.1    Stark, S.M.2    Klein, M.T.3
  • 15
    • 0028410110 scopus 로고
    • Computer-generated pyrolysis modeling - On-the-fly generation of species, reactions, and rates
    • 10.1021/ie00028a003 1:CAS:528:DyaK2cXitFKnu7s%3D
    • Broadbelt LJ, Stark SM, Klein MT (1994) Computer-generated pyrolysis modeling - on-the-fly generation of species, reactions, and rates. Ind Eng Chem Res 33:790-799
    • (1994) Ind Eng Chem Res , vol.33 , pp. 790-799
    • Broadbelt, L.J.1    Stark, S.M.2    Klein, M.T.3
  • 16
    • 0000670212 scopus 로고
    • Termination of computer-generated reaction-mechanisms-species rank-based convergence criterion
    • 10.1021/ie00047a003 1:CAS:528:DyaK2MXntVWksrw%3D
    • Broadbelt LJ, Stark SM, Klein MT (1995) Termination of computer-generated reaction-mechanisms-species rank-based convergence criterion. Ind Eng Chem Res 34:2566-2573
    • (1995) Ind Eng Chem Res , vol.34 , pp. 2566-2573
    • Broadbelt, L.J.1    Stark, S.M.2    Klein, M.T.3
  • 17
    • 22144436255 scopus 로고    scopus 로고
    • Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways
    • DOI 10.1021/ja051586y
    • Gonzalez-Lergier J, Broadbelt LJ, Hatzimanikatis V (2005) Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways. J Chem Soc 127:9930-9938 (Pubitemid 40981557)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.27 , pp. 9930-9938
    • Gonzalez-Lergier, J.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 18
    • 70350501257 scopus 로고    scopus 로고
    • Thermodynamic analysis of biodegradation pathways
    • 10.1002/bit.22489 1:CAS:528:DC%2BD1MXhtlequ73O
    • Finley SD, Broadbelt LJ, Hatzimanikatis V (2009) Thermodynamic analysis of biodegradation pathways. Biotechnol Bioeng 104:1086-1097
    • (2009) Biotechnol Bioeng , vol.104 , pp. 1086-1097
    • Finley, S.D.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 19
    • 77953578214 scopus 로고    scopus 로고
    • Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
    • 1:CAS:528:DC%2BC3cXlsVOlsb4%3D
    • Henry CS, Broadbelt LJ, Hatzimanikatis V (2010) Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 106:462-473
    • (2010) Biotechnol Bioeng , vol.106 , pp. 462-473
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 20
    • 2642513030 scopus 로고    scopus 로고
    • Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space
    • DOI 10.1016/j.jtbi.2004.02.006, PII S0022519304000554
    • Wiback SJ, Famili I, Greenberg HJ, Palsson B∅ (2004) Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol 228:437-447 (Pubitemid 38726066)
    • (2004) Journal of Theoretical Biology , vol.228 , Issue.4 , pp. 437-447
    • Wiback, S.J.1    Famili, I.2    Greenberg, H.J.3    Palsson, B.O.4
  • 21
    • 77955121936 scopus 로고
    • Structure/reactivity relationships for high-performance polyamides-kinetics of the reactions of N,N′-dihexylphthalamides in the presence of added copper iodide and water
    • Broadbelt LJ, Klein MT, Dean BD, Andrews SM (1995) Structure/reactivity relationships for high-performance polyamides-kinetics of the reactions of N,N′-dihexylphthalamides in the presence of added copper iodide and water. J Polym Sci A Polym Chem 33:533-545
    • (1995) J Polym Sci A Polym Chem , vol.33 , pp. 543-545
    • Broadbelt, L.J.1    Klein, M.T.2    Dean, B.D.3    Andrews, S.M.4
  • 22
    • 18844424175 scopus 로고
    • Inertia and driving force of chemical reactions
    • 10.1039/tf9383400011 1:CAS:528:DyaA1cXitVWisg%3D%3D
    • Evans MG, Polanyi M (1938) Inertia and driving force of chemical reactions. Trans Faraday Soc 34:11-24
    • (1938) Trans Faraday Soc , vol.34 , pp. 11-24
    • Evans, M.G.1    Polanyi, M.2
  • 23
    • 73449112657 scopus 로고    scopus 로고
    • Cycloaddition reactions of butadiene and 1,3-dipoles to curved arenes, fullerenes, and nanotubes: Theoretical evaluation of the role of distortion energies on activation barriers
    • 10.1002/chem.200901761 1:CAS:528:DC%2BD1MXhsFektb%2FK
    • Osuna S, Houk KN (2009) Cycloaddition reactions of butadiene and 1,3-dipoles to curved arenes, fullerenes, and nanotubes: theoretical evaluation of the role of distortion energies on activation barriers. Chem Eur J 15:13219-13231
    • (2009) Chem Eur J , vol.15 , pp. 13219-13231
    • Osuna, S.1    Houk, K.N.2
  • 24
    • 79955939745 scopus 로고    scopus 로고
    • Computational screening of novel thiamine-catalyzed decarboxylation reaction of 2-keto acids
    • 10.1007/s00449-010-0481-z
    • Assary RS, Broadbelt LA (2010) Computational screening of novel thiamine-catalyzed decarboxylation reaction of 2-keto acids. Bioprocess Biosyst Eng 34:375-388
    • (2010) Bioprocess Biosyst Eng , vol.34 , pp. 375-388
    • Assary, R.S.1    Broadbelt, L.A.2
  • 25
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic-behavior
    • 10.1103/PhysRevA.38.3098 1:CAS:528:DyaL1cXmtlOhsLo%3D
    • Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys Rev Abstr 38:3098-3100
    • (1988) Phys Rev Abstr , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 26
    • 0000189651 scopus 로고
    • Density-functional thermochemistry.3. The role of exact exchange
    • 10.1063/1.464913 1:CAS:528:DyaK3sXisVWgtrw%3D
    • Becke AD (1993) Density-functional thermochemistry.3. The role of exact exchange. J Chem Phys 98:5648-5652
    • (1993) J Chem Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 27
    • 0345491105 scopus 로고
    • Development of the colle-salvetti correlation-energy formula into a functional of the electron-density
    • 10.1103/PhysRevB.37.785 1:CAS:528:DyaL1cXktFWrtbw%3D
    • Lee CT, Yang WT, Parr RG (1988) Development of the colle-salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B 37:785-789
    • (1988) Phys Rev B , vol.37 , pp. 785-789
    • Lee, C.T.1    Yang, W.T.2    Parr, R.G.3
  • 29
    • 84962361532 scopus 로고    scopus 로고
    • Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules
    • 10.1021/ct049977a
    • Takano Y, Houk KN (2005) Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules. J Chem Theor Comput 1:70-77
    • (2005) J Chem Theor Comput , vol.1 , pp. 70-77
    • Takano, Y.1    Houk, K.N.2
  • 30
    • 84962349001 scopus 로고    scopus 로고
    • Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model
    • 10.1002/jcc.10189 1:CAS:528:DC%2BD3sXivFWqsbc%3D
    • Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669-681
    • (2003) J Comput Chem , vol.24 , pp. 669-681
    • Cossi, M.1    Rega, N.2    Scalmani, G.3    Barone, V.4
  • 31
    • 84961985847 scopus 로고    scopus 로고
    • Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model
    • Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995-2001 (Pubitemid 128591338)
    • (1998) Journal of Physical Chemistry A , vol.102 , Issue.11 , pp. 1995-2001
    • Barone, V.1    Cossi, M.2
  • 32
    • 26844525476 scopus 로고    scopus 로고
    • Theoretical study toward understanding the catalytic mechanism of pyruvate decarboxylase
    • DOI 10.1021/jp052802s
    • Wang J, Dong H, Li S, He H (2005) Theoretical study toward understanding the catalytic mechanism of pyruvate decarboxylase. J Phys Chem B 109:18664-18672 (Pubitemid 41464201)
    • (2005) Journal of Physical Chemistry B , vol.109 , Issue.39 , pp. 18664-18672
    • Wang, J.1    Dong, H.2    Li, S.3    He, H.4
  • 33
    • 67649476220 scopus 로고    scopus 로고
    • Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
    • 10.1007/s00775-009-0511-y 1:CAS:528:DC%2BD1MXlslGms70%3D
    • Siegbahn P, Himo F (2009) Recent developments of the quantum chemical cluster approach for modeling enzyme reactions. J Biol Inorg Chem 14:643-651
    • (2009) J Biol Inorg Chem , vol.14 , pp. 643-651
    • Siegbahn, P.1    Himo, F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.