메뉴 건너뛰기




Volumn 50, Issue 39, 2011, Pages 8302-8310

Role of a mutated residue at the entrance of the substrate access channel in cytochrome P450 engineered for vitamin D 3 hydroxylation activity

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; BINDING FREE ENERGY; BINDING POCKETS; BOUND STATE; COMPUTATIONAL APPROACH; CRYSTAL STRUCTURE ANALYSIS; CYTOCHROME P450; FUTURE CHALLENGES; INTERACTION FORCES; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN DATA BANK; QUANTUM CHEMICAL CALCULATIONS; SALT BRIDGES; STEERED MOLECULAR DYNAMICS; STRUCTURAL CHANGE; THREE DIMENSIONAL COORDINATE; VITAMIN-D; WILD-TYPE ENZYMES;

EID: 80053426513     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi2006493     Document Type: Article
Times cited : (12)

References (45)
  • 2
    • 0033650404 scopus 로고    scopus 로고
    • The natural functions of secondary metabolites
    • Demain, A. L. and Fang, A. (2000) The natural functions of secondary metabolites Adv. Biochem. Eng./Biotechnol. 69, 1-39
    • (2000) Adv. Biochem. Eng./Biotechnol. , vol.69 , pp. 1-39
    • Demain, A.L.1    Fang, A.2
  • 3
    • 0031755168 scopus 로고    scopus 로고
    • Current understanding of the molecular actions of vitamin D
    • Jones, G., Strugnell, S. A., and DeLuca, H. F. (1998) Current understanding of the molecular actions of vitamin D Physiol. Rev. 78, 1193-1231 (Pubitemid 28491953)
    • (1998) Physiological Reviews , vol.78 , Issue.4 , pp. 1193-1231
    • Jones, G.1    Strugnell, S.A.2    DeLuca, H.F.3
  • 4
    • 8544284075 scopus 로고    scopus 로고
    • Enzymes involved in the activation and inactivation of vitamin D
    • DOI 10.1016/j.tibs.2004.10.005, PII S0968000404002701
    • Prosser, D. E. and Jones, G. (2004) Enzymes involved in the activation and inactivation of vitamin D Trends Biochem. Sci. 29, 664-673 (Pubitemid 39491265)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.12 , pp. 664-673
    • Prosser, D.E.1    Jones, G.2
  • 9
    • 0015240863 scopus 로고
    • Identification of 1,25-dihydroxycolestecalciferol, a new kidney hormone controlling calcium metabolism
    • Lawson, D. E. M., Fraser, D. R. F., Kodicek, E., Morris, H. R., and Williams, D. H. (1971) Identification of 1,25-dihydroxycolestecalciferol, a new kidney hormone controlling calcium metabolism Nature 230, 228-230
    • (1971) Nature , vol.230 , pp. 228-230
    • Lawson, D.E.M.1    Fraser, D.R.F.2    Kodicek, E.3    Morris, H.R.4    Williams, D.H.5
  • 11
    • 34548202165 scopus 로고    scopus 로고
    • Vitamin D signalling pathways in cancer: Potential for anticancer therapeutics
    • DOI 10.1038/nrc2196, PII NRC2196
    • Deeb, K. K., Trump, D. L., and Johnson, C. S. (2007) Vitamin D signaling pathways in cancer: Potential for anticancer therapeutics Nat. Rev. Cancer 7, 684-700 (Pubitemid 47327412)
    • (2007) Nature Reviews Cancer , vol.7 , Issue.9 , pp. 684-700
    • Deeb, K.K.1    Trump, D.L.2    Johnson, C.S.3
  • 12
    • 0026614795 scopus 로고
    • Transformation of vitamin D3 to 1α,25-dihydroxyvitamin D3 via 25-hydroxyvitamin D3 using Amycolata sp. strains
    • Sakaki, J., Miyazaki, A., Saito, M., Adachi, T., Mizoue, K., Hanada, K., and Omura, S. (1992) Transformation of vitamin D3 to 1α,25- dihydroxyvitamin D3 via 25-hydroxyvitamin D3 using Amycolata sp. strains Appl. Microbiol. Biotechnol. 38, 152-157
    • (1992) Appl. Microbiol. Biotechnol. , vol.38 , pp. 152-157
    • Sakaki, J.1    Miyazaki, A.2    Saito, M.3    Adachi, T.4    Mizoue, K.5    Hanada, K.6    Omura, S.7
  • 15
    • 77957814994 scopus 로고    scopus 로고
    • Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 Vdh
    • Yasutake, Y., Fujii, Y., Nishioka, T., Cheon, W. K., Arisawa, A., and Tamura, T. (2010) Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 Vdh J. Biol. Chem. 285, 31193-31201
    • (2010) J. Biol. Chem. , vol.285 , pp. 31193-31201
    • Yasutake, Y.1    Fujii, Y.2    Nishioka, T.3    Cheon, W.K.4    Arisawa, A.5    Tamura, T.6
  • 17
    • 0034634393 scopus 로고    scopus 로고
    • Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
    • Lüdemann, S. K., Lounnas, V., and Wade, R. C. (2000) Random expulsion molecular dynamics investigation of ligand access channels and mechanisms J. Mol. Biol. 303, 797-811
    • (2000) J. Mol. Biol. , vol.303 , pp. 797-811
    • Lüdemann, S.K.1    Lounnas, V.2    Wade, R.C.3
  • 18
    • 0037117562 scopus 로고    scopus 로고
    • Comparison of the dynamics of substrate access channels in three cytochrome p450s reveals different opening mechanisms and a novel functional role for a buried arginine
    • DOI 10.1073/pnas.082522999
    • Winn, P. J., Lüdemann, S. K., Gauges, R., Lounnas, V., and Wade, R. C. (2002) Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine Proc. Natl. Acad. Sci. U.S.A. 99, 5361-5366 (Pubitemid 34411553)
    • (2002) Proceedings of the National Academy of Sciences of the United States of America , vol.99 , Issue.8 , pp. 5361-5366
    • Winn, P.J.1    Ludemann, S.K.2    Gauges, R.3    Lounnas, V.4    Wade, R.C.5
  • 20
    • 0030987036 scopus 로고    scopus 로고
    • Molecular dynamics study of unbinding of the avidin-biotin complex
    • Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y., and Schulten, K. (1997) Molecular dynamics study of unbinding of the avidin-biotin complex Biophys. J. 72, 1568-1581 (Pubitemid 27133097)
    • (1997) Biophysical Journal , vol.72 , Issue.4 , pp. 1568-1581
    • Izrailev, S.1    Stepaniants, S.2    Balsera, M.3    Oono, Y.4    Schulten, K.5
  • 21
    • 0034634391 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways
    • Lüdemann, S. K., Lounnas, V., and Wade, R. C. (2000) How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways J. Mol. Biol. 303, 813-830
    • (2000) J. Mol. Biol. , vol.303 , pp. 813-830
    • Lüdemann, S.K.1    Lounnas, V.2    Wade, R.C.3
  • 22
    • 0041691306 scopus 로고    scopus 로고
    • How does Huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations
    • DOI 10.1021/ja029775t
    • Xu, Y., Shen, J., Luo, X., Silman, I., Sussmann, J. L., Chen, K., and Jiang, H. (2003) How does Huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations J. Am. Chem. Soc. 125, 11340-11349 (Pubitemid 37108071)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.37 , pp. 11340-11349
    • Xu, Y.1    Shen, J.2    Luo, X.3    Silman, I.4    Sussman, J.L.5    Chen, K.6    Jiang, H.7
  • 23
    • 0038440651 scopus 로고    scopus 로고
    • Molecular dynamics simulations of lignin peroxidase in solution
    • Gerini, M. F., Roccatano, D., Baciocchi, E., and Nola, A. D. (2003) Molecular dynamics simulations of lignin peroxidase in solution Biophys. J. 84, 3883-3893 (Pubitemid 36637883)
    • (2003) Biophysical Journal , vol.84 , Issue.6 , pp. 3883-3893
    • Gerini, M.F.1    Roccatano, D.2    Baciocchi, E.3    Di Nola, A.4
  • 24
    • 0037380955 scopus 로고    scopus 로고
    • Forced detachment of the CD2-CD58 complex
    • Bayas, M. V., Schulten, K., and Leckband, D. (2003) Forced Detachment of the CD2-CD58 Complex Biophys. J. 84, 2223-2233 (Pubitemid 36373545)
    • (2003) Biophysical Journal , vol.84 , Issue.4 , pp. 2223-2233
    • Bayas, M.V.1    Schulten, K.2    Leckband, D.3
  • 25
    • 33644938813 scopus 로고    scopus 로고
    • Potential of mean force for a acetylcholine unbinding from the α7 nicotinic acetylcholine receptor ligand-binding domain
    • Zhang, D., Gullingsrud, J., and McCammon, J. A. (2006) Potential of mean force for a acetylcholine unbinding from the α7 nicotinic acetylcholine receptor ligand-binding domain J. Am. Chem. Soc. 128, 3019-3026
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 3019-3026
    • Zhang, D.1    Gullingsrud, J.2    McCammon, J.A.3
  • 26
    • 33845571063 scopus 로고    scopus 로고
    • Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol
    • DOI 10.1194/jlr.M600232-JLR200
    • Murcia, M., Faraldo-Gomez, J. D., Maxfield, F. R., and Roux, B. (2006) Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol J. Lipid Res. 47, 2614-2630 (Pubitemid 44936075)
    • (2006) Journal of Lipid Research , vol.47 , Issue.12 , pp. 2614-2630
    • Murcia, M.1    Faraldo-Gomez, J.D.2    Maxfield, F.R.3    Roux, B.4
  • 27
    • 33751285812 scopus 로고    scopus 로고
    • Blocking of the nicotinic acetylcholine receptor ion channel by chlorpromazine, a noncompetitive inhibitor: A molecular dynamics simulation study
    • DOI 10.1021/jp0604591
    • Xu, Y., Barrantes, F. J., Shen, J., Luo, X., Zhu, W., Chen, K., and Jiang, H. (2006) Blocking of the Nicotinic Acetylcholine Receptor Ion Channel by Chlorpromazine, a Noncompetitive Inhibitor: A Molecular Dynamics Simulation Study J. Phys. Chem. B 110, 20640-20648 (Pubitemid 44797496)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.41 , pp. 20640-20648
    • Xu, Y.1    Barrantes, F.J.2    Shen, J.3    Luo, X.4    Zhu, W.5    Chen, K.6    Jiang, H.7
  • 28
    • 55149103351 scopus 로고    scopus 로고
    • Dynamic Mechanism of Fatty Acid Transport across Cellular Membranes through FadL: Molecular Dynamics Simulations
    • Zou, H., Zheng, M., Luo, X., Zhu, W., Chen, K., Shen, J., and Jiang, H. (2008) Dynamic Mechanism of Fatty Acid Transport across Cellular Membranes through FadL: Molecular Dynamics Simulations J. Phys. Chem. B 112, 13070-13078
    • (2008) J. Phys. Chem. B , vol.112 , pp. 13070-13078
    • Zou, H.1    Zheng, M.2    Luo, X.3    Zhu, W.4    Chen, K.5    Shen, J.6    Jiang, H.7
  • 29
    • 44349114473 scopus 로고    scopus 로고
    • Functional and computational studies of the ligand-associated metal binding site of β3 integrins
    • DOI 10.1002/prot.21859
    • Murcia, M., Jirouskova, M., Li, J., Coller, B. S., and Filizola, M. (2008) Functional and computational studies of the ligand-associated metal binding site of β3 integrins Proteins 71, 1779-1791 (Pubitemid 351732934)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.4 , pp. 1779-1791
    • Murcia, M.1    Jirouskova, M.2    Li, J.3    Coller, B.S.4    Filizola, M.5
  • 30
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. (1997) Nonequilibrium equality for free energy differences Phys. Rev. Lett. 78, 2690-2693 (Pubitemid 127655287)
    • (1997) Physical Review Letters , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 32
    • 31344460657 scopus 로고    scopus 로고
    • Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment
    • DOI 10.1110/ps.051842406
    • Midelfort, K. S. and Wittrup, K. D. (2006) Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment Protein Sci. 15, 324-334 (Pubitemid 43145004)
    • (2006) Protein Science , vol.15 , Issue.2 , pp. 324-334
    • Midelfort, K.S.1    Wittrup, K.D.2
  • 33
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J. M., Cieplak, P., and Kollman, P. A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 35
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly, C. I., Cieplak, P., Cornell, W., and Kollman, P. A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model J. Phys. Chem. 97, 10269-10280
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 36
    • 35948961951 scopus 로고    scopus 로고
    • General transition-state force field for cytochrome P450 hydroxylation
    • Rydberg, P., Olsen, L., Norrby, P.-O., and Ryde, U. (2007) General transition-state force field for cytochrome P450 hydroxylation J. Chem. Theory Comput. 3, 1765-1773
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1765-1773
    • Rydberg, P.1    Olsen, L.2    Norrby, P.-O.3    Ryde, U.4
  • 38
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 39
    • 33846823909 scopus 로고
    • Particle Mesh Ewald-an N.Log(N) method for Ewald sums in large systems
    • Darden, T., York, D., and Pedersen, L. (1993) Particle Mesh Ewald-an N.Log(N) method for Ewald sums in large systems J. Chem. Phys. 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 41
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • DOI 10.1016/S0959-440X(00)00194-9
    • Isralewitz, B., Gao, M., and Schulten, K. (2001) Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 11, 224-230 (Pubitemid 32289426)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.2 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 42
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from nonequilibrium molecular dynamics simulations using Jarzynskis equality
    • Park, S., Khalili-Araghi, F., Tajkhorshid, E., and Schulten, K. (2003) Free energy calculation from nonequilibrium molecular dynamics simulations using Jarzynskis equality J. Chem. Phys. 119, 3559-3566
    • (2003) J. Chem. Phys. , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 43
    • 4143087050 scopus 로고    scopus 로고
    • Calculating potentials of mean force from steered molecular dynamics simulations
    • Park, S. and Schulten, K. (2004) Calculating potentials of mean force from steered molecular dynamics simulations J. Chem. Phys. 120, 5946-5961
    • (2004) J. Chem. Phys. , vol.120 , pp. 5946-5961
    • Park, S.1    Schulten, K.2
  • 44
    • 0035826435 scopus 로고    scopus 로고
    • A "fast growth" method of computing free energy differences
    • DOI 10.1063/1.1353552
    • Hendrix, D. A. and Jarzynski, C. (2001) A "fast growth" method of computing free energy differences J. Chem. Phys. 114, 5974-5981 (Pubitemid 32419574)
    • (2001) Journal of Chemical Physics , vol.114 , Issue.14 , pp. 5974-5981
    • Hendrix, D.A.1    Jarzynski, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.