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Volumn 16, Issue 5, 2007, Pages 781-794

CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations

Author keywords

Docking sites; Internal cavities; Ligand migration; Ligand rebinding kinetics; Molecular dynamics

Indexed keywords

CAMPHOR 5 MONOOXYGENASE; CARBON MONOXIDE; XENON;

EID: 34247621201     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062374707     Document Type: Article
Times cited : (9)

References (61)
  • 1
    • 0034813458 scopus 로고    scopus 로고
    • Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics study
    • Amara, P., Andreoletti, P., Jouve, H.M., and Field, M.J. 2001. Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics study. Protein Sci. 10: 1927-1935.
    • (2001) Protein Sci , vol.10 , pp. 1927-1935
    • Amara, P.1    Andreoletti, P.2    Jouve, H.M.3    Field, M.J.4
  • 4
    • 0036606442 scopus 로고    scopus 로고
    • Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty-acid proteins
    • Bakowies, D. and van Gunsteren, W.F. 2002. Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty-acid proteins. Proteins 47: 534-545.
    • (2002) Proteins , vol.47 , pp. 534-545
    • Bakowies, D.1    van Gunsteren, W.F.2
  • 6
    • 2942655520 scopus 로고    scopus 로고
    • Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin
    • Bossa, C., Anselmi, M., Roccatano, D., Amadei, A., Vallone, B., Brunori, M., and Di Nola, A. 2004. Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Biophys. J. 86: 3855-3862.
    • (2004) Biophys. J , vol.86 , pp. 3855-3862
    • Bossa, C.1    Anselmi, M.2    Roccatano, D.3    Amadei, A.4    Vallone, B.5    Brunori, M.6    Di Nola, A.7
  • 7
    • 23244457434 scopus 로고    scopus 로고
    • Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities
    • Bossa, C., Amadei, A., Daidone, I., Anselmi, M., Vallone, B., Brunori, M., and Di Nola, A. 2005. Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities. Biophys. J. 89: 465-474.
    • (2005) Biophys. J , vol.89 , pp. 465-474
    • Bossa, C.1    Amadei, A.2    Daidone, I.3    Anselmi, M.4    Vallone, B.5    Brunori, M.6    Di Nola, A.7
  • 9
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization and molecular dynamics calculations
    • Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M. 1983. CHARMM: A program for macromolecular energy, minimization and molecular dynamics calculations. J. Comput. Chem. 4: 187-217.
    • (1983) J. Comput. Chem , vol.4 , pp. 187-217
    • Brooks, B.1    Bruccoleri, R.2    Olafson, B.3    States, D.4    Swaminathan, S.5    Karplus, M.6
  • 11
    • 0034867130 scopus 로고    scopus 로고
    • Cavities and packing defects in the structural dynamics of myoglobin
    • Brunori, M. and Gibson, Q.H. 2001. Cavities and packing defects in the structural dynamics of myoglobin. EMBO Rep. 2: 674-679.
    • (2001) EMBO Rep , vol.2 , pp. 674-679
    • Brunori, M.1    Gibson, Q.H.2
  • 12
    • 0030031593 scopus 로고    scopus 로고
    • Distal cavity fluctuations in myoglobin: Protein motion and ligand diffusion
    • Carlson, M.L., Regan, R.M., and Gibson, Q.H. 1996. Distal cavity fluctuations in myoglobin: Protein motion and ligand diffusion. Biochemistry 35: 1125-1136.
    • (1996) Biochemistry , vol.35 , pp. 1125-1136
    • Carlson, M.L.1    Regan, R.M.2    Gibson, Q.H.3
  • 13
  • 14
  • 16
    • 0035940433 scopus 로고    scopus 로고
    • Probing the open state of cytochrome P450cam with ruthenium-linker substrates
    • Dunn, A.R., Dmoichowski, I.J., Bilwes, A.M., Gray, H.B., and Crane, B.R. 2001. Probing the open state of cytochrome P450cam with ruthenium-linker substrates. Proc. Natl. Acad. Sci. 98: 12421-12425.
    • (2001) Proc. Natl. Acad. Sci , vol.98 , pp. 12421-12425
    • Dunn, A.R.1    Dmoichowski, I.J.2    Bilwes, A.M.3    Gray, H.B.4    Crane, B.R.5
  • 17
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
    • Elber, R. and Karplus, M. 1990. Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112: 9161-9175.
    • (1990) J. Am. Chem. Soc , vol.112 , pp. 9161-9175
    • Elber, R.1    Karplus, M.2
  • 18
    • 0034028925 scopus 로고    scopus 로고
    • Protein dynamics in an intermediate state of myoglobin: Optical absorption, resonance raman spectroscopy, and X-ray structure analysis
    • Engler, N., Ostermann, A., Gassmann, A., Lamb, D.C., Prusakov, V.E., Schott, J., Schweitzer-Stenner, R., and Parak, F.G. 2000. Protein dynamics in an intermediate state of myoglobin: Optical absorption, resonance raman spectroscopy, and X-ray structure analysis. Biophys. J. 78: 2081-2092.
    • (2000) Biophys. J , vol.78 , pp. 2081-2092
    • Engler, N.1    Ostermann, A.2    Gassmann, A.3    Lamb, D.C.4    Prusakov, V.E.5    Schott, J.6    Schweitzer-Stenner, R.7    Parak, F.G.8
  • 20
    • 0003241140 scopus 로고    scopus 로고
    • Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy
    • Helms, V. and Wade, R.C. 1997. Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. J. Comput. Chem. 18: 449-462.
    • (1997) J. Comput. Chem , vol.18 , pp. 449-462
    • Helms, V.1    Wade, R.C.2
  • 21
    • 7444230904 scopus 로고    scopus 로고
    • Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations
    • Hummer, G., Schotte, F., and Anfinrud, P.A. 2004. Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations. Proc. Natl. Acad. Sci. 101: 15330-15334.
    • (2004) Proc. Natl. Acad. Sci , vol.101 , pp. 15330-15334
    • Hummer, G.1    Schotte, F.2    Anfinrud, P.A.3
  • 23
    • 0030845843 scopus 로고    scopus 로고
    • Model-building and refinement practice
    • Kleywegt, G.J. and Jones, T.A. 1997. Model-building and refinement practice. Methods Enzymol. 277: 208-230.
    • (1997) Methods Enzymol , vol.277 , pp. 208-230
    • Kleywegt, G.J.1    Jones, T.A.2
  • 25
    • 0037023751 scopus 로고    scopus 로고
    • Structural dynamics of myoglobin. Ligand migration among protein cavities studied by FTI/TDS spectroscopy
    • Lamb, D.C., Nienhaus, K., Arcovito, A., Draghi, F., Miele, A.E., Brunori, M., and Nienhaus, G.U. 2002. Structural dynamics of myoglobin. Ligand migration among protein cavities studied by FTI/TDS spectroscopy. J. Biol. Chem. 277: 11636-11644.
    • (2002) J. Biol. Chem , vol.277 , pp. 11636-11644
    • Lamb, D.C.1    Nienhaus, K.2    Arcovito, A.3    Draghi, F.4    Miele, A.E.5    Brunori, M.6    Nienhaus, G.U.7
  • 26
    • 0032190305 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
    • Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., and Subramaniam, S. 1998a. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 33: 1-17.
    • (1998) Proteins , vol.33 , pp. 1-17
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 27
    • 0032189626 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: II. Inacessible cavities in proteins
    • Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., and Subramaniam, S. 1998b. Analytical shape computation of macromolecules: II. Inacessible cavities in proteins. Proteins 33: 18-29.
    • (1998) Proteins , vol.33 , pp. 18-29
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 28
    • 0034634393 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
    • Lüdemann, S.K., Lounnas, V., and Wade, R.C. 2000a. How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. 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
  • 29
    • 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. 2000b. 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
  • 30
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102: 3586-3616.
    • MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102: 3586-3616.
  • 31
    • 0031880931 scopus 로고    scopus 로고
    • Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states
    • Meller, J. and Elber, R. 1998. Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states. Biophys. J. 74: 789-802.
    • (1998) Biophys. J , vol.74 , pp. 789-802
    • Meller, J.1    Elber, R.2
  • 33
    • 23144439273 scopus 로고    scopus 로고
    • Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations
    • Mouawad, L., Marechal, J.-D., and Perahia, D. 2005. Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations. Biochim. Biophys. Acta 1724: 385-393.
    • (2005) Biochim. Biophys. Acta , vol.1724 , pp. 385-393
    • Mouawad, L.1    Marechal, J.-D.2    Perahia, D.3
  • 34
    • 0036157060 scopus 로고    scopus 로고
    • The effect of ligand dynamics on heme electronic transition band III in myoglobin
    • Nienhaus, K., Lamb, D.C., Deng, P., and Nienhaus, G.U. 2002. The effect of ligand dynamics on heme electronic transition band III in myoglobin. Biophys. J. 82: 1059-1067.
    • (2002) Biophys. J , vol.82 , pp. 1059-1067
    • Nienhaus, K.1    Lamb, D.C.2    Deng, P.3    Nienhaus, G.U.4
  • 35
    • 0041742184 scopus 로고    scopus 로고
    • Structural dynamics of myoglobin: Effect of internal cavities on ligand migration and binding
    • Nienhaus, K., Deng, P., Kriegl, J.M., and Nienhaus, G.U. 2003a. Structural dynamics of myoglobin: Effect of internal cavities on ligand migration and binding. Biochemistry 42: 9647-9658.
    • (2003) Biochemistry , vol.42 , pp. 9647-9658
    • Nienhaus, K.1    Deng, P.2    Kriegl, J.M.3    Nienhaus, G.U.4
  • 36
    • 0042242570 scopus 로고    scopus 로고
    • Structural dynamics of myoglobin: Spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W
    • Nienhaus, K., Deng, P., Kriegl, J.M., and Nienhaus, G.U. 2003b. Structural dynamics of myoglobin: Spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W. Biochemistry 42: 9633-9646.
    • (2003) Biochemistry , vol.42 , pp. 9633-9646
    • Nienhaus, K.1    Deng, P.2    Kriegl, J.M.3    Nienhaus, G.U.4
  • 37
    • 0034624691 scopus 로고    scopus 로고
    • Ligand binding and conformational motions in myoglobin
    • Ostermann, A., Waschipky, R., Parak, F.G., and Nienhaus, G.U. 2000. Ligand binding and conformational motions in myoglobin. Nature 404: 205-208.
    • (2000) Nature , vol.404 , pp. 205-208
    • Ostermann, A.1    Waschipky, R.2    Parak, F.G.3    Nienhaus, G.U.4
  • 39
    • 0023645035 scopus 로고
    • High-resolution crystal structure of cytochrome P450cam
    • Poulos, T.L., Finzel, B.C., and Howard, A.J. 1987. High-resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 195: 687-700.
    • (1987) J. Mol. Biol , vol.195 , pp. 687-700
    • Poulos, T.L.1    Finzel, B.C.2    Howard, A.J.3
  • 41
    • 3943081412 scopus 로고    scopus 로고
    • Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s
    • Pylypenko, O. and Schlichting, I. 2004. Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s. Annu. Rev. Biochem. 73: 991-1018.
    • (2004) Annu. Rev. Biochem , vol.73 , pp. 991-1018
    • Pylypenko, O.1    Schlichting, I.2
  • 42
    • 0024974060 scopus 로고
    • Crystal structure of the carbon-monoxide-substrate-cytochrome P-450CAM ternary complex
    • Raag, R. and Poulos, T.L. 1989. Crystal structure of the carbon-monoxide-substrate-cytochrome P-450CAM ternary complex. Biochemistry 28: 7586-7592.
    • (1989) Biochemistry , vol.28 , pp. 7586-7592
    • Raag, R.1    Poulos, T.L.2
  • 43
    • 1842815139 scopus 로고    scopus 로고
    • Kinetic proofreading by the cavity system of myoglobin: Protection from poisoning
    • Radding, W. and Phillips Jr., G.N. 2004. Kinetic proofreading by the cavity system of myoglobin: Protection from poisoning. Bioessays 26: 422-433.
    • (2004) Bioessays , vol.26 , pp. 422-433
    • Radding, W.1    Phillips Jr., G.N.2
  • 45
    • 12944281624 scopus 로고    scopus 로고
    • Lattice models, packing density, and Boltzmann-like distribution of cavities in proteins
    • Rashin, A.A. and Rashin, A.H. 2005. Lattice models, packing density, and Boltzmann-like distribution of cavities in proteins. Proteins 58: 547-559.
    • (2005) Proteins , vol.58 , pp. 547-559
    • Rashin, A.A.1    Rashin, A.H.2
  • 46
    • 0036385795 scopus 로고    scopus 로고
    • Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy
    • Rubin, S.M., Lee, S.-Y., Ruiz, E.J., Pines, A., and Wemmer, D.E. 2002. Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy. J. Mol. Biol. 322: 425-440.
    • (2002) J. Mol. Biol , vol.322 , pp. 425-440
    • Rubin, S.M.1    Lee, S.-Y.2    Ruiz, E.J.3    Pines, A.4    Wemmer, D.E.5
  • 47
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion for 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 for 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
  • 48
    • 0033857394 scopus 로고    scopus 로고
    • Crystallographic structure determination of unstable species
    • Schlichting, I. 2000. Crystallographic structure determination of unstable species. Acc. Chem. Res. 33: 532-538.
    • (2000) Acc. Chem. Res , vol.33 , pp. 532-538
    • Schlichting, I.1
  • 50
    • 0030768765 scopus 로고    scopus 로고
    • Ligand migration in sperm whale myoglobin
    • Scott, E.E. and Gibson, Q.H. 1997. Ligand migration in sperm whale myoglobin. Biochemistry 36: 11909-11917.
    • (1997) Biochemistry , vol.36 , pp. 11909-11917
    • Scott, E.E.1    Gibson, Q.H.2
  • 52
    • 0035923445 scopus 로고    scopus 로고
    • Protein conformational relaxation and ligand migration in myoglobin: A nanosecond to millisecond movie from time-resolved Laue X-ray diffraction
    • Srajer, V., Ren, Z., Teng, T.-Y., Schmidt, M., Ursby, T., Bourgeois, D., Pradervand, C., Schildkamp, W., Wulff, M., and Moffat, K. 2001. Protein conformational relaxation and ligand migration in myoglobin: A nanosecond to millisecond movie from time-resolved Laue X-ray diffraction. Biochemistry 40: 13802-13815.
    • (2001) Biochemistry , vol.40 , pp. 13802-13815
    • Srajer, V.1    Ren, Z.2    Teng, T.-Y.3    Schmidt, M.4    Ursby, T.5    Bourgeois, D.6    Pradervand, C.7    Schildkamp, W.8    Wulff, M.9    Moffat, K.10
  • 53
    • 1642534622 scopus 로고    scopus 로고
    • Myoglobin cavities provide interior ligand pathway
    • Teeter, M.M. 2004. Myoglobin cavities provide interior ligand pathway. Protein Sci. 13: 313-318.
    • (2004) Protein Sci , vol.13 , pp. 313-318
    • Teeter, M.M.1
  • 54
    • 23144435806 scopus 로고    scopus 로고
    • Dominant features of protein reaction dynamics: Conformational relaxation and ligand migration
    • Tetreau, C. and Lavalette, D. 2005. Dominant features of protein reaction dynamics: conformational relaxation and ligand migration. Biochim. Biophys. Acta 1724: 411-424.
    • (2005) Biochim. Biophys. Acta , vol.1724 , pp. 411-424
    • Tetreau, C.1    Lavalette, D.2
  • 55
    • 0346057931 scopus 로고    scopus 로고
    • Competition with xenon elicits ligand migration and escape pathways in myoglobin
    • Tetreau, C., Blouquit, Y., Novikov, E., Quiniou, E., and Lavalette, D. 2004. Competition with xenon elicits ligand migration and escape pathways in myoglobin. Biophys. J. 86: 435-447.
    • (2004) Biophys. J , vol.86 , pp. 435-447
    • Tetreau, C.1    Blouquit, Y.2    Novikov, E.3    Quiniou, E.4    Lavalette, D.5
  • 57
    • 0021766921 scopus 로고
    • Cavities in proteins: Structure of a metmyoglobin-xenon complex solved to 1.9 Å
    • Tilton, R.F., Kuntz, I.D., and Petsko, G.A. 1984. Cavities in proteins: Structure of a metmyoglobin-xenon complex solved to 1.9 Å. Biochemistry 23: 2849-2857.
    • (1984) Biochemistry , vol.23 , pp. 2849-2857
    • Tilton, R.F.1    Kuntz, I.D.2    Petsko, G.A.3
  • 59
    • 0026189146 scopus 로고
    • A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins
    • Wade, R.C., Mazor, M.H., McCannon, J.A., and Quiocho, F.A. 1991. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 8: 919-931.
    • (1991) Biopolymers , vol.8 , pp. 919-931
    • Wade, R.C.1    Mazor, M.H.2    McCannon, J.A.3    Quiocho, F.A.4
  • 60
    • 3042587451 scopus 로고    scopus 로고
    • A survey of active site access channels in cytochromes P450
    • Wade, R.C., Winn, P.J., Schlichting, I., and Sudarko, 2004. A survey of active site access channels in cytochromes P450. J. Inorg. Biochem. 98: 1175-1182.
    • (2004) J. Inorg. Biochem , vol.98 , pp. 1175-1182
    • Wade, R.C.1    Winn, P.J.2    Schlichting, I.3    Sudarko4
  • 61
    • 0028095182 scopus 로고
    • Buried waters and internal cavities in monomeric proteins
    • Williams, M.A., Goodfellow, J.M., and Thornton, J.M. 1994. Buried waters and internal cavities in monomeric proteins. Protein Sci. 3: 1224-1235.
    • (1994) Protein Sci , vol.3 , pp. 1224-1235
    • Williams, M.A.1    Goodfellow, J.M.2    Thornton, J.M.3


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