메뉴 건너뛰기




Volumn 71, Issue 1, 1996, Pages 119-129

Theoretical investigation of the dynamics of the active site lid in Rhizomucor miehei lipase

Author keywords

[No Author keywords available]

Indexed keywords

TRIACYLGLYCEROL LIPASE;

EID: 0029933809     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79207-X     Document Type: Article
Times cited : (93)

References (52)
  • 3
    • 0001842490 scopus 로고
    • B. Bergström and H. L. Brockman, editors. Elsevier Science Publishers, Amsterdam
    • Brockman, H. L. 1984. Lipases. B. Bergström and H. L. Brockman, editors. Elsevier Science Publishers, Amsterdam. 1-46.
    • (1984) Lipases , pp. 1-46
    • Brockman, H.L.1
  • 4
    • 0022780988 scopus 로고
    • The hinge-bending mode of a lysozyme-inhibitor complex
    • Bruccoleri, R. E., M. Karplus, and J. A. McCammon. 1986. The hinge-bending mode of a lysozyme-inhibitor complex. Biopolymers. 25: 1767-1802.
    • (1986) Biopolymers , vol.25 , pp. 1767-1802
    • Bruccoleri, R.E.1    Karplus, M.2    McCammon, J.A.3
  • 6
    • 0017187836 scopus 로고
    • The nature of the accessible and buried surfaces in proteins
    • Chothia, C. 1976. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105:1-14.
    • (1976) J. Mol. Biol. , vol.105 , pp. 1-14
    • Chothia, C.1
  • 7
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program
    • Davis, M. E., J. D. Madura, B. A. Luty, and J. A. McCammon. 1990. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Computer Physics Communications. 62:187-197.
    • (1990) Computer Physics Communications , vol.62 , pp. 187-197
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 8
    • 84988141840 scopus 로고
    • Solving the finite difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods
    • Davis, M. E., and J. A. McCammon. 1989. Solving the finite difference linearized Poisson-Boltzmann equation: a comparison of relaxation and conjugate gradient methods. J. Comput. Chem. 10:386-391.
    • (1989) J. Comput. Chem. , vol.10 , pp. 386-391
    • Davis, M.E.1    McCammon, J.A.2
  • 9
    • 84986522972 scopus 로고
    • Dielectric boundary smoothing in finite difference solutions of the Poisson equation: An approach to improve accuracy and convergence
    • Davis, M. E., and J. A. McCammon. 1991. Dielectric boundary smoothing in finite difference solutions of the Poisson equation: an approach to improve accuracy and convergence. J. Comput. Chem. 7:909-912.
    • (1991) J. Comput. Chem. , vol.7 , pp. 909-912
    • Davis, M.E.1    McCammon, J.A.2
  • 10
    • 49549154895 scopus 로고
    • Surface dipole moments of close-packed un-ionized monolayers at the air-water interface
    • Demchak, R. J., and T. Fort Jr. 1974. Surface dipole moments of close-packed un-ionized monolayers at the air-water interface. J. Colloid Interface Sci. 46:191-202.
    • (1974) J. Colloid Interface Sci. , vol.46 , pp. 191-202
    • Demchak, R.J.1    Fort Jr., T.2
  • 11
    • 0026550733 scopus 로고
    • Catalysis at the interface: The anatomy of a conformational change in a triglyceride lipase
    • Derewenda, U., A. M. Brzozowski, D. M. Lawson, and S. Z. Derewenda. 1992. Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase. Biochemistry. 31:1532-1541.
    • (1992) Biochemistry , vol.31 , pp. 1532-1541
    • Derewenda, U.1    Brzozowski, A.M.2    Lawson, D.M.3    Derewenda, S.Z.4
  • 12
    • 0028295251 scopus 로고
    • Conformational lability of lipases observed in the absence of an oil-water interface: Crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar
    • Derewenda, U., L. Swenson, Y. Wei, R. Green, P. M. Kobos, R. Joerger, M. J. Haas, and Z. S. Derewenda. 1994. Conformational lability of lipases observed in the absence of an oil-water interface: crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar. J. Lipid. Res. 35:524-534.
    • (1994) J. Lipid. Res. , vol.35 , pp. 524-534
    • Derewenda, U.1    Swenson, L.2    Wei, Y.3    Green, R.4    Kobos, P.M.5    Joerger, R.6    Haas, M.J.7    Derewenda, Z.S.8
  • 13
    • 0029039839 scopus 로고
    • A twist in the tale of lipolytic enzymes
    • Derewenda, Z. S. 1995. A twist in the tale of lipolytic enzymes. Nature Struct. Biol. 2:347-349.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 347-349
    • Derewenda, Z.S.1
  • 14
    • 0026786234 scopus 로고
    • The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 angstroms resolution
    • Derewenda, Z. S., U. Derewenda, and G. G. Dodson. 1992. The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 angstroms resolution. J. Mol. Biol. 227:818-839.
    • (1992) J. Mol. Biol. , vol.227 , pp. 818-839
    • Derewenda, Z.S.1    Derewenda, U.2    Dodson, G.G.3
  • 15
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak, D. L., and J. A. McCammon. 1978. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69:1352-1360.
    • (1978) J. Chem. Phys. , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 16
    • 0028049327 scopus 로고
    • Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis
    • Falzone, C. J., P. E. Wright, and S. J. Benkovic. 1994. Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis. Biochemistry. 33:439-442.
    • (1994) Biochemistry , vol.33 , pp. 439-442
    • Falzone, C.J.1    Wright, P.E.2    Benkovic, S.J.3
  • 17
    • 0344909237 scopus 로고
    • The low apparent permittivity of adsorbed water in synthetic zeolites
    • Foster, K. R., and H. A. Resing. 1976. The low apparent permittivity of adsorbed water in synthetic zeolites. J. Chem. Phys. 80:1390-1392.
    • (1976) J. Chem. Phys. , vol.80 , pp. 1390-1392
    • Foster, K.R.1    Resing, H.A.2
  • 18
    • 0027261556 scopus 로고
    • The role of arginines in stabilizing the active open-lid conformation of Rhizomucor miehei lipase
    • Holmquist, M., M. Norin, and K. Hult. 1993. The role of arginines in stabilizing the active open-lid conformation of Rhizomucor miehei lipase. Lipids. 28:721-726.
    • (1993) Lipids , vol.28 , pp. 721-726
    • Holmquist, M.1    Norin, M.2    Hult, K.3
  • 19
    • 0018784438 scopus 로고
    • Surface and side volumes in globular proteins
    • Janin, J. 1979. Surface and side volumes in globular proteins. Nature. 277:491-492.
    • (1979) Nature , vol.277 , pp. 491-492
    • Janin, J.1
  • 20
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 21
    • 0027196872 scopus 로고
    • Movable lobes and flexible loops in proteins. Structural deformations that control biochemical activity
    • Kempner, E. S. 1993. Movable lobes and flexible loops in proteins. Structural deformations that control biochemical activity. FEBS Lett. 326:4-10.
    • (1993) FEBS Lett. , vol.326 , pp. 4-10
    • Kempner, E.S.1
  • 22
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 119:379-400.
    • (1971) J. Mol. Biol. , vol.119 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 23
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • Levitt, M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:59-107.
    • (1976) J. Mol. Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 24
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt, M., and A. Warshel. 1975. Computer simulation of protein folding. Nature. 253:694-698.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 25
    • 0000958642 scopus 로고
    • Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: Electrostatic steering of glyceraldehyde phosphate
    • Luty, B. A., R. C. Wade, J. D. Madura, M. E. Davis, J. M. Briggs, and J. A. McCammon. 1993. Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: electrostatic steering of glyceraldehyde phosphate. J. Phys. Chem. 97:233-237.
    • (1993) J. Phys. Chem. , vol.97 , pp. 233-237
    • Luty, B.A.1    Wade, R.C.2    Madura, J.D.3    Davis, M.E.4    Briggs, J.M.5    McCammon, J.A.6
  • 28
    • 0019421683 scopus 로고
    • Gated binding of ligands to proteins
    • McCammon, J. A., and S. H. Northrup. 1981. Gated binding of ligands to proteins. Nature. 293:316-317.
    • (1981) Nature , vol.293 , pp. 316-317
    • McCammon, J.A.1    Northrup, S.H.2
  • 29
    • 84985740872 scopus 로고
    • Helix-coil transitions in a simple polypeptide model
    • McCammon, J. A., S. H. Northrup, M. Karplus, and R. M. Levy. 1980. Helix-coil transitions in a simple polypeptide model. Biopolymers. 19: 2033-2045.
    • (1980) Biopolymers , vol.19 , pp. 2033-2045
    • McCammon, J.A.1    Northrup, S.H.2    Karplus, M.3    Levy, R.M.4
  • 31
    • 0026487056 scopus 로고
    • Lateral lipid distribution as a major regulator of lipase activity
    • Muderhwa, J. M., and H. L. Brockman. 1992. Lateral lipid distribution as a major regulator of lipase activity. J. Biol. Chem. 267:24184-24192.
    • (1992) J. Biol. Chem. , vol.267 , pp. 24184-24192
    • Muderhwa, J.M.1    Brockman, H.L.2
  • 33
    • 0028146056 scopus 로고
    • Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent
    • Norin, M., F. Haeffner, K. Hult, and O. Edholm. 1994. Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent. Biophys. J. 67:548-559.
    • (1994) Biophys. J. , vol.67 , pp. 548-559
    • Norin, M.1    Haeffner, F.2    Hult, K.3    Edholm, O.4
  • 34
    • 0027332826 scopus 로고
    • Theoretical studies of Rhizomucor miehei lipase activation
    • Norin, M., O. Olsen, A. Svendsen, O. Edholm, and K. Hult. 1993. Theoretical studies of Rhizomucor miehei lipase activation. Protein Eng. 6:855-863.
    • (1993) Protein Eng. , vol.6 , pp. 855-863
    • Norin, M.1    Olsen, O.2    Svendsen, A.3    Edholm, O.4    Hult, K.5
  • 35
    • 36549102274 scopus 로고
    • Brownian dynamics simulation of diffusion-influenced bimolecular reactions
    • Northrup, S. H., S. A. Allinson, and J. A. McCammon. 1984. Brownian dynamics simulation of diffusion-influenced bimolecular reactions. J. Chem. Phys. 80:1517-1524.
    • (1984) J. Chem. Phys. , vol.80 , pp. 1517-1524
    • Northrup, S.H.1    Allinson, S.A.2    McCammon, J.A.3
  • 36
    • 0542362994 scopus 로고
    • Rate theory for gated diffusion-influenced ligand binding to proteins
    • Northrup, S. H., F. Zarin, and J. A. McCammon. 1982. Rate theory for gated diffusion-influenced ligand binding to proteins. J. Phys. Chem. 86:2314-2321.
    • (1982) J. Phys. Chem. , vol.86 , pp. 2314-2321
    • Northrup, S.H.1    Zarin, F.2    McCammon, J.A.3
  • 38
    • 0027629442 scopus 로고
    • Molecular dynamics computer simulations: A tool for the investigation of amphiphilic systems and enzymatic reaction mechanisms on a microscopic level
    • Peters, G. H., S. Toxvaerd, O. H. Olsen, and A. Svendsen. 1993. Molecular dynamics computer simulations: a tool for the investigation of amphiphilic systems and enzymatic reaction mechanisms on a microscopic level. Tenside Surf. Det. 30:264-268.
    • (1993) Tenside Surf. Det. , vol.30 , pp. 264-268
    • Peters, G.H.1    Toxvaerd, S.2    Olsen, O.H.3    Svendsen, A.4
  • 39
    • 0001504479 scopus 로고
    • Modelling of complex biological systems. H. Effect of chainlength on the phase transitions observed in diglyceride monolayers
    • Peters, G. H., S. Toxvaerd, O. H. Olsen, and A. Svendsen. 1995b. Modelling of complex biological systems. H. Effect of chainlength on the phase transitions observed in diglyceride monolayers. Langmuir. 11: 4072-4081.
    • (1995) Langmuir , vol.11 , pp. 4072-4081
    • Peters, G.H.1    Toxvaerd, S.2    Olsen, O.H.3    Svendsen, A.4
  • 40
    • 0001579036 scopus 로고
    • Modeling of complex biological systems. I. Molecular dynamics studies of diglyceride monolayers
    • Peters, G. H., S. Toxvaerd, A. Svendsen, and O. H. Olsen. 1994. Modeling of complex biological systems. I. Molecular dynamics studies of diglyceride monolayers. J. Chem. Phys. 100:5996-6010.
    • (1994) J. Chem. Phys. , vol.100 , pp. 5996-6010
    • Peters, G.H.1    Toxvaerd, S.2    Svendsen, A.3    Olsen, O.H.4
  • 41
    • 0028854555 scopus 로고
    • Identifying the mechanism of protein loop closure: A molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution
    • Philippopoulos, M., Y. Xiang, and C. Lim. 1995. Identifying the mechanism of protein loop closure: a molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution. Protein Eng. 8:565-573.
    • (1995) Protein Eng. , vol.8 , pp. 565-573
    • Philippopoulos, M.1    Xiang, Y.2    Lim, C.3
  • 42
  • 43
    • 0017876485 scopus 로고
    • Geometrical constraints and contact areas
    • Richmond, T. J., and F. M. Richards. 1978. Geometrical constraints and contact areas. J. Mol. Biol. 119:537-555.
    • (1978) J. Mol. Biol. , vol.119 , pp. 537-555
    • Richmond, T.J.1    Richards, F.M.2
  • 44
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 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.C.3
  • 45
    • 0024299305 scopus 로고
    • A model for the molecular mechanism of interfacial activation of phospholipase A2 supporting the substrate theory
    • Thuren, T. 1988. A model for the molecular mechanism of interfacial activation of phospholipase A2 supporting the substrate theory. FEBS Lett. 229:95-99.
    • (1988) FEBS Lett. , vol.229 , pp. 95-99
    • Thuren, T.1
  • 47
    • 0024002142 scopus 로고
    • Hydrated polar groups in lipid monolayers: Effectice local dipole moments and dielectric properties
    • Vogel, V., and D. Mobius. D. 1988. Hydrated polar groups in lipid monolayers: effectice local dipole moments and dielectric properties. Thin Solid Films. 195:73-81.
    • (1988) Thin Solid Films , vol.195 , pp. 73-81
    • Vogel, V.1    D. Mobius, D.2
  • 48
    • 0027446430 scopus 로고
    • Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme
    • Wade, R. C., M. E. Davis, B. A. Luty, J. D. Madura, and J. A. McCammon. 1993. Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys. J. 64:9-15.
    • (1993) Biophys. J. , vol.64 , pp. 9-15
    • Wade, R.C.1    Davis, M.E.2    Luty, B.A.3    Madura, J.D.4    McCammon, J.A.5
  • 50
    • 0026519169 scopus 로고
    • Comparison of the refined crystal structures of liganded and unliganded chicken, yeast and trypanosomal triosephosphate isomerase
    • Wierenga, R. K., M. E. Noble, and R. C. Davenport. 1992. Comparison of the refined crystal structures of liganded and unliganded chicken, yeast and trypanosomal triosephosphate isomerase. J. Mol. Biol 224: 1115-1126.
    • (1992) J. Mol. Biol , vol.224 , pp. 1115-1126
    • Wierenga, R.K.1    Noble, M.E.2    Davenport, R.C.3
  • 51
    • 0025785056 scopus 로고
    • Refined 1.83 Å structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex
    • Wierenga, R. K., M. E. Noble, G. Vriend, S. Nauche, and W. G. Hol. 1991. Refined 1.83 Å structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex. J. Mol. Biol. 220:995-1015.
    • (1991) J. Mol. Biol. , vol.220 , pp. 995-1015
    • Wierenga, R.K.1    Noble, M.E.2    Vriend, G.3    Nauche, S.4    Hol, W.G.5
  • 52
    • 0029000872 scopus 로고
    • Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand gated
    • Williams, J. C., and A. E. McDermott. 1995. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand gated. Biochemistry. 34:8309-8319.
    • (1995) Biochemistry , vol.34 , pp. 8309-8319
    • Williams, J.C.1    McDermott, A.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.