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Volumn 92, Issue 1, 2007, Pages 23-33

Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation

Author keywords

[No Author keywords available]

Indexed keywords

UBIQUINOL CYTOCHROME C REDUCTASE; UBIQUINONE;

EID: 33846008719     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.084715     Document Type: Article
Times cited : (43)

References (49)
  • 1
    • 0022348605 scopus 로고
    • Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3Å resolution
    • Deisenhofer, J., O. Epp, K. Miki, R. Huber, and H. Michel. 1985. Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3Å resolution. Nature. 318:618-624.
    • (1985) Nature , vol.318 , pp. 618-624
    • Deisenhofer, J.1    Epp, O.2    Miki, K.3    Huber, R.4    Michel, H.5
  • 3
    • 0030585121 scopus 로고    scopus 로고
    • The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum
    • Koepke, J., X. C. Hu, C. Muenke, K. Schulten, and H. Michel. 1996. The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. Structure. 4:581-597.
    • (1996) Structure , vol.4 , pp. 581-597
    • Koepke, J.1    Hu, X.C.2    Muenke, C.3    Schulten, K.4    Michel, H.5
  • 5
    • 0028114231 scopus 로고
    • Structure at 2.8-Å resolution of F1-Atpase from bovine heart mitochondria
    • Abrahams, J. P., A. G. W. Leslie, R. Lutter, and J. E. Walker. 1994. Structure at 2.8-Å resolution of F1-Atpase from bovine heart mitochondria. Nature. 370:621-628.
    • (1994) Nature , vol.370 , pp. 621-628
    • Abrahams, J.P.1    Leslie, A.G.W.2    Lutter, R.3    Walker, J.E.4
  • 7
    • 0035909829 scopus 로고    scopus 로고
    • Dynamics of excitation energy transfer in the LH1 and LH2 light-harvesting complexes of photosynthetic bacteria
    • van Grondelle, R., and V. Novoderezhkin. 2001. Dynamics of excitation energy transfer in the LH1 and LH2 light-harvesting complexes of photosynthetic bacteria. Biochemistry. 40:15057-15068.
    • (2001) Biochemistry , vol.40 , pp. 15057-15068
    • van Grondelle, R.1    Novoderezhkin, V.2
  • 8
    • 0033575392 scopus 로고    scopus 로고
    • Unraveling the electronic structure of individual photosynthetic pigment-protein complexes
    • van Oijen, A. M., M. Ketelaars, J. Kohler, T. J. Aartsma, and J. Schmidt. 1999. Unraveling the electronic structure of individual photosynthetic pigment-protein complexes. Science. 285:400-402.
    • (1999) Science , vol.285 , pp. 400-402
    • van Oijen, A.M.1    Ketelaars, M.2    Kohler, J.3    Aartsma, T.J.4    Schmidt, J.5
  • 9
    • 0037426798 scopus 로고    scopus 로고
    • Membrane environment reduces the accessible conformational space available to an integral membrane protein
    • Gerken, U., F. Jelezko, B. Götze, M. Branschadel, C. Tietz, R. Ghosh, and J. Wrachtrup. 2003. Membrane environment reduces the accessible conformational space available to an integral membrane protein. J. Phys. Chem. B. 107:338-343.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 338-343
    • Gerken, U.1    Jelezko, F.2    Götze, B.3    Branschadel, M.4    Tietz, C.5    Ghosh, R.6    Wrachtrup, J.7
  • 10
    • 0042819619 scopus 로고    scopus 로고
    • Circular symmetry of the light-harvesting 1 complex from Rhodospirillum rubrum is not perturbed by interaction with the reaction center
    • Gerken, U., D. Lupo, C. Tietz, J. Wrachtrup, and R. Ghosh. 2003. Circular symmetry of the light-harvesting 1 complex from Rhodospirillum rubrum is not perturbed by interaction with the reaction center. Biochemistry. 42:10354-10360.
    • (2003) Biochemistry , vol.42 , pp. 10354-10360
    • Gerken, U.1    Lupo, D.2    Tietz, C.3    Wrachtrup, J.4    Ghosh, R.5
  • 11
    • 0034696751 scopus 로고    scopus 로고
    • The solution structure of Rhodobacter sphaeroides LH1 β reveals two helical domains separated by a more flexible region: Structural consequences for the LH1 complex
    • Conroy, M. J., W. H. J. Westerhuis, P. S. Parkes-Loach, P. A. Loach, C. N. Hunter, and M. P. Williamson. 2000. The solution structure of Rhodobacter sphaeroides LH1 β reveals two helical domains separated by a more flexible region: structural consequences for the LH1 complex. J. Mol. Biol. 298:83-94.
    • (2000) J. Mol. Biol , vol.298 , pp. 83-94
    • Conroy, M.J.1    Westerhuis, W.H.J.2    Parkes-Loach, P.S.3    Loach, P.A.4    Hunter, C.N.5    Williamson, M.P.6
  • 12
    • 14644440750 scopus 로고    scopus 로고
    • Solution structures of the core light-harvesting α and β polypeptides from Rhodospirillum rubrum: Implications for the pigment-protein and protein-protein interactions
    • Wang, Z. Y., K. Gokan, M. Kobayashi, and T. Nozawa. 2005. Solution structures of the core light-harvesting α and β polypeptides from Rhodospirillum rubrum: implications for the pigment-protein and protein-protein interactions. J. Mol. Biol. 347:465-477.
    • (2005) J. Mol. Biol , vol.347 , pp. 465-477
    • Wang, Z.Y.1    Gokan, K.2    Kobayashi, M.3    Nozawa, T.4
  • 13
    • 0033081638 scopus 로고    scopus 로고
    • Supramolecular organization of the photosynthetic apparatus of Rhodobacter sphaeroides
    • Jungas, C., J. L. Ranck, J. L. Rigaud, P. Joliot, and A. Vermeglio. 1999. Supramolecular organization of the photosynthetic apparatus of Rhodobacter sphaeroides. EMBO J. 18:534-542.
    • (1999) EMBO J , vol.18 , pp. 534-542
    • Jungas, C.1    Ranck, J.L.2    Rigaud, J.L.3    Joliot, P.4    Vermeglio, A.5
  • 14
    • 0028953308 scopus 로고
    • The 8.5-Å projection map of the light-harvesting complex-I from Rhodospirillum rubrum reveals a ring composed of 16 subunits
    • Karrasch, S., P. A. Bullough, and R. Ghosh. 1995. The 8.5-Å projection map of the light-harvesting complex-I from Rhodospirillum rubrum reveals a ring composed of 16 subunits. EMBO J. 14:631-638.
    • (1995) EMBO J , vol.14 , pp. 631-638
    • Karrasch, S.1    Bullough, P.A.2    Ghosh, R.3
  • 15
    • 0036683068 scopus 로고    scopus 로고
    • Projection structure of the photosynthetic reaction centre-antenna complex of Rhodospirillum rubrum at 8.5 Å resolution
    • Jamieson, S. J., P. Y. Wang, P. Qian, J. Y. Kirkland, M. J. Conroy, C. N. Hunter, and P. A. Bullough. 2002. Projection structure of the photosynthetic reaction centre-antenna complex of Rhodospirillum rubrum at 8.5 Å resolution. EMBO J. 21:3927-3935.
    • (2002) EMBO J , vol.21 , pp. 3927-3935
    • Jamieson, S.J.1    Wang, P.Y.2    Qian, P.3    Kirkland, J.Y.4    Conroy, M.J.5    Hunter, C.N.6    Bullough, P.A.7
  • 16
    • 0031575413 scopus 로고    scopus 로고
    • Two-dimensional crystallization of the light-harvesting I reaction centre photounit from Rhodospirillum rubrum
    • Walz, T., and R. Ghosh. 1997. Two-dimensional crystallization of the light-harvesting I reaction centre photounit from Rhodospirillum rubrum. J. Mol. Biol. 265:107-111.
    • (1997) J. Mol. Biol , vol.265 , pp. 107-111
    • Walz, T.1    Ghosh, R.2
  • 18
    • 12544254339 scopus 로고    scopus 로고
    • Structure of the dimeric PufX-containing core complex of Rhodobacter blasticus by in situ atomic force microscopy
    • Scheuring, S., J. Busselez, and D. Levy. 2005. Structure of the dimeric PufX-containing core complex of Rhodobacter blasticus by in situ atomic force microscopy. J. Biol. Chem. 280:1426-1431.
    • (2005) J. Biol. Chem , vol.280 , pp. 1426-1431
    • Scheuring, S.1    Busselez, J.2    Levy, D.3
  • 20
    • 0347717833 scopus 로고    scopus 로고
    • Structural analysis of the reaction center light-harvesting complex I photosynthetic core complex of Rhodospirillum rubrum using atomic force microscopy
    • Fotiadis, D., P. Qian, A. Philippsen, P. A. Bullough, A. Engel, and C. N. Hunter. 2004. Structural analysis of the reaction center light-harvesting complex I photosynthetic core complex of Rhodospirillum rubrum using atomic force microscopy. J. Biol. Chem. 279:2063-2068.
    • (2004) J. Biol. Chem , vol.279 , pp. 2063-2068
    • Fotiadis, D.1    Qian, P.2    Philippsen, A.3    Bullough, P.A.4    Engel, A.5    Hunter, C.N.6
  • 21
    • 0031830394 scopus 로고    scopus 로고
    • The reaction centre of the photounit of Rhodospirillum rubrum is anchored to the light-harvesting complex with four-fold rotational disorder
    • Stahlberg, H., J. Dubochet, H. Vogel, and R. Ghosh. 1998. The reaction centre of the photounit of Rhodospirillum rubrum is anchored to the light-harvesting complex with four-fold rotational disorder. Photosynth. Res. 55:363-368.
    • (1998) Photosynth. Res , vol.55 , pp. 363-368
    • Stahlberg, H.1    Dubochet, J.2    Vogel, H.3    Ghosh, R.4
  • 22
    • 0000388160 scopus 로고
    • NMR studies of ubiquinone location in oriented model membranes: Evidence for a single motionally-averaged population
    • Metz, G., K. P. Howard, W. B. S. Vanliemt, J. H. Prestegard, J. Lugtenburg, and S. O. Smith. 1995. NMR studies of ubiquinone location in oriented model membranes: evidence for a single motionally-averaged population. J. Am. Chem. Soc. 117:564-565.
    • (1995) J. Am. Chem. Soc , vol.117 , pp. 564-565
    • Metz, G.1    Howard, K.P.2    Vanliemt, W.B.S.3    Prestegard, J.H.4    Lugtenburg, J.5    Smith, S.O.6
  • 23
    • 0032502940 scopus 로고    scopus 로고
    • A high diffusion coefficient for coenzyme Q(10) might be related to a folded structure
    • Di Bernardo, S., R. Fato, R. Casadio, P. Fariselli, and G. Lenaz. 1998. A high diffusion coefficient for coenzyme Q(10) might be related to a folded structure. FEBS Lett. 426:77-80.
    • (1998) FEBS Lett , vol.426 , pp. 77-80
    • Di Bernardo, S.1    Fato, R.2    Casadio, R.3    Fariselli, P.4    Lenaz, G.5
  • 24
    • 15744405284 scopus 로고    scopus 로고
    • Functional consequences of the organization of the photosynthetic apparatus in Rhodobacter sphaeroides. II. A study of PufX(-) membranes
    • Comayras, R., C. Jungas, and J. Lavergne. 2005. Functional consequences of the organization of the photosynthetic apparatus in Rhodobacter sphaeroides. II. A study of PufX(-) membranes. J. Biol. Chem. 280:11214-11223.
    • (2005) J. Biol. Chem , vol.280 , pp. 11214-11223
    • Comayras, R.1    Jungas, C.2    Lavergne, J.3
  • 25
    • 0031824352 scopus 로고    scopus 로고
    • Model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides
    • Hu, X., and K. Schulten. 1998. Model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides. Biophys. J. 75:683-694.
    • (1998) Biophys. J , vol.75 , pp. 683-694
    • Hu, X.1    Schulten, K.2
  • 26
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N.Log(N) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 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
  • 27
    • 36449007836 scopus 로고
    • Constant-pressure molecular-dynamics simulation: The Langevin piston method
    • Feller, S. E., Y. H. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant-pressure molecular-dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 29
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
    • MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
  • 30
    • 4444240014 scopus 로고    scopus 로고
    • Classical force field parameters for the heme prosthetic group of cytochrome c
    • Autenrieth, F., E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten. 2004. Classical force field parameters for the heme prosthetic group of cytochrome c. J. Comput. Chem. 25:1613-1622.
    • (2004) J. Comput. Chem , vol.25 , pp. 1613-1622
    • Autenrieth, F.1    Tajkhorshid, E.2    Baudry, J.3    Luthey-Schulten, Z.4
  • 32
    • 41349092888 scopus 로고    scopus 로고
    • Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study
    • Damjanovic, A., I. Kosztin, U. Kleinekathöfer, and K. Schulten. 2002. Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study. Phys. Rev. E. 65:031919.
    • (2002) Phys. Rev. E , vol.65 , pp. 031919
    • Damjanovic, A.1    Kosztin, I.2    Kleinekathöfer, U.3    Schulten, K.4
  • 33
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • Isralewitz, B., M. Gao, and K. Schulten. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11:224-230.
    • (2001) Curr. Opin. Struct. Biol , vol.11 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 34
    • 4143087050 scopus 로고    scopus 로고
    • Calculating potentials of mean force from steered molecular dynamics simulations
    • Park, S., and K. Schulten. 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
  • 35
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
    • Park, S., F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten. 2003. Free energy calculation from steered molecular dynamics simulations using Jarzynski's 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
  • 36
    • 16444385400 scopus 로고
    • Monte-Carlo free-energy estimates using non-Boltzmann sampling.: Application to subcritical Lennard-Jones fluid
    • Torrie, G. M., and J. P. Valleau. 1974. Monte-Carlo free-energy estimates using non-Boltzmann sampling.: application to subcritical Lennard-Jones fluid. Chem. Phys. Lett. 28:578-581.
    • (1974) Chem. Phys. Lett , vol.28 , pp. 578-581
    • Torrie, G.M.1    Valleau, J.P.2
  • 37
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
    • Kumar, S., D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J. Comput. Chem. 13:1011-1021.
    • (1992) J. Comput. Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 38
    • 0000765761 scopus 로고    scopus 로고
    • Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences
    • Crooks, G. E. 1999. Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys. Rev. E. 60:2721-2726.
    • (1999) Phys. Rev. E , vol.60 , pp. 2721-2726
    • Crooks, G.E.1
  • 39
    • 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.
    • (1997) Phys. Rev. Lett , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 40
    • 0035957434 scopus 로고    scopus 로고
    • Free energy reconstruction from nonequilibrium single-molecule pulling experiments
    • Hummer, G., and A. Szabo. 2001. Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc. Natl. Acad. Sci. USA. 98:3658-3661.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 3658-3661
    • Hummer, G.1    Szabo, A.2
  • 41
    • 24644450199 scopus 로고    scopus 로고
    • Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
    • Collin, D., F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco, and C. Bustamante. 2005. Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature. 437:231-234.
    • (2005) Nature , vol.437 , pp. 231-234
    • Collin, D.1    Ritort, F.2    Jarzynski, C.3    Smith, S.B.4    Tinoco, I.5    Bustamante, C.6
  • 42
    • 0037036070 scopus 로고    scopus 로고
    • Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    • Liphardt, J., S. Dumont, S. B. Smith, I. Tinoco, and C. Bustamante. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science. 296:1832-1835.
    • (2002) Science , vol.296 , pp. 1832-1835
    • Liphardt, J.1    Dumont, S.2    Smith, S.B.3    Tinoco, I.4    Bustamante, C.5
  • 43
    • 33749551180 scopus 로고    scopus 로고
    • Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality
    • Kosztin, I., B. Barz, and L. Janosi. 2006. Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality. J. Chem. Phys. 124:64106.
    • (2006) J. Chem. Phys , vol.124 , pp. 64106
    • Kosztin, I.1    Barz, B.2    Janosi, L.3
  • 45
    • 36749116443 scopus 로고
    • 1st Passage Time Approach to Diffusion Controlled Reactions
    • Szabo, A., K. Schulten, and Z. Schulten. 1980. 1st Passage Time Approach to Diffusion Controlled Reactions. J. Chem. Phys. 72:4350-4357.
    • (1980) J. Chem. Phys , vol.72 , pp. 4350-4357
    • Szabo, A.1    Schulten, K.2    Schulten, Z.3
  • 46
    • 8644260166 scopus 로고    scopus 로고
    • Molecular dynamics simulations of substrate channeling through an α-β barrel protein
    • Amaro, R., and Z. Luthey-Schulten. 2004. Molecular dynamics simulations of substrate channeling through an α-β barrel protein. Chem. Phys. 307:147-155.
    • (2004) Chem. Phys , vol.307 , pp. 147-155
    • Amaro, R.1    Luthey-Schulten, Z.2
  • 47
    • 0040583544 scopus 로고    scopus 로고
    • Coupling of cytochrome and quinone turnovers in the photocycle of reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides
    • Osvath, S., and P. Maroti. 1997. Coupling of cytochrome and quinone turnovers in the photocycle of reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides. Biophys. J. 73:972-982.
    • (1997) Biophys. J , vol.73 , pp. 972-982
    • Osvath, S.1    Maroti, P.2
  • 48
    • 0347309220 scopus 로고    scopus 로고
    • Kinetic limitations in turnover of photosynthetic bacterial reaction center protein
    • Gerencsér, L., T. Jánosi, G. Laczkó, and P. Maróti. 2000. Kinetic limitations in turnover of photosynthetic bacterial reaction center protein. Acta Biol. Szeged. 44:45-52.
    • (2000) Acta Biol. Szeged , vol.44 , pp. 45-52
    • Gerencsér, L.1    Jánosi, T.2    Laczkó, G.3    Maróti, P.4
  • 49
    • 0031920484 scopus 로고    scopus 로고
    • Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers
    • Marchal, D., W. Boireau, J. M. Laval, J. Moiroux, and C. Bourdillon. 1998. Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers. Biophys. J. 74:1937-1948.
    • (1998) Biophys. J , vol.74 , pp. 1937-1948
    • Marchal, D.1    Boireau, W.2    Laval, J.M.3    Moiroux, J.4    Bourdillon, C.5


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