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Volumn 19, Issue 9, 2014, Pages 14961-14978

A multi-scale-multi-stable model for the rhodopsin photocycle

Author keywords

Classical molecular dynamics; Coarse grained models; Computer simulations; Multi scale modeling; Rhodopsin

Indexed keywords

RHODOPSIN;

EID: 84907284541     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules190914961     Document Type: Article
Times cited : (11)

References (48)
  • 1
    • 2342460436 scopus 로고    scopus 로고
    • Bacteriorhodopsin
    • Lanyi, J.K. Bacteriorhodopsin. Annu. Rev. Physiol. 2004, 66, 665-688.
    • (2004) Annu. Rev. Physiol. , vol.66 , pp. 665-688
    • Lanyi, J.K.1
  • 2
    • 0034717007 scopus 로고    scopus 로고
    • Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution
    • Kolbe, M.; Besir, H.; Essen L.O.; Oesterhelt, D. Structure of the Light-Driven Chloride Pump Halorhodopsin at 1.8 Å Resolution. Science 2000, 288, 1390-1396.
    • (2000) Science , vol.288 , pp. 1390-1396
    • Kolbe, M.1    Besir, H.2    Essen, L.O.3    Oesterhelt, D.4
  • 3
    • 0037466289 scopus 로고    scopus 로고
    • Mechanism of proton transport in bacteriorhodopsin from crystallographic structures of the K, L, M1, M2, and M2intermediates of the photocycle
    • Lanyi, J.K.; Schobert, B. Mechanism of Proton Transport in Bacteriorhodopsin from Crystallographic Structures of the K, L, M1, M2, and M2Intermediates of the Photocycle. J. Mol. Biol. 2003, 328, 439-450.
    • (2003) J. Mol. Biol. , vol.328 , pp. 439-450
    • Lanyi, J.K.1    Schobert, B.2
  • 4
    • 0035800032 scopus 로고    scopus 로고
    • Advances in determination of a high-resolution three- dimensional structure of rhodopsin, a model of g-protein- coupled receptors (GPCRs)
    • Teller, D. C.; Okada, T.; Behnke, C.A.; Palczewski, K.; Stenkamp, R. E. Advances in Determination of a High-Resolution Three- Dimensional Structure of Rhodopsin, a Model of G-Protein- Coupled Receptors (GPCRs). Biochemistry 2006, 40, 7761-7772.
    • (2006) Biochemistry , vol.40 , pp. 7761-7772
    • Teller, D.C.1    Okada, T.2    Behnke, C.A.3    Palczewski, K.4    Stenkamp, R.E.5
  • 5
    • 0016723355 scopus 로고
    • Bacteriorhodopsin: A light-driven proton pump of Halobacterium Halobium
    • Lozier, R.H.; Bogomolni, R.A.; Stoeckenius, W. Bacteriorhodopsin: A light-driven proton pump of Halobacterium Halobium. Biophys. J. 1975, 15, 955-962.
    • (1975) Biophys. J. , vol.15 , pp. 955-962
    • Lozier, R.H.1    Bogomolni, R.A.2    Stoeckenius, W.3
  • 6
    • 0034632864 scopus 로고    scopus 로고
    • Molecular mechanism of vectorial proton translocation by bacteriorhodopsin
    • Subramaniam, S.; Henderson, R. Molecular mechanism of vectorial proton translocation by bacteriorhodopsin. Nature 2000, 406, 653-657.
    • (2000) Nature , vol.406 , pp. 653-657
    • Subramaniam, S.1    Henderson, R.2
  • 7
    • 0034632821 scopus 로고    scopus 로고
    • Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin
    • Royant, A; Edman, K.; Ursby, T.; Pebay-Peyroula, E.; Landau, E.M.; Neutze R. Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin. Nature 2000, 406, 645-648.
    • (2000) Nature , vol.406 , pp. 645-648
    • Royant, A.1    Edman, K.2    Ursby, T.3    Pebay-Peyroula, E.4    Landau, E.M.5    Neutze, R.6
  • 9
    • 43049134414 scopus 로고    scopus 로고
    • The energetics of the primary proton transfer in bacteriorhodopsin revisited: It is a sequential light-induced charge separation after all
    • Braun-Sand, S.; Sharma, P.K.; Chu, Z.T.; Pisliakov, A.V.; Warshel, A. The energetics of the primary proton transfer in bacteriorhodopsin revisited: It is a sequential light-induced charge separation after all. Biochim. Biophys. Acta 2008, 1777, 441-452.
    • (2008) Biochim. Biophys. Acta , vol.1777 , pp. 441-452
    • Braun-Sand, S.1    Sharma, P.K.2    Chu, Z.T.3    Pisliakov, A.V.4    Warshel, A.5
  • 10
    • 0020741491 scopus 로고
    • Energy storage in the primary step of the photocycle of bacteriorhodopsin
    • Birge, R.R.; Cooper, T.M. Energy storage in the primary step of the photocycle of bacteriorhodopsin. Biophys. J. 1983, 42, 61-69.
    • (1983) Biophys. J. , vol.42 , pp. 61-69
    • Birge, R.R.1    Cooper, T.M.2
  • 11
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M.; McCammon, J A. Molecular Dynamics Simulations of Biomolecules. Nat. Struct. Biol. 2002, 9, 646-652.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 12
    • 0037079577 scopus 로고    scopus 로고
    • Combined QM/MM study of the opsin shift in bacteriorhodopsin
    • Rajamani, R.; Gao, J. Combined QM/MM Study of the Opsin Shift in Bacteriorhodopsin. J. Comput. Chem. 2002, 23, 96-105.
    • (2002) J. Comput. Chem. , vol.23 , pp. 96-105
    • Rajamani, R.1    Gao, J.2
  • 15
    • 84872151984 scopus 로고    scopus 로고
    • Minimalist models for biopolymers: Open problems, latest advances and perspectives
    • Trovato, F.; Tozzini, V. Minimalist Models for Biopolymers: Open Problems, Latest Advances and Perspectives. AIP Conf. Proc. 2012, 1456, 187-200.
    • (2012) AIP Conf. Proc. , vol.1456 , pp. 187-200
    • Trovato, F.1    Tozzini, V.2
  • 16
    • 84907280384 scopus 로고    scopus 로고
    • Hybrid Molecular mechanics/coarse-grained calculations applied to GPCR receptors
    • Capece, L.; Nguyen, H.H.C.; Leguebe, M.; Giorgetti, A.; Carloni, P. Hybrid Molecular Mechanics/Coarse-Grained Calculations Applied to GPCR Receptors. Biophys. J. 2012, 102, 63a.
    • (2012) Biophys. J. , vol.102 , pp. 63a
    • Capece, L.1    Nguyen, H.H.C.2    Leguebe, M.3    Giorgetti, A.4    Carloni, P.5
  • 17
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S.J.; Kollman, P.A; Nguyen, D.T.; Case, D. A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 1986, 7, 230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 18
    • 24344438610 scopus 로고    scopus 로고
    • A coarse grained model for the dynamics of flap opening in HIV-1 Protease
    • Tozzini, V.; McCammon, J. A. A coarse grained model for the dynamics of flap opening in HIV-1 Protease. Chem. Phys. Lett. 2005, 413, 123-128.
    • (2005) Chem. Phys. Lett. , vol.413 , pp. 123-128
    • Tozzini, V.1    McCammon, J.A.2
  • 19
    • 24144478280 scopus 로고    scopus 로고
    • Exploring global motions and correlations in the ribosome
    • TryIska, J.; Tozzini, V.; McCammon. J.A. Exploring global motions and correlations in the ribosome. Biophys. J. 2005, 89, 1455-1463.
    • (2005) Biophys. J. , vol.89 , pp. 1455-1463
    • TryIska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 20
    • 84886636578 scopus 로고    scopus 로고
    • A minimalist model of protein diffusion and interactions: The green fluorescent protein within the cytoplasm
    • Trovato, F.; Nifosì, R.; di Fenza, A.; Tozzini, V. A Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm. Macromolecules 2013, 46, 8311-8322.
    • (2013) Macromolecules , vol.46 , pp. 8311-8322
    • Trovato, F.1    Nifosì, R.2    Di Fenza, A.3    Tozzini, V.4
  • 22
    • 68149162202 scopus 로고    scopus 로고
    • Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition
    • Di Fenza, A.; Rocchia, W.; Tozzini, V. Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition. Proteins 2009, 76, 946-958.
    • (2009) Proteins , vol.76 , pp. 946-958
    • Di Fenza, A.1    Rocchia, W.2    Tozzini, V.3
  • 24
    • 0036968773 scopus 로고    scopus 로고
    • Crystallographic structure of the retinal and the protein after deprotonation of the schiff base: The switch in the bacteriorhodopsin photocycle
    • Lanyi, J.K.; Schobert, B. Crystallographic Structure of the Retinal and the Protein after Deprotonation of the Schiff Base: The Switch in the Bacteriorhodopsin Photocycle. J. Mol. Biol. 2002, 2836, 727-737.
    • (2002) J. Mol. Biol. , vol.2836 , pp. 727-737
    • Lanyi, J.K.1    Schobert, B.2
  • 25
    • 67649342841 scopus 로고    scopus 로고
    • Structural changes in the N and N'states of the bacteriorhodopsin photocycle
    • Chen, D.; Lanyi, J.K. Structural changes in the N and N'states of the bacteriorhodopsin photocycle. Biophys. J. 2009, 96, 2779-2788.
    • (2009) Biophys. J. , vol.96 , pp. 2779-2788
    • Chen, D.1    Lanyi, J.K.2
  • 26
    • 84865981364 scopus 로고    scopus 로고
    • Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin
    • Zhang, J.; Yamazaki, Y.; Hikake, M.; Murakami, M.; Ihara, K.; Kouyama, T. Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin. Proteins 2012, 80, 2384-2396.
    • (2012) Proteins , vol.80 , pp. 2384-2396
    • Zhang, J.1    Yamazaki, Y.2    Hikake, M.3    Murakami, M.4    Ihara, K.5    Kouyama, T.6
  • 28
    • 33645941402 scopus 로고    scopus 로고
    • The OPES potential functions for protins. Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen, W.L.; Tirado-Rives, J. The OPES Potential Functions for Protins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. J. Am. Chem. Soc. 1998, 110, 1666-1671.
    • (1998) J. Am. Chem. Soc. , vol.110 , pp. 1666-1671
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 29
    • 36849057606 scopus 로고    scopus 로고
    • Coarse-grained free energy functions for studying protein conformational changes: A double-well network model
    • Chu, J.-W.; Voth, G.A. Coarse-grained free energy functions for studying protein conformational changes: A double-well network model. Biophys. J. 2007, 93, 3860-3871.
    • (2007) Biophys. J. , vol.93 , pp. 3860-3871
    • Chu, J.-W.1    Voth, G.A.2
  • 30
    • 77955833735 scopus 로고    scopus 로고
    • Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model
    • Tekpinar, M.; Zheng, W. Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model. Proteins 2010, 78, 2469-2481.
    • (2010) Proteins , vol.78 , pp. 2469-2481
    • Tekpinar, M.1    Zheng, W.2
  • 31
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • Maragakis, P.; Karplus, M.; Pasteur, L. Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model : Adenylate Kinase. J. Mol. Biol. 2005, 352, 807-822.
    • (2005) J. Mol. Biol. , vol.352 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2    Pasteur, L.3
  • 35
    • 3843096037 scopus 로고    scopus 로고
    • Crystal structure of the M intermediate of bacteriorhodopsin: Allosteric structural changes mediated by sliding movement of a transmembrane helix
    • Takeda, K.; Matsui, Y.; Kamiya, N.; Adachi, S.; Okumura, H.; Kouyama, T. Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix. J. Mol. Biol. 2004, 341, 1023-1037.
    • (2004) J. Mol. Biol. , vol.341 , pp. 1023-1037
    • Takeda, K.1    Matsui, Y.2    Kamiya, N.3    Adachi, S.4    Okumura, H.5    Kouyama, T.6
  • 36
    • 22944467757 scopus 로고
    • Computer Experiments on classical fluids. I. Thermodynamical properties of Lennad-Jones molecules
    • Verlet, L. Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennad-Jones Molecules. Phys. Rev. 1967, 159, 98-103.
    • (1967) Phys. Rev. , vol.159 , pp. 98-103
    • Verlet, L.1
  • 38
    • 0030175155 scopus 로고    scopus 로고
    • DL-POLY-2.0: A general-purpose parallel molecular dynamics simulation package overall design
    • Smith, W.; Forester, T.R. DL-POLY-2.0: A general-purpose parallel molecular dynamics simulation package Overall design. J. Mol. Graph. 1996, 7855, 136-141.
    • (1996) J. Mol. Graph. , vol.7855 , pp. 136-141
    • Smith, W.1    Forester, T.R.2
  • 39
    • 84907280364 scopus 로고    scopus 로고
    • Blake, R., Ed.; CSE Frontier, STFC Computational Science and Engineering, Daresbury Laboratory: Daresbury, UK
    • Yong, C.W. DL-FIELD-A Force Field and Model Development Tool for DL-POLY; Blake, R., Ed.; CSE Frontier, STFC Computational Science and Engineering, Daresbury Laboratory: Daresbury, UK, 2010; pp. 38-40.
    • (2010) DL-FIELD-A Force Field and Model Development Tool for DL-POLY , pp. 38-40
    • Yong, C.W.1
  • 40
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 41
    • 0035789518 scopus 로고    scopus 로고
    • GROM AC S 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E.; Hess, B.; van der Spoel, D. GROM AC S 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 2001, 7, 306-317.
    • (2001) J. Mol. Mod. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 43
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia, A.E. Large-Amplitude Nonlinear Motions in Proteins. Phys. Rev. Lett. 1992, 68, 2696-2699.
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 46
    • 67349196001 scopus 로고    scopus 로고
    • Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case
    • Papaleo, E.; Mereghetti, P.; Fantucci, P.; Grandori, R.; de Gioia, L. Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations : The myoglobin case. J. Mol. Graph. Model. 2009, 27, 889-899.
    • (2009) J. Mol. Graph. Model. , vol.27 , pp. 889-899
    • Papaleo, E.1    Mereghetti, P.2    Fantucci, P.3    Grandori, R.4    De Gioia, L.5
  • 47
    • 79957788878 scopus 로고    scopus 로고
    • ProDy: Protein dynamics inferred from theory and experiments
    • Bakan, A.; Meireles, L.M.; Bahar, I. ProDy: Protein Dynamics Inferred from Theory and Experiments. Bioinformatics 2011, 27, 1575-1577.
    • (2011) Bioinformatics , vol.27 , pp. 1575-1577
    • Bakan, A.1    Meireles, L.M.2    Bahar, I.3


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