메뉴 건너뛰기




Volumn 165, Issue 1, 2009, Pages 37-46

A dual-scale approach toward structure prediction of retinal proteins

Author keywords

All atom molecular dynamics simulations; Coarse grained protein model; Monte Carlo simulations; Parallel tempering; Retinal proteins; Structure prediction

Indexed keywords

BACTERIORHODOPSIN; HALORHODOPSIN; MEMBRANE PROTEIN; RETINAL; SENSORY RHODOPSIN;

EID: 57149146836     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.10.001     Document Type: Article
Times cited : (9)

References (53)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen C. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.1
  • 3
    • 0027506471 scopus 로고    scopus 로고
    • The probable arrangement of the helices in G protein-coupled receptors
    • Baldwin J.M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J. 12 (1998) 1693-1703
    • (1998) EMBO J. , vol.12 , pp. 1693-1703
    • Baldwin, J.M.1
  • 4
    • 0032996356 scopus 로고    scopus 로고
    • Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin
    • Baudry J., Crouzy S., Roux B., and Smith J.C. Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. Biophys. J. 76 (1999) 1909-1917
    • (1999) Biophys. J. , vol.76 , pp. 1909-1917
    • Baudry, J.1    Crouzy, S.2    Roux, B.3    Smith, J.C.4
  • 5
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman H.M., et al. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 7
    • 28444488355 scopus 로고    scopus 로고
    • Solving the membrane protein folding problem
    • Bowie J.U. Solving the membrane protein folding problem. Nature 438 (2005) 581-589
    • (2005) Nature , vol.438 , pp. 581-589
    • Bowie, J.U.1
  • 8
    • 57149122600 scopus 로고    scopus 로고
    • Case, D.A. et al. 2002. AMBER7.
    • Case, D.A. et al. 2002. AMBER7.
  • 9
    • 4243379922 scopus 로고    scopus 로고
    • Lattice model of transmembrane polypeptide folding
    • Chen C.-M. Lattice model of transmembrane polypeptide folding. Phys. Rev. E. 63 (2000) 010901
    • (2000) Phys. Rev. E. , vol.63 , pp. 010901
    • Chen, C.-M.1
  • 10
    • 0037339560 scopus 로고    scopus 로고
    • Computer simulations of membrane protein folding: structure and dynamics
    • Chen C.-M., and Chen C.-C. Computer simulations of membrane protein folding: structure and dynamics. Biophys. J. 84 (2003) 1902-1908
    • (2003) Biophys. J. , vol.84 , pp. 1902-1908
    • Chen, C.-M.1    Chen, C.-C.2
  • 11
    • 0000314476 scopus 로고    scopus 로고
    • Monte-Carlo simulations of polymer crystallisation in dilute solution
    • Chen C.-M., and Higgs P.G. Monte-Carlo simulations of polymer crystallisation in dilute solution. J. Chem. Phys. 108 (1998) 4305-4314
    • (1998) J. Chem. Phys. , vol.108 , pp. 4305-4314
    • Chen, C.-M.1    Higgs, P.G.2
  • 12
    • 42649115134 scopus 로고    scopus 로고
    • Packing of transmembrane helices in bacteriorhodopsin folding: Structure and thermodynamics
    • Chen C.-C., Wei C.-C., Sun Y.-C., and Chen C.-M. Packing of transmembrane helices in bacteriorhodopsin folding: Structure and thermodynamics. J. Struct. Biol. 162 (2008) 237-247
    • (2008) J. Struct. Biol. , vol.162 , pp. 237-247
    • Chen, C.-C.1    Wei, C.-C.2    Sun, Y.-C.3    Chen, C.-M.4
  • 14
    • 0037110551 scopus 로고    scopus 로고
    • Optimal potentials for predicting inter-helical packing in transmembrane proteins
    • Dobbs H., Orlandini E., Bonaccini R., and Seno F. Optimal potentials for predicting inter-helical packing in transmembrane proteins. Proteins 49 (2002) 342-349
    • (2002) Proteins , vol.49 , pp. 342-349
    • Dobbs, H.1    Orlandini, E.2    Bonaccini, R.3    Seno, F.4
  • 16
    • 0032387685 scopus 로고    scopus 로고
    • Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census
    • Gerstein M. Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 33 (1998) 518-534
    • (1998) Proteins , vol.33 , pp. 518-534
    • Gerstein, M.1
  • 17
    • 0031578972 scopus 로고    scopus 로고
    • Parallel tempering algorithm for conformational studies of biological molecules
    • Hansmann U.H.E. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Lett. 281 (1997) 140-150
    • (1997) Chem. Phys. Lett. , vol.281 , pp. 140-150
    • Hansmann, U.H.E.1
  • 18
    • 0017420381 scopus 로고
    • The purple membrane from Halobacterium halobium
    • Henderson R. The purple membrane from Halobacterium halobium. Annu. Rev. Biophys. Bioeng. 6 (1977) 87-109
    • (1977) Annu. Rev. Biophys. Bioeng. , vol.6 , pp. 87-109
    • Henderson, R.1
  • 19
    • 0032575763 scopus 로고    scopus 로고
    • Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin
    • Herzyk P., and Hubbard R.E. Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin. J. Mol. Biol. 281 (1998) 741-754
    • (1998) J. Mol. Biol. , vol.281 , pp. 741-754
    • Herzyk, P.1    Hubbard, R.E.2
  • 20
    • 0019887931 scopus 로고
    • Refolding of an integral membrane protein. Denaturation, renaturation and reconstitution of intact bacteriorhodopsin and two proteolytic fragments
    • Huang K.-S., Bayley H., Liao M.-J., London E., and Khorana H.G. Refolding of an integral membrane protein. Denaturation, renaturation and reconstitution of intact bacteriorhodopsin and two proteolytic fragments. J. Biol. Chem. 256 (1981) 3802-3809
    • (1981) J. Biol. Chem. , vol.256 , pp. 3802-3809
    • Huang, K.-S.1    Bayley, H.2    Liao, M.-J.3    London, E.4    Khorana, H.G.5
  • 21
    • 0000616967 scopus 로고
    • Phase equilibria in an amphiphilic peptide-phospholipid model membrane by deuterium nuclear magnetic resonance difference spectroscopy
    • Huschilt J.C., Hodges R.S., and Davis J.H. Phase equilibria in an amphiphilic peptide-phospholipid model membrane by deuterium nuclear magnetic resonance difference spectroscopy. Biochemistry 24 (1985) 1377-1386
    • (1985) Biochemistry , vol.24 , pp. 1377-1386
    • Huschilt, J.C.1    Hodges, R.S.2    Davis, J.H.3
  • 22
    • 1642410853 scopus 로고    scopus 로고
    • The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonist and antagonists
    • Kalani M.Y., Vaidehi N., Hall S.E., Trabanino R.J., Freddolino P.L., et al. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonist and antagonists. Proc. Natl. Acad. Sci. USA 101 (2004) 3815-3820
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 3815-3820
    • Kalani, M.Y.1    Vaidehi, N.2    Hall, S.E.3    Trabanino, R.J.4    Freddolino, P.L.5
  • 23
    • 2942639959 scopus 로고    scopus 로고
    • Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange monte carlo simulation
    • Kokubo H., and Okamoto Y. Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange monte carlo simulation. Chem. Phys. Lett. 392 (2004) 168-175
    • (2004) Chem. Phys. Lett. , vol.392 , pp. 168-175
    • Kokubo, H.1    Okamoto, Y.2
  • 24
    • 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., and Oesterhelt D. Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution. Science 288 (2000) 1390-1396
    • (2000) Science , vol.288 , pp. 1390-1396
    • Kolbe, M.1    Besir, H.2    Essen, L.-O.3    Oesterhelt, D.4
  • 25
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 26
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 27
    • 0030902305 scopus 로고    scopus 로고
    • Three-dimensional model of sensory rhodopsin I reveals important restraints between the protein and the chromophore
    • Lin S.L., and Yan B. Three-dimensional model of sensory rhodopsin I reveals important restraints between the protein and the chromophore. Protein Eng. 10 (1997) 197-206
    • (1997) Protein Eng. , vol.10 , pp. 197-206
    • Lin, S.L.1    Yan, B.2
  • 28
    • 0033545962 scopus 로고    scopus 로고
    • Protein structure prediction by global optimization of a potential energy function
    • Liwo A., Lee J., Ripoll D.R., Pillardy J., and Scheraga H.A. Protein structure prediction by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA 96 (1999) 5482-5485
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 5482-5485
    • Liwo, A.1    Lee, J.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 29
    • 0020490831 scopus 로고
    • Denaturation and renaturation of bacteriorhodopsin in detergents and lipid-detergent mixtures
    • London E., and Khorana H.G. Denaturation and renaturation of bacteriorhodopsin in detergents and lipid-detergent mixtures. J. Biol. Chem. 257 (1982) 7003-7011
    • (1982) J. Biol. Chem. , vol.257 , pp. 7003-7011
    • London, E.1    Khorana, H.G.2
  • 30
    • 0026661869 scopus 로고
    • Spontaneous insertion of polypeptide-chains into membranes - a Monte-Carlo model
    • Milik M., and Skolnick J. Spontaneous insertion of polypeptide-chains into membranes - a Monte-Carlo model. Proc. Natl. Acad. Sci. USA 89 (1992) 9391-9395
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 9391-9395
    • Milik, M.1    Skolnick, J.2
  • 32
    • 0028835990 scopus 로고
    • Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water
    • Nina M., Roux B., and Smith J.C. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophys. J. 68 (1995) 25-39
    • (1995) Biophys. J. , vol.68 , pp. 25-39
    • Nina, M.1    Roux, B.2    Smith, J.C.3
  • 33
    • 0016875454 scopus 로고
    • Bacteriorhodopsin as an example of a lightdriven proton pump
    • Oesterhelt D. Bacteriorhodopsin as an example of a lightdriven proton pump. Angew. Chem. Int. Ed. Engl. 15 (1976) 17-24
    • (1976) Angew. Chem. Int. Ed. Engl. , vol.15 , pp. 17-24
    • Oesterhelt, D.1
  • 35
    • 34147122523 scopus 로고    scopus 로고
    • Contact-induced structure transformation in transmembrane prion propagation
    • Ou D.-M., Chen C.-C., and Chen C.-M. Contact-induced structure transformation in transmembrane prion propagation. Biophys. J. 92 (2007) 2704-2710
    • (2007) Biophys. J. , vol.92 , pp. 2704-2710
    • Ou, D.-M.1    Chen, C.-C.2    Chen, C.-M.3
  • 36
    • 0026517309 scopus 로고
    • On the use of the transmembrane domain of bacteriorhodopsin as a template for modeling the three-dimensional structure of guanine nucleotide-binding regulatory protein-coupled receptors
    • Pardo L., Ballesteros J.A., Osman R., and Weinstein H. On the use of the transmembrane domain of bacteriorhodopsin as a template for modeling the three-dimensional structure of guanine nucleotide-binding regulatory protein-coupled receptors. Proc. Natl. Acad. Sci. USA 89 (1992) 4009-4012
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 4009-4012
    • Pardo, L.1    Ballesteros, J.A.2    Osman, R.3    Weinstein, H.4
  • 37
    • 0030864048 scopus 로고    scopus 로고
    • X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases
    • Pebay-Peyroula E., Rummel G., Rosenbusch J.P., and Landau E.M. X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277 (1997) 1676-1681
    • (1997) Science , vol.277 , pp. 1676-1681
    • Pebay-Peyroula, E.1    Rummel, G.2    Rosenbusch, J.P.3    Landau, E.M.4
  • 38
    • 0032932375 scopus 로고    scopus 로고
    • A potential smoothing algorithm accurately predicts transmembrane helix packing
    • Pappu R.V., Marshall G.R., and Ponder J.W. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat. Struct. Biol. 6 (1999) 50-55
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 50-55
    • Pappu, R.V.1    Marshall, G.R.2    Ponder, J.W.3
  • 39
    • 0025249842 scopus 로고
    • Membrane protein folding and oligomerization: The two-stage model
    • Popot J.-L., and Engelman D.M. Membrane protein folding and oligomerization: The two-stage model. Biochemistry 29 (1990) 4031-4037
    • (1990) Biochemistry , vol.29 , pp. 4031-4037
    • Popot, J.-L.1    Engelman, D.M.2
  • 40
    • 0033790343 scopus 로고    scopus 로고
    • Helical membrane protein folding, stability, and evolution
    • Popot J.-L., and Engelman D.M. Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 69 (2000) 881-922
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 881-922
    • Popot, J.-L.1    Engelman, D.M.2
  • 41
    • 36248970132 scopus 로고    scopus 로고
    • Crystal structure of the human b2 adrenergic G-protein-coupled receptor
    • Rasmussen S.G.F., Choi H.-J., Rosenbaum D.M., Kobilka T.S., Thian F.S., et al. Crystal structure of the human b2 adrenergic G-protein-coupled receptor. Nature 450 (2007) 383-388
    • (2007) Nature , vol.450 , pp. 383-388
    • Rasmussen, S.G.F.1    Choi, H.-J.2    Rosenbaum, D.M.3    Kobilka, T.S.4    Thian, F.S.5
  • 43
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons K.T., Kooperberg C., Huang E., and Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268 (1997) 209-225
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 44
    • 0032478081 scopus 로고    scopus 로고
    • Molecular organization and dynamics of 1-palmitoyl-2-oleoylphosphatidylcholine bilayers containing a transmembrane α-helical peptide
    • Subczynski W.K., Lewis R.N.A.H., McElhaney R.N., Hodges R.S., Hyde J.S., and Kusumi A. Molecular organization and dynamics of 1-palmitoyl-2-oleoylphosphatidylcholine bilayers containing a transmembrane α-helical peptide. Biochemistry 37 (1998) 3156-3164
    • (1998) Biochemistry , vol.37 , pp. 3156-3164
    • Subczynski, W.K.1    Lewis, R.N.A.H.2    McElhaney, R.N.3    Hodges, R.S.4    Hyde, J.S.5    Kusumi, A.6
  • 45
    • 0001649232 scopus 로고    scopus 로고
    • a control of the retinal Schiff base: a density functional study
    • a control of the retinal Schiff base: a density functional study. J. Phys. Chem. B. 103 (1999) 4518-4527
    • (1999) J. Phys. Chem. B. , vol.103 , pp. 4518-4527
    • Tajkhorshid, E.1    Paizs, B.2    Suhai, S.3
  • 46
    • 1942487807 scopus 로고    scopus 로고
    • First principles predictions of the structure and function of G-protein-coupled receptors: validation for bovine rhodopsin
    • Trabanino R.J., et al. First principles predictions of the structure and function of G-protein-coupled receptors: validation for bovine rhodopsin. Biophys. J. 86 (2004) 1904-1921
    • (2004) Biophys. J. , vol.86 , pp. 1904-1921
    • Trabanino, R.J.1
  • 47
    • 0025310046 scopus 로고
    • Electrical modulation of membrane proteins
    • Tsong T.Y. Electrical modulation of membrane proteins. Annu. Rev. Biophys. Chem. 19 (1990) 83-106
    • (1990) Annu. Rev. Biophys. Chem. , vol.19 , pp. 83-106
    • Tsong, T.Y.1
  • 48
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E., and von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7 (1998) 1029-1038
    • (1998) Protein Sci. , vol.7 , pp. 1029-1038
    • Wallin, E.1    von Heijne, G.2
  • 49
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: physical principles
    • White S.H., and Wimley W.C. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28 (1999) 319-365
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 50
    • 33644842630 scopus 로고    scopus 로고
    • Multipass membrane protein structure prediction using Rosetta
    • Yarov-Yarovoy V., Schonbrun J., and Baker D. Multipass membrane protein structure prediction using Rosetta. Proteins 62 (2006) 1010-1025
    • (2006) Proteins , vol.62 , pp. 1010-1025
    • Yarov-Yarovoy, V.1    Schonbrun, J.2    Baker, D.3
  • 51
    • 33645793799 scopus 로고    scopus 로고
    • Structure modeling of all identified G protein-coupled receptors in the human genome
    • Zhang Y., DeVries M.E., and Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput. Biol. 2 (2006) 88-99
    • (2006) PLoS Comput. Biol. , vol.2 , pp. 88-99
    • Zhang, Y.1    DeVries, M.E.2    Skolnick, J.3
  • 52
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: a new approach to ab initio protein structure prediction
    • Zhang Y., Kolinski A., and Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys. J. 85 (2003) 1145-1164
    • (2003) Biophys. J. , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.