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Volumn 76, Issue 2, 2009, Pages 271-280

Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor

Author keywords

AMPA; Helicity; iGluR; Importance sampling; Ligand gated ion channel; Peptide folding; REMD; Structure function relationship

Indexed keywords

GLUTAMATE RECEPTOR 2; IONOTROPIC RECEPTOR; MONOMER; PEPTIDE; PROTEIN SUBUNIT; TETRAMER;

EID: 67650252005     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22332     Document Type: Article
Times cited : (2)

References (52)
  • 3
    • 33645321641 scopus 로고    scopus 로고
    • Glutamate receptors at atomic resolution
    • Mayer ML. Glutamate receptors at atomic resolution. Nature 2006;440:456-462.
    • (2006) Nature , vol.440 , pp. 456-462
    • Mayer, M.L.1
  • 4
    • 0032523002 scopus 로고    scopus 로고
    • Evidence for a tetrameric structure of recombinant NMDA receptors
    • Laube B, Kuhse J, Betz H. Evidence for a tetrameric structure of recombinant NMDA receptors. J Neurosci 1998;18:2954-2961.
    • (1998) J Neurosci , vol.18 , pp. 2954-2961
    • Laube, B.1    Kuhse, J.2    Betz, H.3
  • 5
    • 0032486422 scopus 로고    scopus 로고
    • The tetrameric structure of a glutamate receptor channel
    • Rosenmund C, Stern-Bach Y, Stevens CF. The tetrameric structure of a glutamate receptor channel. Science 1998;280:1596-1599.
    • (1998) Science , vol.280 , pp. 1596-1599
    • Rosenmund, C.1    Stern-Bach, Y.2    Stevens, C.F.3
  • 6
    • 0033636314 scopus 로고    scopus 로고
    • Mechanisms for activation and antagonism of an AMPA-Sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core
    • Armstrong N, Gouaux E. Mechanisms for activation and antagonism of an AMPA-Sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core. Neuron 2000;28:165-181.
    • (2000) Neuron , vol.28 , pp. 165-181
    • Armstrong, N.1    Gouaux, E.2
  • 7
    • 0035943408 scopus 로고    scopus 로고
    • Mechanisms for ligand binding to GluR0 ion channels: Crystal structures of the glutamate and serine complexes and a closed apo state
    • Mayer ML, Olson R, Gouaux E. Mechanisms for ligand binding to GluR0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state. J Mol Biol 2001;311:815-836.
    • (2001) J Mol Biol , vol.311 , pp. 815-836
    • Mayer, M.L.1    Olson, R.2    Gouaux, E.3
  • 8
    • 13844266202 scopus 로고    scopus 로고
    • Crystal structures of the GluR5 and GluR6 ligand binding cores: Molecular mechanisms underlying kainate receptor selectivity
    • Mayer ML. Crystal structures of the GluR5 and GluR6 ligand binding cores: molecular mechanisms underlying kainate receptor selectivity. Neuron 2005;45:539-552.
    • (2005) Neuron , vol.45 , pp. 539-552
    • Mayer, M.L.1
  • 9
    • 0035003258 scopus 로고    scopus 로고
    • Structural similarities between glutamate receptor channels and K+ channels examined by scanning mutagenesis
    • Panchenko VA, Glasser CR, Mayer ML. Structural similarities between glutamate receptor channels and K+ channels examined by scanning mutagenesis. J Gen Physiol 2001;117:345-359.
    • (2001) J Gen Physiol , vol.117 , pp. 345-359
    • Panchenko, V.A.1    Glasser, C.R.2    Mayer, M.L.3
  • 10
    • 0037213506 scopus 로고    scopus 로고
    • A common architecture for K+ channels and ionotropic glutamate receptors?
    • Kuner T, Seeburg PH, Guy HR. A common architecture for K+ channels and ionotropic glutamate receptors? Trends Neurosci 2003;26:27-33.
    • (2003) Trends Neurosci , vol.26 , pp. 27-33
    • Kuner, T.1    Seeburg, P.H.2    Guy, H.R.3
  • 11
    • 0033576612 scopus 로고    scopus 로고
    • Functional characterization of a potassium-selective prokaryotic glutamate receptor
    • Chen GQ, Cui C, Mayer ML, Gouaux E. Functional characterization of a potassium-selective prokaryotic glutamate receptor. Nature 1999;402:817-821.
    • (1999) Nature , vol.402 , pp. 817-821
    • Chen, G.Q.1    Cui, C.2    Mayer, M.L.3    Gouaux, E.4
  • 12
    • 0032006303 scopus 로고    scopus 로고
    • Glycine-independent NMDA receptor desensitization: Localization of structural determinants
    • Villarroel A, Regalado PM, Lerma J. Glycine-independent NMDA receptor desensitization: localization of structural determinants. Neuron 1998;20:329-339.
    • (1998) Neuron , vol.20 , pp. 329-339
    • Villarroel, A.1    Regalado, P.M.2    Lerma, J.3
  • 13
    • 0033103522 scopus 로고    scopus 로고
    • NMDAR channel segments forming the extracellular vestibule inferred from the accessibility of substituted cysteines
    • Beck C, Wollmuth LP, Seeburg PH, Sakmann B, Kuner T. NMDAR channel segments forming the extracellular vestibule inferred from the accessibility of substituted cysteines. Neuron 1999;22:559-570.
    • (1999) Neuron , vol.22 , pp. 559-570
    • Beck, C.1    Wollmuth, L.P.2    Seeburg, P.H.3    Sakmann, B.4    Kuner, T.5
  • 14
    • 2442675355 scopus 로고    scopus 로고
    • Block of AMPA receptor desensitization by a point mutation outside the ligand-binding domain
    • Yelshansky MV, Sobolevsky AI, Jatzke C, Wollmuth LP. Block of AMPA receptor desensitization by a point mutation outside the ligand-binding domain. J Neurosci 2004;24:4728-4736.
    • (2004) J Neurosci , vol.24 , pp. 4728-4736
    • Yelshansky, M.V.1    Sobolevsky, A.I.2    Jatzke, C.3    Wollmuth, L.P.4
  • 15
    • 36048978613 scopus 로고    scopus 로고
    • A domain linking the AMPA receptor agonist binding site to the ion pore controls Gating and causes lurcher properties when mutated
    • Schmid SM, Korber C, Herrmann S, Werner M, Hollmann M. A domain linking the AMPA receptor agonist binding site to the ion pore controls Gating and causes lurcher properties when mutated. J Neurosci 2007;27:12230-12241.
    • (2007) J Neurosci , vol.27 , pp. 12230-12241
    • Schmid, S.M.1    Korber, C.2    Herrmann, S.3    Werner, M.4    Hollmann, M.5
  • 16
    • 33646229281 scopus 로고    scopus 로고
    • Folding very short peptides using molecular dynamics
    • Ho BK, Dill KA. Folding very short peptides using molecular dynamics. PLoS Comput Biol 2006;2:228-237.
    • (2006) PLoS Comput Biol , vol.2 , pp. 228-237
    • Ho, B.K.1    Dill, K.A.2
  • 17
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151.
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 19
    • 0037339393 scopus 로고    scopus 로고
    • Helix propensities of short peptides: Molecular dynamics versus bioinformatics
    • Bystroff C, Garde S. Helix propensities of short peptides: molecular dynamics versus bioinformatics. Protein: Struct Funct Genet 2003;50:552-562.
    • (2003) Protein: Struct Funct Genet , vol.50 , pp. 552-562
    • Bystroff, C.1    Garde, S.2
  • 20
    • 34247639441 scopus 로고    scopus 로고
    • Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
    • Lei HX, Wu C, Liu HG, Duan Y. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc Natl Acad Sci USA 2007;104:4925-4930.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 4925-4930
    • Lei, H.X.1    Wu, C.2    Liu, H.G.3    Duan, Y.4
  • 21
    • 23944494644 scopus 로고    scopus 로고
    • Folding cooperativity in a three-stranded β-sheet model
    • Roe DR, Hornak V, Simmerling C. Folding cooperativity in a three-stranded β-sheet model. J Mol Biol 2005;352:370-381.
    • (2005) J Mol Biol , vol.352 , pp. 370-381
    • Roe, D.R.1    Hornak, V.2    Simmerling, C.3
  • 22
    • 1642546396 scopus 로고    scopus 로고
    • Atomic simulations of protein folding, using the replica exchange algorithm
    • Nymeyer H, Gnanakaran S, Garcia AE. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol 2004;83:119-149.
    • (2004) Methods Enzymol , vol.83 , pp. 119-149
    • Nymeyer, H.1    Gnanakaran, S.2    Garcia, A.E.3
  • 23
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002;124:11258-11259.
    • (2002) J Am Chem Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 24
    • 0242322528 scopus 로고    scopus 로고
    • An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins
    • Im W, Feig M, Brooks CL. An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 2003;85:2900-2918.
    • (2003) Biophys J , vol.85 , pp. 2900-2918
    • Im, W.1    Feig, M.2    Brooks, C.L.3
  • 25
    • 33846804141 scopus 로고    scopus 로고
    • Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations
    • Bu LT, Im W, Charles LI. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J 2007;92:854-863.
    • (2007) Biophys J , vol.92 , pp. 854-863
    • Bu, L.T.1    Im, W.2    Charles, L.I.3
  • 26
    • 18744403982 scopus 로고    scopus 로고
    • Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
    • Im W, Brooks CL. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci USA 2005;102:6771-6776.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6771-6776
    • Im, W.1    Brooks, C.L.2
  • 27
    • 0344702698 scopus 로고    scopus 로고
    • Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
    • Nymeyer H, Garcia AE. Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Natl Acad Sci USA 2003;100:13934-13939.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13934-13939
    • Nymeyer, H.1    Garcia, A.E.2
  • 28
    • 0034510764 scopus 로고    scopus 로고
    • Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models
    • Bursulaya BD, Brooks CL. Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models. J Phys Chem B 2000;104:12378-12383.
    • (2000) J Phys Chem B , vol.104 , pp. 12378-12383
    • Bursulaya, B.D.1    Brooks, C.L.2
  • 30
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replica-exchange simulations of "Trp-cage" fly miniproteins
    • Pitera JW, Swope W. Understanding folding and design: replica-exchange simulations of "Trp-cage" fly miniproteins. Proc Natl Acad Sci USA 2003;100:7587-7592.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 31
    • 0347130904 scopus 로고    scopus 로고
    • Heterogeneous folding of the trpzip hairpin: Full atom simulation and experiment
    • Yang WY, Pitera JW, Swope WC, Gruebele M. Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. J Mol Biol 2004;336:241-251.
    • (2004) J Mol Biol , vol.336 , pp. 241-251
    • Yang, W.Y.1    Pitera, J.W.2    Swope, W.C.3    Gruebele, M.4
  • 33
    • 33645722974 scopus 로고    scopus 로고
    • Convergence of replica exchange molecular dynamics
    • Zhang W, Wu C, Duan Y. Convergence of replica exchange molecular dynamics. J Chem Phys 2005;123:154105.
    • (2005) J Chem Phys , vol.123 , pp. 154105
    • Zhang, W.1    Wu, C.2    Duan, Y.3
  • 34
    • 33846106377 scopus 로고    scopus 로고
    • Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
    • Periole X, Mark AE. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. J Chem Phys 2007;126:014903.
    • (2007) J Chem Phys , vol.126 , pp. 014903
    • Periole, X.1    Mark, A.E.2
  • 35
    • 34247234602 scopus 로고    scopus 로고
    • The Alzheimer's peptides A β 40 and 42 adopt distinct conformations in water: A combined MD/NMR study
    • Sgourakis NG, Yan YL, McCallum SA, Wang CY, Garcia AE. The Alzheimer's peptides A β 40 and 42 adopt distinct conformations in water: a combined MD/NMR study. J Mol Biol 2007;368:1448-1457.
    • (2007) J Mol Biol , vol.368 , pp. 1448-1457
    • Sgourakis, N.G.1    Yan, Y.L.2    McCallum, S.A.3    Wang, C.Y.4    Garcia, A.E.5
  • 36
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones DT, Taylor WR, Thornton JM. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 1994;33:3038-3049.
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 37
    • 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, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567-580.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.L.4
  • 40
    • 33646987405 scopus 로고
    • Optimized Monte-Carlo data analysis
    • Ferrenberg AM, Swendsen RH. Optimized Monte-Carlo data analysis. Phys Rev Lett 1989;63:1195-1198.
    • (1989) Phys Rev Lett , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 41
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 1992;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
  • 42
    • 67650229610 scopus 로고    scopus 로고
    • Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Hornak G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman PA. AMBER 8. San Francisco: University of California; 2004.
    • Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Hornak G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman PA. AMBER 8. San Francisco: University of California; 2004.
  • 43
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 44
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized Born solvation model in macromolecular simulations
    • Tsui V, Case DA. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 2000;56:275-291.
    • (2000) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 45
    • 0001411633 scopus 로고
    • Permeability properties of unmodified lipid bilayer membranes
    • Giebish G, editor, New York: Springer;
    • Andersen OS. Permeability properties of unmodified lipid bilayer membranes. In: Giebish G, editor. Membrane transport and biology, Vol. 1. New York: Springer; 1978. pp 349-446.
    • (1978) Membrane transport and biology , vol.1 , pp. 349-446
    • Andersen, O.S.1
  • 46
    • 33947398571 scopus 로고    scopus 로고
    • Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
    • Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J Chem Theory Comput 2007;3:26-41.
    • (2007) J Chem Theory Comput , vol.3 , pp. 26-41
    • Chodera, J.D.1    Swope, W.C.2    Pitera, J.W.3    Seok, C.4    Dill, K.A.5
  • 47
    • 0000998079 scopus 로고
    • The effects of solvent on the conformation and the collective motions of protein - normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum
    • Kitao A, Hirata F, Go N. The effects of solvent on the conformation and the collective motions of protein - normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum. Chem Phys 1991;158:447-472.
    • (1991) Chem Phys , vol.158 , pp. 447-472
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 48
    • 0037165750 scopus 로고    scopus 로고
    • General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation
    • Prompers JJ, Bruschweiler R. General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation. J Am Chem Soc 2002;124:4522-4534.
    • (2002) J Am Chem Soc , vol.124 , pp. 4522-4534
    • Prompers, J.J.1    Bruschweiler, R.2
  • 49
    • 0034828605 scopus 로고    scopus 로고
    • Reorientational eigenmode dynamics: A combined MD/NMR relaxation analysis method for flexible parts in globular proteins
    • Prompers JJ, Bruschweiler R. Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins. J Am Chem Soc 2001;123:7305-7313.
    • (2001) J Am Chem Soc , vol.123 , pp. 7305-7313
    • Prompers, J.J.1    Bruschweiler, R.2
  • 50
    • 0026525048 scopus 로고
    • Molecular dynamics simulations of helix denaturation
    • Daggett V, Levitt M. Molecular dynamics simulations of helix denaturation. J Mol Biol 1992;223:1121-1138.
    • (1992) J Mol Biol , vol.223 , pp. 1121-1138
    • Daggett, V.1    Levitt, M.2
  • 51
    • 0041921002 scopus 로고    scopus 로고
    • Different gating mechanisms in glutamate receptor and K+ channels
    • Sobolevsky AI, Yelshansky MV, Wollmuth LP. Different gating mechanisms in glutamate receptor and K+ channels. J Neurosci 2003;23:7559-7568.
    • (2003) J Neurosci , vol.23 , pp. 7559-7568
    • Sobolevsky, A.I.1    Yelshansky, M.V.2    Wollmuth, L.P.3
  • 52
    • 0032509102 scopus 로고    scopus 로고
    • Proline-induced disruption of a transmembrane α-helix in its natural environment
    • Nilsson I, Saaf A, Whitley P, Gafvelin G, Waller C, von Heijne G. Proline-induced disruption of a transmembrane α-helix in its natural environment. J Mol Biol 1998;284:1165-1175.
    • (1998) J Mol Biol , vol.284 , pp. 1165-1175
    • Nilsson, I.1    Saaf, A.2    Whitley, P.3    Gafvelin, G.4    Waller, C.5    von Heijne, G.6


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