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Volumn 90, Issue C, 2008, Pages 233-265

Chapter 12 Molecular Modeling and Simulation Studies of Ion Channel Structures, Dynamics and Mechanisms

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID A RECEPTOR; ION CHANNEL; MEMBRANE PROTEIN;

EID: 59049094817     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(08)00812-1     Document Type: Review
Times cited : (25)

References (129)
  • 1
    • 0347089020 scopus 로고    scopus 로고
    • Energetics of ion conduction through the gramicidin channel
    • Allen T.W., Andersen O.S., and Roux B. Energetics of ion conduction through the gramicidin channel. Proc. Natl. Acad. Sci. USA 101 (2004) 117-122
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 117-122
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 2
    • 10344245541 scopus 로고    scopus 로고
    • On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation
    • Allen T.W., Andersen O.S., and Roux B. On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J. Gen. Physiol. 124 (2004) 679-690
    • (2004) J. Gen. Physiol. , vol.124 , pp. 679-690
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 3
    • 33646192258 scopus 로고    scopus 로고
    • Ion permeation through a narrow channel: Using gramicidin to ascertain all-atom molecular dynamics potential of mean force
    • Allen T.W., Andersen O.S., and Roux B. Ion permeation through a narrow channel: Using gramicidin to ascertain all-atom molecular dynamics potential of mean force. Biophys. J. 90 (2006) 3447-3468
    • (2006) Biophys. J. , vol.90 , pp. 3447-3468
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 4
    • 0035957523 scopus 로고    scopus 로고
    • Structure and function in bacteriorhodopsin: The effect of the interhelical loops on the protein folding kinetics
    • Allen S.J., Kim J.M., Khorana H.G., Lu H., and Booth P.J. Structure and function in bacteriorhodopsin: The effect of the interhelical loops on the protein folding kinetics. J. Mol. Biol. 308 (2001) 423-435
    • (2001) J. Mol. Biol. , vol.308 , pp. 423-435
    • Allen, S.J.1    Kim, J.M.2    Khorana, H.G.3    Lu, H.4    Booth, P.J.5
  • 6
    • 17844406709 scopus 로고    scopus 로고
    • The a7 nicotinic acetylcholine receptor: Molecular modelling, electrostatics, and energetics
    • Amiri S., Tai K., Beckstein O., Biggin P.C., and Sansom M.S.P. The a7 nicotinic acetylcholine receptor: Molecular modelling, electrostatics, and energetics. Mol. Membr. Biol. 22 (2005) 151-162
    • (2005) Mol. Membr. Biol. , vol.22 , pp. 151-162
    • Amiri, S.1    Tai, K.2    Beckstein, O.3    Biggin, P.C.4    Sansom, M.S.P.5
  • 7
    • 0034690250 scopus 로고    scopus 로고
    • Ion permeation mechanism of the potassium channel
    • Åqvist J., and Luzhkov V. Ion permeation mechanism of the potassium channel. Nature 404 (2000) 881-884
    • (2000) Nature , vol.404 , pp. 881-884
    • Åqvist, J.1    Luzhkov, V.2
  • 8
    • 33746094645 scopus 로고    scopus 로고
    • Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity
    • Asthagiri D., Pratt L.R., and Paulaitis M.E. Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity. J. Chem. Phys. 125 (2006) 024701
    • (2006) J. Chem. Phys. , vol.125 , pp. 024701
    • Asthagiri, D.1    Pratt, L.R.2    Paulaitis, M.E.3
  • 11
    • 0035747672 scopus 로고    scopus 로고
    • Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
    • Bates P.A., Kelley L.A., MacCallum R.M., and Sternberg M.J. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins: Struct. Func. Bioinf. 45 Suppl. 5 (2001) 39-46
    • (2001) Proteins: Struct. Func. Bioinf. , vol.45 , Issue.SUPPL. 5 , pp. 39-46
    • Bates, P.A.1    Kelley, L.A.2    MacCallum, R.M.3    Sternberg, M.J.4
  • 12
    • 33745907550 scopus 로고    scopus 로고
    • A hydrophobic gate in an ion channel: The closed state of the nicotinic acetylcholine receptor
    • Beckstein O., and Sansom M.S.P. A hydrophobic gate in an ion channel: The closed state of the nicotinic acetylcholine receptor. Phys. Biol. 3 (2006) 147-159
    • (2006) Phys. Biol. , vol.3 , pp. 147-159
    • Beckstein, O.1    Sansom, M.S.P.2
  • 13
    • 8844228899 scopus 로고    scopus 로고
    • Not ions alone: Barriers to ion permeation in nanopores and channels
    • Beckstein O., Tai K., and Sansom M.S.P. Not ions alone: Barriers to ion permeation in nanopores and channels. J. Am. Chem. Soc. 126 (2004) 14694-14695
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 14694-14695
    • Beckstein, O.1    Tai, K.2    Sansom, M.S.P.3
  • 19
    • 17044400911 scopus 로고    scopus 로고
    • A gate in the selectivity filter of potassium channels
    • Bernèche S., and Roux B. A gate in the selectivity filter of potassium channels. Structure 13 (2005) 591-600
    • (2005) Structure , vol.13 , pp. 591-600
    • Bernèche, S.1    Roux, B.2
  • 21
    • 34250333069 scopus 로고    scopus 로고
    • + channels is due to topological control of the permanent ion's coordinated state
    • + channels is due to topological control of the permanent ion's coordinated state. Proc. Natl. Acad. Sci. USA 104 (2007) 9260-9265
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 9260-9265
    • Bostick, D.L.1    Brooks, C.L.2
  • 22
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 23
    • 0035902009 scopus 로고    scopus 로고
    • Crystal structure of an ach-binding protein reveals the ligand-binding domain of nicotinic receptors
    • Brejc K., van Dijk W.J., Klaassen R.V., Schuurmans M., van der Oost J., Smit A.B., and Sixma T.K. Crystal structure of an ach-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 411 (2001) 269-276
    • (2001) Nature , vol.411 , pp. 269-276
    • Brejc, K.1    van Dijk, W.J.2    Klaassen, R.V.3    Schuurmans, M.4    van der Oost, J.5    Smit, A.B.6    Sixma, T.K.7
  • 24
    • 0033970022 scopus 로고    scopus 로고
    • Expectations from structural genomics
    • Brenner S.E., and Levitt M. Expectations from structural genomics. Protein Sci. 9 (2000) 197-200
    • (2000) Protein Sci. , vol.9 , pp. 197-200
    • Brenner, S.E.1    Levitt, M.2
  • 26
    • 0031030225 scopus 로고    scopus 로고
    • Permeation through an open channel: Poisson-Nernst-Planck theory of a synthetic ionic channel
    • Chen D., Lear J., and Eisenberg B. Permeation through an open channel: Poisson-Nernst-Planck theory of a synthetic ionic channel. Biophys. J. 72 (1997) 97-116
    • (1997) Biophys. J. , vol.72 , pp. 97-116
    • Chen, D.1    Lear, J.2    Eisenberg, B.3
  • 27
    • 0037736706 scopus 로고    scopus 로고
    • Free energy calculations: The long and winding gilded road
    • Chipot C., and Pearlman D.A. Free energy calculations: The long and winding gilded road. Mol. Simulat. 28 (2002) 1-12
    • (2002) Mol. Simulat. , vol.28 , pp. 1-12
    • Chipot, C.1    Pearlman, D.A.2
  • 29
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C., and Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5 (1986) 823-826
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 33
    • 33846823909 scopus 로고
    • Particle mesh Ewald-An N.log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald-An N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 34
    • 0035935802 scopus 로고    scopus 로고
    • Calculating free energies using average force
    • Davre E., and Pohorille A. Calculating free energies using average force. J. Chem. Phys. 115 (2001) 9169-9183
    • (2001) J. Chem. Phys. , vol.115 , pp. 9169-9183
    • Davre, E.1    Pohorille, A.2
  • 36
    • 43949121752 scopus 로고    scopus 로고
    • Modeling membranes under a transmembrane potential
    • Delemotte L., Dehez F., Treptow W., and Tarek M. Modeling membranes under a transmembrane potential. J. Phys. Chem. B 112 (2008) 5547-5550
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5547-5550
    • Delemotte, L.1    Dehez, F.2    Treptow, W.3    Tarek, M.4
  • 37
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
    • Dolinsky T.J., Nielsen J.E., McCammon J.A., and Baker N.A. PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32 (2004) W665-W667
    • (2004) Nucleic Acids Res. , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 40
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • Dunbrack Jr. R.L. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12 (2002) 431-440
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 431-440
    • Dunbrack Jr., R.L.1
  • 41
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S.R. Profile hidden Markov models. Bioinformatics 14 (1998) 755-763
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 42
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
    • Fischer D. 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor. Proteins: Struct. Func. Bioinf. 51 (2003) 434-441
    • (2003) Proteins: Struct. Func. Bioinf. , vol.51 , pp. 434-441
    • Fischer, D.1
  • 43
    • 0036873086 scopus 로고    scopus 로고
    • The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology
    • Fogolari F., Brigo A., and Molinari H. The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology. J. Mol. Recogn. 15 (2002) 377-392
    • (2002) J. Mol. Recogn. , vol.15 , pp. 377-392
    • Fogolari, F.1    Brigo, A.2    Molinari, H.3
  • 44
    • 36148944514 scopus 로고    scopus 로고
    • Rapid, accurate and precise calculation of relative binding affinities for the SH2 domain using a computational grid
    • Fowler P.W., Geroult S., Jha S., Waksman G., and Coveney P.V. Rapid, accurate and precise calculation of relative binding affinities for the SH2 domain using a computational grid. J. Chem. Theor. Comput. 3 (2007) 1193-1202
    • (2007) J. Chem. Theor. Comput. , vol.3 , pp. 1193-1202
    • Fowler, P.W.1    Geroult, S.2    Jha, S.3    Waksman, G.4    Coveney, P.V.5
  • 45
    • 58149331214 scopus 로고    scopus 로고
    • + ion channels: Testing the hypotheses
    • doi:10.1529/biophysj.108.132035
    • + ion channels: Testing the hypotheses. Biophys. J. (2008) doi:10.1529/biophysj.108.132035
    • (2008) Biophys. J.
    • Fowler, P.W.1    Tai, K.2    Sansom, M.S.P.3
  • 46
    • 33646002994 scopus 로고    scopus 로고
    • Comparative modeling for protein structure prediction
    • Ginalski K. Comparative modeling for protein structure prediction. Curr. Opin. Struct. Biol. 16 (2006) 172-177
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 172-177
    • Ginalski, K.1
  • 47
    • 28544453561 scopus 로고    scopus 로고
    • Principles of selective ion transport in channels and pumps
    • Gouaux E., and MacKinnon R. Principles of selective ion transport in channels and pumps. Science 310 (2005) 1461-1465
    • (2005) Science , vol.310 , pp. 1461-1465
    • Gouaux, E.1    MacKinnon, R.2
  • 48
    • 24944551911 scopus 로고    scopus 로고
    • Conformational dynamics of M2 helices in kirbac channels: Helix flexibility in relation to gating via molecular dynamics simulations
    • Grottesi A., Domene C., and Sansom M.S.P. Conformational dynamics of M2 helices in kirbac channels: Helix flexibility in relation to gating via molecular dynamics simulations. Biochemistry 44 (2005) 14586-14594
    • (2005) Biochemistry , vol.44 , pp. 14586-14594
    • Grottesi, A.1    Domene, C.2    Sansom, M.S.P.3
  • 49
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-pdbviewer: An environment for comparative protein modeling
    • Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-pdbviewer: An environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 50
    • 4344660645 scopus 로고    scopus 로고
    • Overcoming free energy barriers using unconstrained molecular dynamics simulations
    • Hénin J., and Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J. Chem. Phys. 121 (2004) 2904-3004
    • (2004) J. Chem. Phys. , vol.121 , pp. 2904-3004
    • Hénin, J.1    Chipot, C.2
  • 53
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B., and Nicholls A. Classical electrostatics in biology and chemistry. Science 268 (1995) 1144-1149
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 55
    • 0036310711 scopus 로고    scopus 로고
    • On the role of the crystal environment in determining protein side-chain conformations
    • Jacobson M.P., Friesner R.A., Xiang Z., and Honig B. On the role of the crystal environment in determining protein side-chain conformations. J. Mol. Biol. 320 (2002) 597-608
    • (2002) J. Mol. Biol. , vol.320 , pp. 597-608
    • Jacobson, M.P.1    Friesner, R.A.2    Xiang, Z.3    Honig, B.4
  • 57
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
    • Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach. Phys. Rev. E 56 (1997) 5018-5035
    • (1997) Phys. Rev. E , vol.56 , pp. 5018-5035
    • Jarzynski, C.1
  • 58
    • 0037198626 scopus 로고    scopus 로고
    • Crystal structure and mechanism of a calcium-gated potassium channel
    • Jiang Y., Lee A., Chen J., Cadene M., Chait B.T., and MacKinnon R. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417 (2002) 515-522
    • (2002) Nature , vol.417 , pp. 515-522
    • Jiang, Y.1    Lee, A.2    Chen, J.3    Cadene, M.4    Chait, B.T.5    MacKinnon, R.6
  • 61
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones D.T., Taylor W.R., and Thornton J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33 (1994) 3038-3049
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 62
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern-recognition of hydrogen-bonded and geometrical features
    • Kabsch W., and Sander C. Dictionary of protein secondary structure: Pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 63
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105 (2001) 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 64
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
    • Kolodny R., Koehl P., and Levitt M. Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol. 346 (2005) 1173-1188
    • (2005) J. Mol. Biol. , vol.346 , pp. 1173-1188
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3
  • 66
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar S., Bouzida D., Swendsen R.H., Kollman P.A., and Rosenberg J.M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comp. Chem. 13 (1992) 1011-1021
    • (1992) J. Comp. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 68
    • 0345307243 scopus 로고    scopus 로고
    • Physics of ion channels
    • Kuyucak S., and Bastug T. Physics of ion channels. J. Biol. Phys. 29 (2004) 429-446
    • (2004) J. Biol. Phys. , vol.29 , pp. 429-446
    • Kuyucak, S.1    Bastug, T.2
  • 69
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure prediction
    • Lazaridis T., and Karplus M. Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10 (2000) 139-145
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 139-145
    • Lazaridis, T.1    Karplus, M.2
  • 71
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226 (1992) 507-533
    • (1992) J. Mol. Biol. , vol.226 , pp. 507-533
    • Levitt, M.1
  • 75
    • 0035957732 scopus 로고    scopus 로고
    • Mechanisms of tetraethylammonium ion block in the KcsA potassium channel
    • Luzhkov V.B., and Åqvist J. Mechanisms of tetraethylammonium ion block in the KcsA potassium channel. FEBS Lett. 495 (2001) 191-196
    • (2001) FEBS Lett. , vol.495 , pp. 191-196
    • Luzhkov, V.B.1    Åqvist, J.2
  • 76
    • 43649094583 scopus 로고    scopus 로고
    • Distribution of amino acids in a lipid bilayer from computer simulations
    • MacCallum J.L., Bennett W.F.D., and Tieleman D.P. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94 (2008) 3393-3404
    • (2008) Biophys. J. , vol.94 , pp. 3393-3404
    • MacCallum, J.L.1    Bennett, W.F.D.2    Tieleman, D.P.3
  • 77
    • 0038440721 scopus 로고    scopus 로고
    • The role of the dielectric barrier in narrow biological channels: A novel composite approach to modeling single-channel currents
    • Mamonov A.B., Coalson R.D., Nitzan A., and Kurnikova M.G. The role of the dielectric barrier in narrow biological channels: A novel composite approach to modeling single-channel currents. Biophys. J. 84 (2003) 3646-3661
    • (2003) Biophys. J. , vol.84 , pp. 3646-3661
    • Mamonov, A.B.1    Coalson, R.D.2    Nitzan, A.3    Kurnikova, M.G.4
  • 78
    • 1842559320 scopus 로고    scopus 로고
    • Alignment of protein sequences by their profiles
    • Marti-Renom M.A., Madhusudhan M.S., and Sali A. Alignment of protein sequences by their profiles. Protein Sci. 13 (2004) 1071-1087
    • (2004) Protein Sci. , vol.13 , pp. 1071-1087
    • Marti-Renom, M.A.1    Madhusudhan, M.S.2    Sali, A.3
  • 79
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt E.A., and Bacon D.J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 80
    • 0038112088 scopus 로고    scopus 로고
    • Structure and gating mechanism of the acetylcholine receptor pore
    • Miyazawa A., Fujiyoshi Y., and Unwin N. Structure and gating mechanism of the acetylcholine receptor pore. Nature 423 (2003) 949-955
    • (2003) Nature , vol.423 , pp. 949-955
    • Miyazawa, A.1    Fujiyoshi, Y.2    Unwin, N.3
  • 83
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • Moult J. A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 15 (2005) 285-289
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 285-289
    • Moult, J.1
  • 84
    • 0034106946 scopus 로고    scopus 로고
    • Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics
    • Moy G., Corry B., Kuyucak S., and Chung S.H. Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics. Biophys. J. 78 (2000) 2349-2363
    • (2000) Biophys. J. , vol.78 , pp. 2349-2363
    • Moy, G.1    Corry, B.2    Kuyucak, S.3    Chung, S.H.4
  • 85
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 86
    • 34548386717 scopus 로고    scopus 로고
    • Crystal structure of a Kir3.1-prokaryotic Kir channel chimera
    • Nishida M., Cadene M., Chait B.T., and MacKinnon R. Crystal structure of a Kir3.1-prokaryotic Kir channel chimera. EMBO J. 26 (2007) 4005-4015
    • (2007) EMBO J. , vol.26 , pp. 4005-4015
    • Nishida, M.1    Cadene, M.2    Chait, B.T.3    MacKinnon, R.4
  • 87
    • 7244251461 scopus 로고    scopus 로고
    • Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
    • Noskov S.Y., Bernèche S., and Roux B. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834
    • (2004) Nature , vol.431 , pp. 830-834
    • Noskov, S.Y.1    Bernèche, S.2    Roux, B.3
  • 88
    • 33750609826 scopus 로고    scopus 로고
    • Ion selectivity in potassium channels
    • Noskov S.Y., and Roux B. Ion selectivity in potassium channels. Biophys. Chem. 124 (2006) 279-291
    • (2006) Biophys. Chem. , vol.124 , pp. 279-291
    • Noskov, S.Y.1    Roux, B.2
  • 89
    • 33846625994 scopus 로고    scopus 로고
    • Importance of hydration and dynamics on the selectivity of the kcsa and nak channels
    • Noskov S.Y., and Roux B. Importance of hydration and dynamics on the selectivity of the kcsa and nak channels. J. Gen. Physiol. 129 (2007) 135-143
    • (2007) J. Gen. Physiol. , vol.129 , pp. 135-143
    • Noskov, S.Y.1    Roux, B.2
  • 91
    • 0019707626 scopus 로고
    • Polymorphic transitions in single-crystals-A new molecular-dynamics method
    • Parrinello M., and Rahman A. Polymorphic transitions in single-crystals-A new molecular-dynamics method. J. Appl. Phys. 52 (1981) 7182-7190
    • (1981) J. Appl. Phys. , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 92
    • 0029633186 scopus 로고
    • Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman D.A., Case D.A., Caldwell J.W., Ross W.S., Cheatham T.E., Debolt S., Ferguson D., Seibel G., and Kollman P. Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91 (1995) 1-41
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 93
    • 0000008625 scopus 로고    scopus 로고
    • Free energy calculations: Methods and applications
    • von Ragué Schleyer P. (Ed), Wiley, Chichester
    • Pearlman D.A., and Rao B.G. Free energy calculations: Methods and applications. In: von Ragué Schleyer P. (Ed). Encyclopedia of Computational Chemistry (1999), Wiley, Chichester 1036-1061
    • (1999) Encyclopedia of Computational Chemistry , pp. 1036-1061
    • Pearlman, D.A.1    Rao, B.G.2
  • 94
    • 29144526714 scopus 로고    scopus 로고
    • Protein structure prediction: Inroads to biology
    • Petrey D., and Honig B. Protein structure prediction: Inroads to biology. Mol. Cell 20 (2005) 811-819
    • (2005) Mol. Cell , vol.20 , pp. 811-819
    • Petrey, D.1    Honig, B.2
  • 96
    • 33746907422 scopus 로고    scopus 로고
    • Towards accurate solvation dynamics of divalent cations in water using the polarizable AMOEBA force field: From energetics to structure
    • Piquemal J.P., Perera L., Cisneros G.A., Ren P., Pedersen L.G., and Darden T.A. Towards accurate solvation dynamics of divalent cations in water using the polarizable AMOEBA force field: From energetics to structure. J. Chem. Phys. 125 (2006) 054511
    • (2006) J. Chem. Phys. , vol.125 , pp. 054511
    • Piquemal, J.P.1    Perera, L.2    Cisneros, G.A.3    Ren, P.4    Pedersen, L.G.5    Darden, T.A.6
  • 98
    • 17044382128 scopus 로고    scopus 로고
    • Enhancing the accuracy, the efficiency and the scope of free energy simulations
    • Rodinger T., and Pomès R. Enhancing the accuracy, the efficiency and the scope of free energy simulations. Curr. Opin. Struct. Biol. 15 (2005) 164-170
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 164-170
    • Rodinger, T.1    Pomès, R.2
  • 99
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux B. The calculation of the potential of mean force using computer simulations. Comp. Phys. Commun. 91 (1995) 275-282
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 100
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327
    • (1977) J. Comput. Phys. , vol.23 , pp. 327
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 101
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Šali A., and Blundell T.L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Šali, A.1    Blundell, T.L.2
  • 102
    • 11144342719 scopus 로고    scopus 로고
    • Atomistic simulations of biologically realistic transmembrane potential gradients
    • Sachs J.N., Crozier P.S., and Woolf T.B. Atomistic simulations of biologically realistic transmembrane potential gradients. J. Chem. Phys. 121 (2004) 10847-10851
    • (2004) J. Chem. Phys. , vol.121 , pp. 10847-10851
    • Sachs, J.N.1    Crozier, P.S.2    Woolf, T.B.3
  • 103
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede T., Kopp J., Guex N., and Peitsch M.C. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31 (2003) 3381-3385
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 106
    • 17744375780 scopus 로고    scopus 로고
    • Structural similarity to bridge sequence space: Finding new families on the bridges
    • Shah P.K., Aloy P., Bork P., and Russell R.B. Structural similarity to bridge sequence space: Finding new families on the bridges. Protein Sci. 14 (2005) 1305-1314
    • (2005) Protein Sci. , vol.14 , pp. 1305-1314
    • Shah, P.K.1    Aloy, P.2    Bork, P.3    Russell, R.B.4
  • 108
    • 22244439883 scopus 로고    scopus 로고
    • Assessing strategies for improved superfamily recognition
    • Sillitoe I., Dibley M., Bray J., Addou S., and Orengo C. Assessing strategies for improved superfamily recognition. Protein Sci. 14 (2005) 1800-1810
    • (2005) Protein Sci. , vol.14 , pp. 1800-1810
    • Sillitoe, I.1    Dibley, M.2    Bray, J.3    Addou, S.4    Orengo, C.5
  • 109
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • 262
    • Sippl M.J. Recognition of errors in three-dimensional structures of proteins. Proteins: Struct. Func. Genet. 17 (1993) 355 262
    • (1993) Proteins: Struct. Func. Genet. , vol.17 , pp. 355
    • Sippl, M.J.1
  • 110
    • 0031042584 scopus 로고    scopus 로고
    • A novel method for structure-based prediction of ion channel conductance properties
    • Smart O.S., Breed J., Smith G.R., and Sansom M.S.P. A novel method for structure-based prediction of ion channel conductance properties. Biophys. J. 72 (1997) 1109-1126
    • (1997) Biophys. J. , vol.72 , pp. 1109-1126
    • Smart, O.S.1    Breed, J.2    Smith, G.R.3    Sansom, M.S.P.4
  • 111
    • 0001433241 scopus 로고
    • Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
    • Sutcliffe M.J., Haneef I., Carney D., and Blundell T.L. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1 (1987) 377-384
    • (1987) Protein Eng. , vol.1 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 112
    • 62949137785 scopus 로고    scopus 로고
    • Ion channel gates: Comparative analysis of energy barriers
    • doi:10.1007/S00249-008-0377-x
    • Tai K., Haider S., Grottesi A., and Sansom M.S.P. Ion channel gates: Comparative analysis of energy barriers. Eur. Biophys. J. (2008) doi:10.1007/S00249-008-0377-x
    • (2008) Eur. Biophys. J.
    • Tai, K.1    Haider, S.2    Grottesi, A.3    Sansom, M.S.P.4
  • 113
    • 0344873345 scopus 로고    scopus 로고
    • On the role of structural information in remote homology detection and sequence alignment: New methods using hybrid sequence profiles
    • Tang C.L., Xie L., Koh I.Y., Posy S., Alexov E., and Honig B. On the role of structural information in remote homology detection and sequence alignment: New methods using hybrid sequence profiles. J. Mol. Biol. 334 (2003) 1043-1062
    • (2003) J. Mol. Biol. , vol.334 , pp. 1043-1062
    • Tang, C.L.1    Xie, L.2    Koh, I.Y.3    Posy, S.4    Alexov, E.5    Honig, B.6
  • 115
    • 35348997382 scopus 로고    scopus 로고
    • The predominant role or coordination number in potassium channel selectivity
    • Thomas M., Jayatilaka D., and Corry B. The predominant role or coordination number in potassium channel selectivity. Biophys. J. 93 (2007) 2635-2643
    • (2007) Biophys. J. , vol.93 , pp. 2635-2643
    • Thomas, M.1    Jayatilaka, D.2    Corry, B.3
  • 116
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte-Carlo free energy distributions: Umbrella sampling
    • Torrie G.M., and Valleau J.P. Nonphysical sampling distributions in Monte-Carlo free energy distributions: Umbrella sampling. J. Comp. Phys. 23 (1977) 187-199
    • (1977) J. Comp. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 117
    • 33751229926 scopus 로고    scopus 로고
    • + conduction in the selectivity filter of potassium channels is monitored by the charge distribution along their sequence
    • + conduction in the selectivity filter of potassium channels is monitored by the charge distribution along their sequence. Biophys. J. 91 (2006) L81-L83
    • (2006) Biophys. J. , vol.91
    • Treptow, W.1    Tarek, M.2
  • 118
    • 33746725967 scopus 로고    scopus 로고
    • Molecular restraints in the permeation pathway of ion channels
    • Treptow W., and Tarek M. Molecular restraints in the permeation pathway of ion channels. Biophys. J. 91 (2006) L26-L28
    • (2006) Biophys. J. , vol.91
    • Treptow, W.1    Tarek, M.2
  • 119
    • 13444271681 scopus 로고    scopus 로고
    • Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution
    • Unwin N. Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution. J. Mol. Biol. 346 (2005) 967-989
    • (2005) J. Mol. Biol. , vol.346 , pp. 967-989
    • Unwin, N.1
  • 121
    • 34548262701 scopus 로고    scopus 로고
    • Tuning ion coordination architectures to enable selective partitioning
    • Varma S., and Rempe S.B. Tuning ion coordination architectures to enable selective partitioning. Biophys. J. 93 (2007) 1093-1099
    • (2007) Biophys. J. , vol.93 , pp. 1093-1099
    • Varma, S.1    Rempe, S.B.2
  • 122
    • 38049095537 scopus 로고    scopus 로고
    • + selectivity in K channels and valinomycin: Over-coordination versus cavity-size constraints
    • + selectivity in K channels and valinomycin: Over-coordination versus cavity-size constraints. J. Mol. Biol. 376 (2008) 13-22
    • (2008) J. Mol. Biol. , vol.376 , pp. 13-22
    • Varma, S.1    Sabo, D.2    Rempe, S.B.3
  • 123
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms
    • Wallin E., and von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms. Protien Sci. 7 (1998) 1029-1038
    • (1998) Protien Sci. , vol.7 , pp. 1029-1038
    • Wallin, E.1    von Heijne, G.2
  • 124
    • 33845985262 scopus 로고    scopus 로고
    • SGTx1, a Kv channel gating-modifier toxin, binds to the interfacial region of lipid bilayers
    • Wee C.L., Bemporad D., Sands Z.A., Gavaghan D., and Sansom M.S.P. SGTx1, a Kv channel gating-modifier toxin, binds to the interfacial region of lipid bilayers. Biophys. J. 92 (2007) L07-L09
    • (2007) Biophys. J. , vol.92
    • Wee, C.L.1    Bemporad, D.2    Sands, Z.A.3    Gavaghan, D.4    Sansom, M.S.P.5
  • 126
    • 0031176369 scopus 로고    scopus 로고
    • Use of the Poisson-Boltzmann equation to estimate the electrostatic free energy barrier for dielectric models of biological ion channels
    • Weetman P., Goldman S., and Gray C.G. Use of the Poisson-Boltzmann equation to estimate the electrostatic free energy barrier for dielectric models of biological ion channels. J. Phys. Chem. 101 (1997) 6073-6078
    • (1997) J. Phys. Chem. , vol.101 , pp. 6073-6078
    • Weetman, P.1    Goldman, S.2    Gray, C.G.3
  • 127
    • 84986518863 scopus 로고
    • AMBER-assisted model-building with energy refinement-a general program for modeling molecules and their interactions
    • Weiner P.K., and Kollman P.A. AMBER-assisted model-building with energy refinement-a general program for modeling molecules and their interactions. J. Comp. Chem. 2 (1981) 287-303
    • (1981) J. Comp. Chem. , vol.2 , pp. 287-303
    • Weiner, P.K.1    Kollman, P.A.2
  • 128
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations
    • Xiang Z.X., and Honig B. Extending the accuracy limits of prediction for side-chain conformations. J. Mol. Biol. 311 (2001) 421-430
    • (2001) J. Mol. Biol. , vol.311 , pp. 421-430
    • Xiang, Z.X.1    Honig, B.2


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