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Volumn 48, Issue 36, 2009, Pages 8758-8763

Ion-blocking sites of the Kir2.1 channel revealed by multiscale modeling

Author keywords

[No Author keywords available]

Indexed keywords

BLOCKING SITES; CYTOPLASMIC DOMAINS; EN-ROUTE; INTERACTION SITE; INTRACELLULAR DOMAIN; INWARD-RECTIFYING; MOLECULAR DYNAMICS SIMULATIONS; MULTI-SCALE MODELING; MULTIVALENT IONS; POTASSIUM CHANNELS;

EID: 70149115914     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9007808     Document Type: Article
Times cited : (13)

References (43)
  • 3
    • 0037932785 scopus 로고    scopus 로고
    • Electrophysiological remodeling in human atrial fibrillation
    • van Wagoner, D. R. (2003) Electrophysiological remodeling in human atrial fibrillation. Pacing Clin. Electrophysiol. 26 (Part 2), 1572-1575.
    • (2003) Pacing Clin. Electrophysiol. , vol.26 , Issue.PART 2 , pp. 1572-1575
    • Van Wagoner, D.R.1
  • 4
    • 0242667036 scopus 로고    scopus 로고
    • Spermine is fit to block inward rectifier (Kir) channels
    • Stanfield, P. R., and Sutcliffe, M. J. (2003) Spermine is fit to block inward rectifier (Kir) channels. J. Gen. Physiol. 2003, 481-484.
    • (2003) J. Gen. Physiol. 2003 , pp. 481-484
    • Stanfield, P.R.1    Sutcliffe, M.J.2
  • 5
    • 0028227239 scopus 로고
    • A single aspartate residue is involved in both intrinsic gating and blockage by Mg2+ of the inward rectified, IRK1
    • Stanfield, P. R., Davies, N. W., Shelton, P. A., Sutcliffe, M. J., Khan, I. A., Brammar, W. J., and Conley, E. C. (1994) A single aspartate residue is involved in both intrinsic gating and blockage by Mg2+ of the inward rectified, IRK1. J. Physiol. 478, 1-6.
    • (1994) J. Physiol. , vol.478 , pp. 1-6
    • Stanfield, P.R.1    Davies, N.W.2    Shelton, P.A.3    Sutcliffe, M.J.4    Khan, I.A.5    Brammar, W.J.6    Conley, E.C.7
  • 6
    • 26444584556 scopus 로고    scopus 로고
    • Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography
    • DOI 10.1016/j.str.2005.07.011, PII S0969212605002704
    • Kuo, A. L., Domene, C., Johnson, L. N., Doyle, D. A., and Vénien-Bryan, C. (2005) Two different conformational states of the Kir-Bac3.1 potassium channel revealed by electron crystallography. Structure 13, 1463-1472. (Pubitemid 41427586)
    • (2005) Structure , vol.13 , Issue.10 , pp. 1463-1472
    • Kuo, A.1    Domene, C.2    Johnson, L.N.3    Doyle, D.A.4    Venien-Bryan, C.5
  • 7
    • 33746047139 scopus 로고    scopus 로고
    • Andersen's syndrome mutation effects on the structure and assembly of the cytoplasmic domains of Kir2.1
    • DOI 10.1021/bi060653d
    • Pegan, S., Arrabit, C., Slesinger, P. A., and Choe, S. (2006) Andersen's syndrome mutation effects on the structure and sssembly of the cytoplasmic domains of Kir2.1. Biochemistry 45, 8599-8606. (Pubitemid 44078880)
    • (2006) Biochemistry , vol.45 , Issue.28 , pp. 8599-8606
    • Pegan, S.1    Arrabit, C.2    Slesinger, P.A.3    Choe, S.4
  • 8
    • 14544298750 scopus 로고    scopus 로고
    • Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification
    • Pegan, S., Arrabit, C., Zhou, W., Kwiatkowski, W., Collins, A., Slesinger, P. A., and Choe, S. (2005) Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification. Nat. Neurosci. 8, 279-287.
    • (2005) Nat. Neurosci. , vol.8 , pp. 279-287
    • Pegan, S.1    Arrabit, C.2    Zhou, W.3    Kwiatkowski, W.4    Collins, A.5    Slesinger, P.A.6    Choe, S.7
  • 9
    • 33947709389 scopus 로고    scopus 로고
    • Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: A comparative study
    • DOI 10.1021/bi062210f
    • Haider, S., Khalid, S., Tucker, S. J., Ashcroft, F. M., and Sansom, M. S. P. (2007) Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study. Biochemistry 46, 3643-3652. (Pubitemid 46493465)
    • (2007) Biochemistry , vol.46 , Issue.12 , pp. 3643-3652
    • Haider, S.1    Khalid, S.2    Tucker, S.J.3    Ashcroft, F.M.4    Sansom, M.S.P.5
  • 10
    • 34548386717 scopus 로고    scopus 로고
    • Crystal structure of a Kir3.1-prokaryotic Kir channel chimera
    • DOI 10.1038/sj.emboj.7601828, PII 7601828
    • Nishida, M., Cadene, M., Chait, B. T., and MacKinnon, R. (2007) Crystal structure of a Kir3.1-prokaryotic Kir channel chimera. EMBO J. 26, 4005-4015. (Pubitemid 47367496)
    • (2007) EMBO Journal , vol.26 , Issue.17 , pp. 4005-4015
    • Nishida, M.1    Cadene, M.2    Chait, B.T.3    MacKinnon, R.4
  • 12
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 14
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 16
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt, G. J., and Jones, T. A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D50, 178-185.
    • (1994) Acta Crystallogr , vol.D50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 19
    • 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. (2004) Not ions alone: Barriers to ion permeation in nanopores and channels. J. Am. Chem. Soc. 126, 14694-14695.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 14694-14695
    • Beckstein, O.1    Tai, K.2    Sansom, M.S.P.3
  • 20
    • 0030404988 scopus 로고    scopus 로고
    • HOLE: A program for the analysis of the pore dimensions of ion channel structural models
    • DOI 10.1016/S0263-7855(97)00009-X, PII S026378559700009X
    • Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A., and Sansom, M. S. P. (1996) HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graphics 14, 354-360. (Pubitemid 27302826)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.6 , pp. 354-360
    • Smart, O.S.1    Neduvelil, J.G.2    Wang, X.3    Wallace, B.A.4    Sansom, M.S.P.5
  • 21
    • 33749223814 scopus 로고
    • Reevaluation of the Born model of ion hydration
    • Rashin, A. A., and Honig, B. (1985) Reevaluation of the Born model of ion hydration. J. Phys. Chem. 89, 5588-5593.
    • (1985) J. Phys. Chem. , vol.89 , pp. 5588-5593
    • Rashin, A.A.1    Honig, B.2
  • 22
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., and Baker, N. A. (2004) PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665-W667.
    • (2004) Nucleic Acids Res. , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 23
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J., Cieplak, P., and Kollman, P. A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049-1074.
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 25
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • Bond, P. J., Holyoake, J., Ivetac, A., Khalid, S., and Sansom, M. S. P. (2007) Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 157, 593-605.
    • (2007) J. Struct. Biol. , vol.157 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivetac, A.3    Khalid, S.4    Sansom, M.S.P.5
  • 27
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log N method for Ewald sums in large systems
    • Darden, T., York, D., and Pedersen, L. (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
  • 31
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
    • Schuettelkopf, A. W., and van Aalten, D. M. F. (2004) PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D60, 1355-1363.
    • (2004) Acta Crystallogr , vol.D60 , pp. 1355-1363
    • Schuettelkopf, A.W.1    Van Aalten, D.M.F.2
  • 32
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127-134.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 33
    • 0025398721 scopus 로고
    • WHAT IF. a molecular modeling and drug design program
    • DOI 10.1016/0263-7855(90)80070-V
    • Vriend, G. (1990) WHAT IF: A molecular modeling and drug design program. J. Mol. Graphics 8, 52-56. (Pubitemid 20717037)
    • (1990) Journal of Molecular Graphics , vol.8 , Issue.1 , pp. 52-56
    • Vriend, G.1
  • 34
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and and empirical binding free energy function
    • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998) Automated docking using a Lamarckian genetic algorithm and and empirical binding free energy function. J. Comput. Chem. 19, 1639-1662.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 35
    • 59649091228 scopus 로고    scopus 로고
    • Long-pore electrostatics in inward-rectifier potassium channels
    • Robertson, J. L., Palmer, L. G., and Roux, B. (2008) Long-pore electrostatics in inward-rectifier potassium channels. J. Gen. Physiol. 132, 613-632.
    • (2008) J. Gen. Physiol. , vol.132 , pp. 613-632
    • Robertson, J.L.1    Palmer, L.G.2    Roux, B.3
  • 36
    • 34547621771 scopus 로고    scopus 로고
    • The role of the cytoplasmic pore in inward rectification of Kir2.1 channels
    • Kurata, H. T., Cheng, W. W., Arrabit, C., Slesinger, P. A., and Nichols, C. G. (2007) The role of the cytoplasmic pore in inward rectification of Kir2.1 channels. J. Gen. Physiol. 130, 145-155.
    • (2007) J. Gen. Physiol. , vol.130 , pp. 145-155
    • Kurata, H.T.1    Cheng, W.W.2    Arrabit, C.3    Slesinger, P.A.4    Nichols, C.G.5
  • 37
    • 0028857962 scopus 로고
    • The mechanism of inward rectification of potassium channels: "long-pore plugging" by cytoplasmic polyamines
    • Lopatin, A. N., Makhina, E. N., and Nichols, C. G. (1995) The mechanism of inward rectification of potassium channels: "long-pore plugging" by cytoplasmic polyamines. J. Gen. Physiol. 106, 923-955.
    • (1995) J. Gen. Physiol. , vol.106 , pp. 923-955
    • Lopatin, A.N.1    Makhina, E.N.2    Nichols, C.G.3
  • 40
    • 13344262697 scopus 로고
    • Determination of the subunit stoichiometry of an inwardly rectifying potassium channel
    • DOI 10.1016/0896-6273(95)90021-7
    • Yang, J., Jan, Y. N., and Jan, L. Y. (1995) Determination of the subunit stoichiometry of an inwardly rectifying potassium channel. Neuron 15, 1441-1447. (Pubitemid 26005380)
    • (1995) Neuron , vol.15 , Issue.6 , pp. 1441-1447
    • Yang, J.1    Jan, Y.N.2    Jan, L.Y.3
  • 41
    • 0036020151 scopus 로고    scopus 로고
    • Spermine block of the strong inward rectifier potassium channel Kir2.1: Dual roles of surface charge screening and pore block
    • Xie, L.-H., John, S. A., and Weiss, J. N. (2002) Spermine block of the strong inward rectifier potassium channel Kir2.1: dual roles of surface charge screening and pore block. J. Gen. Physiol. 120, 53-66.
    • (2002) J. Gen. Physiol. , vol.120 , pp. 53-66
    • Xie, L.-H.1    John, S.A.2    Weiss, J.N.3
  • 43
    • 33645325379 scopus 로고    scopus 로고
    • Functional roles of charged amino acid residues on the wall of the cytoplasmic pore of Kir2.1
    • Fujiwara, Y., and Kubo, Y. (2006) Functional roles of charged amino acid residues on the wall of the cytoplasmic pore of Kir2.1. J. Gen. Physiol. 127, 401-419.
    • (2006) J. Gen. Physiol. , vol.127 , pp. 401-419
    • Fujiwara, Y.1    Kubo, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.