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Volumn 95, Issue 8, 2008, Pages 3850-3860

Generation, comparison, and merging of pathways between protein conformations: Gating in K-channels

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; POTASSIUM CHANNEL; PROKARYOTIC POTASSIUM CHANNEL;

EID: 56049102616     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.135285     Document Type: Article
Times cited : (16)

References (54)
  • 6
    • 23244456428 scopus 로고    scopus 로고
    • Crystal structure of a mammalian voltage-dependent Shaker family K1 channel
    • Long, S. B., E. B. Campbell, and R. Mackinnon. 2005. Crystal structure of a mammalian voltage-dependent Shaker family K1 channel. Science. 309:897-903.
    • (2005) Science , vol.309 , pp. 897-903
    • Long, S.B.1    Campbell, E.B.2    Mackinnon, R.3
  • 8
    • 23244441222 scopus 로고    scopus 로고
    • Voltage sensor of Kv1.2: Structural basis of electromechanical coupling
    • Long, S. B., E. B. Campbell, and R. Mackinnon. 2005. Voltage sensor of Kv1.2: structural basis of electromechanical coupling. Science. 309:903-908.
    • (2005) Science , vol.309 , pp. 903-908
    • Long, S.B.1    Campbell, E.B.2    Mackinnon, R.3
  • 9
    • 34548386717 scopus 로고    scopus 로고
    • Crystal structure of a Kir3.1-prokaryotic Kir channel chimera
    • Nishida, M., M. Cadene, B. T. Chait, and R. MacKinnon. 2007. Crystal structure of a Kir3.1-prokaryotic Kir channel chimera. EMBO J. 26:4005-4015.
    • (2007) EMBO J , vol.26 , pp. 4005-4015
    • Nishida, M.1    Cadene, M.2    Chait, B.T.3    MacKinnon, R.4
  • 11
    • 0037198626 scopus 로고    scopus 로고
    • Crystal structure and mechanism of a calcium-gated potassium channel
    • Jiang, Y., A. Lee, J. Chen, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. Crystal structure and mechanism of a calcium-gated potassium channel. Nature. 417:515-522.
    • (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
  • 13
    • 0037387189 scopus 로고    scopus 로고
    • Potassium channel gating observed with site-directed mass tagging
    • Kelly, B. L., and A. Gross. 2003. Potassium channel gating observed with site-directed mass tagging. Nat. Struct. Biol. 10:280-284.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 280-284
    • Kelly, B.L.1    Gross, A.2
  • 14
    • 33646145322 scopus 로고    scopus 로고
    • Structural characterization and pH-induced conformational transition of full-length KcsA
    • Zimmer, J., D. A. Doyle, and J. G. Grossmann. 2006. Structural characterization and pH-induced conformational transition of full-length KcsA. Biophys. J. 90:1752-1766.
    • (2006) Biophys. J , vol.90 , pp. 1752-1766
    • Zimmer, J.1    Doyle, D.A.2    Grossmann, J.G.3
  • 15
    • 33748802222 scopus 로고    scopus 로고
    • Surface structure and its dynamic rearrangements of the KcsA potassium channel upon gating and tetrabutylammonium blocking
    • Iwamoto, M., H. Shimizu, F. Inoue, T. Konno, Y. C. Sasaki, and S. Oiki. 2006. Surface structure and its dynamic rearrangements of the KcsA potassium channel upon gating and tetrabutylammonium blocking. J. Biol. Chem. 281:28379-28386.
    • (2006) J. Biol. Chem , vol.281 , pp. 28379-28386
    • Iwamoto, M.1    Shimizu, H.2    Inoue, F.3    Konno, T.4    Sasaki, Y.C.5    Oiki, S.6
  • 18
    • 36849022651 scopus 로고    scopus 로고
    • + channel: Monte Carlo normal mode following simulations
    • + channel: Monte Carlo normal mode following simulations. Structure. 15:1654-1662.
    • (2007) Structure , vol.15 , pp. 1654-1662
    • Miloshevsky, G.V.1    Jordan, P.C.2
  • 19
    • 33744926664 scopus 로고    scopus 로고
    • Common mechanism of pore opening shared by five different potassium channels
    • Shrivastava, I. H., and I. Bahar. 2006. Common mechanism of pore opening shared by five different potassium channels. Biophys. J. 90:3929-3940.
    • (2006) Biophys. J , vol.90 , pp. 3929-3940
    • Shrivastava, I.H.1    Bahar, I.2
  • 20
    • 37649021608 scopus 로고    scopus 로고
    • Global twisting motion of single molecular KcsA potassium channel upon gating
    • Shimizu, H., M. Iwamoto, T. Konno, A. Nihei, Y. C. Sasaki, and S. Oiki. 2008. Global twisting motion of single molecular KcsA potassium channel upon gating. Cell. 132:67-78.
    • (2008) Cell , vol.132 , pp. 67-78
    • Shimizu, H.1    Iwamoto, M.2    Konno, T.3    Nihei, A.4    Sasaki, Y.C.5    Oiki, S.6
  • 21
    • 0036787715 scopus 로고    scopus 로고
    • Open-state models of a potassium channel
    • Biggin, P. C., and M. S. Sansom. 2002. Open-state models of a potassium channel. Biophys. J. 83:1867-1876.
    • (2002) Biophys. J , vol.83 , pp. 1867-1876
    • Biggin, P.C.1    Sansom, M.S.2
  • 22
    • 4444261061 scopus 로고    scopus 로고
    • + channel by lateral forces applied to the C-termini of inner helices
    • + channel by lateral forces applied to the C-termini of inner helices. Biophys. J. 87:1526-1536.
    • (2004) Biophys. J , vol.87 , pp. 1526-1536
    • Tikhonov, D.B.1    Zhorov, B.S.2
  • 23
  • 24
    • 0001209809 scopus 로고    scopus 로고
    • Motion planning: A journey of robots, molecules, digital actors, and other artifacts
    • Latombe, J.-C. 1999. Motion planning: a journey of robots, molecules, digital actors, and other artifacts. Int. J. Robot. Res. 10:1119-1128.
    • (1999) Int. J. Robot. Res , vol.10 , pp. 1119-1128
    • Latombe, J.-C.1
  • 25
    • 20744432838 scopus 로고    scopus 로고
    • Algorithmic motion planning
    • 2nd ed. J. E. Goodman and J. O'Rourke, editors. CRC Press, Boca Raton
    • Sharir, M. 2004. Algorithmic motion planning. In Handbook of Discrete and Computational Geometry, 2nd ed. J. E. Goodman and J. O'Rourke, editors. CRC Press, Boca Raton. 1037-1064.
    • (2004) Handbook of Discrete and Computational Geometry , pp. 1037-1064
    • Sharir, M.1
  • 30
    • 77952010176 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge, UK
    • Lavalle, S. M. 2006. Planning Algorithms. Cambridge University Press, Cambridge, UK.
    • (2006) Planning Algorithms
    • Lavalle, S.M.1
  • 31
    • 0242438173 scopus 로고    scopus 로고
    • Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures
    • Amato, N. M., K. A. Dill, and G. Song. 2003. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. J. Comput. Biol. 10:239-255.
    • (2003) J. Comput. Biol , vol.10 , pp. 239-255
    • Amato, N.M.1    Dill, K.A.2    Song, G.3
  • 36
    • 37349101940 scopus 로고    scopus 로고
    • An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
    • Kirillova, S., J. Cortes, A. Stefaniu, and T. Simeon. 2008. An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins. Proteins. 70:131-143.
    • (2008) Proteins , vol.70 , pp. 131-143
    • Kirillova, S.1    Cortes, J.2    Stefaniu, A.3    Simeon, T.4
  • 37
    • 33846688205 scopus 로고    scopus 로고
    • Prediction and simulation of motion in pairs of transmembrane alpha-helices
    • Enosh, A., S. J. Fleishman, N. Ben-Tal, and D. Halperin. 2007. Prediction and simulation of motion in pairs of transmembrane alpha-helices. Bioinformatics. 23:e212-e218.
    • (2007) Bioinformatics , vol.23
    • Enosh, A.1    Fleishman, S.J.2    Ben-Tal, N.3    Halperin, D.4
  • 40
    • 0014129195 scopus 로고
    • Hierarchical clustering schemes
    • Johnson, S. C. 1967. Hierarchical clustering schemes. Psychometrika. 2:241-254.
    • (1967) Psychometrika , vol.2 , pp. 241-254
    • Johnson, S.C.1
  • 43
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu, A. A., A. A. Shelenkov, and R. L. Dunbrack, Jr. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12:2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 44
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang, C., O. Schueler-Furman, and D. Baker. 2005. Improved side-chain modeling for protein-protein docking. Protein Sci. 14:1328-1339.
    • (2005) Protein Sci , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 45
  • 46
    • 0000390120 scopus 로고
    • Taboo search: An approach to the multiple minima problem
    • Cvijovicacute, D., and J. Klinowski. 1995. Taboo search: an approach to the multiple minima problem. Science. 267:664-666.
    • (1995) Science , vol.267 , pp. 664-666
    • Cvijovicacute, D.1    Klinowski, J.2
  • 47
    • 33645858263 scopus 로고    scopus 로고
    • Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR
    • Lange, A., K. Giller, S. Hornig, M. F. Martin-Eauclaire, O. Pongs, S. Becker, and M. Baldus. 2006. Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR. Nature. 440:959-962.
    • (2006) Nature , vol.440 , pp. 959-962
    • Lange, A.1    Giller, K.2    Hornig, S.3    Martin-Eauclaire, M.F.4    Pongs, O.5    Becker, S.6    Baldus, M.7
  • 49
    • 4143116650 scopus 로고    scopus 로고
    • Computational studies of membrane channels
    • Roux, B., and K. Schulten. 2004. Computational studies of membrane channels. Structure. 12:1343-1351.
    • (2004) Structure , vol.12 , pp. 1343-1351
    • Roux, B.1    Schulten, K.2
  • 51
    • 35648943768 scopus 로고    scopus 로고
    • Toward high-resolution prediction and design of transmembrane helical protein structures
    • Barth, P., J. Schonbrun, and D. Baker. 2007. Toward high-resolution prediction and design of transmembrane helical protein structures. Proc. Natl. Acad. Sci. USA. 104:15682-15687.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 15682-15687
    • Barth, P.1    Schonbrun, J.2    Baker, D.3
  • 52
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink, C., A. Villa, A. E. Mark, and W. F. van Gunsteren. 2004. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25:1656-1676.
    • (2004) J. Comput. Chem , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 53
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria, E., S. Fischer, and M. Karplus. 1996. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105:1902-1921.
    • (1996) J. Chem. Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 54
    • 0037246863 scopus 로고    scopus 로고
    • MolMovDB: Analysis and visualization of conformational change and structural flexibility
    • Echols, N., D. Milburn, and M. Gerstein. 2003. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31:478-482.
    • (2003) Nucleic Acids Res , vol.31 , pp. 478-482
    • Echols, N.1    Milburn, D.2    Gerstein, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.