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Volumn 96, Issue 10, 2009, Pages 4006-4012

Importance of the peptide backbone description in modeling the selectivity filter in potassium channels

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL DERIVATIVE; POTASSIUM CHANNEL KCSA; POTASSIUM CHANNEL KV1.2; SHAKER POTASSIUM CHANNEL; UNCLASSIFIED DRUG; PEPTIDE;

EID: 68049122041     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.02.041     Document Type: Article
Times cited : (22)

References (35)
  • 1
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
    • MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
  • 2
    • 0038054912 scopus 로고    scopus 로고
    • Force field influence on the observation of p-helical protein structures in molecular dynamics simulations
    • Feig, A., A. D. MacKerell, Jr., and C. L. Brooks. 2003. Force field influence on the observation of p-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B. 107:2831-2836.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 2831-2836
    • Feig, A.1    MacKerell Jr., A.D.2    Brooks, C.L.3
  • 3
    • 1642576012 scopus 로고    scopus 로고
    • Improved treatment of the protein backbone in empirical force fields
    • MacKerell, A. D., M. Feig, and C. L. Brooks. 2004. Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 126:698-699.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 698-699
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 4
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • MacKerell, A. D., M. Feig, and C. L. Brooks. 2004. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.
    • (2004) J. Comput. Chem , vol.25 , pp. 1400-1415
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 5
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • MacKerell, A. D. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25:1584-1606.
    • (2004) J. Comput. Chem , vol.25 , pp. 1584-1606
    • MacKerell, A.D.1
  • 6
    • 33645786604 scopus 로고    scopus 로고
    • Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme
    • Buck, M., S. Bouguet-Bonnet, R. W. Friesner, and A. D. MacKerell, Jr. 2006. Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys. J. 90:L36-L38.
    • (2006) Biophys. J , vol.90
    • Buck, M.1    Bouguet-Bonnet, S.2    Friesner, R.W.3    MacKerell Jr., A.D.4
  • 7
    • 23044465669 scopus 로고    scopus 로고
    • Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties
    • Li, X. F., S. A. Hassan, and E. L. Mehler. 2005. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties. Proteins. 60:464-484.
    • (2005) Proteins , vol.60 , pp. 464-484
    • Li, X.F.1    Hassan, S.A.2    Mehler, E.L.3
  • 8
    • 10344264957 scopus 로고    scopus 로고
    • Exploring peptide energy landscapes: A test of force fields and implicit solvent models
    • Steinbach, P. J. 2004. Exploring peptide energy landscapes: a test of force fields and implicit solvent models. Proteins. 57:665-677.
    • (2004) Proteins , vol.57 , pp. 665-677
    • Steinbach, P.J.1
  • 9
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple AMBER force fields and development of improved protein backbone parameters
    • Hornak, V., R. Abel, A. Okur, B. Strockbine, A. Roitberg, et al. 2006. Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins. 65:712-725.
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5
  • 12
    • 0035705881 scopus 로고    scopus 로고
    • Simulation approaches to ion channel structure-function relationships
    • Tieleman, D. P., P. C. Biggin, G. R. Smith, and M. S. P. Sansom. 2001. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34:473-561.
    • (2001) Q. Rev. Biophys , vol.34 , pp. 473-561
    • Tieleman, D.P.1    Biggin, P.C.2    Smith, G.R.3    Sansom, M.S.P.4
  • 13
    • 3142652094 scopus 로고    scopus 로고
    • Theoretical and computational models of biological ion channels
    • Roux, B., T. Allen, S. Bernèche, and W. Im. 2004. Theoretical and computational models of biological ion channels. Q. Rev. Biophys. 37:15-103.
    • (2004) Q. Rev. Biophys , vol.37 , pp. 15-103
    • Roux, B.1    Allen, T.2    Bernèche, S.3    Im, W.4
  • 15
    • 34547092180 scopus 로고    scopus 로고
    • Molecular dynamics simulations of potassium channels
    • Domene, C. 2007. Molecular dynamics simulations of potassium channels. Cent. Eur. J. Chem. 5:653-671.
    • (2007) Cent. Eur. J. Chem , vol.5 , pp. 653-671
    • Domene, C.1
  • 18
    • 0034730689 scopus 로고    scopus 로고
    • A computational study of ion binding and protonation states in the KcsA potassium channel
    • Luzhkov, V. B., and J. Aqvist. 2000. A computational study of ion binding and protonation states in the KcsA potassium channel. Biochim. Biophys. Acta. 1481:360-370.
    • (2000) Biochim. Biophys. Acta , vol.1481 , pp. 360-370
    • Luzhkov, V.B.1    Aqvist, J.2
  • 22
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics: The Langevin piston method
    • Feller, S., Y. Zhang, R. Pastor, and B. Brooks. 1995. Constant pressure molecular dynamics: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys , vol.103 , pp. 4613-4621
    • Feller, S.1    Zhang, Y.2    Pastor, R.3    Brooks, B.4
  • 23
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge, D. L., and F. M. DiCapua. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-492.
    • (1989) Annu. Rev. Biophys. Biophys. Chem , vol.18 , pp. 431-492
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 24
    • 33744944511 scopus 로고    scopus 로고
    • Energetics of ion permeation, rejection, binding and block in gramicidin A from free energy simulations
    • Bastug, T., and S. Kuyucak. 2006. Energetics of ion permeation, rejection, binding and block in gramicidin A from free energy simulations. Biophys. J. 90:3941-3950.
    • (2006) Biophys. J , vol.90 , pp. 3941-3950
    • Bastug, T.1    Kuyucak, S.2
  • 25
    • 17044400911 scopus 로고    scopus 로고
    • A gate in the selectivity filter of potassium channels
    • Berneche, S., and B. Roux. 2005. A gate in the selectivity filter of potassium channels. Structure. 13:591-600.
    • (2005) Structure , vol.13 , pp. 591-600
    • Berneche, S.1    Roux, B.2
  • 26
    • 7244251461 scopus 로고    scopus 로고
    • Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
    • Noskov, S. Y., S. Berneche, and B. Roux. 2004. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature. 431:830-834.
    • (2004) Nature , vol.431 , pp. 830-834
    • Noskov, S.Y.1    Berneche, S.2    Roux, B.3
  • 29
    • 33750609826 scopus 로고    scopus 로고
    • Ion selectivity in potassium channels
    • Noskov, S. Y., and B. Roux. 2006. Ion selectivity in potassium channels. Biophys. Chem. 124:279-291.
    • (2006) Biophys. Chem , vol.124 , pp. 279-291
    • Noskov, S.Y.1    Roux, B.2
  • 30
    • 33746094645 scopus 로고    scopus 로고
    • Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity
    • Asthagiri, D., L. R. Pratt, and M. E. Paulaitis. 2006. Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity. J. Chem. Phys. 125:024701.
    • (2006) J. Chem. Phys , vol.125 , pp. 024701
    • Asthagiri, D.1    Pratt, L.R.2    Paulaitis, M.E.3
  • 31
    • 34250333069 scopus 로고    scopus 로고
    • + channels is due to topological control of the permeant ion's coordinated state
    • + channels is due to topological control of the permeant ion's coordinated state. Proc. Natl. Acad. Sci. USA. 104:9260-9265.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 9260-9265
    • Bostick, D.L.1    Brooks, C.L.2
  • 32
    • 35348997382 scopus 로고    scopus 로고
    • The predominant role of coordination number in potassium channel selectivity
    • Thomas, M., D. Jayatilaka, and B. Corry. 2007. The predominant role of coordination number in potassium channel selectivity. Biophys. J. 93:2635-2643.
    • (2007) Biophys. J , vol.93 , pp. 2635-2643
    • Thomas, M.1    Jayatilaka, D.2    Corry, B.3
  • 33
    • 34548262701 scopus 로고    scopus 로고
    • Tuning ion coordination architectures to enable selective partitioning
    • Varma, S., and S. B. Rempe. 2007. Tuning ion coordination architectures to enable selective partitioning. Biophys. J. 93:1093-1099.
    • (2007) Biophys. J , vol.93 , pp. 1093-1099
    • Varma, S.1    Rempe, S.B.2
  • 34
    • 33746725967 scopus 로고    scopus 로고
    • Molecular restraints in the permeation pathway of ion channels
    • Treptow, W., and M. Tarek. 2006. Molecular restraints in the permeation pathway of ion channels. Biophys. J. 91:26-28.
    • (2006) Biophys. J , vol.91 , pp. 26-28
    • Treptow, W.1    Tarek, M.2
  • 35
    • 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. 91:81-83.
    • (2006) Biophys. J , vol.91 , pp. 81-83
    • Treptow, W.1    Tarek, M.2


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