메뉴 건너뛰기




Volumn 1838, Issue 9, 2014, Pages 2319-2325

Free energy analysis of conductivity and charge selectivity of M2GlyR-derived synthetic channels

Author keywords

Anion selectivity; Cystic fibrosis; Ion channels; Molecular dynamics; Peptide design; Potential of mean force

Indexed keywords

CHLORIDE ION; GLYCINE RECEPTOR; POTASSIUM ION; PROLYLALANYLARGINYLVALYLGLYCYLLEUCYLGLYCYLISOLEUCYLTHREONYLTHREONYLVALYLLEUCYLTHREONYLMETHIONYLTHREONYLTHREONYLGLUTAMINYLSERYLSERYLGLYCYLSERYLARGINYLALANINE; THREONINE; UNCLASSIFIED DRUG;

EID: 84903770867     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2014.02.016     Document Type: Article
Times cited : (5)

References (47)
  • 1
    • 15244355046 scopus 로고    scopus 로고
    • Fifty years of progress in ion channel research
    • DOI 10.1109/TNB.2004.842467
    • P.C. Jordan Fifty years of progress in ion channel research IEEE Trans. Nanobioscience 4 2005 3 9 (Pubitemid 40384642)
    • (2005) IEEE Transactions on Nanobioscience , vol.4 , Issue.1 , pp. 3-9
    • Jordan, P.C.1
  • 2
    • 31944452776 scopus 로고    scopus 로고
    • Mechanisms of valence selectivity in biological ion channels
    • DOI 10.1007/s00018-005-5405-8
    • B. Corry, and S.H. Chung Mechanisms of valence selectivity in biological ion channels Cell. Mol. Life Sci. 63 2006 301 315 (Pubitemid 43202312)
    • (2006) Cellular and Molecular Life Sciences , vol.63 , Issue.3 , pp. 301-315
    • Corry, B.1    Chung, S.-H.2
  • 3
    • 0027162649 scopus 로고
    • Molecular mechanisms of CFTR chloride channel dysfunction in cystic fibrosis
    • DOI 10.1016/0092-8674(93)90353-R
    • M.J. Welsh, and A.E. Smith Molecular mechanisms of CFTR chloride channel dysfunction in cystic-fibrosis Cell 73 1993 1251 1254 (Pubitemid 23201140)
    • (1993) Cell , vol.73 , Issue.7 , pp. 1251-1254
    • Welsh, M.J.1    Smith, A.E.2
  • 4
    • 33947495204 scopus 로고    scopus 로고
    • Physiologic principles underlying ion channelopathies
    • DOI 10.1016/j.nurt.2007.01.015, PII S1933721307000153
    • S.C. Cannon Physiologic principles underlying ion channelopathies Neurotherapeutics 4 2007 174 183 (Pubitemid 46467549)
    • (2007) Neurotherapeutics , vol.4 , Issue.2 , pp. 174-183
    • Cannon, S.C.1
  • 5
    • 84892581415 scopus 로고    scopus 로고
    • Non-selective ion channel activity of polymorphic human islet amyloid polypeptide (amylin) double channels
    • J. Zhao, R. Hu, M.F. Sciacca, J.R. Brender, H. Chen, A. Ramamoorthy, and J. Zheng Non-selective ion channel activity of polymorphic human islet amyloid polypeptide (amylin) double channels Phys. Chem. Chem. Phys. 16 2014 2368 2377
    • (2014) Phys. Chem. Chem. Phys. , vol.16 , pp. 2368-2377
    • Zhao, J.1    Hu, R.2    Sciacca, M.F.3    Brender, J.R.4    Chen, H.5    Ramamoorthy, A.6    Zheng, J.7
  • 6
    • 0036083537 scopus 로고    scopus 로고
    • Molecular structure and physiological function of chloride channels
    • T.J. Jentsch, V. Stein, F. Weinreich, and A.A. Zdebik Molecular structure and physiological function of chloride channels Physiol. Rev. 82 2002 503 568 (Pubitemid 34654460)
    • (2002) Physiological Reviews , vol.82 , Issue.2 , pp. 503-568
    • Jentsch, T.J.1    Stein, V.2    Weinreich, F.3    Zdebik, A.A.4
  • 8
    • 0027209828 scopus 로고
    • Synthetic peptides and four-helix bundle proteins as model systems for the pore-forming structure of channel proteins. I. Transmembrane segment M2 of the nicotinic cholinergic receptor channel is a key pore-lining structure
    • M. Oblatt-Montal, L.K. Buhler, T. Iwamoto, J.M. Tomich, and M. Montal Synthetic peptides and 4-helix bundle proteins as model systems for the pore-forming structure of channel proteins.1. Transmembrane segment M2 of the nicotinic cholinergic receptor-channel is a key pore-lining structure J. Biol. Chem. 268 1993 14601 14607 (Pubitemid 23206594)
    • (1993) Journal of Biological Chemistry , vol.268 , Issue.20 , pp. 14601-14607
    • Oblatt-Montal, M.1    Buhler, L.K.2    Iwamoto, T.3    Tomich, J.M.4    Montal, M.5
  • 9
    • 0027255102 scopus 로고
    • Synthetic peptides and four-helix bundle proteins as model systems for the pore-forming structure of channel proteins. II. Transmembrane segment M2 of the brain glycine receptor is a plausible candidate for the pore-lining structure
    • G.L. Reddy, T. Iwamoto, J.M. Tomich, and M. Montal Synthetic peptides and four-helix bundle proteins as model systems for the pore-forming structure of channel proteins. II. Transmembrane segment M2 of the brain glycine receptor is a plausible candidate for the pore-lining structure J. Biol. Chem. 268 1993 14608 14615 (Pubitemid 23206595)
    • (1993) Journal of Biological Chemistry , vol.268 , Issue.20 , pp. 14608-14615
    • Reddy, G.L.1    Iwamoto, T.2    Tomich, J.M.3    Montal, M.4
  • 10
    • 60549108729 scopus 로고    scopus 로고
    • Solid-state NMR and molecular dynamics simulations reveal the oligomeric ion-channels of TM2-GABA(A) stabilized by intermolecular hydrogen bonding
    • S.K. Kandasamy, D.K. Lee, R.P. Nanga, J. Xu, J.S. Santos, R.G. Larson, and A. Ramamoorthy Solid-state NMR and molecular dynamics simulations reveal the oligomeric ion-channels of TM2-GABA(A) stabilized by intermolecular hydrogen bonding Biochim. Biophys. Acta 1788 2009 686 695
    • (2009) Biochim. Biophys. Acta , vol.1788 , pp. 686-695
    • Kandasamy, S.K.1    Lee, D.K.2    Nanga, R.P.3    Xu, J.4    Santos, J.S.5    Larson, R.G.6    Ramamoorthy, A.7
  • 16
    • 0037062632 scopus 로고    scopus 로고
    • Distinct structural elements that direct solution aggregation and membrane assembly in the channel-forming peptide M2GlyR
    • DOI 10.1021/bi016053q
    • J.R. Broughman, L.P. Shank, W. Takeguchi, B.D. Schultz, T. Iwamoto, K.E. Mitchell, and J.M. Tomich Distinct structural elements that direct solution aggregation and membrane assembly in the channel-forming peptide M2GlyR Biochemistry (Mosc) 41 2002 7350 7358 (Pubitemid 34602452)
    • (2002) Biochemistry , vol.41 , Issue.23 , pp. 7350-7358
    • Broughman, J.R.1    Shank, L.P.2    Takeguchi, W.3    Schultz, B.D.4    Iwamoto, T.5    Mitchell, K.E.6    Tomich, J.M.7
  • 18
    • 33645974334 scopus 로고    scopus 로고
    • Redesigning channel-forming peptides: Amino acid substitutions that enhance rates of supramolecular self-assembly and raise ion transport activity
    • L.P. Shank, J.R. Broughman, W. Takeguchi, G. Cook, A.S. Robbins, L. Hahn, G. Radke, T. Iwamoto, B.D. Schultz, and J.M. Tomich Redesigning channel-forming peptides: amino acid substitutions that enhance rates of supramolecular self-assembly and raise ion transport activity Biophys. J. 90 2006 2138 2150
    • (2006) Biophys. J. , vol.90 , pp. 2138-2150
    • Shank, L.P.1    Broughman, J.R.2    Takeguchi, W.3    Cook, G.4    Robbins, A.S.5    Hahn, L.6    Radke, G.7    Iwamoto, T.8    Schultz, B.D.9    Tomich, J.M.10
  • 20
  • 21
    • 40449137981 scopus 로고    scopus 로고
    • Immunity to a self-derived, channel-forming peptide in the respiratory tract
    • DOI 10.1128/CVI.00319-07
    • F.W. van Ginkel, T. Iwamoto, B.D. Schultz, and J.M. Tomich Immunity to a self-derived, channel-forming peptide in the respiratory tract Clin. Vaccine Immunol. 15 2008 260 266 (Pubitemid 352025531)
    • (2008) Clinical and Vaccine Immunology , vol.15 , Issue.2 , pp. 260-266
    • Van Ginkel, F.W.1    Iwamoto, T.2    Schultz, B.D.3    Tomich, J.M.4
  • 22
    • 41149168686 scopus 로고    scopus 로고
    • X-ray structure of a prokaryotic pentameric ligand-gated ion channel
    • (375-U312)
    • R.J.C. Hilf, and R. Dutzler X-ray structure of a prokaryotic pentameric ligand-gated ion channel Nature 452 2008 (375-U312)
    • (2008) Nature , vol.452
    • Hilf, R.J.C.1    Dutzler, R.2
  • 23
  • 24
    • 58149242730 scopus 로고    scopus 로고
    • Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel
    • (115-U122)
    • R.J.C. Hilf, and R. Dutzler Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel Nature 457 2009 (115-U122)
    • (2009) Nature , vol.457
    • Hilf, R.J.C.1    Dutzler, R.2
  • 27
    • 34447131659 scopus 로고    scopus 로고
    • Barriers to ion translocation in cationic and anionic receptors from the cys-loop family
    • DOI 10.1021/ja070778l
    • I. Ivanov, X.L. Cheng, S.M. Sine, and J.A. McCammon Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family J. Am. Chem. Soc. 129 2007 8217 8224 (Pubitemid 47035135)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.26 , pp. 8217-8224
    • Ivanov, I.1    Cheng, X.2    Sine, S.M.3    McCammon, J.A.4
  • 28
    • 77955788241 scopus 로고    scopus 로고
    • Structural characterization of two pore-forming peptides: Consequences of introducing a C-terminal tryptophan
    • A.I. Herrera, A. Al-Rawi, G.A. Cook, J. Gao, T. Iwamoto, O. Prakash, J.M. Tomich, and J. Chen Structural characterization of two pore-forming peptides: consequences of introducing a C-terminal tryptophan Proteins 78 2010 2238 2250
    • (2010) Proteins , vol.78 , pp. 2238-2250
    • Herrera, A.I.1    Al-Rawi, A.2    Cook, G.A.3    Gao, J.4    Iwamoto, T.5    Prakash, O.6    Tomich, J.M.7    Chen, J.8
  • 29
    • 0342929614 scopus 로고
    • Non-physical sampling distributions in Monte-Carlo free-energy estimation - Umbrella sampling
    • G.M. Torrie, and J.P. Valleau Non-physical sampling distributions in Monte-Carlo free-energy estimation - umbrella sampling J. Comput. Phys. 23 1977 187 199
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 30
    • 33750606030 scopus 로고    scopus 로고
    • Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels
    • DOI 10.1016/j.bpc.2006.04.015, PII S0301462206001311
    • T.W. Allen, O.S. Andersen, and B. Roux Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels Biophys. Chem. 124 2006 251 267 (Pubitemid 44692362)
    • (2006) Biophysical Chemistry , vol.124 , Issue.3 , pp. 251-267
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 31
    • 33646192258 scopus 로고    scopus 로고
    • Ion permeation through a narrow channel: Using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields
    • T.W. Allen, O.S. Andersen, and B. Roux Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields 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
  • 35
    • 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
    • A.D. Mackerell, M. Feig, and C.L. Brooks 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 2004 1400 1415
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • Mackerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 37
    • 33646940952 scopus 로고
    • Numerical-integration of Cartesian equations of motion of a system with constraints - Molecular-dynamics of N-alkanes
    • J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes J. Comput. Phys. 23 1977 327 341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 38
    • 33846823909 scopus 로고
    • Particle mesh ewald - An N. Log(N) method for Ewald Sums in large systems
    • T. Darden, D. York, and L. Pedersen 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
  • 39
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules.1. The method
    • S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules.1. The method J. Comput. Chem. 13 1992 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
  • 40
    • 41149134824 scopus 로고    scopus 로고
    • Automated builder and database of protein/membrane complexes for molecular dynamics simulations
    • S. Jo, T. Kim, and W. Im Automated builder and database of protein/membrane complexes for molecular dynamics simulations PLoS One 2 2007 e880
    • (2007) PLoS One , vol.2 , pp. 880
    • Jo, S.1    Kim, T.2    Im, W.3
  • 41
    • 0036301334 scopus 로고    scopus 로고
    • Ions and counterions in a biological channel: A molecular dynamics simulation of ompf porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution
    • DOI 10.1016/S0022-2836(02)00380-7
    • W. Im, and B. Roux Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution J. Mol. Biol. 319 2002 1177 1197 (Pubitemid 34729427)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.5 , pp. 1177-1197
    • Im, W.1    Roux, B.2
  • 42
    • 33748583013 scopus 로고
    • Ion-transport in a gramicidin-like channel - Dynamics and mobility
    • B. Roux, and M. Karplus Ion-transport in a gramicidin-like channel - dynamics and mobility J. Phys. Chem. 95 1991 4856 4868
    • (1991) J. Phys. Chem. , vol.95 , pp. 4856-4868
    • Roux, B.1    Karplus, M.2
  • 44
    • 13244259427 scopus 로고    scopus 로고
    • Charge selectivity of the Cys-loop family of ligand-gated ion channels
    • DOI 10.1111/j.1471-4159.2004.02883.x
    • M.L. Jensen, A. Schousboe, and P.K. Ahring Charge selectivity of the Cys-loop family of ligand-gated ion channels J. Neurochem. 92 2005 217 225 (Pubitemid 40194013)
    • (2005) Journal of Neurochemistry , vol.92 , Issue.2 , pp. 217-225
    • Jensen, M.L.1    Schousboe, A.2    Ahring, P.K.3
  • 45
    • 0035999831 scopus 로고    scopus 로고
    • Cation-selective mutations in the M2 domain of the inhibitory glycine receptor channel reveal determinants of ion-charge selectivity
    • DOI 10.1085/jgp.20028552
    • A. Keramidas, A.J. Moorhouse, K.D. Pierce, P.R. Schofield, and P.H. Barry Cation-selective mutations in the M2 domain of the inhibitory glycine receptor channel reveal determinants of ion-charge selectivity J. Gen. Physiol. 119 2002 393 410 (Pubitemid 34522287)
    • (2002) Journal of General Physiology , vol.119 , Issue.5 , pp. 393-410
    • Keramidas, A.1    Moorhouse, A.J.2    Pierce, K.D.3    Schofield, P.R.4    Barry, P.H.5
  • 46
    • 84888374562 scopus 로고    scopus 로고
    • Effect of diaminopropionic acid (Dap) on the biophysical properties of a modified synthetic channel-forming peptide
    • U. Bukovnik, M. Sala-Rabanal, S. Francis, S.J. Frazier, B.D. Schultz, C.G. Nichols, and J.M. Tomich Effect of diaminopropionic acid (Dap) on the biophysical properties of a modified synthetic channel-forming peptide Mol. Pharm. 10 2013 3959 3966
    • (2013) Mol. Pharm. , vol.10 , pp. 3959-3966
    • Bukovnik, U.1    Sala-Rabanal, M.2    Francis, S.3    Frazier, S.J.4    Schultz, B.D.5    Nichols, C.G.6    Tomich, J.M.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.