메뉴 건너뛰기




Volumn 37, Issue 12, 2011, Pages 975-985

Dynamic structure of the polytheonamide B channel studied by normal mode analysis

Author keywords

Gramicidin A; Ion channel; Normal mode analysis; Peptide libration; Polytheonamide B

Indexed keywords

CHANNEL WALL; COMMON FEATURES; CORRELATION FACTORS; DYNAMIC STRUCTURE; DYNAMICAL PROPERTIES; ELASTIC ROD; GRAMICIDIN A; HELIX STRUCTURES; ION CHANNEL; L-AMINO ACIDS; LIBRATIONAL MOTIONS; LOW FREQUENCY; LOW-FREQUENCY MODES; NORMAL MODE ANALYSIS; POLYTHEONAMIDE B; ROOT MEAN SQUARES;

EID: 81255152587     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2011.561433     Document Type: Article
Times cited : (12)

References (42)
  • 1
    • 0028118767 scopus 로고
    • Polytheonamides unprecedented highly cytotoxic polypeptides from the marine sponge Theonella swinhoei: 1. Isolation and component amino acids
    • T. Hamada, T. Sugawara, S. Matsunaga, and N. Fusetani, Polytheonamides, unprecedented highly cytotoxic polypeptides, from the marine sponge Theonella swinhoei: 1. Isolation and component amino acids, Tetrahedron Lett. 35 (1994), pp. 719-720.
    • (1994) Tetrahedron Lett. , vol.35 , pp. 719-720
    • Hamada, T.1    Sugawara, T.2    Matsunaga, S.3    Fusetani, N.4
  • 2
    • 11844280935 scopus 로고    scopus 로고
    • Polytheonamides A and B, highly cytotoxic, linear polypeptides with unprecedented structural features, from the marine sponge, Theonella swinhoei
    • DOI 10.1021/ja045749e
    • T. Hamada, S. Matsunaga, G. Yano, and N. Fusetani, Polytheon- amides A and B, highly cytotoxic, linear polypeptides with unprecedented structural features, from the marine sponge, Theonella swinhoei, J. Am. Chem. Soc. 127 (2005), pp. 110-118. (Pubitemid 40094375)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.1 , pp. 110-118
    • Hamada, T.1    Matsunaga, S.2    Yano, G.3    Fusetani, N.4
  • 3
    • 0028196647 scopus 로고
    • Polytheonamides unprecedented highly cytotoxic polypeptides from the marine sponge Theonella swinhoei: 2. Structure elucidation
    • T. Hamada, T. Sugawara, S. Matsunaga, and N. Fusetani, Polytheonamides, unprecedented highly cytotoxic polypeptides, from the marine sponge Theonella swinhoei: 2. Structure elucidation, Tetrahedron Lett. 35 (1994), pp. 609-612.
    • (1994) Tetrahedron Lett. , vol.35 , pp. 609-612
    • Hamada, T.1    Sugawara, T.2    Matsunaga, S.3    Fusetani, N.4
  • 5
    • 77956921248 scopus 로고    scopus 로고
    • A cytotoxic peptidefrom a marine sponge exhibits ion channel activity through vectorial-insertion into the membrane
    • M. Iwamoto, H. Shimizu, I. Muramatsu, and S. Oiki, A cytotoxic peptidefrom a marine sponge exhibits ion channel activity through vectorial-insertion into the membrane, FEBS Lett. 584 (2010), pp. 3995-3999.
    • (2010) FEBS Lett. , vol.584 , pp. 3995-3999
    • Iwamoto, M.1    Shimizu, H.2    Muramatsu, I.3    Oiki, S.4
  • 7
    • 0031830332 scopus 로고    scopus 로고
    • Recent advances in the high resolution structures of bacterial channels: Gramicidin A
    • DOI 10.1006/jsbi.1997.3948
    • BA. Wallace, Recent advances in the high resolution structures of bacterial channels: Gramicidin A, J. Struct. Biol. 121 (1998), pp. 123-141. (Pubitemid 28361441)
    • (1998) Journal of Structural Biology , vol.121 , Issue.2 , pp. 123-141
    • Wallace, B.A.1
  • 9
    • 0028931417 scopus 로고
    • Voltage-dependent gating of an asymmetric gramicidin channel
    • S. Oiki, R.E. Koeppe, II, and O.S. Andersen, Voltage-dependent gating of an asymmetric gramicidin channel, Proc. Natl Acad. Sci. USA 92 (1995), pp. 2121-2125.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 2121-2125
    • Oiki, S.1    Koeppe, I.I.R.E.2    Andersen, O.S.3
  • 10
    • 0024339854 scopus 로고
    • Transmembrane channels based on tartaric acid-gramicidin A hybrids
    • C.J. Stankovic, S.H. Heinemann, J.M. Delfino, F.J. Sigworth, and S.L. Schreiber, Transmembrane channels based on tartaric acid-gramicidin A hybrids, Science 244 (1989), pp. 813-817. (Pubitemid 19163868)
    • (1989) Science , vol.244 , Issue.4906 , pp. 813-817
    • Stankovic, C.J.1    Heinemann, S.H.2    Delfino, J.M.3    Sigworth, F.J.4    Schreiber, S.L.5
  • 11
    • 0037304680 scopus 로고    scopus 로고
    • Theoretical study of the structure and dynamic fluctuations of dioxolane-linked gramicidin channels
    • C.H. Yu, S. Cukierman, and R. Pomès, Theoretical study of the structure and dynamic fluctuations of dioxolane-linked gramicidin channels, Biophys. J. 84 (2003), pp. 816-831. (Pubitemid 36133410)
    • (2003) Biophysical Journal , vol.84 , Issue.2 , pp. 816-831
    • Yu, C.-H.1    Cukierman, S.2    Pomes, R.3
  • 12
    • 0028321565 scopus 로고
    • Moleculardynamics simulations of the gramicidin channel
    • B. Roux and M. Karplus, Moleculardynamics simulations of the gramicidin channel, Annu. Rev. Biophys. Biomol. Struct. 23 (1994), pp. 731-761.
    • (1994) Annu. Rev. Biophys. Biomol. Struct. , vol.23 , pp. 731-761
    • Roux, B.1    Karplus, M.2
  • 13
    • 0037134267 scopus 로고    scopus 로고
    • Control of the selectivity of the aquaporin water channel family by global orientational tuning
    • DOI 10.1126/science.1067778
    • E. Tajkhorshid, P. Nollert, M.Ø. Jensen, L.J.W. Miercke, J. O'Connell, R.M. Stroud, and K. Schulten, Control of the selectivity of the aquaporin water channel family by global orientational tuning, Science 296 (2002), pp. 525-530. (Pubitemid 34413590)
    • (2002) Science , vol.296 , Issue.5567 , pp. 525-530
    • Tajkhorshid, E.1    Nollert, P.2    Jensen, M.O.3    Miercke, L.J.W.4    O'Connell, J.5    Stroud, R.M.6    Schulten, K.7
  • 14
    • 0141534474 scopus 로고    scopus 로고
    • The mechanism of proton exclusion in the aquaporin-1 water channel
    • DOI 10.1016/j.jmb.2003.08.003
    • B.L. de Groot, T. Frigato, V. Helms, and H. Grubmüller, The mechanism of proton exclusion in the aquaporin-1 water channel, J. Mol. Biol. 333 (2003), pp. 279-293. (Pubitemid 37188572)
    • (2003) Journal of Molecular Biology , vol.333 , Issue.2 , pp. 279-293
    • De Groot, B.L.1    Frigato, T.2    Helms, V.3    Grubmuller, H.4
  • 15
    • 33646134384 scopus 로고    scopus 로고
    • The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF
    • S. Varma, S.W. Chiu, andE. Jakobsson, The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF, Biophys. J. 90 (2006), pp. 112-123.
    • (2006) Biophys. J. , vol.90 , pp. 112-123
    • Varma, S.1    Chiu, S.W.2    Jakobsson, E.3
  • 16
    • 0036151669 scopus 로고    scopus 로고
    • Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations
    • S.H. Chung, T.W. Allen, and S. Kuyucak, Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations, Biophys. J. 82 (2002), pp. 628-645. (Pubitemid 34111206)
    • (2002) Biophysical Journal , vol.82 , Issue.2 , pp. 628-645
    • Chung, S.-H.1    Allen, T.W.2    Kuyucak, S.3
  • 17
    • 0036389892 scopus 로고    scopus 로고
    • Ion permeation and selectivity ofOmpFporin: A theoretical study based on molecular dynamics Brownian dynamics and continuum electrodiffusion theory
    • W. Im and B. Roux, Ion permeation and selectivity ofOmpFporin: A theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory, J. Mol. Biol. 322 (2002), pp. 851-869.
    • (2002) J Mol. Biol. , vol.322 , pp. 851-869
    • Im, W.1    Roux, B.2
  • 18
    • 0030050164 scopus 로고    scopus 로고
    • A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: The origin of cation selectivity
    • V. Dorman, M.B. Partenskii, and P.C. Jordan, A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: The origin of cation selectivity, Biophys. J. 70 (1996), pp. 121-134. (Pubitemid 26021454)
    • (1996) Biophysical Journal , vol.70 , Issue.1 , pp. 121-134
    • Dorman, V.1    Partenskii, M.B.2    Jordan, P.C.3
  • 19
    • 0034271520 scopus 로고    scopus 로고
    • Monte Carlo simulations of the mechanism for channel selectivity: The competition between volume exclusion and charge neutrality
    • D. Boda, D.D. Busath, D. Henderson, and S. Sokolowski, Monte Carlo simulations of the mechanism for channel selectivity: The competition between volume exclusion and charge neutrality, J. Phys. Chem. B 104 (2000), pp. 8903-8910.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 8903-8910
    • Boda, D.1    Busath, D.D.2    Henderson, D.3    Sokolowski, S.4
  • 20
    • 0043238084 scopus 로고    scopus 로고
    • Dynamical properties of the MscL of Escherichia coli: A normal mode analysis
    • DOI 10.1016/S0022-2836(03)00851-9
    • H. Valadié, J.J. Lacapčre, Y.H. Sanejouand, and C. Etchebest, Dynamical properties of the MscL of Escherichia coli: A normal mode analysis, J. Mol. Biol. 332 (2003), pp. 657-674. (Pubitemid 37075988)
    • (2003) Journal of Molecular Biology , vol.332 , Issue.3 , pp. 657-674
    • Valadie, H.1    Lacapcre, J.J.2    Sanejouand, Y.-H.3    Etchebest, C.4
  • 21
    • 28844448877 scopus 로고    scopus 로고
    • Channel opening motion of α7 nicotinic acetylcholine receptor as suggested by normal mode analysis
    • DOI 10.1016/j.jmb.2005.10.039, PII S0022283605012830
    • X.L. Cheng, B.Z. Lu, B. Grant, R.J. Law, and JA. McCammon, Channel opening motion of a7 nicotinic acetylcholine receptor as suggested by normal mode analysis, J. Mol. Biol. 355 (2006), pp. 310-324. (Pubitemid 41774133)
    • (2006) Journal of Molecular Biology , vol.355 , Issue.2 , pp. 310-324
    • Cheng, X.1    Lu, B.2    Grant, B.3    Law, R.J.4    McCammon, J.A.5
  • 22
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • N. Gō, T. Noguti, and T. Nishikawa, Dynamics of a small globular protein in terms of low-frequency vibrational modes, Proc. Natl Acad. Sci. USA 80 (1983), pp. 3696-3700.
    • (1983) Proc. Natl Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 24
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • M. Levitt, C. Sander, and P.S. Stern, Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol. 181 (1985), pp. 423-447.
    • (1985) J Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 25
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change ofproteins arisingfromnormalmodecalculations
    • F. Tama and Y.H. Sanejouand, Conformational change ofproteins arisingfromnormalmodecalculations, ProteinEng. 14(2001),pp. 1-6.
    • (2001) ProteinEng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 26
    • 0023863112 scopus 로고
    • The normal modes of the gramicidin-A dimer channel
    • B. Roux and M. Karplus, The normal modes of the gramicidin-A dimer channel, Biophys. J. 53 (1988), pp. 297-309. (Pubitemid 18074196)
    • (1988) Biophysical Journal , vol.53 , Issue.3 , pp. 297-309
    • Roux, B.1    Karplus, M.2
  • 27
    • 0022539798 scopus 로고
    • Vibrational analysis of the structure of gramicidin A. I. Normal mode analysis
    • V.M. Naik and S. Krimm, Vibrational analysis of the structure of gramicidin A.I. Normal mode analysis, Biophys. J. 49 (1986), pp. 1131-1145. (Pubitemid 16083826)
    • (1986) Biophysical Journal , vol.49 , Issue.6 , pp. 1131-1145
    • Naik, V.M.1    Krimm, S.2
  • 28
    • 2742586768 scopus 로고
    • Vibrational spectroscopic studies of LD-alternating valinepeptides
    • V.M. Naik, Vibrational spectroscopic studies of L,D-alternating valinepeptides, Vib. Spectrosc. 3 (1992), pp. 105-113.
    • (1992) Vib. Spectrosc. , vol.3 , pp. 105-113
    • Naik, V.M.1
  • 29
    • 0027171104 scopus 로고
    • Vibrational spectroscopic studies of L,D-alternating phenylalanine peptides
    • V.M. Naik, Vibrational spectroscopic studies of L,D-alternating phenylalanine peptides, Int. J. Pept. Protein Res. 42 (1993), pp. 125-131. (Pubitemid 23240239)
    • (1993) International Journal of Peptide and Protein Research , vol.42 , Issue.2 , pp. 125-131
    • Naik, V.M.1
  • 30
    • 33746794687 scopus 로고    scopus 로고
    • The open state gating mechanism of gramicidin A requires relative opposed monomer rotation and simultaneous lateral displacement
    • DOI 10.1016/j.str.2006.06.007, PII S0969212606002905
    • G.V. Miloshevsky and P.C. Jordan, The open state gating mechanism of gramicidin A requires relative opposed monomer rotation and simultaneous lateral displacement, Structure 14 (2006), pp. 1241-1249. (Pubitemid 44176369)
    • (2006) Structure , vol.14 , Issue.8 , pp. 1241-1249
    • Miloshevsky, G.V.1    Jordan, P.C.2
  • 33
    • 0008075262 scopus 로고    scopus 로고
    • Atomistic models and force fields
    • O.M. Becker, A.D. MacKerell, Jr, B. Roux, and M. Watanabe, eds. Marcel Dekker, New York
    • A.D. MacKerell, Jr, Atomistic models and force fields, in Computational Biochemistry and Biophysics, O.M. Becker, A.D. MacKerell, Jr, B. Roux, and M. Watanabe, eds., Marcel Dekker, New York, 2001, pp. 7-38.
    • (2001) Computational Biochemistry and Biophysics , pp. 7-38
    • MacKerell Jr., A.D.1
  • 34
    • 0037075407 scopus 로고    scopus 로고
    • A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations
    • DOI 10.1021/jp013658n
    • M.L. Strader and S.E. Feller, A flexible all-atom model of dimethyl sulfoxideformoleculardynamics simulations, J. Phys. Chem. A 106 (2002), pp. 1074-1080. (Pubitemid 35275913)
    • (2002) Journal of Physical Chemistry A , vol.106 , Issue.6 , pp. 1074-1080
    • Strader, M.L.1    Feller, S.E.2
  • 36
    • 0027497596 scopus 로고
    • 6.3-helix
    • 6. -helix, Biophys. J. 64 (1993), pp. 36-43. (Pubitemid 23063925)
    • (1993) Biophysical Journal , vol.64 , Issue.1 , pp. 36-43
    • Monoi, H.1
  • 37
    • 0017172843 scopus 로고
    • Fluctuations and mechanical strength of a-helices of polyglycine and poly(L-alanine)
    • Y. Suezaki and N. Gō, Fluctuations and mechanical strength of a-helices of polyglycine and poly(L-alanine), Biopolymers 15 (1976), pp. 2137-2153.
    • (1976) Biopolymers , vol.15 , pp. 2137-2153
    • Suezaki, Y.1    Go, N.2
  • 38
    • 0000319912 scopus 로고    scopus 로고
    • Dynamicproperties ofdouble-stranded DNA by normal mode analysis
    • A. Matsumoto and N. Gō, Dynamicproperties ofdouble-stranded DNA by normal mode analysis, J. Chem. Phys. 110 (1999), pp. 11070-11075.
    • (1999) J. Chem. Phys. , vol.110 , pp. 11070-11075
    • Matsumoto, A.1    Go, N.2
  • 39
    • 84985649741 scopus 로고
    • Vibrational approach to the dynamics of an a-helix
    • R.M. Levy and M. Karplus, Vibrational approach to the dynamics of an a-helix, Biopolymers 18 (1979), pp. 2465-2495.
    • (1979) Biopolymers , vol.18 , pp. 2465-2495
    • Levy, R.M.1    Karplus, M.2
  • 41
    • 84986436997 scopus 로고
    • Theoretical analysis of gramicidin a transmembrane channel. II. Energetics of helical librationalstates ofthe channel
    • C.M. Venkatachalam and D.W. Urry, Theoretical analysis of gramicidin a transmembrane channel. II. Energetics of helical librationalstates ofthe channel, J. Comput. Chem. 5 (1984), pp. 64-71.
    • (1984) J. Comput. Chem. , vol.5 , pp. 64-71
    • Venkatachalam, C.M.1    Urry, D.W.2
  • 42
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • B.R. Brooks, D. Janežič, and M. Karplus, Harmonic analysis of large systems. I. Methodology, J. Comput. Chem. 16 (1995), pp. 1522-1542.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janežič, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.