Hostname: page-component-cd9895bd7-hc48f Total loading time: 0 Render date: 2024-12-28T05:24:38.142Z Has data issue: false hasContentIssue false
  • English
  • Français

Energy profiles in the gramicidin A channel

Published online by Cambridge University Press:  17 March 2009

A. Pullman
A. Pullman
Affiliation:
Laboratoire de Biochimie Theorique associé au C.N.R.S., Institut de Biologic Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
Get access Rights & Permissions [Opens in a new window]

Extract

Gramicidin A (GA) is a linear pentadecapeptide made of alternating D and L residues, in which the N-and C-terminals are blocked by a formyl group (head) and an ethanolamine end (tail), respectively (Sarges & Witkop, 1964):

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 20 , Issue 3-4 , November 1987 , pp. 173 - 200
Copyright
Copyright © Cambridge University Press 1987

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Andersen, O. S. (1984). Gramicidin channels. A. Rev. Physiol. 46, 531–548.CrossRefGoogle ScholarPubMed
Arseniev, A. S., Barsukov, I. L., Bystrov, V. F., Lomize, A. L. & Ovchinnikov, Yu. A. (1985). 1H-NMR study of gramicidin A transmembrane ion channel. Head-to-head right-handed single-stranded helices. FEBS Lett. 186, 168–174.CrossRefGoogle ScholarPubMed
Arseniev, A. S., Barsukov, I. L., Bystrov, V. F. & Ovchinnikov, Yu. A. (1986). Spatial structure of gramicidin A transmembrane ion channel – NMR analysis in micelles. Biological Membranes (URSS) 3, 437–462 (edition in Russian).Google Scholar
Bamberg, E. & Läuger, P. (1977). Blocking of the gramicidin A channel by divalent cations. J. Membrane Biol. 35, 351–375.CrossRefGoogle Scholar
Bamberg, E., Noda, K., Gross, E. & Läuger, P. (1976). Single-channel parameters of gramicidin A, B and C. Biochim. biophys. Acta 419, 223–228.CrossRefGoogle ScholarPubMed
Barrett-Russell, E. W., Weiss, L. B., Navetta, F. I., Koeppe, R. E. II. & Andersen, O. S. (1986). Single-channel studies on linear gramicidins with altered amino-acid side chains. Effects of altering the polarity of the side chain at position 1 in gramicidin A. Biophys. J. 49, 673–686.CrossRefGoogle Scholar
Busath, D. & Waldbillig, R. C. (1983). Photolysis of gramicidin A channels in lipid bilayers. Biochim. biophys. Acta 736, 28–38.CrossRefGoogle Scholar
Eisenman, G., Dani, J. A. & Sandblom, J. (1985). Recent studies on the energy profiles underlying permeation and ion-selectivity of the gramicidin and acetylcholine receptor channel. In Ion Measurements in Physiology and Medicine (ed. Kessler, M.), pp. 54–66. Springer-Verlag: Berlin Heidelberg.CrossRefGoogle Scholar
Eisenman, G. & Horn, R. (1983). Ionic selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Membrane Biol. 76, 197–225.CrossRefGoogle ScholarPubMed
Eisenman, G. & Sandblom, J. P. (1983). Energy barriers in ionic channels: data for gramicidin A interpreted using a single-file (3B4S) model having 3 barriers separating 4 sites. In Physical Chemistry of Transmembrane Ion Motions (ed. Spach, G.), pp. 329–348. Amsterdam: Elsevier Science Publishers.Google Scholar
Etchebest, C. & Pullman, A. (1984). The gramicidin A channel. Role of the ethanolamine end chain on the energy profiles for single occupancy by Na+. FEBS Lett. 170, 191–195.CrossRefGoogle Scholar
Etchebest, C. & Pullman, A. (1985). The effect of the amino-acid side chains on the energy profiles for ion transport in the gramicidin A channel. J. Biomol. Structure and Dynamics 2, 859–870.CrossRefGoogle ScholarPubMed
Etchebest, C. & Pullman, A. (1986 a). The gramicidin A channel. Energetics and structural characteristics of the progression of a sodium ion in the presence of water. J. Biomol. Structure and Dynamics 3, 805–825.CrossRefGoogle ScholarPubMed
Etchebest, C. & Pullman, A. (1986 b). The gramicidin A channel. The energy profile calculated for Na+ in the presence of water with inclusion of the flexibility of the ethanolamine tail. FEBS Lett. 204, 261–265.CrossRefGoogle Scholar
Etchebest, C., Pullman, A. & Ranganathan, S. (1985). The gramicidin A channel: theoretical energy profile computed for single occupancy by a divalent cation. Ca2+. Biochim. biophys. Acta 818, 23–30.CrossRefGoogle Scholar
Etchebest, C., Ranganathan, S. & Pullman, A. (1984). The gramicidin A channel: comparison of the energy profiles of Na+, K+ and Cs+. Influence of the flexibility of the ethanolamine end chain on the profiles. FEBS Lett. 173, 301–306.CrossRefGoogle Scholar
Finkelstein, A. & Andersen, O. S. (1981). The gramicidin A channel: a review of its permeability characteristics with special reference to the single-file aspect of transport. J. Membrane Biol. 59, 155–171.CrossRefGoogle Scholar
Fischer, W., Brickmann, J. & Läuger, P. (1981). Molecular dynamics study of ion transport in transmembrane protein channels. Biophys. Chem. 13, 105–116.CrossRefGoogle ScholarPubMed
Furois-Corbin, S. & Pullman, A. (1986 a). Theoretical study of the packing of α-helices by energy minimization: effect of the length of the helices on the packing energy and on the optimal configuration of a pair. Chem. Phys. Lett. 123, 305–310.CrossRefGoogle Scholar
Furois-Corbin, S. & Pullman, A. (1986 b). Theoretical study of the packing of α-helices of poly(L-alanine) into transmembrane bundles. Possible significance for ion-transfer. Biochim. biophys. Acta 860, 165–177.CrossRefGoogle Scholar
Furois-Corbin, S. & Pullman, A. (1987). Theoretical study of potential ion channels formed by a bundle of α-helices: effect of the presence of polar residues along the channel inner wall. J. molec. Structure and Dynamics 4, 589–598.CrossRefGoogle ScholarPubMed
Goodall, M. C. (1971). Thickness dependence in the action of gramicidin A on lipid bilayers. Archs Biochem. Biophys. 147, 129–135.CrossRefGoogle ScholarPubMed
Gresh, N., Claverie, P. & Pullman, A. (1979). Intermolecular interactions: reproduction of the results of ab initio supermolecule computations by an additive procedure. Int. J. Quantum Chem. S13, 243–253.Google Scholar
Gresh, N., Claverie, P. & Pullman, A. (1984). Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison with ab initio SCF computations. Theor. chim. Acta (Berl.) 66, 1–20.CrossRefGoogle Scholar
Gresh, N., Pullman, A. & Claverie, P. (1985 a). Theoretical studies of molecular conformation. II. Application of the SIBFA procedure to molecules containing carbonyl and carboxylate oxygens and amide nitrogens. Theor. chitn. Acta (Berl.) 67, 11–32.CrossRefGoogle Scholar
Gresh, N., Pullman, A. & Claverie, P. (1985 b). Cation-ligand interactions: reproduction of extended basis set ab initio SCF computations by the SIBFA-2 additive procedure. Int. J. Quantum Chem. 28, 757–771.CrossRefGoogle Scholar
Haydon, D. A. & Hladky, S. B. (1972). Ion transport across thin lipid membranes: a critical discussion of mechanisms in selected systems. Q. Rev. Biophys. 5, 187–282.CrossRefGoogle ScholarPubMed
Heitz, F., Spach, G. & Trudelle, Y. (1982). Single channels of 9, 11, 13, 15-oestryptophyl-phenylalanyl-gramicidin A Biophys. J. 39, 87–89.CrossRefGoogle Scholar
Hladky, S. B. & Haydon, D. A. (1972). Ion transfer across lipid membranes in the presence of gramicidin A. I. Studies of the unit conductance channel. Biochim. biophys. Acta 274, 294–312.CrossRefGoogle ScholarPubMed
Jones, D., Hayon, E. & Busath, D. (1986). Tryptophan photolysis is responsible for gramicidin-channel inactivation by ultra-violet light. Biochim. biophys. Acta 861, 62–66.CrossRefGoogle Scholar
Jordan, P. C. (1984). The total electrostatic potential in a gramicidin A channel. J. Membrane Biol. 78, 91–102.CrossRefGoogle Scholar
Läuger, P. (1973). Ion transport through pores: a rate-theory analysis. Biochim. biophys. Acta 311, 423–441.CrossRefGoogle Scholar
Läuger, P. (1980). Kinetic properties of ion-carriers and channels. J. Membrane Biol. 57, 163–178.CrossRefGoogle ScholarPubMed
Läuger, P. (1982). Microscopic calculation of ion-transport rates in membrane channels. Biophys. Chem. 15, 89–100.CrossRefGoogle ScholarPubMed
Lavery, R., Sklenar, H., Zakrzewska, K. & Pullman, B. (1986 a). The flexibility of the nucleic acids. II. The calculation of internal energy and applications to mononucleotide repeat DNA. J. Biomol. Structure and Dynamics 3, 989–1014.CrossRefGoogle Scholar
Lavery, R., Sklenar, H. & Pullman, B. (1986 b). The flexibility of the nucleic acids (III) the interaction of an aliphatic diamine, putrescine, with flexible B-DNA. Biomol. Structure and Dynamics 3, 1015–1031.CrossRefGoogle ScholarPubMed
Levitt, D. G. (1978 a). Electrostatic calculations for an ion-channel. I. Energy and potential profiles and interactions between ions. Biophys. J. 22, 209–219.CrossRefGoogle ScholarPubMed
Levitt, D. G. (1978 b). Electrostatic calculations for an ion channel. II. Kinetic behaviour of the gramicidin A channel. Biophys. J. 22, 221–247.CrossRefGoogle ScholarPubMed
Mackay, D. H. J., Berens, P. H., Wilson, K. R. & Hagler, A. T. (1984). Structure and dynamics of ion transport through gramicidin A. Biophys. J. 46, 229–247.CrossRefGoogle ScholarPubMed
Mazet, J. L., Andersen, O. S. & Koeppe, R. E. II (1984). Single-channel studies on linear gramicidins with altered amino acid sequences. A comparison of phenylalanine, tryptophan and tyrosine substitution at positions 1 and 11. Biophys. J. 45, 263–276.CrossRefGoogle ScholarPubMed
Parsegian, A. (1969). Energy of an ion crossing a low dielectric membrane: solutions to four relevant electrostatic problems. Nature (London) 221, 844–846.CrossRefGoogle Scholar
Parsegian, A. (1975). Ion membrane interactions as structural forces. Ann. N.Y. Acad. Sci. 264, 161–174.CrossRefGoogle ScholarPubMed
Pullman, A. & Etchebest, C. (1983). The gramicidin A channel: the energy profile for single and double occupancy in a head-to-head helical dimer backbone. FEBS. Lett. 163, 199–202.CrossRefGoogle Scholar
Pullman, A. & Etchebest, C. (1987). The effect of molecular structure and of water on the energy profiles in the gramicidin A channel. In Ion Transport through Membranes ed. Yagi, K. and Pullman, B.), pp. 277–293. Tokyo: Academic Press.Google Scholar
Sarges, R. & Witkop, B. (1964). Formyl, a novel NH2-terminal blacking group in a naturally occurring peptide. The identity of sec-gramicidin with desformylgramicidin. J. Am. chem. Soc. 86, 1861–1862.CrossRefGoogle Scholar
Schroeder, H. (1983). Rate-theoretical analysis of ion-transport in membrane channels with elastically bound ligands. In Physical Chemistry of Trans-membrane Ion Motions (ed. Spach, G.), pp. 425–436. Amsterdam: Elsevier.Google Scholar
Schroeder, H. (1985). A molecular model for ion-selectivity in membrane channels. Eur. Biophys. J. 11, 157–165.Google Scholar
Tosteson, D. C., Andreoli, T. E., Tieffenberg, M. & Cook, P. (1968). The effects of macrocyclic compounds on cation transport in sheep red cells and thin and thick lipid membranes. J. gen. Physiol. 51, 373–384S.CrossRefGoogle ScholarPubMed
Urry, D. W. (1971). The gramicidin A transmembrane channel: a proposed π(L, D) helix. Proc. natn. Acad. Sci. USA 68, 672–676.CrossRefGoogle Scholar
Urry, D. W. (1973). Polypeptide conformation and biological function. β-helices (πL, D-helices) as permselective transmembrane channels. In Conformation of Biological Molecules and Polymers, Jerusalem Symposium on Quantum Chemistry and Biochemistry (ed. Pullman, B.), vol. 5, pp. 723–736. Israel Academy of Sciences and Humanities.Google Scholar
Urry, D. W., Alonso-Romanowski, S., Venkatachalam, C. M., Trapane, T. L. & Prasad, K. U. (1984). The source of the dispersity of gramicidin A single-channel conductances. The L-Leu5-gramicidin A analog. Biophys. J. 46, 259–266.CrossRefGoogle ScholarPubMed
Urry, D. W., Prasad, K. U. & Trapane, T. L. (1982 a). Location of monovalent cation binding sites in the gramicidin A channel. Proc. natn. Acad. Sci. USA 79, 390–394.CrossRefGoogle Scholar
Urry, D. W., Trapane, T. L. & Prasad, K. L. (1982 b). Molecular structure and ionic mechanisms of an ion-selective transmembrane channel: monovalent versus divalent cation selectivity. Int. J. Quantum Chem., Quantum Biol. Symp. 9, 31–40.Google Scholar
Urry, D. W., Trapane, T. L. & Venkatachalam, C. M. (1986). Potassium-39 NMR of K+-interaction with the gramicidin A channel and NMR-derived conductance ratios for Na+, K+ and Rb+. J. Membrane Biol. 89, 107–111.CrossRefGoogle Scholar
Urry, D. W., Venkatachalam, C. M., Prasad, K. U., Bradley, R. J., Parenticastelli, G. & Lenaz, G. (1981). Conduction processes of the gramicidin A channel. Int. J. Quantum Chem. Quantum Biol. Symp. 8, 385–389.CrossRefGoogle Scholar
Urry, D. W., Venkatachalam, C. M., Spisni, A., Läuger, P. & Khaled, Md. A. (1980). Rate-theory calculation of gramicidin A single-channel currents using NMR derived rate constants. Proc. natn. Acad. Sci. USA 77, 2028–2032.CrossRefGoogle ScholarPubMed
Venkatachalam, C. M. & Urry, D. W. (1983). Theoretical conformational analysis of the gramicidin A transmembrane channel. 1. Helix sense and energetics of head-to-head dimerization. J. comp. Chem. 4, 461–469.CrossRefGoogle Scholar
Venkatachala, C. M. & Urry, D. W. (1984). Theoretical analysis of gramicidin A transmembrane channel. II. Energetics of helical librational states of the channel. J. comp. Chem. 5, 64–71.CrossRefGoogle Scholar
Wallace, B. A. (1983). Gramicidin A adopts distinctly different conformations in membranes and in organic solvents. Biopolymers 22, 397–402.CrossRefGoogle Scholar
Wallace, B. A. (1984). Ion-bound forms of the gramicidin A transmembrane channel. Biophys. J. 45, 114–116.CrossRefGoogle Scholar
Weiler-Feichenfeld, H., Pullman, A., Berthod, H. & Giessner-Prettre, C. (1970). Experimental and quantum-chemical studies of the dipole moments of quinoleine and indole. J. molec. Structure 6, 297–304.CrossRefGoogle Scholar
Weinstein, S., Durkin, J. T., Veatch, W. R. & Blout, E. R. (1985). Conformation of the gramicidin A channel in phospholipid vesicles: a fluorine 19 NMR study. Biochemistry 24, 4374.CrossRefGoogle Scholar