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Journal articles on the topic 'Gramicidin channel and MJ0305 channel'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Koeppe, R. E., and O. S. Anderson. "Engineering the Gramicidin Channel." Annual Review of Biophysics and Biomolecular Structure 25, no. 1 (June 1996): 231–58. http://dx.doi.org/10.1146/annurev.bb.25.060196.001311.

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2

Etchebest, Catherine, and Alberte Pullman. "The gramicidin A channel." FEBS Letters 204, no. 2 (August 18, 1986): 261–65. http://dx.doi.org/10.1016/0014-5793(86)80824-9.

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3

Goulian, M., O. N. Mesquita, D. K. Fygenson, C. Nielsen, O. S. Andersen, and A. Libchaber. "Gramicidin Channel Kinetics under Tension." Biophysical Journal 74, no. 1 (January 1998): 328–37. http://dx.doi.org/10.1016/s0006-3495(98)77790-2.

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4

Roux, BenoÎt. "Computational Studies of the Gramicidin Channel." Accounts of Chemical Research 35, no. 6 (June 2002): 366–75. http://dx.doi.org/10.1021/ar010028v.

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5

Markham, Jeffrey C., Joseph A. Gowen, Timothy A. Cross, and David D. Busath. "Comparison of gramicidin A and gramicidin M channel conductance dispersities." Biochimica et Biophysica Acta (BBA) - Biomembranes 1513, no. 2 (August 2001): 185–92. http://dx.doi.org/10.1016/s0005-2736(01)00353-4.

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6

Koeppe, Roger E., Jean A. Paczkowski, and William L. Whaley. "Gramicidin K, a new linear channel-forming gramicidin from Bacillus brevis." Biochemistry 24, no. 12 (June 4, 1985): 2822–26. http://dx.doi.org/10.1021/bi00333a002.

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7

Nelson, Andrew. "Conducting Gramicidin Channel Activity in Phospholipid Monolayers." Biophysical Journal 80, no. 6 (June 2001): 2694–703. http://dx.doi.org/10.1016/s0006-3495(01)76238-8.

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8

Rostovtseva, Tatiana K., Horia I. Petrache, Namdar Kazemi, Elnaz Hassanzadeh, and Sergey M. Bezrukov. "Interfacial Polar Interactions Affect Gramicidin Channel Kinetics." Biophysical Journal 94, no. 4 (February 2008): L23—L25. http://dx.doi.org/10.1529/biophysj.107.120261.

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9

Pullman, A. "Energy profiles in the gramicidin A channel." Quarterly Reviews of Biophysics 20, no. 3-4 (November 1987): 173–200. http://dx.doi.org/10.1017/s0033583500004170.

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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):

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10

Seoh, S. A., and D. Busath. "Gramicidin tryptophans mediate formamidinium-induced channel stabilization." Biophysical Journal 68, no. 6 (June 1995): 2271–79. http://dx.doi.org/10.1016/s0006-3495(95)80409-1.

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11

Deamer, D. W. "Visualizing proton conductance in the gramicidin channel." Biophysical Journal 71, no. 1 (July 1996): 5. http://dx.doi.org/10.1016/s0006-3495(96)79202-0.

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12

Roux, B., and M. Karplus. "Molecular Dynamics Simulations of the Gramicidin Channel." Annual Review of Biophysics and Biomolecular Structure 23, no. 1 (June 1994): 731–61. http://dx.doi.org/10.1146/annurev.bb.23.060194.003503.

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13

Sung, Shen-Shu, and Peter C. Jordan. "The channel properties of possible gramicidin dimers." Journal of Theoretical Biology 140, no. 3 (October 1989): 369–80. http://dx.doi.org/10.1016/s0022-5193(89)80093-1.

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14

Lundbaek, J. "Gramicidin and Related Ion channel-Forming Peptides." Cell Biology International 24, no. 12 (December 2000): 910. http://dx.doi.org/10.1006/cbir.2000.0600.

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15

Weinrich, Michael, David L. Worcester, and Sergey M. Bezrukov. "Lipid nanodomains change ion channel function." Nanoscale 9, no. 35 (2017): 13291–97. http://dx.doi.org/10.1039/c7nr03926c.

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16

Urry, Dan W., Naijie Jing, and K. U. Prasad. "On the mechanism of channel-length dependence of gramicidin single-channel conductance." Biochimica et Biophysica Acta (BBA) - Biomembranes 902, no. 1 (August 1987): 137–44. http://dx.doi.org/10.1016/0005-2736(87)90144-1.

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17

Dzikovski, Boris G., Petr P. Borbat, and Jack H. Freed. "Spin-Labeled Gramicidin A: Channel Formation and Dissociation." Biophysical Journal 87, no. 5 (November 2004): 3504–17. http://dx.doi.org/10.1529/biophysj.104.044305.

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18

Song, Hyun Deok, and Thomas L. Beck. "Temperature Dependence of Gramicidin Channel Transport and Structure." Journal of Physical Chemistry C 117, no. 8 (February 18, 2013): 3701–12. http://dx.doi.org/10.1021/jp305557s.

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19

Xie, Xiulan, Lo'ay Al-Momani, Philipp Reiß, Christian Griesinger, and Ulrich Koert. "An asymmetric ion channel derived from gramicidin A." FEBS Journal 272, no. 4 (February 2005): 975–86. http://dx.doi.org/10.1111/j.1742-4658.2004.04531.x.

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20

Oiki, S., R. E. Koeppe, and O. S. Andersen. "Voltage-dependent gating of an asymmetric gramicidin channel." Proceedings of the National Academy of Sciences 92, no. 6 (March 14, 1995): 2121–25. http://dx.doi.org/10.1073/pnas.92.6.2121.

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21

Roux, Benoit. "ChemInform Abstract: Computational Studies of the Gramicidin Channel." ChemInform 33, no. 36 (May 20, 2010): no. http://dx.doi.org/10.1002/chin.200236295.

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22

Schatz, A., A. Linke-Hommes, and J. Neubert. "Gravity dependency of the gramicidin A channel conductivity." European Biophysics Journal 25, no. 1 (October 11, 1996): 37–41. http://dx.doi.org/10.1007/s002490050014.

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23

Glowka, M. L., A. Olczak, J. Bojarska, M. Szczesio, and W. L. Duax. "Crystal structures puzzle of the DSDH gramicidin channel." Acta Crystallographica Section A Foundations of Crystallography 61, a1 (August 23, 2005): c273. http://dx.doi.org/10.1107/s0108767305088367.

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24

Allen, T. W., O. S. Andersen, and B. Roux. "Energetics of ion conduction through the gramicidin channel." Proceedings of the National Academy of Sciences 101, no. 1 (December 22, 2003): 117–22. http://dx.doi.org/10.1073/pnas.2635314100.

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25

Sträszle, M., and G. Stark. "PHOTODYNAMIC INACTIVATION OF AN ION CHANNEL: GRAMICIDIN A." Photochemistry and Photobiology 55, no. 3 (March 1992): 461–63. http://dx.doi.org/10.1111/j.1751-1097.1992.tb04262.x.

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26

Duax, W. L., B. Burkhart, V. Pletnev, N. Li, and W. Pangborn. "Novel Ion Coordination in Gramicidin, a Membrane Channel." Acta Crystallographica Section A Foundations of Crystallography 56, s1 (August 25, 2000): s265. http://dx.doi.org/10.1107/s0108767300025678.

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27

Davis, Ryan W., Elizabeth L. Patrick, Lauren A. Meyer, Theodore P. Ortiz, Jason A. Marshall, David J. Keller, Susan M. Brozik, and James A. Brozik. "Thermodynamic Properties of Single Ion Channel Formation: Gramicidin." Journal of Physical Chemistry B 108, no. 39 (September 2004): 15364–69. http://dx.doi.org/10.1021/jp049686y.

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28

Bridal, Terry R., and David Busath. "Inhibition of gramicidin channel activity by local anesthetics." Biochimica et Biophysica Acta (BBA) - Biomembranes 1107, no. 1 (June 1992): 31–38. http://dx.doi.org/10.1016/0005-2736(92)90325-g.

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29

Arasteh, Shima, Mohammad Hosein Karimi-Jafari, and Bahram Goliaei. "Molecular Dynamics Simulation Study of Gramicidin like Channel." Biophysical Journal 106, no. 2 (January 2014): 555a. http://dx.doi.org/10.1016/j.bpj.2013.11.3089.

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30

Roeske, Roger W., Tanya P. Hrinyo-Pavlina, Richard S. Pottorf, Terry Bridal, Xian-Zheng Jin, and David Busath. "Synthesis and channel properties of [Tau16]gramicidin A." Biochimica et Biophysica Acta (BBA) - Biomembranes 982, no. 2 (July 1989): 223–27. http://dx.doi.org/10.1016/0005-2736(89)90058-8.

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31

Kelkar, Devaki A., and Amitabha Chattopadhyay. "The gramicidin ion channel: A model membrane protein." Biochimica et Biophysica Acta (BBA) - Biomembranes 1768, no. 9 (September 2007): 2011–25. http://dx.doi.org/10.1016/j.bbamem.2007.05.011.

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32

Cole, Chad D., Adam S. Frost, Nephi Thompson, Myriam Cotten, Timothy A. Cross, and David D. Busath. "Noncontact Dipole Effects on Channel Permeation. VI. 5F- and 6F-Trp Gramicidin Channel Currents." Biophysical Journal 83, no. 4 (October 2002): 1974–86. http://dx.doi.org/10.1016/s0006-3495(02)73959-3.

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33

Lopez-Escalera, Ricardo, Robert J. French, and Paul P. M. Schnetkamp. "Cation fluxes and cation channels in outer segment membranes of bovine retinal rods: contamination by antibiotics applied to cattle?" Canadian Journal of Physiology and Pharmacology 72, no. 6 (June 1, 1994): 650–58. http://dx.doi.org/10.1139/y94-092.

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Membrane vesicles were prepared from intact rod outer segments (ROSs) isolated from bovine retinas and were examined for the presence of cation-selective conductances. We performed macroscopic flux measurements in an ensemble of ROS membrane vesicles and single-channel measurements after fusion of ROS membrane vesicles with planar bilayer membranes. Two K+-permeable conductances were observed, the well-established cyclic GMP (cGMP) gated channel and an apparently new K+ channel with some unusual properties. Flux and single-channel data showed that the new conductance passed K+, Rb+, and Cs+ equally well but was much less permeable to Na+, Li+ and protons. Single-channel measurements revealed a linear current–voltage relationship and three unitary conductance states of 15, 11, and 8 pS, using symmetric 150 mM KCl solutions. Measured macroscopic K+ fluxes varied considerably among different preparations, suggesting some unknown regulation of the channel; the variability appeared to arise from variation in the channel's open probability, not the unit conductance or the number of channels present. The recorded single-channel events and the selectivity data are remarkably similar to those reported for antibiotic channel-forming ionophore gramicidin. We believe that the variability in both macroscopic permeability experiments and single-channel experiments may reflect a variable contamination with gramicidin applied to the animals as the topical antibiotic V-Sporin.Key words: cyclic GMP gated channel, ion channel, rod photoreceptor, gramicidin.

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34

Poxleitner, M., J. Seitz-Beywl, and K. Heinzinger. "Ion Transport through Gramicidin A. Water Structure and Functionality." Zeitschrift für Naturforschung C 48, no. 7-8 (August 1, 1993): 654–65. http://dx.doi.org/10.1515/znc-1993-7-820.

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Dynamics (MD) simulations were performed on a gramicidin A dimer model representing a transmembrane channel. Different from previous simulations the peptide was in contact with bulk water at both ends of the dimer to guarantee a realistic description of the hydration of the biomolecule. The flexible BJH model for water was employed in the simulations and the gramicidin-water, gramicidin-ion and ion-water potentials used are based on molecular orbital calculations. The water structure near the gramicidin was investigated first by a simulation without ions, while for the energy profiles of the ion transport through the channel a potassium or a sodium ion was added. These investigations provide a detailed and conclusive picture on a molecular level of the role of water in the ion transport through a gramicidin A channel and can explain the experimental results on the selectivity between alkali ions, their double or even triple occupancy, the exclusion or permeability of anions depending upon cation concentration and the consequences of differences in the ionic charge. The investigation demonstrate that the water molecules around the gramicidin behave as an integral part of the peptide and the functionality is the result of the whole complex biomolecule-water.

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35

Kaliman, I. A., A. A. Moskovsky, S. S. Konyukhov, and A. V. Nemukhin. "Simulation of proton transport in the gramicidin A channel." Moscow University Chemistry Bulletin 63, no. 5 (October 2008): 241–44. http://dx.doi.org/10.3103/s0027131408050015.

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36

Rokitskaya, T. I., Y. N. Antonenko, E. A. Kotova, A. Anastasiadis, and F. Separovic. "Effect of Avidin on Channel Kinetics of Biotinylated Gramicidin." Biochemistry 39, no. 42 (October 2000): 13053–58. http://dx.doi.org/10.1021/bi0007876.

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37

Wallace, B. A. "Crystallographic studies of a transmembrane ion channel, gramicidin A." Progress in Biophysics and Molecular Biology 57, no. 2 (January 1992): 59–69. http://dx.doi.org/10.1016/0079-6107(92)90004-p.

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38

Roux, B., and M. Karplus. "The normal modes of the gramicidin-A dimer channel." Biophysical Journal 53, no. 3 (March 1988): 297–309. http://dx.doi.org/10.1016/s0006-3495(88)83107-2.

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39

Sawyer, D. B., R. E. Koeppe, and O. S. Andersen. "Gramicidin single-channel properties show no solvent-history dependence." Biophysical Journal 57, no. 3 (March 1990): 515–23. http://dx.doi.org/10.1016/s0006-3495(90)82567-4.

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40

Providence, L. L., O. S. Andersen, D. V. Greathouse, R. E. Koeppe, and R. Bittman. "Gramicidin Channel Function Does Not Depend on Phospholipid Chirality." Biochemistry 34, no. 50 (December 1995): 16404–11. http://dx.doi.org/10.1021/bi00050a022.

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41

Huo, S., S. Arumugam, and T. A. Cross. "Hydrogen exchange in the lipid bilayer-bound gramicidin channel." Solid State Nuclear Magnetic Resonance 7, no. 3 (December 1996): 177–83. http://dx.doi.org/10.1016/s0926-2040(96)01260-x.

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42

Langs, David A. "Structure of the ion channel peptide antibiotic gramicidin A." Biopolymers 28, no. 1 (January 1989): 259–66. http://dx.doi.org/10.1002/bip.360280126.

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43

Sung, Shen-Shu, and Peter C. Jordan. "The interaction of Cl− with a gramicidin-like channel." Biophysical Chemistry 27, no. 1 (July 1987): 1–6. http://dx.doi.org/10.1016/0301-4622(87)80041-8.

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44

Sokolov, Yuri V., Saskia C. Milton, Charles G. Glabe, and James E. Hall. "Amyloid Oligomers Alter The Conductance Of The Gramicidin Channel." Biophysical Journal 96, no. 3 (February 2009): 158a. http://dx.doi.org/10.1016/j.bpj.2008.12.719.

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45

Rokitskaya, Tatyana I., Elena A. Kotova, and Yuri N. Antonenko. "Tandem Gramicidin Channels Cross-linked by Streptavidin." Journal of General Physiology 121, no. 5 (April 28, 2003): 463–76. http://dx.doi.org/10.1085/jgp.200208780.

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The interaction of biotin-binding proteins with biotinylated gramicidin (gA5XB) was studied by monitoring single-channel activity and sensitized photoinactivation kinetics. It was discovered that the addition of streptavidin or avidin to the bathing solutions of a bilayer lipid membrane (BLM) with incorporated gA5XB induced the opening of a channel characterized by approximately doubled single-channel conductance and extremely long open-state duration. We believe that the deceleration of the photoinactivation kinetics observed here with streptavidin and previously (Rokitskaya, T.I., Y.N. Antonenko, E.A. Kotova, A. Anastasiadis, and F. Separovic. 2000. Biochemistry. 39:13053–13058) with avidin reflects the formation of long-lived channels of this type. Both opening and closing of the double-conductance channels occurred via a transient sub-state of the conductance coinciding with that of the usual single-channel transition. The appearance of the double-conductance channels after the addition of streptavidin was preceded by bursts of fast fluctuations of the current with the open state duration of the individual events of 60 ms. The streptavidin-induced double-conductance channels appeared to be inherent only to the gramicidin analogue with a biotin group linked to the COOH terminus through a long linker arm. Including biotinylated phosphatidylethanolamine into the BLM prevented the formation of the double-conductance channels even with the excess streptavidin. In view of the results obtained here, it is suggested that the double-conductance channel represents a tandem of two neighboring gA5XB channels with their COOH termini being cross-linked by the bound streptavidin at both sides of the BLM. The finding that streptavidin induces the formation of the tandem gramicidin channel comprising two channels functioning in concert is considered to be relevant to the physiologically important phenomenon of ligand-induced receptor oligomerization.

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46

Lundbæk, Jens A., Pia Birn, Anker J. Hansen, Rikke Søgaard, Claus Nielsen, Jeffrey Girshman, Michael J. Bruno, et al. "Regulation of Sodium Channel Function by Bilayer Elasticity." Journal of General Physiology 123, no. 5 (April 26, 2004): 599–621. http://dx.doi.org/10.1085/jgp.200308996.

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Membrane proteins are regulated by the lipid bilayer composition. Specific lipid–protein interactions rarely are involved, which suggests that the regulation is due to changes in some general bilayer property (or properties). The hydrophobic coupling between a membrane-spanning protein and the surrounding bilayer means that protein conformational changes may be associated with a reversible, local bilayer deformation. Lipid bilayers are elastic bodies, and the energetic cost of the bilayer deformation contributes to the total energetic cost of the protein conformational change. The energetics and kinetics of the protein conformational changes therefore will be regulated by the bilayer elasticity, which is determined by the lipid composition. This hydrophobic coupling mechanism has been studied extensively in gramicidin channels, where the channel–bilayer hydrophobic interactions link a “conformational” change (the monomer↔dimer transition) to an elastic bilayer deformation. Gramicidin channels thus are regulated by the lipid bilayer elastic properties (thickness, monolayer equilibrium curvature, and compression and bending moduli). To investigate whether this hydrophobic coupling mechanism could be a general mechanism regulating membrane protein function, we examined whether voltage-dependent skeletal-muscle sodium channels, expressed in HEK293 cells, are regulated by bilayer elasticity, as monitored using gramicidin A (gA) channels. Nonphysiological amphiphiles (β-octyl-glucoside, Genapol X-100, Triton X-100, and reduced Triton X-100) that make lipid bilayers less “stiff”, as measured using gA channels, shift the voltage dependence of sodium channel inactivation toward more hyperpolarized potentials. At low amphiphile concentration, the magnitude of the shift is linearly correlated to the change in gA channel lifetime. Cholesterol-depletion, which also reduces bilayer stiffness, causes a similar shift in sodium channel inactivation. These results provide strong support for the notion that bilayer–protein hydrophobic coupling allows the bilayer elastic properties to regulate membrane protein function.

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47

Hianik, T., V. I. Passechnik, F. Paltauf, and A. Hermetter. "Nonlinearity of current-voltage characteristics of the gramicidin channel and the structure of gramicidin molecule." Bioelectrochemistry and Bioenergetics 34, no. 1 (June 1994): 61–68. http://dx.doi.org/10.1016/0302-4598(94)80010-3.

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48

Fyles, Thomas M., Tony D. James, and Katharine C. Kaye. "Biomimetic ion transport: on the mechanism of ion transport by an artificial ion channel mimic." Canadian Journal of Chemistry 68, no. 6 (June 1, 1990): 976–78. http://dx.doi.org/10.1139/v90-153.

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The influx of cations into vesicles mediated by a synthetic transporter is coupled to proton efflux and may be quantified by a pH-stat technique. The dependence of the transport upon cation type and concentration, upon transporter concentration, and upon temperature has been examined. The synthetic transporter is closely similar to the natural channel forming compound gramicidin, and significantly different from the carrier valinomycin, with respect to the variables examined. Keywords: ion transport, vesicle membrane, channel, gramicidin, transport mechanism.

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49

Goforth, Robyn L., Aung K. Chi, Denise V. Greathouse, Lyndon L. Providence, Roger E. Koeppe, and Olaf S. Andersen. "Hydrophobic Coupling of Lipid Bilayer Energetics to Channel Function." Journal of General Physiology 121, no. 5 (April 28, 2003): 477–93. http://dx.doi.org/10.1085/jgp.200308797.

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The hydrophobic coupling between membrane-spanning proteins and the lipid bilayer core causes the bilayer thickness to vary locally as proteins and other “defects” are embedded in the bilayer. These bilayer deformations incur an energetic cost that, in principle, could couple membrane proteins to each other, causing them to associate in the plane of the membrane and thereby coupling them functionally. We demonstrate the existence of such bilayer-mediated coupling at the single-molecule level using single-barreled as well as double-barreled gramicidin channels in which two gramicidin subunits are covalently linked by a water-soluble, flexible linker. When a covalently attached pair of gramicidin subunits associates with a second attached pair to form a double-barreled channel, the lifetime of both channels in the assembly increases from hundreds of milliseconds to a hundred seconds—and the conductance of each channel in the side-by-side pair is almost 10% higher than the conductance of the corresponding single-barreled channels. The double-barreled channels are stabilized some 100,000-fold relative to their single-barreled counterparts. This stabilization arises from: first, the local increase in monomer concentration around a single-barreled channel formed by two covalently linked gramicidins, which increases the rate of double-barreled channel formation; and second, from the increased lifetime of the double-barreled channels. The latter result suggests that the two barrels of the construct associate laterally. The underlying cause for this lateral association most likely is the bilayer deformation energy associated with channel formation. More generally, the results suggest that the mechanical properties of the host bilayer may cause the kinetics of membrane protein conformational transitions to depend on the conformational states of the neighboring proteins.

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50

Tang, Pei, Pravat K. Mandal, and Martha Zegarra. "Effects of Volatile Anesthetic on Channel Structure of Gramicidin A." Biophysical Journal 83, no. 3 (September 2002): 1413–20. http://dx.doi.org/10.1016/s0006-3495(02)73912-x.

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