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Das S, Ben Haj Salah K, Djibo M, Inguimbert N. Peptaibols as a model for the insertions of chemical modifications. Arch Biochem Biophys 2018; 658:16-30. [DOI: 10.1016/j.abb.2018.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
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2
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2014.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:98-105. [PMID: 24071593 DOI: 10.1016/j.bbamem.2013.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.
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Affiliation(s)
- Asif Rahaman
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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Larda ST, Bokoch MP, Evanics F, Prosser RS. Lysine methylation strategies for characterizing protein conformations by NMR. JOURNAL OF BIOMOLECULAR NMR 2012; 54:199-209. [PMID: 22960995 DOI: 10.1007/s10858-012-9664-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 08/17/2012] [Indexed: 05/20/2023]
Abstract
In the presence of formaldehyde and a mild reducing agent, reductive methylation is known to achieve near complete dimethylation of protein amino groups under non-denaturing conditions, in aqueous media. Amino methylation of proteins is employed in mass spectrometric, crystallographic, and NMR studies. Where biosynthetic labeling is prohibitive, amino (13)C-methylation provides an attractive option for monitoring folding, kinetics, protein-protein and protein-DNA interactions by NMR. Here, we demonstrate two improvements over traditional (13)C-reductive methylation schemes: (1) By judicious choice of stoichiometry and pH, ε-aminos can be preferentially monomethylated. Monomethyl tags are less perturbing and generally exhibit improved resolution over dimethyllysines, and (2) By use of deuterated reducing agents and (13)C-formaldehyde, amino groups can be labeled with (13)CH(2)D tags. Use of deutero-(13)C-formaldehyde affords either (13)CHD(2), or (13)CD(3) probes depending on choice of reducing agent. Making use of (13)C-(2)H scalar couplings, we demonstrate a filtering scheme that eliminates natural abundance (13)C signal.
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Affiliation(s)
- Sacha Thierry Larda
- Department of Chemical and Physical Sciences, University of Toronto, UTM, 3359 Mississauga Rd. North, Mississauga, ON L5L 1C6, Canada.
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Zhang R, Lev B, Cuervo JE, Noskov SY, Salahub DR. A Guide to QM/MM Methodology and Applications. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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6
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Gokel GW, Barkey N. Transport of chloride ion through phospholipid bilayers mediated by synthetic ionophores. NEW J CHEM 2009. [DOI: 10.1039/b817245p] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Futaki S, Asami K. Ligand-induced extramembrane conformation switch controlling alamethicin assembly and the channel current. Chem Biodivers 2007; 4:1313-22. [PMID: 17589883 DOI: 10.1002/cbdv.200790112] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this review, we describe our approach to creating artificial receptor-channel proteins or sensor systems, using an extramembrane segment conformationally switchable by external stimuli. Alamethicin is known to self-assemble in membranes to form ion channels with various open states. Employment of an alpha-helical leucine-zipper segment resulted in the effective modulation of the association states of alamethicin to produce a single predominant channel-open state. A decrease in the helical content of the extramembrane segments was found to induce a channel-current increase. Therefore, conformational changes in the extramembrane segments induced by the interaction with ligands can be reflected in the current levels.
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Affiliation(s)
- Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
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Leitgeb B, Szekeres A, Manczinger L, Vágvölgyi C, Kredics L. The history of alamethicin: a review of the most extensively studied peptaibol. Chem Biodivers 2007; 4:1027-51. [PMID: 17589875 DOI: 10.1002/cbdv.200790095] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Balázs Leitgeb
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, Hungary
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Abstract
In this short review article, the effects of covalent tethering of alamethicin molecules on channel-forming behavior are described. Broadly speaking, these chemical modifications have provided insight into all three aspects of channel behavior: the structure of the conducting state, the ion-selectivity and ion-permeation properties, and the voltage dependence. Each of these aspects are discussed in turn.
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Affiliation(s)
- G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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Abstract
A recently developed implicit membrane model (IMM1) is supplemented with a Gouy-Chapman term describing counterion-screened electrostatic interactions of a solute with negatively charged membrane lipids. The new model is tested on peptides that bind to anionic membranes. Pentalysine binds just outside the plane of negative charge, whereas Lys-Phe peptides insert their aromatic rings into the hydrophobic core. Melittin and magainin 2 bind more strongly to anionic than to neutral membranes and in both cases insert their hydrophobic residues into the hydrocarbon core. The third domain of Antennapedia homeodomain (penetratin) binds as an alpha-helix in the headgroup region. Cardiotoxin II binds strongly to anionic membranes but marginally to neutral ones. In all cases, the location and configuration of the peptides are consistent with experimental data, and the effective energy changes upon binding compare favorably with experimental binding free energies. The model opens the way to exploring the effect of membrane charge on the location, conformation, and dynamics of a large variety of biologically active peptides on membranes.
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Mottamal M, Lazaridis T. Voltage-dependent energetics of alamethicin monomers in the membrane. Biophys Chem 2006; 122:50-7. [PMID: 16542770 DOI: 10.1016/j.bpc.2006.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/11/2006] [Accepted: 02/11/2006] [Indexed: 11/18/2022]
Abstract
The implicit membrane model IMM1 is extended to include the effect of transmembrane potential and used to investigate the optimal membrane binding configurations and energies for alamethicin helices. In the absence of voltage, the lowest energy configuration is on the membrane surface with a tilt allowing the N terminus to be fully buried. Slightly higher in energy is an also tilted configuration with the N terminus deeper in the membrane and almost crossing the membrane. In 26A membranes and in the presence of 0.1V voltage, the TM orientation becomes lower in energy. This is consistent with the assumption that voltage induces a transition from the interfacial to the inserted (TM) orientation. This effect of voltage is smaller in thicker membranes. The results are compared to previous experimental and theoretical studies and the findings are discussed in relation to the mechanism of channel formation by alamethicin.
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Affiliation(s)
- Madhusoodanan Mottamal
- Department of Chemistry, City College of New York/CUNY, 138th St. and Convent Ave, New York, NY 10031, USA
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Peggion C, Coin I, Toniolo C. Total synthesis in solution of alamethicin F50/5 by an easily tunable segment condensation approach. Biopolymers 2005; 76:485-93. [PMID: 15499566 DOI: 10.1002/bip.20161] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A total synthesis in solution of the 19-mer peptide component F50/5 of alamethicin, the most extensively investigated among the channel-former peptaibol antibiotics, is reported. Three peptide segments (A, B, C) were prepared and assembled, followed by incorporation of the acetylated N-terminal amino acid. The synthetic modules B and C are characterized by three Glu(OMe) residues (at positions 7, 18, and 19) that, after completion of the synthesis, were reacted with ammonia to provide alamethicin F50/5. By use of this general strategy, we also prepared the [Gln7, Glu(OMe)18,19] alamethicin F50/5 analogue. The purity and conformation of the final products were assessed by chromatographic, spectrometric, and spectroscopic techniques. This tunable segment condensation approach will pave the way for an easy synthesis of alamethicin analogues bearing amino acid residues with desired side-chain probes even at the N-terminus and in internal positions of the sequence.
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Affiliation(s)
- Cristina Peggion
- Department of Chemistry, University of Padova, 35131 Padova, Italy
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Ash WL, Zlomislic MR, Oloo EO, Tieleman DP. Computer simulations of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:158-89. [PMID: 15519314 DOI: 10.1016/j.bbamem.2004.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.
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Affiliation(s)
- Walter L Ash
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB, Canada T2N 1N4
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Srinivas G, Discher DE, Klein ML. Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics. NATURE MATERIALS 2004; 3:638-44. [PMID: 15300242 DOI: 10.1038/nmat1185] [Citation(s) in RCA: 268] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Accepted: 06/17/2004] [Indexed: 05/03/2023]
Abstract
Block-copolymer amphiphiles have been observed to assemble into vesicles and other morphologies long known for lipids but with remarkably different properties. Coarse-grain molecular dynamics (CG-MD) is used herein to elaborate the structures and properties of diblock copolymer assemblies in water. By varying the hydrophilic/hydrophobic ratio of the copolymer in line with experiment, bilayer, cylindrical and spherical micelle morphologies spontaneously assemble. Varying the molecular weight (MW) with hydrophilic/hydrophobic ratio appropriate to a bilayer yields a hydrophobic core thickness that scales for large MW as a random coil polymer, in agreement with experiment. The extent of hydrophobic-segment overlap in the core increases nonlinearly with MW, indicative of chain entanglements and consistent with the dramatic decrease reported for lateral mobility in polymer vesicles. Calculated trends with MW as well as hydrophilic/hydrophobic ratio thus agree with experiment, demonstrating that CG-MD simulations provide a rational design tool for diblock copolymer assemblies.
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Affiliation(s)
- Goundla Srinivas
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA
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Schaldach CM, Bourcier WL, Paul PH, Wilson WD. Electrostatic potentials and fields in the vicinity of engineered nanostructures. J Colloid Interface Sci 2004; 275:601-11. [PMID: 15178293 DOI: 10.1016/j.jcis.2004.02.092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Accepted: 02/25/2004] [Indexed: 10/26/2022]
Abstract
We have developed a method for calculating the electrostatic potentials and fields in the vicinity of geometrically complex engineered nanostructures composed of varying materials in electrolytes of arbitrary pH and ionic strength. The method involves direct summation of charged Debye-Hückel spheres composing the nanostructural surfaces and, by including charge redistribution on the surface of conducting materials held at constant potential, is applicable to mixed boundary conditions. The method is validated by comparison to analytical solutions for an infinite plane (Gouy-Chapman), an infinite cylinder (Bessel functions), and an infinite plane which contains a hole and which is held at constant potential. Excellent agreement between the potentials obtained by our numerical method and the closed form solutions is found for these conditions. The method is applied to the calculation of the electric field enhancement in the vicinity of a nanomembrane whose pore wall is held at constant charge and whose membrane surfaces are held at constant potential. The electric field is found to be enhanced by the charge buildup in the rim of the hole of the nanomembrane; the buildup results from the potential being held constant in the conducting region. Ion concentrations are also calculated. Positive ion rejection is found to be enhanced by this charge buildup in the region of the rim when a constant positive potential is applied.
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Affiliation(s)
- C M Schaldach
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
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Lougheed T, Zhang Z, Andrew Woolley G, Borisenko V. Engineering charge selectivity in model ion channels. Bioorg Med Chem 2004; 12:1337-42. [PMID: 15018905 DOI: 10.1016/j.bmc.2003.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2003] [Revised: 06/03/2003] [Accepted: 06/08/2003] [Indexed: 11/21/2022]
Abstract
Most ion channel proteins exhibit some degree of charge selectivity, that is, an ability to conduct ions of one charge more efficiently than ions of the opposite charge. The structural origins of charge selectivity remain incompletely understood despite recent advances in the determination of cation-selective and anion-selective channel protein structures. Helix bundle channels formed via self-assembly of the peptide alamethicin provide a tractable model system for exploring the structural basis of charge selectivity. We synthesized covalently-linked alamethicin dimers, with amino acid substitutions at position 18 [lysine (Lys), arginine (Arg), glutamine (Gln), 2,3-diaminopropionic acid (Dpr)] in each helix, to assess the role of this position as a charge-selectivity determinant in alamethicin channels. Of the position 18 substitutions investigated, the Lys derivative exhibited the greatest degree of anion selectivity. Arg-containing channels were slightly less anion-selective than Lys. Interestingly, Dpr channels showed cation selectivity nearly equivalent to that exhibited by the neutral Gln derivative. We suggest that this result is due to a wider pore diameter that permits a greater number of counter-ions leading to enhanced charge screening and a lower effective side-chain positive charge.
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Affiliation(s)
- Tyler Lougheed
- Department of Chemistry, 80 St George St University of Toronto, Toronto, Ontario, Canada M5S 3H6
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Mafé S, Ramı́rez P, Alcaraz A. Simple molecular model for the binding of antibiotic molecules to bacterial ion channels. J Chem Phys 2003. [DOI: 10.1063/1.1606438] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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