The Experts below are selected from a list of 189 Experts worldwide ranked by ideXlab platform
Isaiah T. Arkin - One of the best experts on this subject based on the ideXlab platform.
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Multiple site-specific Infrared Dichroism of CD3-ζ, a transmembrane helix bundle
Journal of molecular biology, 2002Co-Authors: Jaume Torres, John A. G. Briggs, Isaiah T. ArkinAbstract:The structure of the transmembrane domain of CD3-ζ a component of the T-cell receptor involved in signal transduction, has been studied in its native state (a lipid bilayer) by multiple site-specific Infrared Dichroism. For the first time, the transmembrane domain has been labelled at multiple positions along the sequence, representing a total of 11 samples, each labelled at a different residue with an isotopically modified carbonyl group, 13C18O. A strategy is outlined that, based on the above data, can yield the rotational orientation and the local helix tilt for each labelled residue, giving a detailed description of helix geometry. The results obtained indicate that the transmembrane segment is in an α-helical conformation throughout, with an average helix tilt of 12 °. The N-terminal side of the helix is more tilted than the C-terminal. In an accompanying paper we describe the implementation of the Infrared data in a model-building study of the CD3-ζ transmembrane complex. The model obtained is entirely consistent with results based on evolutionary conservation data. Taken together, this study represents the first step towards elucidation of the backbone structure of a transmembrane α-helical bundle by Infrared spectroscopy.
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C-Deuterated Alanine: A New Label to Study Membrane Protein Structure Using Site-Specific Infrared Dichroism
Biophysical journal, 2002Co-Authors: Jaume Torres, Isaiah T. ArkinAbstract:The helix tilt and rotational orientation of the transmembrane segment of M2, a 97-residue protein from the Influenza A virus that forms H(+)-selective ion channels, have been determined by attenuated total reflection site-specific Infrared Dichroism using a novel labeling approach. Triple C-deuteration of the methyl group of alanine in the transmembrane domain of M2 was used, as such modification shifts the asymmetric and symmetric stretching vibrations of the methyl group to a transparent region of the Infrared spectrum. Structural information can then be obtained from the dichroic ratios corresponding to these two vibrations. Two consecutive alanine residues were labeled to enhance signal intensity. The results obtained herein are entirely consistent with previous site-specific Infrared Dichroism and solid-state nuclear magnetic resonance experiments, validating C-deuterated alanine as an Infrared structural probe that can be used in membrane proteins. This new label adds to the previously reported (13)C [double bond] (18)O and C-deuterated glycine as a tool to analyze the structure of simple transmembrane segments and will also increase the feasibility of the study of polytopic membrane proteins with site-specific Infrared Dichroism.
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Structure of the Influenza C Virus CM2 Protein Transmembrane Domain Obtained by Site-specific Infrared Dichroism and Global Molecular Dynamics Searching
The Journal of biological chemistry, 2000Co-Authors: Andreas Kukol, Isaiah T. ArkinAbstract:The 115-residue protein CM2 from Influenza C virus has been recently characterized as a tetrameric integral membrane glycoprotein. Infrared spectroscopy and site-directed Infrared Dichroism were utilized here to determine its transmembrane structure. The transmembrane domain of CM2 is alpha-helical, and the helices are tilted by beta = (14.6 +/- 3.0) degrees from the membrane normal. The rotational pitch angle about the helix axis omega for the 1-(13)C-labeled residues Gly(59) and Leu(66) is omega = (218 +/- 17) degrees, where omega is defined as zero for a residue pointing in the direction of the helix tilt. A detailed structure was obtained from a global molecular dynamics search utilizing the orientational data as an energy refinement term. The structure consists of a left-handed coiled-coil with a helix crossing angle of Omega = 16 degrees. The putative transmembrane pore is occluded by the residue Met(65). In addition hydrogen/deuterium exchange experiments show that the core is not accessible to water.
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vpu Transmembrane Peptide Structure Obtained by Site-Specific Fourier Transform Infrared Dichroism and Global Molecular Dynamics Searching
Biophysical journal, 1999Co-Authors: Andreas Kukol, Isaiah T. ArkinAbstract:Abstract The recently developed method of site-directed Fourier transform Infrared Dichroism for obtaining orientational constraints of oriented polymers is applied here to the transmembrane domain of the vpu protein from the human immunodeficiency virus type 1 (HIV-1). The Infrared spectra of the 31-residue-long vpu peptide reconstituted in lipid vesicles reveal a predominantly α -helical structure. The Infrared Dichroism data of the 13 C-labeled peptide yielded a helix tilt β =(6.5±1.7)° from the membrane normal. The rotational pitch angle ω, defined as zero for a residue located in the direction of the helix tilt, is ω=(283±11)° for the 13 C labels Val 13 /Val 20 and ω=(23±11)° for the 13 C labels Ala 14 /Val 21 . A global molecular dynamics search protocol restraining the helix tilt to the experimental value was performed for oligomers of four, five, and six subunits. From 288 structures for each oligomer, a left-handed pentameric coiled coil was obtained, which best fits the experimental data. The structure reveals a pore occluded by Trp residues at the intracellular end of the transmembrane domain.
Andreas Kukol - One of the best experts on this subject based on the ideXlab platform.
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The Transmembrane Domain of the Oncogenic Mutant ErbB-2 Receptor: A Structure Obtained from Site-specific Infrared Dichroism and Molecular Dynamics
Journal of molecular biology, 2006Co-Authors: Andrew J. Beevers, Andreas KukolAbstract:ErbB-2 is a member of the family of epidermal growth factor receptors, which shows an oncogenic mutation in the rat gene neu, Val664Glu in the transmembrane domain that causes permanent dimerisation and subsequently leads to uncontrollable cell division and tumour formation. We have obtained the a-helical structure of the mutant transmembrane domain dimer experimentally with site-specific Infrared Dichroism (SSID) based on six transmembrane peptides with (CO)-C-13-O-18 carbonyl group-labelled residues. The derived orientational data indicate a local helix tilt ranging from 28(6) to 22(4). Altogether using orientational constraints from SSID and experimental a-helical constraints while performing a systematic conformational search including molecular dynamics simulation in a lipid bilayer, we have obtained a unique experimentally defined atomic structure. The resulting structure consists of a right handed a-helical bundle with the residues Ile659, Val663, Leu667, Ile671, Val674 and Leu679 in the dimerisation interface. The right-handed bundle is in contrast to the left-handed structures obtained in previous modelling efforts. In order to facilitate tight helical packing, the spacious Glu664 residues do not interact directly but with water molecules that enter the bilayer. (c) 2006 Elsevier Ltd. All rights reserved.
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Structure of the Influenza C Virus CM2 Protein Transmembrane Domain Obtained by Site-specific Infrared Dichroism and Global Molecular Dynamics Searching
The Journal of biological chemistry, 2000Co-Authors: Andreas Kukol, Isaiah T. ArkinAbstract:The 115-residue protein CM2 from Influenza C virus has been recently characterized as a tetrameric integral membrane glycoprotein. Infrared spectroscopy and site-directed Infrared Dichroism were utilized here to determine its transmembrane structure. The transmembrane domain of CM2 is alpha-helical, and the helices are tilted by beta = (14.6 +/- 3.0) degrees from the membrane normal. The rotational pitch angle about the helix axis omega for the 1-(13)C-labeled residues Gly(59) and Leu(66) is omega = (218 +/- 17) degrees, where omega is defined as zero for a residue pointing in the direction of the helix tilt. A detailed structure was obtained from a global molecular dynamics search utilizing the orientational data as an energy refinement term. The structure consists of a left-handed coiled-coil with a helix crossing angle of Omega = 16 degrees. The putative transmembrane pore is occluded by the residue Met(65). In addition hydrogen/deuterium exchange experiments show that the core is not accessible to water.
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vpu Transmembrane Peptide Structure Obtained by Site-Specific Fourier Transform Infrared Dichroism and Global Molecular Dynamics Searching
Biophysical journal, 1999Co-Authors: Andreas Kukol, Isaiah T. ArkinAbstract:Abstract The recently developed method of site-directed Fourier transform Infrared Dichroism for obtaining orientational constraints of oriented polymers is applied here to the transmembrane domain of the vpu protein from the human immunodeficiency virus type 1 (HIV-1). The Infrared spectra of the 31-residue-long vpu peptide reconstituted in lipid vesicles reveal a predominantly α -helical structure. The Infrared Dichroism data of the 13 C-labeled peptide yielded a helix tilt β =(6.5±1.7)° from the membrane normal. The rotational pitch angle ω, defined as zero for a residue located in the direction of the helix tilt, is ω=(283±11)° for the 13 C labels Val 13 /Val 20 and ω=(23±11)° for the 13 C labels Ala 14 /Val 21 . A global molecular dynamics search protocol restraining the helix tilt to the experimental value was performed for oligomers of four, five, and six subunits. From 288 structures for each oligomer, a left-handed pentameric coiled coil was obtained, which best fits the experimental data. The structure reveals a pore occluded by Trp residues at the intracellular end of the transmembrane domain.
Jaume Torres - One of the best experts on this subject based on the ideXlab platform.
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Multiple site-specific Infrared Dichroism of CD3-ζ, a transmembrane helix bundle
Journal of molecular biology, 2002Co-Authors: Jaume Torres, John A. G. Briggs, Isaiah T. ArkinAbstract:The structure of the transmembrane domain of CD3-ζ a component of the T-cell receptor involved in signal transduction, has been studied in its native state (a lipid bilayer) by multiple site-specific Infrared Dichroism. For the first time, the transmembrane domain has been labelled at multiple positions along the sequence, representing a total of 11 samples, each labelled at a different residue with an isotopically modified carbonyl group, 13C18O. A strategy is outlined that, based on the above data, can yield the rotational orientation and the local helix tilt for each labelled residue, giving a detailed description of helix geometry. The results obtained indicate that the transmembrane segment is in an α-helical conformation throughout, with an average helix tilt of 12 °. The N-terminal side of the helix is more tilted than the C-terminal. In an accompanying paper we describe the implementation of the Infrared data in a model-building study of the CD3-ζ transmembrane complex. The model obtained is entirely consistent with results based on evolutionary conservation data. Taken together, this study represents the first step towards elucidation of the backbone structure of a transmembrane α-helical bundle by Infrared spectroscopy.
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C-Deuterated Alanine: A New Label to Study Membrane Protein Structure Using Site-Specific Infrared Dichroism
Biophysical journal, 2002Co-Authors: Jaume Torres, Isaiah T. ArkinAbstract:The helix tilt and rotational orientation of the transmembrane segment of M2, a 97-residue protein from the Influenza A virus that forms H(+)-selective ion channels, have been determined by attenuated total reflection site-specific Infrared Dichroism using a novel labeling approach. Triple C-deuteration of the methyl group of alanine in the transmembrane domain of M2 was used, as such modification shifts the asymmetric and symmetric stretching vibrations of the methyl group to a transparent region of the Infrared spectrum. Structural information can then be obtained from the dichroic ratios corresponding to these two vibrations. Two consecutive alanine residues were labeled to enhance signal intensity. The results obtained herein are entirely consistent with previous site-specific Infrared Dichroism and solid-state nuclear magnetic resonance experiments, validating C-deuterated alanine as an Infrared structural probe that can be used in membrane proteins. This new label adds to the previously reported (13)C [double bond] (18)O and C-deuterated glycine as a tool to analyze the structure of simple transmembrane segments and will also increase the feasibility of the study of polytopic membrane proteins with site-specific Infrared Dichroism.
Steve Granick - One of the best experts on this subject based on the ideXlab platform.
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Infrared Dichroism and Surface Conformational Dynamics of Adsorbed Poly(dimethylsiloxane)
Macromolecules, 1998Co-Authors: Iwao Soga, Steve GranickAbstract:We examined polymer conformations at a strongly adsorbing solid surface and their evolution with elapsed time during the adsorption process. Poly(dimethylsiloxane) (PDMS: Mw = 118 000; Mw/Mn = 1.1...
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Chain flattening and Infrared Dichroism of adsorbed poly(ethylene oxide)
Colloids and Surfaces A: Physicochemical and Engineering Aspects, 1996Co-Authors: Erwin P. Enriquez, Steve GranickAbstract:Abstract The adsorption of poly(ethylene oxide), PEO, from dilute solutions in 1 mM aqueous NaCl to germanium at 30°C, was investigated by polarized Infrared spectroscopy in attenuated total internal reflection (ATR). PEO aggregation could be prevented with careful sample preparation. After adsorption, chain anisotropy was deduced from the COC stretching vibrations along the polymer backbone and found to indicate substantial backbone alignment parallel to the surface.
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Infrared Dichroism chain flattening and the bound fraction histogram in adsorbed poly methyl methacrylate layers
Macromolecules, 1995Co-Authors: Peter Frantz, Steve GranickAbstract:We examine the distribution of adsorption substates, in contrast to their average. The distribution of Infrared Dichroism and bound fraction were determined in a model system (poly(methyl methacrylate) adsorbed chiefly by hydrogen bonding onto oxidized silicon from CCl 4 ). The method was Infrared spectroscopy in attenuated total reflection (FTIR-ATR). From the surface excess (Γ), dichroic ratio (D zx ), and fraction of carbonyl groups bound to the surface (p), a broad distribution of conformations was found to prevail, from severely flattened (p 0.5 and D zx << 1 for the asymmetric methyl stretch) to nearly solution-like (p 0.1 and D zx 1 for the asymmetric methyl stretch). The extent of flattening depended mainly on the number of adsorption sites available to each chain at the time it deposited to the surface ; chains that adsorbed later, finding fewer and fewer surface sites available, then became attached by fewer and fewer segments. This in turn implied that chains which arrived initially had the center-of-mass closer to the solid surface than those which arrived later. Conformational rearrangements were not observed on the experimental time scale of 3 h ; this allowed determination of the distribution of conformational substates by subtraction of sequentially-acquired Infrared spectra. The broad and asymmetric distribution of conformational substates appeared to originate, predictably, from the piecemeal process by which the surface was coated. It presents analogies with issues of random sequential adsorption.
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Infrared Dichroism, Chain Flattening, and the Bound Fraction Histogram in Adsorbed Poly(methyl methacrylate) Layers
Macromolecules, 1995Co-Authors: Peter Frantz, Steve GranickAbstract:We examine the distribution of adsorption substates, in contrast to their average. The distribution of Infrared Dichroism and bound fraction were determined in a model system (poly(methyl methacrylate) adsorbed chiefly by hydrogen bonding onto oxidized silicon from CCl 4 ). The method was Infrared spectroscopy in attenuated total reflection (FTIR-ATR). From the surface excess (Γ), dichroic ratio (D zx ), and fraction of carbonyl groups bound to the surface (p), a broad distribution of conformations was found to prevail, from severely flattened (p 0.5 and D zx
Lucien Monnerie - One of the best experts on this subject based on the ideXlab platform.
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Relaxation Dynamics in Bimodal Polystyrene Melts: A Fourier-Transform Infrared Dichroism and Small-Angle Neutron Scattering Study
Macromolecules, 1996Co-Authors: C. Hayes, Liliane Bokobza, François Boué, Eduardo Mendes, Lucien MonnerieAbstract:Polymer chain orientational relaxation has been studied in bimodal polystyrene melts composed of long hydrogenated chains and 20 wt % short deuterated chains. Thin polymer films were uniaxially stretched above the glass transition temperature, relaxed, and then quenched after different relaxation times. The chain orientation in the deformed samples was analyzed on different length scales using two different techniquesFourier-transform Infrared Dichroism (FTIRD) and small-angle neutron scattering (SANS). The local orientational relaxation of the long matrix chains, as well as that of the short deuterated chains, is measured using FTIRD. It is shown that the relaxation of the long chains (Mw ∼2 × 106) is not affected by the presence of the short chains, for the particular weight fraction of short chains (20%), and for the two different short chain masses used: Mw ∼27 000 and Mw ∼188 000. The SANS isointensity patterns are elliptical in shape for short relaxation times but take the form of lozenges when the...
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Analysis of orientational relaxation in binary blends of long and short polystyrene chains by fourier transform Infrared Dichroism and small‐angle neutron scattering
Macromolecular Symposia, 1995Co-Authors: C. Hayes, Liliane Bokobza, François Boué, Eduardo Mendes, Lucien MonnerieAbstract:Measurements of the local orientational order and average chain anisotropy in non-uniform polystyrene are reported. Fourier-transform Infrared Dichroism spectroscopy has been used to determine the effects of short deuterated chains (Mw = 500 to 188 000) on the orientational relaxation of long entangled chains (Mw = 2 000 000) in bidisperse melts uniaxially deformed above the glass transition temperature. While the long-chain relaxation is found to be dependent on the short-chain concentration, the local orientational order of the latter is molecular weight dependent consistent with the classical relaxation theories. The FTIR experiments are also combined with small-angle neutron scattering measurements which probe the deuterated-chain anisotropy in the defomed melts. There is evidence, from the combination of the two techniques, that although the short chains possess a negligible local orientational order, there exists an important anisotopy in the short chain distribution in space.