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Bengt Norden - One of the best experts on this subject based on the ideXlab platform.

  • tryptophan orientations in membrane bound gramicidin and melittin a comparative Linear Dichroism study on transmembrane and surface bound peptides
    Biochimica et Biophysica Acta, 2011
    Co-Authors: Frida Svensson, Bengt Norden, Per Lincoln, Elin K Esbjorner
    Abstract:

    In the search for methods to study structure and function of membrane-associated proteins and peptides flow Linear Dichroism, LD, spectroscopy has emerged as a promising technique. Using shear-aligned lipid vesicles, conformations and binding geometries of membrane-bound bio-macromolecules can be assessed. Here we investigate anchoring properties and specific orientations of tryptophan relative to the peptide backbone and to the membrane normal for the model peptides gramicidin and melittin. We have monitored the conformational change associated with the refolding of non-channel gramicidin into its channel form, and quantitatively determined the average orientations of its tryptophan transition moments, suggesting that these residues adopt a well-defined orientation at the membrane interface. An important conclusion regards the structural variation of gramicidin between these two distinct transmembrane forms. Whilst circular Dichroism (CD) spectra, as has been reported before, vary strongly between the two forms suggesting their structures might be quite different, the LD results clearly evidence both the peptide backbone orientation and tryptophan side-chain positioning to be very similar. The latter are oriented in accord with what is expected from their role to anchor peptide termini to the membrane surface. The variations in CD could be due to, the in LD observed, minor shifts in mutual orientation and distance between neighbouring tryptophans sensitively determining their exciton interactions. Our data dispute that the non-channel form of membrane-bound gramicidin would be any of the intertwined forms often observed in crystal as the positioning of tryptophans along the peptide axis would not be compatible with the strong interfacial positioning observed here. The general role of tryptophans as interfacial anchors is further assessed for melittin whose conformation shows considerable angular spread, consistent with a carpet model of its mechanism for induced membrane leakage, and a predominantly surface-aligned membrane orientation governed by amphipathic interactions.

  • Linear Dichroism and Circular Dichroism: A Textbook on Polarized-Light Spectroscopy
    2010
    Co-Authors: Bengt Norden, Alison Rodger, Timothy R. Dafforn
    Abstract:

    Spectroscopy, chirality, and oriented systems Circular Dichroism of biomolecules Linear Dichroism of biomolecules Linear Dichroism of small molecules Analysis of circular Dichroism: electric dipole allowed transitions Analysis of circular Dichroism: magnetic dipole allowed transitions and magnetic CD Circular Dichroism formalism Appendices

  • circular Dichroism and Linear Dichroism
    1997
    Co-Authors: Bengt Norden, Alison Rodger
    Abstract:

    Circular Dichroism (CD) is the difference in absorption, A, of left and right circularly polarized light, Equation (1): (1) For randomly oriented systems such as solutions of molecules, only chiral molecules will show any CD intensity corresponding to their absorption bands. Chiral molecules are those molecules that cannot be superposed on their mirror images. Chiral is derived from the Greek word χϵιρ meaning hand, hence the alternate term for chirality, ‘handedness’. Two molecules that are mirror images of each other are often referred to as enantiomers, and equimolar mixtures of two enatiomers form a racemic mixture, which has no net CD intensity in solution. CD can be used to analyze chiral structures such as protein secondary structure in molecules and to probe interactions between chiral molecules and other molecules. Linear Dichroism (LD) is the difference in absorption of light Linearly polarized parallel and perpendicular to an orientation axis, Equation (2): (2) LD can be used to provide orientation information about subunits of a molecular system such as small molecules absorbed onto stretched films, flow-oriented DNAs and fibrous proteins, and lipid bilayer systems.

  • structure of uvrabc excinuclease uv damaged dna complexes studied by flow Linear Dichroism dna curved by uvrb and uvrc
    FEBS Letters, 1992
    Co-Authors: Masayuki Takahashi, Elisabeth Bertrandburggraf, Robert P P Fuchs, Bengt Norden
    Abstract:

    The interaction between UvrABC excinuclease from Escherichia coli and ultraviolet light- (UV) damaged DNA was studied by flow Linear Dichroism. The Dichroism signal from DNA was drastically decreased in intensity upon incubation with UvrA and UvrB or whole enzyme in the presence of effector ATP. The change was specific for UV-damaged DNA, and a concluded suppressed DNA orientation suggests the wrapping of DNA around the protein. The incubation with the UvrC subunit alone also somewhat reduces the signal, however, in this case the change was smaller and not specific for UV-damaged DNA. The structural modification of DNA, promoted by the (UvrA2-UvrB) complex, probably facilitates or stabilizes the interaction of the UvrC subunit with DNA for the excision.

Richard A Palmer - One of the best experts on this subject based on the ideXlab platform.

  • humidity dependent dynamic infrared Linear Dichroism study of a poly ester urethane
    Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2007
    Co-Authors: Jon R Schoonover, Warren P Steckle, Jonathan D Cox, Cliff T Johnston, Yanqia Wang, Angela Gillikin, Richard A Palmer
    Abstract:

    Abstract Fourier transform infrared techniques, infrared difference spectroscopy and dynamic infrared Linear Dichroism (DIRLD), have been utilized to explore the effects of humidity and water absorption on a poly(ester urethane). An environmental infrared microbalance cell was used to measure the infrared spectra as a function of humidity and accompanying weight change for the absorption–desorption processes. The infrared difference data indicate that exposure to humidity affects the hydrogen-bonding interactions in the polymer. Dynamic infrared Linear Dichroism studies in tensile deformation mode as a function of humidity demonstrate how changes in water content affect the orientational response of functional groups. Complex behavior as a function of humidity for functional groups involved in hydrogen bonding indicates that water absorbed by the polymer affects the micro-environments near these functional groups.

  • dynamic mechanical analysis and dynamic infrared Linear Dichroism study of the frequency dependent viscoelastic behavior of a poly ester urethane
    Vibrational Spectroscopy, 2006
    Co-Authors: Yanqia Wang, Jon R Schoonover, Richard A Palmer, Steven R Aubuchon
    Abstract:

    Abstract Dynamic infrared Linear Dichroism (DIRLD) data have been collected as a function of strain modulation frequency in a simultaneous DIRLD-dynamic mechanical analysis experiment. The frequency range is limited, but the DIRLD data indicate some similarities to the temperature-dependent data. The frequency-dependent infrared data do not show the direct correlation with the mechanical data that was evident in the temperature-dependent study. However, the frequency-dependent infrared data do provide some molecular insight, with a similarity to the temperature-dependent results in the 1800–1320 cm −1 region, a quadrature signal increasing with increasing frequency in the 1320–1000 cm −1 region, and complex changes in the low wavenumber region that are interpreted as polymer chain responses as a function of frequency.

  • dynamic infrared Linear Dichroism study of the temperature dependent viscoelastic behavior of a poly ester urethane
    Applied Spectroscopy, 2005
    Co-Authors: Yanqia Wang, Jon R Schoonover, Steven R Aubuchon, Mark E Smith, Richard A Palmer
    Abstract:

    In the study reported here, of the poly(ester urethane), Estane®5703, simultaneous dynamic mechanical analysis (DMA) and dynamic infrared Linear Dichroism (DIRLD) measurements have been carried out at continuously variable temperatures from −50 to +30 °C. Multivariate curve resolution–alternating least squares (MCR-ALS) analysis of the spectral data has been correlated with the thermo-mechanical properties. Spectral changes, analyzed as a function of temperature, are compared with the storage and loss moduli to provide insight into viscoelastic behavior at the molecular level. In addition, the data for pure Estane have been compared to those for plasticized Estane samples, which contain 10 and 30% plasticizer by weight. These comparisons show a strong and consistent correlation between the macroscopic rheological properties and the microscopic (molecular, inter-molecular, and sub-molecular) responses of this block co-polymer.

  • infrared Linear Dichroism study of a hydrolytically degraded poly ester urethane
    Polymer Degradation and Stability, 2001
    Co-Authors: Jon R Schoonover, Darla Graff Thompson, Jill C Osborn, Bruce E Orler, Debra A Wrobleski, Anderson L Marsh, Haochuan Wang, Richard A Palmer
    Abstract:

    Static and dynamic infrared Linear Dichroism data have been used to supply additional insight into changes in tensile properties as a consequence of hydrolytic degradation of a segmented poly(ester urethane). Unaged material responds to tensile deformation with the soft (polyester) segments supplying the elasticity and the hard (polyurethane) segments supplying strength. Upon hydrolytic degradation, the static and dynamic data indicate altered orientational responses at the molecular-level, which are interpreted as resulting from cleavage of the soft segment chains and altered hydrogen-bonding interactions for both segments.

Jon R Schoonover - One of the best experts on this subject based on the ideXlab platform.

  • humidity dependent dynamic infrared Linear Dichroism study of a poly ester urethane
    Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2007
    Co-Authors: Jon R Schoonover, Warren P Steckle, Jonathan D Cox, Cliff T Johnston, Yanqia Wang, Angela Gillikin, Richard A Palmer
    Abstract:

    Abstract Fourier transform infrared techniques, infrared difference spectroscopy and dynamic infrared Linear Dichroism (DIRLD), have been utilized to explore the effects of humidity and water absorption on a poly(ester urethane). An environmental infrared microbalance cell was used to measure the infrared spectra as a function of humidity and accompanying weight change for the absorption–desorption processes. The infrared difference data indicate that exposure to humidity affects the hydrogen-bonding interactions in the polymer. Dynamic infrared Linear Dichroism studies in tensile deformation mode as a function of humidity demonstrate how changes in water content affect the orientational response of functional groups. Complex behavior as a function of humidity for functional groups involved in hydrogen bonding indicates that water absorbed by the polymer affects the micro-environments near these functional groups.

  • dynamic mechanical analysis and dynamic infrared Linear Dichroism study of the frequency dependent viscoelastic behavior of a poly ester urethane
    Vibrational Spectroscopy, 2006
    Co-Authors: Yanqia Wang, Jon R Schoonover, Richard A Palmer, Steven R Aubuchon
    Abstract:

    Abstract Dynamic infrared Linear Dichroism (DIRLD) data have been collected as a function of strain modulation frequency in a simultaneous DIRLD-dynamic mechanical analysis experiment. The frequency range is limited, but the DIRLD data indicate some similarities to the temperature-dependent data. The frequency-dependent infrared data do not show the direct correlation with the mechanical data that was evident in the temperature-dependent study. However, the frequency-dependent infrared data do provide some molecular insight, with a similarity to the temperature-dependent results in the 1800–1320 cm −1 region, a quadrature signal increasing with increasing frequency in the 1320–1000 cm −1 region, and complex changes in the low wavenumber region that are interpreted as polymer chain responses as a function of frequency.

  • dynamic infrared Linear Dichroism study of the temperature dependent viscoelastic behavior of a poly ester urethane
    Applied Spectroscopy, 2005
    Co-Authors: Yanqia Wang, Jon R Schoonover, Steven R Aubuchon, Mark E Smith, Richard A Palmer
    Abstract:

    In the study reported here, of the poly(ester urethane), Estane®5703, simultaneous dynamic mechanical analysis (DMA) and dynamic infrared Linear Dichroism (DIRLD) measurements have been carried out at continuously variable temperatures from −50 to +30 °C. Multivariate curve resolution–alternating least squares (MCR-ALS) analysis of the spectral data has been correlated with the thermo-mechanical properties. Spectral changes, analyzed as a function of temperature, are compared with the storage and loss moduli to provide insight into viscoelastic behavior at the molecular level. In addition, the data for pure Estane have been compared to those for plasticized Estane samples, which contain 10 and 30% plasticizer by weight. These comparisons show a strong and consistent correlation between the macroscopic rheological properties and the microscopic (molecular, inter-molecular, and sub-molecular) responses of this block co-polymer.

  • infrared Linear Dichroism study of a hydrolytically degraded poly ester urethane
    Polymer Degradation and Stability, 2001
    Co-Authors: Jon R Schoonover, Darla Graff Thompson, Jill C Osborn, Bruce E Orler, Debra A Wrobleski, Anderson L Marsh, Haochuan Wang, Richard A Palmer
    Abstract:

    Static and dynamic infrared Linear Dichroism data have been used to supply additional insight into changes in tensile properties as a consequence of hydrolytic degradation of a segmented poly(ester urethane). Unaged material responds to tensile deformation with the soft (polyester) segments supplying the elasticity and the hard (polyurethane) segments supplying strength. Upon hydrolytic degradation, the static and dynamic data indicate altered orientational responses at the molecular-level, which are interpreted as resulting from cleavage of the soft segment chains and altered hydrogen-bonding interactions for both segments.

Masayuki Takahashi - One of the best experts on this subject based on the ideXlab platform.

  • structure of uvrabc excinuclease uv damaged dna complexes studied by flow Linear Dichroism dna curved by uvrb and uvrc
    FEBS Letters, 1992
    Co-Authors: Masayuki Takahashi, Elisabeth Bertrandburggraf, Robert P P Fuchs, Bengt Norden
    Abstract:

    The interaction between UvrABC excinuclease from Escherichia coli and ultraviolet light- (UV) damaged DNA was studied by flow Linear Dichroism. The Dichroism signal from DNA was drastically decreased in intensity upon incubation with UvrA and UvrB or whole enzyme in the presence of effector ATP. The change was specific for UV-damaged DNA, and a concluded suppressed DNA orientation suggests the wrapping of DNA around the protein. The incubation with the UvrC subunit alone also somewhat reduces the signal, however, in this case the change was smaller and not specific for UV-damaged DNA. The structural modification of DNA, promoted by the (UvrA2-UvrB) complex, probably facilitates or stabilizes the interaction of the UvrC subunit with DNA for the excision.

David S Kliger - One of the best experts on this subject based on the ideXlab platform.

  • microviscosity in e coli cells from time resolved Linear Dichroism measurements
    Journal of Physical Chemistry B, 2018
    Co-Authors: Eefei Chen, Raymond M Esquerra, Philipp A Melendez, Sita S Chandrasekaran, David S Kliger
    Abstract:

    A protein’s folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity—the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved Linear Dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules. This study reports the microviscosity experienced by myoglobin in the E. coli cell’s heterogeneous cytoplasm by using TRLD to measure rotational diffusion times. The results show that photolyzed deoxyMb ensembles randomize through environment-dependent rotational diffusion with a lifetime of 34 ± 6 ns. This value corresponds to a microviscosity of 2.82 ± 0.42 cP, which is consistent with prev...

  • time resolved Linear Dichroism measurements of carbonmonoxy myoglobin as a probe of the microviscosity in crowded environments
    Journal of Physical Chemistry B, 2017
    Co-Authors: Eefei Chen, David S Kliger
    Abstract:

    The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved Linear Dichroism spectroscopy. The results of these studies offer simple empirically determined Linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecul...

  • Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments
    2017
    Co-Authors: Eefei Chen, David S Kliger
    Abstract:

    The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)­viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)­viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved Linear Dichroism spectroscopy. The results of these studies offer simple empirically determined Linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells