Lise Arleth

University of Copenhagen, København, Capital Region, Denmark

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Publications (57)191.19 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Small-angle X-ray and neutron scattering have become increasingly popular owing to improvements in instrumentation and developments in data analysis, sample handling and sample preparation. For some time, it has been suggested that a more systematic approach to the quantification of the information content in small-angle scattering data would allow for a more optimal experiment planning and a more reliable data analysis. In the present article, it is shown how ray-tracing techniques in combination with a statistically rigorous data analysis provide an appropriate platform for such a systematic quantification of the information content in scattering data. As examples of applications, it is shown how the exposure time at different instrumental settings or contrast situations can be optimally prioritized in an experiment. Also, the gain in information by combining small-angle X-ray and neutron scattering is assessed. While solution small-angle scattering data of proteins and protein–lipid complexes are used as examples in the present case study, the approach is generalizable to a wide range of other samples and experimental techniques. The source code for the algorithms and ray-tracing components developed for this study has been made available on-line.
    Journal of Applied Crystallography 12/2014; 47(6). · 3.95 Impact Factor
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    ABSTRACT: The high flux at European Spallation Source (ESS) will allow for performing experiments with relatively small beam-sizes while maintaining a high intensity of the incoming beam. The pulsed nature of the source makes the facility optimal for time-of-flight small-angle neutron scattering (ToF-SANS). We find that a relatively compact SANS instrument becomes the optimal choice in order to obtain the widest possible q -range in a single setting and the best possible exploitation of the neutrons in each pulse and hence obtaining the highest possible flux at the sample position. The instrument proposed in the present article is optimised for performing fast measurements of small scattering volumes, typically down to 2×2×2 mm3, while covering a broad q -range from about 0.005 1/Å to 0.5 1/Å in a single instrument setting. This q -range corresponds to that available at a typical good BioSAXS instrument and is relevant for a wide set of biomacromolecular samples. A central advantage of covering the whole q -range in a single setting is that each sample has to be loaded only once. This makes it convenient to use the fully automated high-throughput flow-through sample changers commonly applied at modern synchrotron BioSAXS-facilities. The central drawback of choosing a very compact instrument is that the resolution in terms of δλ/λδλ/λ obtained with the short wavelength neutrons becomes worse than what is usually the standard at state-of-the-art SANS instruments. Our McStas based simulations of the instrument performance for a set of characteristic biomacromolecular samples show that the resulting smearing effects still have relatively minor effects on the obtained data and can be compensated for in the data analysis. However, in cases where a better resolution is required in combination with the large simultaneous q-range characteristic of the instrument, we show that this can be obtained by inserting a set of choppers.
    Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment 11/2014; 764:133–141. · 1.32 Impact Factor
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    ABSTRACT: Phosphatidylcholine (PC) is a major component of eukaryotic cell membranes and one of the most commonly used phospholipids for reconstitution of membrane proteins into carrier systems such as lipid vesicles, micelles and nanodiscs. Selectively deuterated versions of this lipid have many applications, especially in structural studies using techniques such as NMR, neutron reflectivity and small-angle neutron scattering. Here we present a comprehensive study of selective deuteration of phosphatidylcholine through biosynthesis in a genetically modified strain of Escherichia coli. By carefully tuning the deuteration level in E. coli growth media and varying the deuteration of supplemented carbon sources, we show that it is possible to achieve a controlled deuteration for three distinct parts of the PC lipid molecule, namely the (a) lipid head group, (b) glycerol backbone and (c) fatty acyl tail. This biosynthetic approach paves the way for the synthesis of specifically deuterated, physiologically relevant phospholipid species which remain difficult to obtain through standard chemical synthesis.
    Applied microbiology and biotechnology. 10/2014;
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    ABSTRACT: The thermodynamics and structural properties of flexible and rigid nonionic water/oil/surfactant microemulsions have been investigated using a two level-cut Gaussian random field method based on the Helfrich formalism. Ternary stability diagrams and scattering spectra have been calculated for different surfactant rigidities and spontaneous curvatures. A more important contribution of the Gaussian elastic constants compared to the bending one is observed on the ternary stability diagrams. Furthermore, influence of the spontaneous curvature of the surfactant points out a displacement of the instability domains which corresponds to the difference between the spontaneous and effective curvatures. We enlighten that a continuous transition from a connected water in oil droplets to a frustrated locally lamellar (oil in water in oil droplets) microstructure is found to occur when increasing the temperature for an oil-rich microemulsion. This continuous transition translated in a shift in the scattering functions, points out that the phase inversion phenomenon occurs by a coalescence of the water droplets.
    The Journal of Chemical Physics 04/2014; 140(16):164711. · 3.12 Impact Factor
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    ABSTRACT: Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial nanoscale bilayer disc carriers that mimic the native bilayer environment allows the handling of membrane proteins in solution. This enables the use of small-angle scattering techniques for fast and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly nontrivial fashion, making subsequent data analysis challenging. Here, an elegant solution to circumvent the intrinsic complexity brought about by the presence of the carrier disc is presented. In combination with small-angle neutron scattering (SANS) and the D2O/H2O-based solvent contrast-variation method, it is demonstrated that it is possible to prepare specifically deuterated carriers that become invisible to neutrons in 100% D2O at the length scales relevant to SANS. These `stealth' carrier discs may be used as a general platform for low-resolution structural studies of membrane proteins using well established data-analysis tools originally developed for soluble proteins.
    Acta Crystallographica Section D Biological Crystallography 02/2014; 70(Pt 2):317-328. · 7.23 Impact Factor
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    ABSTRACT: Monomeric bacteriorhodopsin (bR) reconstituted into POPC/POPG-containing nanodiscs was investigated by combined small-angle neutron and X-ray scattering. A novel hybrid approach to small-angle scattering data analysis was developed. In combination, these provided direct structural insight into membrane-protein localization in the nanodisc and into the protein-lipid interactions. It was found that bR is laterally decentred in the plane of the disc and is slightly tilted in the phospholipid bilayer. The thickness of the bilayer is reduced in response to the incorporation of bR. The observed tilt of bR is in good accordance with previously performed theoretical predictions and computer simulations based on the bR crystal structure. The result is a significant and essential step on the way to developing a general small-angle scattering-based method for determining the low-resolution structures of membrane proteins in physiologically relevant environments.
    Acta Crystallographica Section D Biological Crystallography 02/2014; 70(Pt 2):371-383. · 7.23 Impact Factor
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    ABSTRACT: New methods to handle membrane bound proteins, e.g. G-protein coupled receptors (GPCRs), are highly desirable. Recently, apoliprotein A1 (ApoA1) based lipoprotein particles have emerged as a new platform for studying membrane proteins, and it has been shown that they can self-assemble in combination with phospholipids to form discoidal shaped particles that can stabilize membrane proteins. In the present study, we have investigated an ApoA1 mimetic peptide with respect to its solution structure when in complex with phospholipids. This was achieved using a powerful combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) supported by coarse-grained molecular dynamics simulations. The detailed structure of the discs was determined in unprecedented detail and it was found that they adopt a discoidal structure very similar to the ApoA1 based nanodiscs. We furthermore show that, like the ApoA1 and derived nanodiscs, these peptide discs can accommodate and stabilize a membrane protein. Finally, we exploit their dynamic properties and show that the 18A discs may be used for transferring membrane proteins and associated phospholipids directly and gently into phospholipid nanodiscs.
    Soft Matter 01/2014; 10(5):738-52. · 4.15 Impact Factor
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    ABSTRACT: A software framework for analysis of small-angle scattering data is presented. On the basis of molecular constraints and prior knowledge of the chemical composition of the sample, the software is capable of simultaneously fitting small-angle X-ray and neutron scattering data to analytical or semi-analytical models of biomacromolecules. The software features various fitting routines along with the possibility of incorporating instrumental resolution effects on the fit. Finally, trust region estimation, based on the profile likelihood strategy, is implemented. The algorithms and models are written in C, whereas the user interface is written in Python. Parallelization is implemented using the OpenMP extensions to C. The source code is available for free upon request or via the associated code repository. The software runs on Linux, Windows and OSX and is available as an open-source initiative published under the General Publishing License.
    Journal of Applied Crystallography 12/2013; 46(6):1894-1898. · 3.95 Impact Factor
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    ABSTRACT: In most temperate bacteriophages, regulation of the choice of lysogenic or lytic life cycle is controlled by a CI repressor protein. Inhibition of transcription is dependent on a helix-turn-helix motif, often located in the N-terminal domain (NTD), which binds to specific DNA sequences (operator sites). Here the crystal structure of the NTD of the CI repressor from phage TP901-1 has been determined at 1.6 Å resolution, and at 2.6 Å resolution in complex with a 9 bp double-stranded DNA fragment that constitutes a half-site of the OL operator. This N-terminal construct, comprising residues 2-74 of the CI repressor, is monomeric in solution as shown by nuclear magnetic resonance (NMR), small angle X-ray scattering, and gel filtration and is monomeric in the crystal structures. The binding interface between the NTD and the half-site in the crystal is very similar to the interface that can be mapped by NMR in solution with a full palindromic site. The interactions seen in the complexes (in the crystal and in solution) explain the observed affinity for the OR site that is lower than that for the OL site and the specificity for the recognized DNA sequence in comparison to that for other repressors. Compared with many well-studied phage repressor systems, the NTD from TP901-1 CI has a longer extended scaffolding helix that, interestingly, is strongly conserved in putative repressors of Gram-positive pathogens. On the basis of sequence comparisons, we suggest that these bacteria also possess repressor/antirepressor systems similar to that found in phage TP901-1.
    Biochemistry 09/2013; · 3.38 Impact Factor
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    ABSTRACT: COMPLETE AUTHOR LIST PLEASE ACCESS ESS, the European Spallation Source, will be a major user facility at which researchers from academia and industry will investigate scientific questions using neutron beams. Neutron methods provide insights about the molecular building blocks of matter not available by other means. They are used for both basic and applied research. ESS will be a slow neutron source of unparallelled power and scientific performance. It will deliver its first protons to a solid, rotating tungsten target in 2019, which will in turn generate neutrons for delivery to an initial suite of seven neutron scattering research instruments. ESS will reach its full design specifications in 2025, with a suite of 22 research instruments. The publication of the Technical Design Report in 2013 represents an important milestone for the ESS project, marking its readiness to move forward with construction activities. This executive overview provides a brief summary of the key insights and findings of the Technical Design Report.
    04/2013; , ISBN: 978-91-980173-2-8
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    ABSTRACT: The swelling behaviour of water-oil microemulsions - considering a surfactant layer between oil and water - has been studied using a two level-cuts Gaussian random field approach based on the Helfrich formalism. Microstructures and scattering properties of microemulsions have been calculated for different amounts of oil (and water) for flexible and rigid microemulsions. When the stiffness, the spontaneous curvature of the interfacial film, and the surface to volume ratio of the immiscible fluids are varied, the microemulsion topology and morphology change in order to minimize the microemulsion free energy. Our simulations point out a change in the microemulsion morphology as a function of the surfactant film rigidity and the composition of oil, water and the surfactant. Locally lamellar structures are found for rigid microemulsions, whereas for more flexible ones, the connected-droplet and/or bicontinuous structures are preferred. Furthermore, we show that the microemulsion swelling versus the volume fraction gives a specific signature of the microemulsion microstructure. This allows for discriminating between different types of microemulsions: flexible, frustrated and unfrustrated (close to bi-liquid foams), and connected structures as molten hexagonal and cubic phases. The universal swelling behaviour is compared to different analytic expressions of Disordered Open Connected (DOC) models for the microemulsion swelling versus the volume fraction.
    Physical Chemistry Chemical Physics 04/2013; · 4.20 Impact Factor
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    ABSTRACT: α-Helical coiled coil structures, which are noncovalently associated heptad repeat peptide sequences, are ubiquitous in nature. Similar amphipathic repeat sequences have also been found in helix-containing proteins and have played a central role in de novo design of proteins. In addition, they are promising tools for the construction of nanomaterials. Small-angle X-ray scattering (SAXS) has emerged as a new biophysical technique for elucidation of protein topology. Here, we describe a systematic study of the self-assembly of a small ensemble of coiled coil sequences using SAXS and analytical ultracentrifugation (AUC), which was correlated with molecular dynamics simulations. Our results show that even minor sequence changes have an effect on the folding topology and the self-assembly and that these differences can be observed by a combination of AUC, SAXS, and circular dichroism spectroscopy. A small difference in these methods was observed, as SAXS for one peptide and revealed the presence of a population of longer aggregates, which was not observed by AUC. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
    Journal of Peptide Science 03/2013; · 1.86 Impact Factor
  • International Conference on Neutron Scattering - ICNS 2013; 01/2013
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    ABSTRACT: Precise control of the oligomeric state of proteins is of central importance for biological function and for the properties of biopharmaceutical drugs. Here, the self-assembly of 2,2'-bipyridine conjugated monomeric insulin analogues, induced through coordination to divalent metal ions, was studied. This protein drug system was designed to form non-native homo-oligomers through selective coordination of two divalent metal ions, Fe(II) and Zn(II), respectively. The insulin type chosen for this study is a variant designed for a reduced tendency toward native dimer formation at physiological concentrations. A small-angle X-ray scattering analysis of the bipyridine-modified insulin system confirmed an organization into a novel well-ordered structure based on insulin trimers, as induced by the addition of Fe(II). In contrast, unmodified monomeric insulin formed larger and more randomly structured assemblies upon addition of Fe(II). The addition of Zn(II), on the other hand, led to the formation of small quantities of insulin hexamers for both the bipyridine-modified and the unmodified monomeric insulin. Interestingly, the location of the bipyridine-modification significantly affects the tendency to hexamer formation as compared to the unmodified insulin. Our study shows how combining a structural study and chemical design can be used to obtain molecular understanding and control of the self-assembly of a protein drug. This knowledge may eventually be employed to develop an optimized in vivo drug release profile.
    Langmuir 08/2012; 28(33):12159-70. · 4.38 Impact Factor
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    ABSTRACT: Immune stimulating complex (ISCOM) particles consisting of a mixture of Quil-A, cholesterol, and phospholipids were structurally characterized by small-angle x-ray scattering (SAXS). The ISCOM particles are perforated vesicles of very well-defined structures. We developed and implemented a novel (to our knowledge) modeling method based on Monte Carlo simulation integrations to describe the SAXS data. This approach is similar to the traditional modeling of SAXS data, in which a structure is assumed, the scattering intensity is calculated, and structural parameters are optimized by weighted least-squares methods when the model scattering intensity is fitted to the experimental data. SAXS data from plain ISCOM matrix particles in aqueous suspension, as well as those from complete ISCOMs (i.e., with an antigen (tetanus toxoid) incorporated) can be modeled as a polydisperse distribution of perforated bilayer vesicles with icosahedral, football, or tennis ball structures. The dominating structure is the tennis ball structure, with an outer diameter of 40 nm and with 20 holes 5-6 nm in diameter. The lipid bilayer membrane is 4.6 nm thick, with a low-electron-density, 2.0-nm-thick hydrocarbon core. Surprisingly, in the ISCOMs, the tetanus toxoid is located just below the membrane inside the particles.
    Biophysical Journal 05/2012; 102(10):2372-80. · 3.83 Impact Factor
  • Biophysical Journal 01/2012; 102(3):236-. · 3.83 Impact Factor
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    ABSTRACT: The self-assembly of biopharmaceutical peptides into multimeric, nanoscale objects, as well as their disassembly to monomers, is central for their mode of action. Here, we describe a bioorthogonal strategy, using a non-native recognition principle, for control of protein self-assembly based on intermolecular fluorous interactions and demonstrate it for the small protein insulin. Perfluorinated alkyl chains of varying length were attached to desB30 human insulin by acylation of the ε-amine of the side-chain of LysB29. The insulin analogues were formulated with Zn(II) and phenol to form hexamers. The self-segregation of fluorous groups directed the insulin hexamers to self-assemble. The structures of the systems were investigated by circular dichroism (CD) spectroscopy and synchrotron small-angle X-ray scattering. Also, the binding affinity to the insulin receptor was measured. Interestingly, varying the length of the perfluoroalkyl chain provided three different scenarios for self-assembly; the short chains hardly affected the native hexameric structure, the medium-length chains induced fractal-like structures with the insulin hexamer as the fundamental building block, while the longest chains lead to the formation of structures with local cylindrical geometry. This hierarchical self-assembly system, which combines Zn(II) mediated hexamer formation with fluorous interactions, is a promising tool to control the formation of high molecular weight complexes of insulin and potentially other proteins.
    Langmuir 11/2011; 28(1):593-603. · 4.38 Impact Factor
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    ABSTRACT: Nanodiscs are self-assembled nanostructures composed of a belt protein and a small patch of lipid bilayer, which can solubilize membrane proteins in a lipid bilayer environment. We present a method for the alignment of a well-defined two-dimensional layer of nanodiscs at the air-water interface by careful design of an insoluble surfactant monolayer at the surface. We used neutron reflectivity to demonstrate the feasibility of this approach and to elucidate the structure of the nanodisc layer. The proof of concept is hereby presented with the use of nanodiscs composed of a mixture of two different lipid (DMPC and DMPG) types to obtain a net overall negative charge of the nanodiscs. We find that the nanodisc layer has a thickness or 40.9 ± 2.6 Å with a surface coverage of 66 ± 4%. This layer is located about 15 Å below a cationic surfactant layer at the air-water interface. The high level of organization within the nanodiscs layer is reflected by a low interfacial roughness (~4.5 Å) found. The use of the nanodisc as a biomimetic model of the cell membrane allows for studies of single membrane proteins isolated in a confined lipid environment. The 2D alignment of nanodiscs could therefore enable studies of high-density layers containing membrane proteins that, in contrast to membrane proteins reconstituted in a continuous lipid bilayer, remain isolated from influences of neighboring membrane proteins within the layer.
    Langmuir 11/2011; 27(24):15065-73. · 4.38 Impact Factor
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    ABSTRACT: A new microfluidic sample-preparation system is presented for the structural investigation of proteins using small-angle X-ray scattering (SAXS) at synchrotrons. The system includes hardware and software features for precise fluidic control, sample mixing by diffusion, automated X-ray exposure control, UV absorbance measurements and automated data analysis. As little as 15 l of sample is required to perform a complete analysis cycle, including sample mixing, SAXS measurement, continuous UV absorbance measurements, and cleaning of the channels and X-ray cell with buffer. The complete analysis cycle can be performed in less than 3 min. Bovine serum albumin was used as a model protein to characterize the mixing efficiency and sample consumption of the system. The N2 fragment of an adaptor protein (p120-RasGAP) was used to demonstrate how the device can be used to survey the structural space of a protein by screening a wide set of conditions using high-throughput techniques. © 2011 International Union of Crystallography.
    Journal of Applied Crystallography 08/2011; 44(5):1090-1099. · 3.95 Impact Factor
  • Nicholas Skar-Gislinge, Lise Arleth
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    ABSTRACT: Nanodiscs™ consist of small phospholipid bilayer discs surrounded and stabilized by amphiphilic protein belts. Nanodiscs and their confinement and stabilization of nanometer sized pieces of phospholipid bilayer are highly interesting from a membrane physics point of view. We demonstrate how the detailed structure of Di-Lauroyl-Phosphatidyl Choline (DLPC) nanodiscs may be determined by simultaneous fitting of a structural model to small-angle scattering data from the nanodiscs as investigated in three different contrast situations, respectively two SANS contrasts and one SAXS contrast. The article gives a detailed account of the underlying structural model for the nanodiscs and describe how additional chemical and biophysical information can be incorporated in the model in terms of molecular constraints. We discuss and quantify the contribution from the different elements of the structural model and provide very strong experimental support for the nanodiscs as having an elliptical cross-section and with poly-histidine tags protruding out from the rim of the protein belt. The analysis also provides unprecedented information about the structural conformation of the phospholipids when these are localized in the nanodiscs. The model paves the first part of the way in order to reach our long term goal of using the nanodiscs as a platform for small-angle scattering based structural investigations of membrane proteins in solution.
    Physical Chemistry Chemical Physics 02/2011; 13(8):3161-70. · 4.20 Impact Factor

Publication Stats

579 Citations
191.19 Total Impact Points


  • 2009–2014
    • University of Copenhagen
      • • Niels Bohr Institute
      • • Faculty of Science
      • • Faculty of Life Sciences
      København, Capital Region, Denmark
  • 2013
    • French National Centre for Scientific Research
      • Institut de Chimie Séparative de Marcoule (ICSM)
      Montpellier, Languedoc-Roussillon, France
  • 2010–2013
    • IT University of Copenhagen
      København, Capital Region, Denmark
    • University of California, San Francisco
      San Francisco, California, United States
  • 2005–2011
    • Roskilde University
      • Department of Science, Systems and Models (NSM)
      Roskilde, Zealand, Denmark
  • 2006
    • Atomic Energy and Alternative Energies Commission
      Fontenay, Île-de-France, France
  • 2004
    • Los Alamos National Laboratory
      • Los Alamos Neutron Science Center
      Los Alamos, California, United States