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  • 1.
    Almqvist, Nils
    et al.
    Luleå University of Technology, Department of Engineering Sciences and Mathematics, Material Science.
    Bhatia, R
    Neuroscience Research Institute, University of California, Santa Barbara.
    Primbs, G
    Neuroscience Research Institute, University of California, Santa Barbara.
    Desai, N
    NutraSweet Company, Chicago.
    Banerjee, S
    Department of Chemical Engineering, University of California, Santa Barbara.
    Lal, R
    Neuroscience Research Institute, University of California, Santa Barbara.
    Elasticity and adhesion force mapping reveals real-time clustering of growth factor receptors and associated changes in local cellular rheological properties2004In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 86, no 3, p. 1753-1762Article in journal (Refereed)
    Abstract [en]

    Cell surface macromolecules such as receptors and ion channels serve as the interface link between the cytoplasm and the extracellular region. Their density, distribution, and clustering are key spatial features influencing effective and proper physical and biochemical cellular responses to many regulatory signals. In this study, the effect of plasma-membrane receptor clustering on local cell mechanics was obtained from maps of interaction forces between antibody-conjugated atomic force microscope tips and a specific receptor, a vascular endothelial growth factor (VEGF) receptor. The technique allows simultaneous measurement of the real-time motion of specific macromolecules and their effect on local rheological properties like elasticity. The clustering was stimulated by online additions of VEGF, or antibody against VEGF receptors. VEGF receptors are found to concentrate toward the cell boundaries and cluster rapidly after the online additions commence. Elasticity of regions under the clusters is found to change remarkably, with order-of-magnitude stiffness reductions and fluidity increases. The local stiffness reductions are nearly proportional to. receptor density and, being concentrated near the cell edges, provide a mechanism for cell growth and angiogenesis.

  • 2.
    Antzutkin, Oleg
    et al.
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Balbach, John J.
    National Institutes of Health.
    Tycko, Robert
    National Institutes of Health.
    Site-Specific Identification of Non-ß-Strand Conformations in Alzheimer's ß-Amyloid Fibrils by Solid-State NMR2003In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, no 5, p. 3326-3335Article in journal (Refereed)
    Abstract [en]

    The most well-established structural feature of amyloid fibrils is the cross-ß motif, an extended ß-sheet structure formed by ß-strands oriented perpendicular to the long fibril axis. Direct experimental identification of non-ß-strand conformations in amyloid fibrils has not been reported previously. Here we report the results of solid-state NMR measurements on amyloid fibrils formed by the 40-residue ß-amyloid peptide associated with Alzheimer's disease (Aß1-40), prepared synthetically with pairs of 13C labels at consecutive backbone carbonyl sites. The measurements probe the peptide backbone conformation in residues 24-30, a segment where a non-ß-strand conformation has been suggested by earlier sequence analysis, cross-linking experiments, and molecular modeling. Data obtained with the fpRFDR-CT, DQCSA, and 2D MAS exchange solid-state NMR techniques, which provide independent constraints on the and backbone torsion angles between the labeled carbonyl sites, indicate non-ß-strand conformations at G25, S26, and G29. These results represent the first site-specific identification and characterization of non-ß-strand peptide conformations in an amyloid fibril

  • 3.
    Balbach, John J.
    et al.
    National Institutes of Health.
    Petkova, Aneta T.
    National Institutes of Health.
    Oyler, Nathan A.
    National Institutes of Health.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Gordon, David J.
    University of Chicago.
    Supramolecular structure in full-length Alzheimer's -amyloid fibrils: evidence for a parallel -sheet organization from solid-state nuclear magnetic resonance2002In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 83, no 2, p. 1205-1216Article in journal (Refereed)
  • 4.
    Huang, Rick K.
    et al.
    Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland.
    Baxa, Ulrich
    Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland.
    Aldrian, Gudrun
    Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2.
    Ahmed, Abdullah B.
    Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2.
    Wall, Joseph P.
    Department of Biology, Brookhaven National Laboratory, Upton New York.
    Mizuno, Naoko
    Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Steven, Alasdair C.
    Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland.
    Kajava, Andrey V.
    Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier 1 and 2.
    Conformational Switching in PolyGln Amyloid Fibrils Resulting from a Single Amino Acid Insertion2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 10, p. 2134-2142Article in journal (Refereed)
    Abstract [en]

    The established correlation between neurodegenerative disorders and intracerebral deposition of polyglutamine aggregates motivates attempts to better understand their fibrillar structure. We designed polyglutamines with a few lysines inserted to overcome the hindrance of extreme insolubility and two D-lysines to limit the lengths of β-strands. One is 33 amino acids long (PolyQKd-33) and the other has one fewer glutamine (PolyQKd-32). Both form well-dispersed fibrils suitable for analysis by electron microscopy. Electron diffraction confirmed cross-β structures in both fibrils. Remarkably, the deletion of just one glutamine residue from the middle of the peptide leads to substantially different amyloid structures. PolyQKd-32 fibrils are consistently 10–20% wider than PolyQKd-33, as measured by negative staining, cryo-electron microscopy, and scanning transmission electron microscopy. Scanning transmission electron microscopy analysis revealed that the PolyQKd-32 fibrils have 50% higher mass-per-length than PolyQKd-33. This distinction can be explained by a superpleated β-structure model for PolyQKd-33 and a model with two β-solenoid protofibrils for PolyQKd-32. These data provide evidence for β-arch-containing structures in polyglutamine fibrils and open future possibilities for structure-based drug design.

  • 5.
    Song, Z.
    et al.
    Stockholm University.
    Antzutkin, Oleg
    Lee, Y. K.
    Stockholm University.
    Shekar, S.C.
    Stockholm University.
    Rupprecht, A.
    Stockholm University.
    Levitt, M.H.
    Stockholm University.
    Conformational transitions of the phosphodiester backbone in native DNA: two-dimensional magic-angle-spinning 31P-NMR of DNA fibers1997In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 73, no 3, p. 1539-1552Article in journal (Refereed)
    Abstract [en]

    Solid-state 31P-NMR is used to investigate the orientation of the phosphodiester backbone in NaDNA-, LiDNA-, MgDNA-, and NaDNA-netropsin fibers. The results for A- and B-DNA agree with previous interpretations. We verify that the binding of netropsin to NaDNA stabilizes the B form, and find that in NaDNA, most of the phosphate groups adopt a conformation typical of the A form, although there are minor components with phosphate orientations close to the B form. For LiDNA and MgDNA samples, on the other hand, we find phosphate conformations that are in variance with previous models. These samples display x-ray diffraction patterns that correspond to C-DNA. However, we find two distinct phosphate orientations in these samples, one resembling that in B-DNA, and one displaying a twist of the PO4 groups about the O3-P-O4 bisectors. The latter conformation is not in accordance with previous models of C-DNA structure.

  • 6. Thomson, Neil H.
    et al.
    Smith, Bettye L.
    Almqvist, Nils
    Luleå University of Technology, Department of Engineering Sciences and Mathematics, Material Science.
    Schmitt, Lutz
    Kashlev, Mikhail
    Kool, Eric T.
    Hansma, Paul K.
    Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study1999In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 76, no 2, p. 1024-1033Article in journal (Refereed)
    Abstract [en]

    RNA polymerase (RNAP) molecules to be imaged under aqueous buffer using tapping-mode atomic force microscopy (AFM). Recombinant RNAP molecules containing histidine tags (hisRNAP) on the C-terminus were specifically immobilized on ultraflat gold via a mixed monolayer of two different Ω-functionalized alkanethiols. One alkanethiol was terminated in an ethylene-glycol (EG) group, which resists protein adsorption, and the other was terminated in an N-nitrilotriacetic acid (NTA) group, which binds the histidine tag through two coordination sites with a nickel ion. AFM images showed that these two alkanethiols phase-segregate. Specific binding of the hisRNAP molecules was followed in situ by injecting proteins directly into the AFM fluid cell. The activity of the hisRNAP bound to the NTA groups was confirmed with a 42-base circular single-stranded DNA template (rolling circle), which the RNAP uses to produce huge RNA transcripts. These transcripts were imaged in air after the samples were rinsed and dried, since RNA also has low affinity for the EG-thiol and cannot be imaged under the buffers we used.

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