Protein Science

Cover image for Vol. 23 Issue 9

Edited By: Brian W. Matthews

Impact Factor: 2.861

ISI Journal Citation Reports © Ranking: 2013: 146/291 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • An osmolyte mitigates the destabilizing effect of protein crowding

    An osmolyte mitigates the destabilizing effect of protein crowding

    Backbone of CI2 colored by stability changes in kcal/mol. (a) ΔGopo′ in buffered 100.0 g/L protein lysate minus ΔGopo′ in buffer alone. (b) ΔGopo′ in buffered 100.0 g/L protein lysate with 0.4 M glycine betaine minus ΔGopo′in buffered 0.4 M glycine betaine.

  • Role of β-lactamase residues in a common interface for binding the structurally unrelated inhibitory proteins BLIP and BLIP-II

    Role of β‐lactamase residues in a common interface for binding the structurally unrelated inhibitory proteins BLIP and BLIP‐II

    Structural comparison of BLIP-TEM-1 (PDB 1JTG) (A) and BLIP-II-TEM-1 (PDB 1JTD) (B). The protruding loop-helix region (red) and the catalytic serine 70 (blue space fill) of TEM-1 (gray) is shown as the primary binding region for both BLIP and BLIP-II (orange).

  • Structural and thermodynamic characterization of the recognition of the S100-binding peptides TRTK12 and p53 by calmodulin

    Structural and thermodynamic characterization of the recognition of the S100‐binding peptides TRTK12 and p53 by calmodulin

    Changes in backbone 1H and 15N chemical shifts for TRTK12 (A) and p53 (B) binding to Ca2+-bound CaM (PDB: 2L7L). Residues are color coded according to the degree of combined backbone 1H and 15N chemical-shift perturbations (c.s.p.) on TRTK12 (C) and p53 (D) binding. Color assignment was done as follows: c.s.p. 0.3–0.4 (yellow), c.s.p. 0.4–0.5 (orange), and c.s.p. > 0.5 (red). Selected residues are labeled for orientation only.

  • Intracellular selection of peptide inhibitors that target disulphide-bridged Aβ42 oligomers

    Intracellular selection of peptide inhibitors that target disulphide‐bridged Aβ42 oligomers

    The PCA for amyloid systems. Selection is undertaken using SHuffle cells that harbor an oxidizing cytoplasmic environment to promote disulphide bond formation. Library members that bind to Aβ42cc lead to the recombination of murine DHFR and lead to a colony under selective conditions (bacterial DHFR is specifically inhibited using trimethoprim). Subsequent competition selection in liquid media isolates winners of highest efficacy. Those library members that bind the target and are able to confer faster growth rates by reducing the toxic effects of the amyloid protein most effectively will be selected. As the assay is performed in the cytoplasm of E.coli, any nonspecific, unstable, aggregation prone (insoluble), protease susceptible members are removed.

  • A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein

    A maximum entropy approach to the study of residue‐specific backbone angle distributions in α‐synuclein, an intrinsically disordered protein

    Dynamic correction [Eq. ] to J(0) for sequential Hα[BOND]HN couplings as a function of the weighted population [Eq. (8)] in the extended configuration. Results are shown for each residue at three temperatures (blue squares: 300 K; green circles: 310 K; red triangles: 320 K). The lines show least-squares straight-line fits for each of the temperatures. The ratio of the factors extrapolated to weights of 1 and 0 are 2.45, 2.80, and 2.28 at T = 300, 310, and 320 K, respectively. A global fit of all data gives a ratio of 2.51 ± 0.20, with the error determined by the bootstrap method. The simulation estimates for the correction are therefore fully consistent with the functional form of Eq. and the maximum magnitude of 2.5 for the correction factor used in the analysis of the experimental NOE data.

  • Method to increase the yield of eukaryotic membrane protein expression in Saccharomyces cerevisiae for structural and functional studies

    Method to increase the yield of eukaryotic membrane protein expression in Saccharomyces cerevisiae for structural and functional studies

    A modified S. cerevisiae expression system for eukaryotic MP production. (A) Vector map of pDDGFP2-Leu2d vector. The vector allows for dual selection using either the uracil or leucine markers. The gene for the recombinant protein is inserted via homologous recombination into the smaI site and is, then, expressed under the control of the GAL1 promoter as a tev cleavable C terminal tagged GFP-His fusion. (B) Comparison of expression level between the use of either the URA3 (selection using medium lacking uracil) or LEU2 genes (selection using medium lacking leucine) as selective markers for a number of different membrane proteins (see Table for details). (C) As (B) but looking at yeast strain dependence of the system for the expression of two constructs.

  • Life at the border: Adaptation of proteins to anisotropic membrane environment

    Life at the border: Adaptation of proteins to anisotropic membrane environment

    Conformational rearrangements of bacterial pore-forming toxins (PFT) upon binding to membranes. (A–C) Structures of β-PFT from Staphylococcus aureus: (A) soluble form of LukF monomer, a homologue of α-hemolysin (1PVL), (B) monomer of α-hemolysin from the oligomer (7AHL), (C) α-hemolysin heptamer (7AHL). Conformational changes in α-hemolysin include release of an amphiphilic β-hairpin (residues 108–147), oligomerization of seven molecules to create a stem domain with the central hydrophilic channel, and insertion of the stem domain into the membrane. (D–F) Structures of α-PFT from E. coli: (D) soluble form of ClyA monomer from E. coli (1QOY), (E) monomer of ClyA from the oligomer (2WCD), (F) ClyA dodecamer (2WCD). Conformational transitions of the ClyA toxin include detachment of β-tongue domain (residues 176–202) from the α-bundle, rearrangement of N-terminal α-helix, and formation of oligomers (octamers, dodecamers, or tridecamers) with circular pore inside the hydrophobic membrane core. The β-sheet is shown in yellow, the α-helices are shown in red, membrane-bound segments are shown in orange with side chains shown by sticks. Location of hydrophobic membrane boundaries are shown by lines: inner membrane leaflet is colored blue, outer leaflet is colored red.

  • An osmolyte mitigates the destabilizing effect of protein crowding
  • Role of β‐lactamase residues in a common interface for binding the structurally unrelated inhibitory proteins BLIP and BLIP‐II
  • Structural and thermodynamic characterization of the recognition of the S100‐binding peptides TRTK12 and p53 by calmodulin
  • Intracellular selection of peptide inhibitors that target disulphide‐bridged Aβ42 oligomers
  • A maximum entropy approach to the study of residue‐specific backbone angle distributions in α‐synuclein, an intrinsically disordered protein
  • Method to increase the yield of eukaryotic membrane protein expression in Saccharomyces cerevisiae for structural and functional studies
  • Life at the border: Adaptation of proteins to anisotropic membrane environment

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