Protein Science

Cover image for Vol. 23 Issue 8

Edited By: Brian W. Matthews

Impact Factor: 2.735

ISI Journal Citation Reports © Ranking: 2012: 150/290 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats

    Capping motifs stabilize the leucine‐rich repeat protein PP32 and rigidify adjacent repeats

    Structure and sequence of PP32. A: Schematic representation of the hAnp32A. The folded N-terminal LRR domain is shown as colored shapes (N-terminal capping motif in purple, repeats 1–5 in red, green, blue, magenta, and orange, respectively, the C-terminal capping motif in cyan), and the C-terminal acidic region is shown as a black line. Ribbon representation of (B) the crystal structure of the LRR domain of human Anp32A (PP32) and (C) the NMR structure of the LRR domain of mouse Anp32A. The conserved hydrogen-bonded Y131 and D146 are shown in black. D: Sequence alignment of the five LRRs of hAnp32 1-154. Conserved hydrophobic residues and asparagines are highlighted in cyan. The conserved hydrogen bond donor and acceptor Y131 and D146 are bolded. The five C-terminal residues included in this study (residues 150–154) are highlighted in yellow. Construct hAnp32A 1-149 is missing the residues highlighted in yellow. Construct hAnp32A 1-145 is missing residues in the red box.

  • Crystal structure of toxin HP0892 from Helicobacter pylori with two Zn(II) at 1.8 Å resolution

    Crystal structure of toxin HP0892 from Helicobacter pylori with two Zn(II) at 1.8 Å resolution

    Comparison of the NMR structure of apo-HP0892 and crystal structure of metal-bound HP0892. (A) The NMR structure of apo-HP0892 exhibited β1-α1-α2-β2-β3-β4-β5-α3 topology. (B) The crystal structure of the zinc-bound form of HP0892 at 1.8 Å resolution (PDB code 4NRN) exhibited similar β1-α1-α2-β2-β3-β4-η1-β5-α3 topology. Two zinc ions are shown as orange spheres. Minor changes were observed in the terminal α-region and in loop regions. Hydrophobic residues in the metal-bound form are shown in (C) and (D). Electrostatic (Coulombic) surface charge shown in (E) and (F) is colored at a level of +10 (blue) and −10 (red) kcal/mol·e as shown by Chimera. The orientation of the molecule in (C) and (E) is the same as that in (A), and the molecule is rotated 180° about the y-axis in (D) and (F). (G and H) Topological models of NMR and crystal structures, respectively, generated by Pro-origami interface. The figures were made using PyMOL.

  • Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains

    Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains

    Increase in both Tmax and ΔHc due to the addition of DDM or phospholipids into the NBD1/LPG14 complex. A, the effect of added DDM. The total detergent concentrations were held constant at 10 mM, while the DDM/LPG14 ratio was increased. DSC curve in the presence of 4 mM LPG14 is shown as the control because LPG14 caused complete denaturation at 10 mM. B, the effect of added phospholipids. LPG14 and lipid concentrations are shown in the data labels. When lipids were added with delay, the delay time was 4 hrs. The composition of the lipids was POPC: POPE = 4:1 (w/w).

  • The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors

    The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors

    (A) Monomers C (orange) and D (green) make up dimer CD. (B) A secondary structure alignment of monomer A from the Love et al. dimer (blue) with each monomer C and D shows an extension of β-strand B3 from Val 75 to Arg 78. (C) Hydrogen bonds are formed between residues Ile 74 O and Arg 78 NH, Gly 76 NH and Gly 76 O, forming a total of four hydrogen bonds in the CD dimer.

  • The dynamic duo: Combining NMR and small angle scattering in structural biology

    The dynamic duo: Combining NMR and small angle scattering in structural biology

    Utility of subunit-selective deuteration of protein complexes with SANS measurements. (A) A ternary complex, consisting of protein A (blue), B (orange), and RNA (red) is assumed. (B) In 0% D2O solution without any deuteration SANS does provide information about the overall shape of the complex, comparable to SAXS (but with lower sensitivity). (C) In 42% D2O solution, deuterated protein components have a positive contrast, while the protonated components match the contrast of the buffer and are “invisible.” Under these conditions the shape and center-of-mass distances between the deuterated component and the RNA can be determined. (D) In 70% D2O solution, the contrast of RNA is matched by the buffer, and the shape and center-of-mass distances between the deuterated components (positive contrast), and protonated components (negative contrast) can be determined.

  • Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment

    Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment

    (a) Fluorescence quenching of Trp residues in CLRR2 is shown as a function of MDP concentration. Error bars are the standard deviation from three measurements. The Kd was determined to be 2.0 ± 0.4 µM. (b) The MUSTER model of CLRR2 showing location of Trp residues (red) on the concave face of the protein that are the proposed binding site of MDP. The terminal repeats are shown in blue and the internal repeats are shown in cyan.

  • Capping motifs stabilize the leucine‐rich repeat protein PP32 and rigidify adjacent repeats
  • Crystal structure of toxin HP0892 from Helicobacter pylori with two Zn(II) at 1.8 Å resolution
  • Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains
  • The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors
  • The dynamic duo: Combining NMR and small angle scattering in structural biology
  • Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment

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