Protein Science

Cover image for Vol. 23 Issue 11

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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  • Molecular determinants of tetramerization in the KcsA cytoplasmic domain

    Molecular determinants of tetramerization in the KcsA cytoplasmic domain

    The KcsA C-terminal domain four-helix bundle. Shown are two adjacent helices in the CTD bundle (as depicted in the inset) and key residues referred to in the text. Left, back view of the two helices highlighting residues in the hydrophobic core of the helical bundle. Right, front view highlighting residues on the outer surface of the helices. Residues mutated to alanine in this study are shown in stick mode, with hydrophobic, positively- and negatively-charged residues shown in green, blue and red, respectively.

  • Contribution of each Trp residue toward the intrinsic fluorescence of the Giα1 protein

    Contribution of each Trp residue toward the intrinsic fluorescence of the Giα1 protein

    Model of WT Giα1 depicting its carbon backbone, GDP nucleotide, three Trp residues, W131 (blue), W211 (orange), and W258 (green), and R208 (red).

  • Double trouble—Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments

    Double trouble—Buffer selection and His‐tag presence may be responsible for nonreproducibility of biomedical experiments

    Conformational change of PA4794 upon binding HEPES. The apo structure is shown in gray, and the HEPES-bound structure is shown in green. Upon binding of HEPES we observe a flip of the main chain of Gly79 and Asn80, a shift in the main chain of residues 28 and 29, and a conformational change of the Cys29 side chain.

  • Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake

    Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake

    The ligand binding site. The binding site is located at one end of the β-barrel as identified from binding of a UNL (red spheres). (A) Stereo view of the UNL and its interaction with the protein in BACOVA_00364 (pdb code 4gzv). Omit map is contoured at 1.25 σ level above the mean density. The residues interacting with the UNL are shown in stick representation. Arg163 that interacts with the UNL comes from an adjacent protomer in the biological tetramer. (B) and (C) are the corresponding UNL binding sites for BACUNI_03039 (pdb code 4iab) and BACEGG_00036 (pdb code 4i95), respectively, where the same or similar UNL is bound.

  • Understanding the determinants of substrate specificity in IMP family metallo-β-lactamases: The importance of residue

    Understanding the determinants of substrate specificity in IMP family metallo‐β‐lactamases: The importance of residue

    IMP-1 active site with Zn(II) ligands and residue 262. Serine 262 is highlighted with a red circle. The six remaining residues are Zn(II) ligands coordinating their respective Zn(II) ion (depicted as gray spheres). The enzyme backbone is represented as a cyan cartoon and residues as sticks with atoms colored in green (carbon), red (oxygen), blue (nitrogen), and yellow (sulfur). The top left Zn(II) ion is Zn1 in the 3H site and the bottom right one Zn2 in the DCH site. The image was created using PyMOL (www.pymol.org/) and PDB entry 1DD6 (Ref. ).

  • Probing structurally altered and aggregated states of therapeutically relevant proteins using GroEL coupled to bio-layer interferometry

    Probing structurally altered and aggregated states of therapeutically relevant proteins using GroEL coupled to bio‐layer interferometry

    Assessment of FGF-1 stability in the presence and absence of heparin by the GroEL-BLI biosensor assay. (A) The experimental steps of a typical BLI experiment are shown. The step numbers correspond with the step numbers shown on the BLI sensograms in (B). (B) A representative BLI sensogram of FGF-1, with and without heating at 40°C for 5 min, followed by assessment by GroEL-BLI assay. Note, the diminished binding in presence of 3:1 (w/w) ratio of heparin:FGF-1. (C) The normalized binding amplitudes of FGF-1 to GroEL after the association phase was quantified. The bar chart is an average of three independent experiments with the error bars representing the standard deviation.

  • Engineering deamidation-susceptible asparagines leads to improved stability to thermal cycling in a lipase

    Engineering deamidation‐susceptible asparagines leads to improved stability to thermal cycling in a lipase

    Characterization of 6B and mutC: (A) Far-UV CD spectra of 6B (•) and mutC (○) at 25°C. (B) Near-UV CD spectra of 6B (•) and mutC (○) at 25°C. (C) Unfolding (▪, •) and refolding (□, ○) of mutC (circle) and 6B (square) was monitored by change in ellipticity at 222 nm as a function of temperature.

  • Molecular determinants of tetramerization in the KcsA cytoplasmic domain
  • Contribution of each Trp residue toward the intrinsic fluorescence of the Giα1 protein
  • Double trouble—Buffer selection and His‐tag presence may be responsible for nonreproducibility of biomedical experiments
  • Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake
  • Understanding the determinants of substrate specificity in IMP family metallo‐β‐lactamases: The importance of residue
  • Probing structurally altered and aggregated states of therapeutically relevant proteins using GroEL coupled to bio‐layer interferometry
  • Engineering deamidation‐susceptible asparagines leads to improved stability to thermal cycling in a lipase

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