Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 83 Issue 7

Edited By: Bertrand Garcia-Moreno

Impact Factor: 2.627

ISI Journal Citation Reports © Ranking: 2014: 37/73 (Biophysics); 148/289 (Biochemistry & Molecular Biology)

Online ISSN: 1097-0134

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  • Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor

    Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor

    Structure prediction and selection of functional amino acids for mutagenesis. (A) A comparative model of inducer-binding domain of ΔL141-pobR dimer (green and cyan for each domain) overlaid on a template of known structure (PDB code: 2IA2) (gray). (B) Magnified view of domain crossing loop in ΔL141-pobR comparative model. The loop in modeled pobR (cyan) is in excess from template (gray) by four amino acids. The modeled loop and template loop are marked with arrows. One amino acid at position 141 on this loop was deleted in native pobR sequence (hence ΔL141-pobR) to keep consistency with another transcription factor, pcaU, in the IclR family. (C) Ligand docking and estimation of first-shell residues in inducer-binding pocket of pobR model. Top three unique binding orientations of 34DHB ligand in ΔL141-pobR dimer model is shown in magenta. First-shell residues (distance cutoff from any ligand orientation 4 Å) are shown in sticks. Amino acid numbering is based on native pobR sequence. V143 in parentheses denotes residue from a different chain. The images were generated using PyMOL software (The PyMOL Molecular Graphics System, Version 0.99, Schrödinger, LLC).

  • Structural diversity of the epigenetics pocketome

    Structural diversity of the epigenetics pocketome

    Structural coverage of the epigenetics pocketome. The ensemble of structures collected in the PDB covers 163 binding pockets (highlighted in red) across 18 classes of protein domains that write, read and erase post-translational modifications on histones, DNA and RNA. The structures of representative pockets (green: hydrophobic; red/blue: polar) occupied by endogenous ligands (purple) are shown.

  • Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations

    Folding thermodynamics of β‐hairpins studied by replica‐exchange molecular dynamics simulations

    Most populated structure of studied β-hairpins based on backbone clustering with 0.15 nm cutoff distance. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Exploring proteome-wide occurrence of clusters of charged residues in eukaryotes

    Exploring proteome‐wide occurrence of clusters of charged residues in eukaryotes

    The workflow of FCCP. The main steps of FCCP performance are shown below, the downstream and the upstream steps are also shown. The beginning and the end of the program are indicated. To get more details (a, b, c) see the text.

  • Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering

    Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure‐guided surface engineering

    The crystal structure of eCGP123. A: Three views of the structure with a cutaway view showing the chromophore (shown in yellow) and the adjacent coaxial helix. B: The QYG chromophore (chemical identifier: CRQ) shown in stick representation with 2mFo-DFc electron density from the refined structure contoured at 1.5 σ. C: The chromophore environment with critical residues discussed in the text is shown. Red spheres represented ordered water molecules modeled in the structure. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Finding off-targets, biological pathways, and target diseases for chymase inhibitors via structure-based systems biology approach

    Finding off‐targets, biological pathways, and target diseases for chymase inhibitors via structure‐based systems biology approach

    Crystal structure of human chymase and the zoomed view of its active site which clearly shows the catalytic triad and important binding site residues such as G193, K192, and R217. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Structural analysis of the polo-box domain of human Polo-like kinase 2

    Structural analysis of the polo‐box domain of human Polo‐like kinase 2

    Phosphopeptide-binding models of Plk2-PBD. Plk2-PBD (violet) in a complex with a peptide MQSpTPL (green; A) or MQTSpTPK (cyan; B) are modeled based on the structural superposition on Plk1-PBD (yellow) bound to the MQSpTPL peptide (PDB code 3P34). Labeled are the whole peptide residues and the Plk1 or Plk2 residues involving the intermolecular interactions. Dotted lines represent intermolecular hydrogen bonds. Among them, bonds only shown in (B) are in orange. Dashed red circle highlights ionic interactions mediated by phosphothreonine, and black circles exhibited intermolecular hydrophobic interactions.

  • Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor
  • Structural diversity of the epigenetics pocketome
  • Folding thermodynamics of β‐hairpins studied by replica‐exchange molecular dynamics simulations
  • Exploring proteome‐wide occurrence of clusters of charged residues in eukaryotes
  • Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure‐guided surface engineering
  • Finding off‐targets, biological pathways, and target diseases for chymase inhibitors via structure‐based systems biology approach
  • Structural analysis of the polo‐box domain of human Polo‐like kinase 2

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Special Issue: Antibody Modeling Assessment II

Edited by Gary L. Gilliland

To assess the state of the art in antibody 3D modeling, 11 unpublished high-resolution x-ray Fab crystal structures from diverse species and covering a wide range of antigen-binding site conformations were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. In this Special Issue, Proteins present an overview of the organization, participants and main results of this second antibody modeling assessment (AMA-II).

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