Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 82 Issue 9

Edited By: Bertrand Garcia-Moreno

Impact Factor: 2.921

ISI Journal Citation Reports © Ranking: 2013: 32/74 (Biophysics); 139/291 (Biochemistry & Molecular Biology)

Online ISSN: 1097-0134

Featured

  • Rebuilding a macromolecular membrane complex at the atomic scale: Case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2

    Rebuilding a macromolecular membrane complex at the atomic scale: Case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2

    Superimposition of the docking models of µ-OR, CXCR4, and Kv1.2 with their respective X-ray structure. The superimposition is operated on the Cα of monomer A for µ-OR and CXCR4 and on the Cα of the channel domain for Kv1.2. A. Superimposition of the PDB structure 4DKL and the docking model at rank 4. B. Superimposition of the PDB structure 3ODU and the docking model at rank #1 (without T4L). C. Superimposition of the PDB structure 3ODU and the docking model at rank #9 (with T4L). D. Superimposition of the PDB structure 3LUT and the docking model at rank #3 (with distance restraint). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Functional and structural studies of pullulanase from Anoxybacillus sp. LM18-11

    Functional and structural studies of pullulanase from Anoxybacillus sp. LM18‐11

    Detailed interaction networks of the N1 domain and polysaccharides. The PulA-apo structure (gray) is superimposed on those of PulA-maltotriose (A; cyan) and PulA-maltotetraose (B; green). The substrate molecules are shown as sticks. The detailed interaction networks of (C) PulA and maltotriose and (D) PulA and maltotetraose are shown in stereo.

  • Cation–π, amino–π, π–π, and H-bond interactions stabilize antigen–antibody interfaces

    Cation–π, amino–π, π–π, and H‐bond interactions stabilize antigen–antibody interfaces

    Selected views of antigen–antibody interfaces that show cation/amino–π and π–π chain motifs. Protein chains are displayed as ribbons, and the side chains of interest as sticks. (A) Chains of cation/amino–π interactions in the interface between the major respiratory grass pollen allergen Phl p 2 and specific human immunoglobulin E (PDB code: 2vxq). Epitope residues are shown in purple, the heavy chain residues of the antibody in lime and its light chain residues in blue. The two cation/amino–π chains involve the residues W41/Y32-R67-Y102 and N76-Y33-R98. (B) Chain of π–π interactions in the interface between the intermediate affinity I domain of integrin LFA-1 and its antibody AL-57 (PDB code: 3hi6). Epitope residues are shown in purple and the heavy chain residues of the antibody in lime. The π–π chain involves the residues W52-H264-W103-F102.

  • A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases

    A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases

    Mean values 〈DOO〉 of the average inter-carboxyl O…O distances DOO determined for structures within each class of GH family: α-retaining (yellow), β-retaining (green), α-inverting (red), and β-inverting (blue). The histogram is arranged from left to right in ascending order of magnitude of 〈DOO〉.

  • A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family

    A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family

    Model structures for TctA_ar and TctA_ct derived from 3VVN (top) and 4K1C (bottom). The structures are shown in cyan ribbons, highlighting in red ribbons the 20-amino acid repeat. G107 is shown as yellow spheres. The horizontal lines mark the approximate location of a lipid bilayer. The extracellular/vacuolar space lies at the top of the figure.

  • Incorporating replacement free energy of binding-site waters in molecular docking

    Incorporating replacement free energy of binding‐site waters in molecular docking

    Predicted binding-site waters in (A) crystal complex structure of αFABP (PDB ID: 2NNQ) and (B) corresponding apo-like structure (excluding the ligand). The crystal ligand is colored in forest green, the crystal waters are colored in magenta, and the protein residues are colored in light gray. Note that the crystal waters from an apo structure (PDBID: 3Q6L) are included in the apo-like system for comparison. The predicted binding-site water is colored based on the calculated replacement free energy ΔGSPA, from unfavorable (red) to highly favorable (green), and its calculated occupancy is represented by its size of the oxygen atom. Molecular images were generated with UCSF Chimera.

  • Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment

    Molecular dynamics simulation of the phosphorylation‐induced conformational changes of a tau peptide fragment

    DSSPPPII plots of secondary structure (colored as per legend) over simulation time - for simulations 0p (a), Tp (c), Sp (e), and 2p (g). Also shown are the bar charts for simulations 0p (b), Tp (d), Sp (f), and 2p (h), indicating the average percentage of secondary structure content per residue during the simulation. Helical turns and 310 helices (cyan), α-helices (blue), bends (yellow), and undefined structures (white) are shown above the x-axis, whereas β (red) and PPII (purple) structures are shown below the x-axis of the bar chart. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Rebuilding a macromolecular membrane complex at the atomic scale: Case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2
  • Functional and structural studies of pullulanase from Anoxybacillus sp. LM18‐11
  • Cation–π, amino–π, π–π, and H‐bond interactions stabilize antigen–antibody interfaces
  • A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases
  • A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family
  • Incorporating replacement free energy of binding‐site waters in molecular docking
  • Molecular dynamics simulation of the phosphorylation‐induced conformational changes of a tau peptide fragment

Recently Published Issues

See all

SEO Tips for Authors

SEO Author

Keep Current

Register

Register for email table of contents alerts and be the first to know when Proteins: Structure, Function, and Bioinformatics has published new research.

Why sign up?

It’s Free – you don’t have to have a subscription to receive email table of content alerts

Convenient Delivery – each alert is delivered straight to your inbox.

User-Friendly – as each issue publishes, you get an at-a-glance listing of new content with direct links to the full-text of each article

Saves Time – allows you to keep up-to-date with issues as they publish, saving you valuable time

No Commitment – you can opt-out of receiving email table of content alerts at any time, no questions asked

SEARCH

SEARCH BY CITATION