Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 83 Issue 1

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

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  • Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning

    Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning

    Conformational densities of the residues in the N-terminal segment of the G head domain. The four ensembles of these residues are color coded, and each ensemble is represented using 15 snapshots. The X-ray structure of the head domain is also shown in the background as a cartoon. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Detecting local residue environment similarity for recognizing near-native structure models

    Detecting local residue environment similarity for recognizing near‐native structure models

    Examples of residue-wise energies by SDE and other potentials. Two decoy sets included in the Lmds set, 1fc2 and 1bba, were used. As shown in Table , SDE and MRE successfully identified the native structure among 501 decoys for these two decoy sets. A to E are comparison between the SDE and GOAP energies at individual residues in the native structure of 1fc2 and the lowest GOAP energy decoy, 1fc2.60276.pdb. F to H are comparison between the SDE and DFIRE energies at each residue in the native of 1bba and the lowest DFIRE energy decoy, 1bba.1697.pdb. A: Energy difference at each residue between the native 1fc2 and the decoy 1fc2.60276.pdb by GOAP, DFIRE, MRE, and SDE. The y-axis shows the residue-wise energy difference between the native and the decoy. A negative value indicates that the residue has a lower energy in the native than the decoy. SDE and MRE scores are negated so that they have the same sign as the other two potentials. B: The structure of the decoy 1fc2.60276.pdb. ILE12 is shown in red, and three residues that have preferable GOAP energy between 1LE12, namely, PHE26, LEU30, and LEU41 are shown in yellow, green, and cyan, respectively. C: The native structure of 1fc2. ILE12, PHE26, LEU30, and LEU41 are shown in the same colors as in the Panel B. D: The pairwise GOAP energies between ILE12 and the other residues in the decoy 1fc2.60276.pdb. E: The Euclidean distance of side-chain centroids of each residue in the native and the decoy after the two structures are superimposed by the LGA program. A high distance (y-axis) indicates that the residue position in the decoy is far off from its correct position. F: Energy difference at each residue between the native 1bba and the decoy 1bba.1697.pdb by GOAP, DFIRE, MRE, and SDE. G: Superimposition of the native structure (pink) of 1bba and the decoy 1bba.1697.pdb (cyan). LEU24 are shown in the stick representation in red and blue in the native and the decoy, respectively. H: Pairwise DFIRE energies between LEU24 and each residue in the native (filled circles) and in the decoy 1bba.1697.pdb (open circles).

  • Dual effects of familial Alzheimer's disease mutations (D7H, D7N, and H6R) on amyloid β peptide: Correlation dynamics and zinc binding

    Dual effects of familial Alzheimer's disease mutations (D7H, D7N, and H6R) on amyloid β peptide: Correlation dynamics and zinc binding

    Correlation dynamics between the N-terminal Aβ(1–16) and the C-terminal Aβ(17–42) regions. The corresponding correlation dynamics of Zn2+-bound Aβ42 is also shown for comparison. The error bars show the standard deviations using the block average method.

  • Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site

    Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site

    Left: The host in reality. Right: The host as described by the solvation model, in terms of its contributions to the cavitation energy. In the model, the surface area of the buried pocket is added to the cavitation energy contribution of the host, providing a qualitatively wrong description of the host. ΔSASA is the difference in the solvent accessible surface area between the complex and host. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures

    The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures

    3D structure of mjSHMT. A) The G monomer of holo-mjSHMT is colored by domain type: yellow, small N-terminal α-helix (residues 1–24); purple, catalytic domain (residues 25–282); green, C-terminal domain (residues 283–410); orange, 24 C-terminal residues (411–429). PLP is shown as spheres and colored red. B) G/H dimer. The G monomer is colored as in panel A, the H monomer is cyan and the PLP blue. C) Ribbon representation of mjSHMT holo G and apo A monomers after least square structure superposition of the structurally conserved regions (SCRs-mj, see Methods and Supporting Information Table S3). The SCRs-mj of both proteins are colored green, the remaining regions of the holo and apo dimers are blue and orange, respectively. Both PLP molecules bound to holo-mjSHMT G/H dimer are shown as sticks and colored red. The picture was generated with PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC).

  • Application of information theory to a three-body coarse-grained representation of proteins in the PDB: Insights into the structural and evolutionary roles of residues in protein structure

    Application of information theory to a three‐body coarse‐grained representation of proteins in the PDB: Insights into the structural and evolutionary roles of residues in protein structure

    Definition of residue triplets to compute mutual information I2. Centroids representing the sidechains of residues A, B, and C are shown as spheres. The distances r1 between bodies B and A, and r2 between bodies B and C respectively comprise the variable sampled in the probability distributions ρAB, ρBC, and ρABC used in this work.

  • Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions

    Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH‐Π interactions

    Interaction of XXXG with X-2 L110F. (A) XXXG labeled according to the crystal structure. The heptasaccharide was numbered first taking into account the backbone glucoses (BGC1-4) followed by the xylose branches (XYS5-7). BGC4 and XYS7 at the non-reducing end of the oligomer constitute the first X in the XXXG oligomer. (B) The three ligands, XXXG (blue), xylopentaose (green) and cellopentaose (brown), are not positioned in the same way in the binding cleft. Instead the branching xylose of XXXG at the non-reducing end lifts the glucose it is connected to, making room for itself in the binding cleft. However both XXXG (C) and xylopentaose (D) are bound along a similar path in the binding cleft of X-2 L110F. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning
  • Detecting local residue environment similarity for recognizing near‐native structure models
  • Dual effects of familial Alzheimer's disease mutations (D7H, D7N, and H6R) on amyloid β peptide: Correlation dynamics and zinc binding
  • Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
  • The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures
  • Application of information theory to a three‐body coarse‐grained representation of proteins in the PDB: Insights into the structural and evolutionary roles of residues in protein structure
  • Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH‐Π interactions

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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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