Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 83 Issue 5

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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  • Native fold and docking pose discrimination by the same residue-based scoring function

    Native fold and docking pose discrimination by the same residue‐based scoring function

    A case in which a hydrophilic residue (LYS) and a hydrophobic one (PHE) make a hydrophobic contact at the interface between two subunits, here colored in blue and red. To this contact a favorable energy value should be associated. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Inferring the microscopic surface energy of protein–protein interfaces from mutation data

    Inferring the microscopic surface energy of protein–protein interfaces from mutation data

    An overview of the model derivation procedure, exemplified using the mutation of P1 leucine of Streptomyces griseus protease B (SGPB) to aspartic acid, in the interaction with the turkey ovomucoid third domain (OMTKY3). Voronoï diagrams (left) are constructed for the wild-type and mutant protein. The P1 residue is shown, as is OMTKY3 Pro-138, with which it interacts. The diagrams are used to calculate interaction type areas (center), the difference between which are the changes in interaction type area on mutation (top right). These are used to construct a linear equation for this mutant (bottom right). In this case, the mutation is dominated by a loss of 87.4 Å2 area between neutral surfaces, and the gain of 84.7 Å2 of interaction between neutral surface and H-bond acceptor surface, with smaller changes between other surfaces, such as acceptor–acceptor surface. Such an equation is generated for each mutation, which are collectively used to find the γ values which best agree with the experimental ΔΔG data. Voronoï images created using Voroprot.

  • Prediction of VH–VL domain orientation for antibody variable domain modeling

    Prediction of VH–VL domain orientation for antibody variable domain modeling

    The 11 antibodies (Ab01–Ab11) of the AMAII dataset positioned in ABangle VH–VL orientation space, with nomenclature adapted from Ref. . As Ab01 and Ab10 have been crystallized with two Fv structures in the asymmetric unit, the markers “ab01a” and “ab01b” refer to 4MA3_BA and 4MA3_HL, while “ab10a” and “ab10b” refer to 4M61_BA and 4M61_DC (PDB ID and heavy/light chain identifier), respectively. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • The near-symmetry of proteins

    The near‐symmetry of proteins

    Homomeric protein structures analyzed in this study (see Table ). Each subunit is indicated by a different color. (a) Porin, (b) Decameric amyloid P, (c) Tobacco mosaic virus disc, (d) Alcohol dehydrogenase, (e) Hemoglobin, (f) Neuraminidase, (g) GroEL, (h) Wheat germ agglutinin, (i) Triose phosphate isomerase, (j) Light-harvesting comp.2, (k) Beta-subunit of types 1&2 heat-labile enterotoxin, (l) C-reactive protein, (m) HIV proteinase, (n) trp RNA-binding attenuation protein, (o) Purine nucleoside phosphorylase, (p) Aspartate transcarbamoylase, and (q) Glutamine synthetase.

  • Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge-like mechanism

    Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge‐like mechanism

    Overview of colocalization of the interdomain linker with structural elements: (a) the inward-occluded state and (b) the outward-occluded state of LacY. The interdomain linker, the loop between TMSs 2 and 3, the mid-TMS4 linker, and TMS11 are highlighted in purple, green, yellow, and orange, respectively. All of these elements generate strong signals on the Δ-distance maps (Fig. ; Tables and ) and are colocalized with the interdomain linker. In general, the same pattern holds true for XylE, except that there is a long loop between TMSs 3 and 4, which is located on the extracellular side of the protein that displays independent movement (Table ).

  • Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+-ATPase

    Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca2+‐ATPase

    The reaction cycle of SR Ca2+-ATPase and its crystal structures. (A) The E1/E2-reaction cycle of SR Ca2+-ATPase. (B) The crystal structure in the E1·ATP state. The cytoplasmic domains and transmembrane helices are listed in the sequence.

  • Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants

    Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants

    Ligand migration channels in Mb. A: A cartoon image of Mb (pdb id: 1A6G) overlaid with cavities (green spheres), portals (purple spheres with labels that start with P), and nine channels (rugged blue tubes) identified by both our method (see the full list in Table II) and MD. B: Different conformation changes needed to open these channels as determined by our method. The thickness along the backbone trace shows the magnitude of the motions of the residues as each channel opens up. The RMSD deviations between the final conformations and the initial minimized structure and their potential energy differences are also given. C: The primary sequence of Mb and its secondary structures (helices A–H). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Native fold and docking pose discrimination by the same residue‐based scoring function
  • Inferring the microscopic surface energy of protein–protein interfaces from mutation data
  • Prediction of VH–VL domain orientation for antibody variable domain modeling
  • The near‐symmetry of proteins
  • Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge‐like mechanism
  • Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca2+‐ATPase
  • Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants

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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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