Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 83 Issue 3

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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  • Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa

    Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa

    The cavity available to the cis anionic chromophore in the M159T structure (yellow surface) is enlarged relative to dronpa (white surface) as a result of the reduced side chain as well as a 1.4 Å “outward retraction” of the side chain (Dronpa-M159T: yellow scheme/dronpa: green scheme 2Z1O). The cavity volume shown does not include crystal waters. The 2Fo − Fc electron density is contoured at the 2.0 sigma level for chromophore and residues 156–171 for the Dronpa-M159T structure. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis–tau peptide

    Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self‐association of cis–tau peptide

    Free energy profile of the ω bonds of pThr231-Pro232 and Pro232- Pro233. Three major conformational preferences (trans–trans, trans–cis, and cis–trans) are indicated at their corresponding wells. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Evaluation of transmembrane helix predictions in 2014

    Evaluation of transmembrane helix predictions in 2014

    Transmembrane helix prediction performance. Qok scores for all 12 prediction methods on various sets of TMPs. Qok denotes the percentage of proteins for which all TMHs were correctly predicted (A: TMH endpoints within five or less residues of either OPM or PDBTM annotation for the whole protein, Methods). Above the bars are the numbers of proteins in each dataset. Error bars are the sample standard deviation generated by bootstrapping with 1000 draws of half the set size each (cf. Methods). B: Qok is plotted for 190 redundancy-reduced TMPs followed by 44 new (not used for development) and 146 old (used for development, either the protein itself or homologous proteins) TMPs. All methods clearly performed worse for more recently determined protein structures. The old–new difference for TopPred2 suggested that a significant fraction of the differences might not be explained by over-training. C: All methods reached higher Qoks for eukaryotes than for bacteria. Note that we excluded the nine archaeal and two sequences of viral origin. D: Performance declines from bitopic TMPs to those with 2–5 TMHs or more. For (D), the number in brackets behind the set size denotes the number of TMHs in the respective subset.

  • BioGPS: Navigating biological space to predict polypharmacology, off-targeting, and selectivity

    BioGPS: Navigating biological space to predict polypharmacology, off‐targeting, and selectivity

    Cavity characterization. (a) MIFs computation (shape in yellow wireframe, hydrophobic in green surface, H-bond donor in blue surface, H-bond acceptor in red surface). (b) Selection of representative points and generation of quadruplets (all possible quadruplets are generated, here for clarity only three quadruplets are reported). (c) Data structure of quadruplets (six distances: d1-d6, four point feature: f1-f4, 3D arrangement: V). (d) All quadruplets are represented as a bitstring that constitutes the “Common Reference Framework.”

  • The structure of S. lividans acetoacetyl-CoA synthetase shows a novel interaction between the C-terminal extension and the N-terminal domain

    The structure of S. lividans acetoacetyl‐CoA synthetase shows a novel interaction between the C‐terminal extension and the N‐terminal domain

    The C-terminal Domain of SlAacS. (A) Ribbon diagrams for the C-terminal domains of SeAcs (cyan), ScAcs (red) and SlAacS (green). The hinge residue at the start of the C-terminal domain is shown. Dashed lines represent regions that were disordered in the crystal structures including the loop that spans the two C-terminal helices. (B) Stereo illustration of the interactions between the C-terminal extension in SlAacS and the N-terminal domain. Residues Asn637 through Ser640 interact with the N-terminal helix from residues Arg183 through Arg188 and the P-loop at positions Ser272 through Gly277. Note that the side chains of Ser272, Ser273, Thr275, and Thr276 are not shown for clarity as the only interactions occur with main chain carbonyl atoms. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin

    Atomic resolution crystal structure of HV‐BBI protease inhibitor from amphibian skin in complex with bovine trypsin

    The protease binding loop is structurally conserved in BBI inhibitors. The superposition of HV-BBI(3-18) (orange), ORB2-K (green), and SFTI-1 (yellow) inhibitors.

  • Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262

    Crystal structure of a fully glycosylated HIV‐1 gp120 core reveals a stabilizing role for the glycan at Asn262

    Location and interactions of the Asn262 glycan in CD4-bound gp120. (A) The Asn262 glycan (N262) is shown as green and red ball-and-sticks in the context of the inner and outer domains of the gp120 core. Visible N-linked glycosylation sites are indicated by green circles and locations of other potential glycosylation sites by nonfilled circles. (B) The solvent accessible surface of the weakly negatively charged cleft into which the Asn262 glycan inserts is displayed and colored according to surface electrostatic potential [−10 kT/e (red) to 10 kT/e (blue)] as calculated by the adaptive Poisson–Boltzmann solver (APBS). The cleft is shown with and without glycan. (C) The interaction of Asn262 glycan with the cleft in gp120 around the largely buried GlcNAc core. The blue mesh represents the 2Fobs–Fcalc electron density map at a 1σ contour level. The side chains of protein residues that constitute the cleft around the glycan base are shown in ball-and-stick representation and labelled. (D) The organization of other gp120 glycans in proximity to the Asn262 glycan. The closest distances between the glycans are labelled. The positions of the V3 loop and the Asn301 glycan that are absent in the YU2 gp120 core construct are approximated.

  • Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa
  • Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self‐association of cis–tau peptide
  • Evaluation of transmembrane helix predictions in 2014
  • BioGPS: Navigating biological space to predict polypharmacology, off‐targeting, and selectivity
  • The structure of S. lividans acetoacetyl‐CoA synthetase shows a novel interaction between the C‐terminal extension and the N‐terminal domain
  • Atomic resolution crystal structure of HV‐BBI protease inhibitor from amphibian skin in complex with bovine trypsin
  • Crystal structure of a fully glycosylated HIV‐1 gp120 core reveals a stabilizing role for the glycan at Asn262

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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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