Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 82 Issue 11

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

  • Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models

    Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models

    P(χ1, χ2) for a dipeptide mimetic versus α-helical segment for aromatic residues: Comparison of the observed and calculated probability distributions of side-chain dihedral angles P(χ1, χ2) for Phe (Left column), Tyr (Middle column), and Trp (Right column). Row (a): Observed P(χ1, χ2) for Phe, Tyr, and Trp residues in an α-helical backbone conformation. Row (b): Calculated P(χ1, χ2) for Phe, Tyr, and Trp dipeptide mimetics with φ and ψ angles within ±10° of the canonical α-helix values (φ = −57°, ψ = −47°). Row (c): Calculated P(χ1, χ2) for Phe, Tyr, and Trp in α-helical segments. Row (d): Observed P(χ1, χ2) for Phe, Tyr, and Trp residues in a β-sheet backbone conformation. Row (e): Calculated P(χ1, χ2) for Phe, Tyr, and Trp dipeptide mimetics with φ and ψ angles within ±10° of the canonical β-sheet values (φ = −119°, ψ = 113°). The probabilities are normalized such that ∫P(χ1, χ2) dχ1 dχ2 = 1. The probability values, expressed as percentages, are defined by regions between the two vertical dotted lines. The probabilities increase from white to yellow to orange to black. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Crystal structure of a feruloyl esterase belonging to the tannase family: A disulfide bond near a catalytic triad

    Crystal structure of a feruloyl esterase belonging to the tannase family: A disulfide bond near a catalytic triad

    Dimer (A), monomer (B), and active site (C) structures of AoFaeB. The catalytic α/β-hydrolase domain (green) and the lid domain (magenta) are shown. GlcNAc residues of N-glycans, the catalytic triad and a calcium ion are shown as cyan sticks, yellow sticks and an orange sphere, respectively. Disulfide bonds are shown as sticks with the sulfur atoms in yellow. In (C), the |Fo| – |Fc| omit map (4.0σ) of the catalytic triad and the Cys202-Cys458 disulfide bond residues are shown.

  • Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily

    Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily

    (A) Conformational clusters of UDP-Glc, UDP-Gal, and UDP-4KH bound to w.t. eGALE and its mutants. (B) Conformational clusters of NAD + and NADH bound to w.t eGALE and its mutants. The occupancy values depict the relative numerical strength of each cluster. The simulations from which ligand conformations were obtained are indicated by the colors and hatching patterns and described in the key shown on the bottom right. The codes for the individual simulations are: Wtglc, Y177Fglc, H243Iglc, and S122Vglc; UDP-Glc bound to w.t. eGALE and its Y177F, H243I and S122V mutants respectively. Wtgal, Y177Fgal, H243Igal and S122Vgal; UDP-Gal bound to w.t. eGALE and its Y177F, H243I, and S122V mutants respectively. Wt4kh, Y177F4kh, H243I4kh, and S122V4kh; UDP-4KH bound to w.t. eGALE and its Y177F, H243I, and S122V mutants, respectively. Wtrst, Y177Frst, H243Irst, and S122Vrst; the resting state containing NAD + but no substrates/intermediates of w.t. eGALE and its mutants Y177F, H243I, and S122V respectively. EmNADH represents a simulation of eGALE with bound NADH but without any substrate or intermediate.

  • Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations

    Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations

    Cartoon representation of GOx. Colors legend: monomers (ice-blue and blue), FAD (green), sugars (pink), and dimer interface (red). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Cytotoxicity of the Vibrio vulnificus MARTX toxin Effector DUF5 is linked to the C2A Subdomain

    Cytotoxicity of the Vibrio vulnificus MARTX toxin Effector DUF5 is linked to the C2A Subdomain

    C2A is the cytotoxic subdomain of DUF5Vv. (A) Schematic of proteins expressed in the panel. (B–H) Epifluorescent and DIC images (3200) of HeLa epithelial cells transfected with pEGFP-N3 plasmid clones expressing EGFP (B), DUF5Vv-EGFP (C), C2Vv-EGFP (D). Expression of proteins in transfected cells is shown by western blot (E), and average of percent rounded cells in each cell type is quantified from three independent experiments (F).

  • Extracting representative structures from protein conformational ensembles

    Extracting representative structures from protein conformational ensembles

    Some atoms have curved distributions, where simply taking the mean leads to an unrealistic average position. (A) Highly nonlinear distribution of positions for the terminal nitrogen of a lysine side chain. The protein backbone is white and the lysine side chain is red. Each sphere represents a position of the terminal nitrogen group from the ensemble. The spheres are colored blue or orange to emphasize the curved shape. (B) Schematic 2D illustration of a complex nonlinear distribution of atom positions. The mean position lies in a region of space that is never sampled. A better representative position is shown.

  • Hot-spot analysis to dissect the functional protein–protein interface of a tRNA-modifying enzyme

    Hot‐spot analysis to dissect the functional protein–protein interface of a tRNA‐modifying enzyme

    Directional interface contacts of the Tgt dimer. The color code of the subfigures is the same as in Figure . Individual residues are shown in stick representation with nitrogen atoms in blue, oxygen atoms in red, and sulfur atoms in orange. Water molecules are shown as red spheres. H-bonds and salt bridges are indicated by dashed gray lines. (A) The Lys52···Glu339′ salt bridge as well as the Ala48···His333′ and Ala49···Tyr330′ H-bonds as present in the high-resolution crystal structure of wild-type Tgt in complex with a competitive inhibitor (pdb-code: 2z7k). The Lys52···Glu339′ salt bridge is observed in only about two thirds of all deposited Tgt crystal structures while in the remaining ones Lys52 adopts an alternative conformation allowing an H-bond to the backbone carbonyl of Thr285. (B) The Lys55···Glu348′ salt bridge and a water mediated interaction between the side chain carboxylate of Glu57 and the side chain ammonium of Lys325′ are observed in the crystal structure of wild-type apo-Tgt (pdb-code: 1pud). While in some crystal structures of Tgt the latter residues directly form a salt bridge via their side chain functional groups, in some structures no interaction between these residues is formed. (C) Aromatic hot-spot region formed by residues Phe92, Trp326′, Tyr330′, and His333′ (pdb-code ???: 1pud). This hydrophobic interface contact region is shielded from water access by Leu86 and Leu311′ on one side and by the β1α1-loop (omitted for the sake of clarity) on the opposite side. (D) Same detail as in (C) but from Tgt(Cys158Ser/Cys281Ser/Trp326Glu/Glu339Gln) (pdb-code: 3uvi). The empty space generated by the Trp326′Glu exchange is filled by six water molecules making H-bonds to the Glu326′ side chain carboxylate. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

  • Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models
  • Crystal structure of a feruloyl esterase belonging to the tannase family: A disulfide bond near a catalytic triad
  • Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily
  • Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations
  • Cytotoxicity of the Vibrio vulnificus MARTX toxin Effector DUF5 is linked to the C2A Subdomain
  • Extracting representative structures from protein conformational ensembles
  • Hot‐spot analysis to dissect the functional protein–protein interface of a tRNA‐modifying enzyme

Recently Published Issues

See all

Recently Published Articles

SEO Tips for Authors

SEO Author

Special Issue

Special Issue




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).

Click here to read more

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