Protein Science

Cover image for Vol. 25 Issue 10

Edited By: Brian W. Matthews

Impact Factor: 3.039

ISI Journal Citation Reports © Ranking: 2015: 118/289 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • Landscape of protein–small ligand binding modes

    Landscape of protein–small ligand binding modes

    Comparison of the binding modes between tyrosine hydroxylase (PDB ID: 2TOH) and phenylalanine hydroxylase (PDB ID: 1TG2) complexed with 7,8-dihydrobiopterin. The gray and green molecules indicate 2TOH and 1TG2, respectively. The molecules depicted by sticks at the center of the figure are 7,8-dihydrobiopterin. The leucine and tyrosine residues, described in the main text, are shown as sticks.

  • Network representation of protein interactions: Theory of graph description and analysis

    Network representation of protein interactions: Theory of graph description and analysis

    Display of the correlation network of the OPN/heparin interaction. It is represented with three pronounced hubs as indicated by the blue loops. These hubs correspond to the binding site, the affected site and residual correlated residues Isolated nodes are ignored. Every spot corresponds to a node, that is, to a diagonal element of the adjacency matrix and every line indicates an edge between two nodes, that is, a nonzero off-diagonal matrix elements of A. The residue patches of the primary sequence corresponding to the nodes are indicated at the bottom; see Figure 3 for the corresponding nodes in the adjacency matrix. The clustering was performed by means of binary hierarchical clustering using an Euclidean distance norm and a predefined number of three clusters. The graphical visualization was done using Mathematica 10's spring electrical embedding method.

  • The interplay between effector binding and allostery in an engineered protein switch

    The interplay between effector binding and allostery in an engineered protein switch

    MalE complementation assay for estimating maltose affinity. (A) Schematic diagrams of in vivo of the malE complementation assay. (B) A heat map representation of minimum growth concentration of maltose (MGCMal) for the malE knockout E. coli strain PM9F' as a function of the mutation in the MBP domain. (C) Average MGCMal for types of residues as categorized in (B) for each target residue. All MGCMal values can be found in Supplementary Data S1.

  • Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin

    Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin

    Best models of S6(Rpt1) generated by different programs. (A) Robetta, (B) I-TASSER, (C) QUARK. Coloring from N (blue) to C (brown) terminus. Both the front view and transverse view is depicted.

  • Destruction-and-diffraction by X-ray free-electron laser

    Destruction‐and‐diffraction by X‐ray free‐electron laser

    Relative loss of scattering powers of Cu, Zn, and S atoms in the XFEL 3WG7 data set revealed from the F(2DYR)-F(3WG7) difference Fourier map. (a, b) The first and second copies of CcO molecules in the structure for the di-copper cluster. (c, d) The first and second copies of CcO molecules in the structure for the Zn-(Cys)4 motif. The map is contoured at ±6.5σ (green and red) and superimposed onto the 2DYR model.

  • Current view on regulation of voltage-gated sodium channels by calcium and auxiliary proteins

    Current view on regulation of voltage‐gated sodium channels by calcium and auxiliary proteins

    Ca2+-dependent conformational changes of CaM bound to the NaVCTD and their involvement in channelopathies. (A) Overlay of the NaVCTD ternary complexes in the presence of Ca2+ (NaV1.2) and the absence of Ca2+ (NaV1.5). Colors for NaV1.2: NaV1.2CTD (blue), FHF (brown), Ca2+ (cyan), and CaM (red). Colors for NaV1.5: NaV1.5CTD (green), FHF (gold), and CaM (purple). (B) Zoomed-in view of the IQ domain and CaM with the same orientation as (A). (C) Zoomed-in view of the CaM N-lobe interactions with the IQ domain. Residue numbering is based on NaV1.2; numbering for NaV1.5 is shown in parentheses. (D) Zoomed-in view of the NaV1.5 ternary complex in the absence of Ca2+ showing the ternary interactions between Arg1898 (Arg1902 in NaV1.2) in the Nav1.5 CTD, Lys95 in CaM via Glu1901 (Glu1905 in NaV1.2), and Tyr98 in FGF13 (FHF). (E) Zoomed-in view of the NaVCTD ternary complexes in the presence of Ca2+ (NaV1.2) and the absence of Ca2+ (NaV1.5). The overlaid structures demonstrate the Ca2+-dependent changes in the interaction between the NaVCTD and the C-lobe and interlobular linker of CaM. The residue numbering is based on NaV1.2; numbering for NaV1.5 is shown in parentheses.

  • Landscape of protein–small ligand binding modes
  • Network representation of protein interactions: Theory of graph description and analysis
  • The interplay between effector binding and allostery in an engineered protein switch
  • Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin
  • Destruction‐and‐diffraction by X‐ray free‐electron laser
  • Current view on regulation of voltage‐gated sodium channels by calcium and auxiliary proteins

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Special Issue in Honor of Ron Levy

Protein Science Awards

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2016 Best Paper Award Winners
We are pleased to announce the winners of the 2016 Protein Science Best Paper Award:

Tracy Clinton
Air Force Biochemist

Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets
Tracy R. Clinton, Matthew T. Weinstock, Michael T. Jacobsen, Nicolas Szabo-Fresnais, Maya J. Pandya, Frank G. Whitby, Andrew S. Herbert, Laura I. Prugar, Rena McKinnon, Christopher P. Hill, Brett D. Welch, John M. Dye, Debra M. Eckert and Michael S. Kay
Protein Sci. 24:446-463, 2015.

Michael Thompson
Postdoctoral Fellow
Department of Bioengineering and Therapeutic Sciences at University of California, San Francisco

An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein
Michael C. Thompson, Duilio Cascio, David J. Leibly and Todd O. Yeates
Protein Sci. 24:956-975, 2015.

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2016 Young Investigator Award Winner

The Protein Science Young Investigator Award recognizes a scientist generally within the first 8 years of an independent career who has made an important contribution to the study of proteins. The 2016 winner is Dr. Benjamin Garcia (University of Pennsylvania Perelman School of Medicine).

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More information on our awards can be found here.

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