Protein Science

Cover image for Vol. 25 Issue 8

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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  • The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7

    The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7

    Model of the HDAC-MTA1-RBBP4 portion of the NuRD complex. The model has been made by simply juxtaposing the HDAC-MTA1 crystal structure with two copies of our model of the RBBP4-MTA1449–715 complex and adding the crystal structure of the nucleosome (1AOI). The HDAC1 active sites are shown as yellow spheres and the histone H3 binding site on RBBP4 is circled. The N-terminal 40-residue tail of histone H3 is indicated schematically to show that it is within reach of both the histone-H3-binding site on RBBP4 and the HDAC1 active site. Similar interactions are possible for the right-hand RBBP4 subunits, which could interact with the second histone H3 tail on the back of the model as drawn.

  • Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations

    Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations

    Salt bridge and H-bond contacts (magenta dashed lines) around the C-terminus of Ang. The RNH1 backbone is shown in gray ribbon. The Ang backbone is shown in cartoon and colored by secondary structure. Positively and negatively charged residues that form salt bridges are labeled in blue and red, respectively. Main-chain and side-chain atoms are shown in sticks and balls, respectively. (A) RNH1-Ang WT preserves a salt-bridge/H-bond network throughout the simulation. (B) In RNH1-Ang GGRRmut, AngQ117 side chain swings between the original position (such as in RNH1-Ang WT) and a solvent-exposed one (shown here) where it forms an H-bond with RNH1N406. (C) RNH1-Ang QGmut maintains the same C-terminal conformation and intra-/intermolecular interactions as those in RNH1-Ang WT, except for the H-bonds involving the mutated Ang residue 117. (D) Ang GGRR/QGmut C-terminus adjusts its position with respect to RNH1 and forms stable salt bridges with the latter via AngR121 and AngR122.

  • Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

    Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

    V26A Ubiquitin at pH 2.0 is a late folding intermediate of Ubiquitin. The contact maps of (a) wt Ubiquitin, (b) V26A Ubiquitin at pH 6 and (c) V26A Ubiquitin at pH 2. The red circle shows regions where the major contacts are disrupted at pH 2. (d) The structure of wt Ubiquitin. The regions that show major differences in contact map at pH 2 are colored in green. (e) The structure of wt Ubiquitin is shown in a different orientation to show the hydrophobic contacts, H-bond and salt bridges that stabilize the A46–Q62 region against helix α1. (f) The structure of V26A Ubiquitin at pH 2 in same orientation shows disruption of these contacts. An ensemble of lowest forty energy structures for (g) V26A Ubiquitin at pH 6, (h) V26A Ubiquitin pH 2 and (i) cluster F1 from MD simulations.

  • Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding

    Molecular dynamic study of MlaC protein in Gram‐negative bacteria: conformational flexibility, solvent effect and protein‐phospholipid binding

    Correlation map of MlaC protein. The correlation map of the MlaC protein from Ralstonia solanacearum are on the left. The MlaC protein (gray) and phospholipid (colored bonds) are shown on the right. The red box shows that α7 appears correlated motions with β2 and β3; and the yellow box indicates the correlations between α7 and α2.

  • Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition

    Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition

    (A) Overlay of 1H-15N HSQC spectra of TC-1 in the absence (black) and presence (red) of full-length Cby at a 1:2 ratio (TC-1 60 μM:Cby 120 μM). (B) Overlay of 1H-15N HSQC spectra of TC-1 in the absence (black) and presence (cyan) of CbyΔC20 at a 1:2 ratio (TC-1 60 μM:CbyΔC20 120 μM). (C) Intensity ratios (I/Io) for assigned TC-1 amide resonances in the presence (I) or absence (Io) of either full-length Cby or CbyΔC20. Yellow shaded areas correspond to the three regions on TC-1 with high-helical propensity as determined by chemical shift analysis.

  • X-ray radiation-induced addition of oxygen atoms to protein residues

    X‐ray radiation‐induced addition of oxygen atoms to protein residues

    Oxygen additions of glu364 (a) and Glu364 (b). In this article, lowercase amino acid abbreviations are used to designate residues in the lowercase monomer defined in the 3ARC model, and abbreviations that start with an uppercase letter designate residues belonging to the second monomer. Original chain identification numbers are omitted for clarity. E-maps are contoured typically at +8σ (cyan), +5σ (blue), and +2σ (green) as indicated for nearly all the figures unless otherwise indicated. The original 3ARC model is shown in yellow, and all other models of oxygenated residues are shown in varying colors. When multiple extra peaks are observed, simple interpretations are made, for example, each extra peak corresponding to one molecule. Heights of peaks in E-maps original non-H atoms are labeled in black, and heights for extra peaks being interpreted as oxygen additions are in red. Model-phased F-maps are contoured at +1.0σ level (magenta) before and after sharpening. An ordered water molecule to which the peroxide species is anchored is not shown next to Glu364. A small peak next to the Cγ atom of glu364 about +2σ is another oxygenation species, but not modeled.

  • The ribosome in action: Tuning of translational efficiency and protein folding

    The ribosome in action: Tuning of translational efficiency and protein folding

    Schematic representation of a cross-section of the ribosome with the nascent peptide. The peptide exit tunnel (overall length 100 Å) can be separated into three folding zones, as indicated. Ribosomal proteins uL4 and uL22 form the constriction. Protein uL23 and residues of 23S rRNA in the upper tunnel region (indicated by glow) can signal events in the tunnel to the PTC and the ribosome surface in the vicinity of the exit port.

  • The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7
  • Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations
  • Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR
  • Molecular dynamic study of MlaC protein in Gram‐negative bacteria: conformational flexibility, solvent effect and protein‐phospholipid binding
  • Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition
  • X‐ray radiation‐induced addition of oxygen atoms to protein residues
  • The ribosome in action: Tuning of translational efficiency and protein folding

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Author Jimin Wang on his recently published Protein Science paper entitled "X-ray radiation-induced addition of oxygen atoms to protein residues." Read the paper here

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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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