Protein Science

Cover image for Vol. 25 Issue 5

Edited By: Brian W. Matthews

Impact Factor: 2.854

ISI Journal Citation Reports © Ranking: 2014: 136/290 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • NlpC/P60 domain-containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan

    NlpC/P60 domain‐containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan

    Three-dimensional structures of NlpC/P60 domains from MAP_1272c and MAP_1204. (A) Refined 1.75 Å resolution structure of MAP_1272c and 2.4 Å resolution structure of MAP_1204. The proteins are rendered as cartoons with the N-terminus in red and the C-terminus in blue. (B) Molecular surface of MAP_1272c and MAP_1204, where residues of the catalytic triad are colored light orange. Note that the dashed white lines represent the boundaries of putative substrate/ligand-binding channels in each protein. (C) Distribution of electrostatic potential at the surface of each protein contoured at ±5e/kT. The orientation of all structures has been kept constant in each panel for clarity.

  • Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11

    Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11

    HDX and structures of PI4KIIIβ bound to GTPγS and GDP loaded Rab11. A: The hydrogen exchange levels of PI4KIIIβ at 3 s of exchange at 21°C were mapped onto the structure of PI4KIIIβ according to the legend. Predicted intrinsically disordered loops are indicated in red. B: Structure of PI4KIIIβ bound to GTPγS loaded Rab11. Helical domain is shown in blue, with the kinase domain shown in red and yellow. Rab11 is colored in green, with the switch regions colored orange. C: Structure of PI4KIIIβ bound to GDP loaded Rab11. Proteins are coloured accorded to the scheme described in B.

  • The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops

    The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops

    Diverse conformations of long H3 loops. A) Antibody structures with diverse H3 loop conformations. The structures of antibody variable regions are shown. The CDR loops are colored cyan, orange, green, blue, pink, and yellow for H1, H2, H3, L1, L2, and L3, respectively. All the figures were drawn by using the interactive molecular viewer, jV. From the left, the structures of antibodies in PDBID 3vg9, 4m62, and 5e8e are shown, whose H3 loops consist of 17, 20, and 18 residues and have straight, bend and broad conformations in the nonstem region, respectively. B) Hydrogen bonds between main-chain atoms at positions 4 and N-3 in H3 loops in the antibodies shown in 3A. The positions 4 and N-3 are shown in ball and stick model. The numbers of the hydrogen bonds are also indicated.

  • Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone

    Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone

    Comparison of AraC-TAL1 crystal structure with wt-AraC. (A) Overlay of the apo structures of wt-AraC (red) and AraC-TAL1 (blue) reveals strong similarities between the two structures. (B) The substituted residues of AraC-TAL1 (blue) are oriented similarly to the native residues of wt-AraC (red), extending into the ligand pocket. The amino acid substitution H80G shows a shift in the beta sheet β2. (C) Each asymmetric unit of the AraC-TAL1 crystal structure contained three monomers. Two of the monomers (shown in orange and blue) appear to directly interact through the N-terminal β-barrels. (D) The β-kiss of the two monomers. Residues Y31 and W95 are highlighted, which interact in the apo form of wt-AraC, but do not form the same interaction in AraC-TAL1.

  • One ring to rule them all: Current trends in combating bacterial resistance to the β-lactams

    One ring to rule them all: Current trends in combating bacterial resistance to the β‐lactams

    Representative β-lactam uptake and efflux systems in Gram-negative E. coli. β-Lactams enter the periplasm through outer membrane porins such as OmpF (PDB ID 2ZFG), where they inhibit periplasmic PBP targets. Dianionic β-lactams such as carbenicillin can be expelled from the cell via RND efflux pumps, represented by the AcrAB-TolC complex (PDB ID 2F1M, 1OYE, 1EK9), where the drug is captured from the periplasmic or periplasmic-cytoplasmic interface. Siderophore conjugated β-lactam drugs can use cognate siderophore receptors for entry as represented here by FhuA complexed with TonB/ExbB/ExbD (FhuA and C-terminus of TonB: PDB ID 2GRX; ExbD: PDB ID 2PFU). The TonB complex couples the proton motive force across the inner membrane to facilitate the active transport mechanism of FhuA across the outer membrane.

  • Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

    Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

    The cartoon representation of monomers of the proteins used in the comparison: (A) AAOR, (B) AFR, (C) A-zyme, (D) BVR, (E) DD, (F) G6DP, (G) Gal80p, (H) IDH, (I) GFOR, (J) WlbA, (K) KijD10. The N-terminal nucleotide-binding domains are in green and the C-terminal domains in red.

  • NlpC/P60 domain‐containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan
  • Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11
  • The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops
  • Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone
  • One ring to rule them all: Current trends in combating bacterial resistance to the β‐lactams
  • Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

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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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