Protein Science

Cover image for Vol. 24 Issue 2

Edited By: Brian W. Matthews

Impact Factor: 2.861

ISI Journal Citation Reports © Ranking: 2013: 146/291 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses

    Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses

    Structural aspects of rTP0435. (A) Ribbons representation of the structure. The β-strands are shown in purple, α-helices are shown in green, and regions with no regular secondary structure depicted are in light blue. The amino- (N) and carboxyl- (C) termini are marked, and the designations of the secondary-structural elements are shown (strands are numbered, helices are lettered). (B) A topology diagram of the structure. The coloration is the same as in part (A). (C) The basin of rTP0435. A cut-away view of the protein's surface is shown. The basin is marked, and basin-lining residues are shown in green. The orientation of the protein is the same as that depicted in part (A). (D) The electrostatic surface potential of rTP0435. A legend to the coloration is shown. The upper part of this panel shows the basin of the protein, rotated 90° toward the viewer compared with panel C. In the lower part, there are two copies of the protein; the two A helices of the proteins meet in the center, and the two basins are oriented to the left and right.

  • Molecular dynamics of the P450cam–Pdx complex reveals complex stability and novel interface contacts

    Molecular dynamics of the P450cam–Pdx complex reveals complex stability and novel interface contacts

    Stability of the P450cam–Pdx throughout the simulation. A) Shown are the RMSD evolutions for the backbone Cα atoms of P450cam (black), Pdx (Red), and the full P450cam–Pdx complex (Teal) throughout the course of the 100 nanosecond simulation. B) Calculated RMSF values for each Cα atom and an overlay of snapshots from every 10 ns throughout the simulation for both P450cam and C) Pdx. Both P450cam and Pdx show a high degree of stability individually and only minor changes as a complex. D) The three P450 structures, the cross-linked reduced of Tripathi et al. (green), the noncovalent complex of Hiruma et al. (Cyan), and a snapshot taken from near the end of the 100 ns simulation presented in this report (magenta) are overlaid by aligning all three along the backbone of P450cam. While the crystal structures overlap greatly, the MD structure shows significant differences in both helix C and a rotation of Pdx relative to P450cam in addition to small conformational changes in loops at the P450cam–Pdx interface.

  • Actin-induced dimerization of palladin promotes actin-bundling

    Actin‐induced dimerization of palladin promotes actin‐bundling

    Intramolecular crosslinking of palladin Ig3–4 domains displays cause and effect relationship with actin binding and bundling. A: Lane 1 contains Ig3–4 (10 µM), BS3 (30 µM), and F-actin (10 µM) that were incubated together for 1 h. Lane 2 is Ig3–4 treated with BS3 for 1 h at RT in the absence of F-actin to allow the formation of intramolecular crosslinked monomers (star), followed by a 1 h incubation with F-actin. Lane 3 is Ig3–4 incubated with F-actin for 1 h, before addition of BS3. B: Quantification of the intramolecular crosslinked (ICL) Ig3–4 species from lanes in A. C and D: Ig3–4 was treated with the thiol-cleavable BS3 analog DSP for 1 h in the absence of F-actin to yield intramolecularly crosslinked monomers (ICL). Following a 30 min incubation in either the absence or the presence of 50 mM DTT (C), the binding of DSP treated Ig3–4 to Factin was assessed by a co-sedimentation assay followed by SDS-PAGE and quantification of Ig3–4 band by densitometry. D: Bundling of F-actin by DSP treated Ig3–4 was also assessed by a differential sedimentation assay and the actin bands were quantified in similar manner. The percentage of actin present in each fraction is represented as supernatant (light gray), pellet (dark gray), and bundle (black).

  • Solution NMR characterization of WTCXCL8 monomer and dimer binding to CXCR1 N-terminal domain

    Solution NMR characterization of WTCXCL8 monomer and dimer binding to CXCR1 N‐terminal domain

    A schematic of CXCL8 dimer. The different secondary structural regions and the receptor binding sites are highlighted in one of the monomers.

  • D-AKAP2:PKA RII:PDZK1 ternary complex structure: Insights from the nucleation of a polyvalent scaffold

    D‐AKAP2:PKA RII:PDZK1 ternary complex structure: Insights from the nucleation of a polyvalent scaffold

    Crystal structure of the D-AKAP2AKB: RIIα D/D: PDZK1D4 ternary complex. (a) Domain organization of D-AKAP2 and its interacting proteins. The RGS domains (RGS-A and RGS-B) interact with the small GTPases Rab4 and Rab11, the D-AKAP2AKB interacts with the D/D domains of PKA RI and RII subunits and the C-terminal type I PDZ motif, represented as –TKL, is known to interact with PDZK1 and NHERF1. The putative PKA phosphorylation site is shown as KKAS. The domains of the three proteins (D-AKAP2AKB, RIIα D/D, and PDZK1D4) used in this study are circled. The sequence of D-AKAP2AKB used for crystallization is shown and numbered, and every tenth residue indicated by a dot. Residues not modeled and modeled as an Ala in the structure are indicated in black and blue, respectively. Residues involved in an α-helix (interacting with RIIα D/D) and β-strand (interacting with PDZK1D4) are indicated by a solid bar and an arrow respectively. (b) Overall structure of the D-AKAP2AKB: RIIα D/D: PDZK1D4 ternary complex. The monomers of RIIα D/D are depicted in gold and brown, D-AKAP2AKB in red and PDZK1D4 in dark cyan. The N- and C-termini of each protein are indicated. D-AKAP2AKB has been divided into three clusters: the N-terminal region that interacts with RIIα D/D through an α-helix, the C-terminal region that interacts with PDZK1D4 through a β-strand and finally, the linker region that connects the N- and C-termini clusters. All structural figures were prepared using Pymol (http://www.pymol.org). (c) Surface representation of the ternary complex showing the importance of the D-AKAP2 linker in separating the RIIα D/D and PDZK1D4 molecules. For simplicity, the orientation and the coloring scheme match that of Figure b.

  • Use of a structural alphabet to find compatible folds for amino acid sequences

    Use of a structural alphabet to find compatible folds for amino acid sequences

    Local threading of a protein sequence that contains two domains against SCOP dataset filtered at 70% sequence identity. This query is a 700 residues long glycosyl hydrolase that contains a catalytic domain and a carbohydrate binding module. Our method reports the catalytic domain (with Z-score = 13.9) and the concanavalin A-like lectin domain (with Z-score = 8.3) correctly as first two hits. Both Z-scores were above the threshold of 7.4 which was defined for 95% specificity.

  • Structure of the lysine specific protease Kgp from Porphyromonas gingivalis, a target for improved oral health

    Structure of the lysine specific protease Kgp from Porphyromonas gingivalis, a target for improved oral health

    Cartoon representation showing orthogonal views of Kgp. Protein colored from the N-terminus (blue) to C-terminus (red). Covalently bound TCLK inhibitor represented as spheres, carbon atoms colored salmon, oxygen colored red, nitrogen colored blue and sulfur colored yellow. Bound lead atom shown as black sphere.

  • Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses
  • Molecular dynamics of the P450cam–Pdx complex reveals complex stability and novel interface contacts
  • Actin‐induced dimerization of palladin promotes actin‐bundling
  • Solution NMR characterization of WTCXCL8 monomer and dimer binding to CXCR1 N‐terminal domain
  • D‐AKAP2:PKA RII:PDZK1 ternary complex structure: Insights from the nucleation of a polyvalent scaffold
  • Use of a structural alphabet to find compatible folds for amino acid sequences
  • Structure of the lysine specific protease Kgp from Porphyromonas gingivalis, a target for improved oral health

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2015 Protein Science Best Paper Award

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We are pleased to announce the winners of the 2015 Protein Science Best Paper Award:

Chih-Chia (Jack) Su
Assistant Scientist, Biological Systems
Department of Chemistry at Iowa State University

Crystal structure of the Campylobacter jejuni CmeC outer membrane channel
Chih-Chia Su, Abhijith Radhakrishnan, Nitin Kumar, Feng Long, Jani Reddy Bolla, Hsiang-Ting Lei, Jared A. Delmar, Sylvia V. Do, Tsung-Han Chou, Kanagalaghatta R. Rajashankar, Qijing Zhang, Edward W. Yu,
Protein Sci. 23:954-961, 2014.

Minttu Virkki
Graduate Student
Department of Biochemistry and Biophysics at Stockholm University

Folding of aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core
Minttu Virkki, Nitin Agrawal, Elin Edsbacker, Susana Cristobal, Arne Elofsson, Anni Kauko
Protein Sci. 23:981-992, 2014.

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