Glycan-Targeted Virus-like Nanoparticles for Photodynamic Therapy

Virus-like particles (VLPs) have proven to be versatile platforms for chemical and genetic functionalization for a variety of purposes in biomedicine, catalysis, and materials science. We describe here the simultaneous modification of the bacteriophage Qβ VLP with a metalloporphyrin derivative for photodynamic therapy and a glycan ligand for specific targeting of cells bearing the CD22 receptor. This application benefits from the presence of the targeting function and the delivery of a high local concentration of singlet oxygen-generating payload

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties-2

<p><b>Copyright information:</b></p><p>Taken from "Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties"</p><p>http://www.biomedcentral.com/1472-6807/7/47</p><p>BMC Structural Biology 2007;7():47-47.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1936996.</p><p></p>from archaeon and the mesophilic brefeldin A esterase (BFAE) from (PDB code ). The regions encompassing EstE1 dimerization motifs and the sequence blocks showing the amino acids involved in the formations of the catalytic triad and oxyanion hole are presented. Identical and similar residues have a grey background. Symbols: ●, amino acids forming a catalytic triad; ○, amino acids involved in oxynion hole formation; □ and ▯, amino acid residues involved in hydrophobic and ionic interactions at 1JJI dimeric interface, respectively; ▯, amino acid residues involved in ionic interactions at 1JKM dimeric interface; ■ and ▲ amino acid residues involved in hydrophobic and ionic interactions at EstE1 dimeric interface, respectively. Amino acid sequence alignment was performed as described previously [5]

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties-1

<p><b>Copyright information:</b></p><p>Taken from "Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties"</p><p>http://www.biomedcentral.com/1472-6807/7/47</p><p>BMC Structural Biology 2007;7():47-47.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1936996.</p><p></p>ck representation. Val274, Phe276, and Leu299 are involved in the hydrophobic interactions. Arg270-Asp291 and Lys177-Glu295 form salt bridges. (B) The centrosymmetric conformation of the interface between the two monomers, consisting of centric hydrophobic interactions (red circle) and salt bridges. (C) A detailed view of the salt bridges that support the dimeric conformation of EstE1. The side chain of Arg270on the loop between the α8 helix and the β8 strand forms a salt bridge with Asp291on the α9 helix. An additional salt bridge is formed between the side chains of Lys177on the β6 strand and Glu295on the α9 helix. (D) A detailed view of the hydrophobic interaction interface observed in the EstE1 dimer. The hydrophobic core residues (Leu299 on the α9 helix, and Phe276 and Val274 on the β8 strand) are indicated. (E) A detailed view of the interface observed in a current AFEST dimer model [19]. Dimeric interactions of AFEST are supported by hydrogen bonds between Tyr280 and Gln303, and by a weak hydrophobic interaction through Val278

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties-5

<p><b>Copyright information:</b></p><p>Taken from "Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties"</p><p>http://www.biomedcentral.com/1472-6807/7/47</p><p>BMC Structural Biology 2007;7():47-47.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1936996.</p><p></p> and EstE1(▯), in 20 mM potassium phosphate buffer (pH 7.0) were incubated at 80°C for the indicated times. Residual activities were then determined by measuring the amount of -nitrophenol released by esterase-catalyzed hydrolysis. The activity of a non-incubated sample was defined as 100

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties-6

<p><b>Copyright information:</b></p><p>Taken from "Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties"</p><p>http://www.biomedcentral.com/1472-6807/7/47</p><p>BMC Structural Biology 2007;7():47-47.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1936996.</p><p></p>elical segments and β-strands are shown in blue and yellow, respectively. G2 and G3 represent 3-helices. Helix α1 is not shown because of its disordered electron map. The catalytic triad containing residues Ser154, Asp251, and His281, are shown in stick representation. N and C denote the N and C termini, respectively

MOESM1 of Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea

Additional file 1: Figure S1. A photomicrograph of Clostridium perfringens strain CBA7123 using Variable Pressure Field Emission Scanning Electron Microscope (VP-FE-SEM). Figure S2. Comparison of genomic structure between Clostridium perfringens CBA7123 and strains FORC 003, FORC 025, JP55, and JP838, using a progressive alignment algorithm in Mauve. The locally collinear blocks with identical colors represent highly homologous regions. The genomes were figured based on scale of the genome of strain CBA7123

Heparin Binding to an Engineered Virus-like Nanoparticle Antagonist

The anticoagulant activity of heparin administered during medical interventions must be reversed to restore normal clotting, typically by titrating with protamine. Given the acute toxicity associated with protamine, we endeavored to generate safer heparin antagonists by engineering bacteriophage Qβ virus-like particles (VLPs) to display motifs that bind heparin. A particle bearing a single amino acid change from wild-type (T18R) was identified as a promising candidate for heparin antagonism. Surface potential maps generated through molecular modeling reveal that the T18R mutation adds synergistically to adjacent positive charges on the particle surface, resulting in a large solvent-accessible cationic region that is replicated 180 times over the capsid. Chromatography using a heparin-sepharose column confirmed a strong interaction between heparin and the T18R particle. Binding studies using fluorescein-labeled heparin (HepFL) resulted in a concentration-dependent change in fluorescence intensity, which could be perturbed by the addition of unlabeled heparin. Analysis of the fluorescence data yielded a dissociation constant of approximately 1 nM and a 1:1 binding stoichiometry for HepFL:VLP. Dynamic light scattering (DLS) experiments suggested that T18R forms discrete complexes with heparin when the VLP:heparin molar ratios are equivalent, and in vitro clotting assays confirmed the 1:1 binding stoichiometry as full antagonism of heparin is achieved. Biolayer interferometry and backscattering interferometry corroborated the strong interaction of T18R with heparin, yielding <i>K</i>_d ∼ 1–10 nM. These biophysical measurements further validated T18R, and VLPs in general, for potential clinical use as effective, nontoxic heparin antagonists

Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease

The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the <i>T</i>_m of apo-PR by 3.5–5 °C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR

Effect of rtL269I and other substitutions on resistance to lamivudine (LMV).

<p>(A) HBV DNA constructs were transfected into Huh7 cells, which were treated with LMV for 3 days. The intracellular HBV DNA was prepared for Southern blot analysis. A representative result has been shown. (B) The relative replication levels of each HBV mutant (no drug <i>vs</i> LMV treatment) were calculated based on the results of Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136728#pone.0136728.g002" target="_blank">2C</a> and 3A. (C) The relative replication ability of the HBV mutants treated with LMV were determined by Southern blotting and quantified by Phosphorimager (*, <i>P</i> < 0.05). The relative replication levels of each HBV construct was shown as the mean value of at least three independent experiments.</p

rtL269I substitution enhances the replication of both WT and drug-resistant hepatitis B virus (HBV).

<p>(A) Schematic diagram of each HBV mutant construct used in this study. (B–C) Effect of mutations at positions 204, 173, 129, 337, and 269 on HBV DNA replication. Huh7 cells cultured in six-well plates were transfected with HBV plasmids. HBV DNA levels were analyzed by Southern blotting. HBeAg in culture supernatant was determined by ELISA. (D) Phosphor-imager analysis of the relative replication capacities of the HBV mutants. The standard deviation from three independent experiments was calculated (**, <i>P</i> < 0.01; ***, <i>P</i> < 0.001).</p