Antisense oligonucleotide treatment ameliorates IFN-γ-induced proteinuria in APOL1-transgenic mice

African Americans develop end-stage renal disease at a higher rate compared with European Americans due to 2 polymorphisms (G1 and G2 risk variants) in the apolipoprotein L1 (APOL1) gene common in people of African ancestry. Although this compelling genetic evidence provides an exciting opportunity for personalized medicine in chronic kidney disease, drug discovery efforts have been greatly hindered by the fact that APOL1 expression is lacking in rodents. Here, we describe a potentially novel physiologically relevant genomic mouse model of APOL1-associated renal disease that expresses human APOL1 from the endogenous human promoter, resulting in expression in similar tissues and at similar relative levels as humans. While naive APOL1-transgenic mice did not exhibit a renal disease phenotype, administration of IFN-γ was sufficient to robustly induce proteinuria only in APOL1 G1 mice, despite inducing kidney APOL1 expression in both G0 and G1 mice, serving as a clinically relevant "second hit." Treatment of APOL1 G1 mice with IONIS-APOL1Rx, an antisense oligonucleotide (ASO) targeting APOL1 mRNA, prior to IFN-γ challenge robustly and dose-dependently inhibited kidney and liver APOL1 expression and protected against IFN-γ-induced proteinuria, indicating that the disease-relevant cell types are sensitive to ASO treatment. Therefore, IONIS-APOL1Rx may be an effective therapeutic for APOL1 nephropathies and warrants further development.

A strategy to obtain backbone resonance assignments of deuterated proteins in the presence of incomplete amide 2H/1H back-exchange

Replacement of non-exchangeable protons by deuterons has become a standard tool in structural studies of proteins on the order of 30-40 kDa to overcome problems arising from rapid (1)H and (13)C transverse relaxation. However, (1)H nuclei are required at exchangeable sites to maintain the benefits of proton detection. Protein expression in D(2)O-based media containing deuterated carbon sources yields protein deuterated in all positions. Subsequent D/H-exchange is commonly used to reintroduce protons in labile positions. Since this strategy may fail for large proteins with strongly inhibited exchange we propose to express the protein in fully deuterated algal lysate medium in 100% H(2)O. As a side-effect partial C(alpha) protonation occurs in a residue-type dependent manner. Samples obtained by this protocol are suitable for complementary (1)H(N)- and (1)H(alpha)-based triple resonance experiments allowing complete backbone resonance assignments in cases where back-exchange of amide protons is very slow after expression in D(2)O and refolding of chemically denatured protein is not feasible. This approach is explored using a 35-kDa protein as a test case. The degree of C(alpha) protonation of individual amino acids is determined quantitatively and transverse relaxation properties of (1)H(N) and (15)N nuclei of the partially deuterated protein are investigated and compared to the fully protonated and perdeuterated species. Based on the deviations of assigned chemical shifts from random coil values its solution secondary structure can be established.

Sequence-specific assignment of histidine and tryptophan ring 1H, 13C and 15N resonances in 13C/15N- and 2H/13C/15N-labelled proteins

Methods are described to correlate aromatic 1H(delta)2/13C(delta)2 or 1H(epsilon)1/15N(epsilon)1 with aliphatic 13C(beta) chemical shifts of histidine and tryptophan residues, respectively. The pulse sequences exclusively rely on magnetization transfers via one-bond scalar couplings and employ [15N, 1H]- and/or [13C, 1H]-TROSY schemes to enhance sensitivity. In the case of histidine imidazole rings exhibiting slow HN-exchange with the solvent, connectivities of these proton resonances with beta-carbons can be established as well. In addition, their correlations to ring carbons can be detected in a simple [15N, 1H]-TROSY-H(N)Car experiment, revealing the tautomeric state of the neutral ring system. The novel methods are demonstrated with the 23-kDa protein xylanase and the 35-kDa protein diisopropyl-fluorophosphatase, providing nearly complete sequence-specific resonance assignments of their histidine delta-CH and tryptophan epsilon-NH groups.

Thermoinactivation of diisopropylfluorophosphatase-containing polyurethane polymers

The thermoinactivation of native diisopropylfluorophosphatase (DFPase, EC 3.8.2.1) is highly calcium dependent, first-order kinetic. Deactivation is coupled with a simultaneous reduction in beta-sheet content. We report herein our attempts to enhance the thermostability of DFPase by irreversibly incorporating the enzyme into polyurethane polymers. Immobilized DFPase has biphasic deactivation kinetics. Our data demonstrate that the initial rapid deactivationof immobilized DFPase leads to the formation of a hyperstable and still active form of enzyme. Like native DFPase, DFPase-containing polyurethanes exhibit a calcium-dependent thermostability. Since bioplastics cannot be analyzed by spectroscopy, the structural mechanisms involved in thermoinactivation of immobilized DFPase were determined using PEG-modified DFPase. The thermoinactivation profile of highly modified DFPase mirrors the stepwise deactivation pattern of bioplastics. Spectroscopic studies enable a structural analysis of the hyperstable intermediate.

Insights into the reaction mechanism of the diisopropyl fluorophosphatase from Loligo vulgaris by means of kinetic studies, chemical modification and site-directed mutagenesis

Kinetic measurements, chemical modification and site-directed mutagenesis have been employed to gain deeper insights into the reaction mechanism of the diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris. Analysis of the kinetics of diisopropyl fluorophosphate hydrolysis reveals optimal enzyme activity at pH >/=8, 35 degrees C and an ionic strength of 500 mM NaCl, where k(cat) reaches a limiting value of 526 s(-1). The pH rate profile shows that full catalytic activity requires the deprotonation of an ionizable group with an apparent pK(a) of 6.82, DeltaH(ion) of 42 kJ/mol and DeltaS(ion) of 9.8 J/mol K at 25 degrees C. Chemical modification of aspartate, glutamate, cysteine, arginine, lysine and tyrosine residues indicates that these amino acids are not critical for catalysis. None of the six histidine residues present in DFPase reacts with diethyl pyrocarbonate (DEPC), suggesting that DEPC has no accessibility to the histidines. Therefore, all six histidine residues have been individually replaced by asparagine in order to identify residues participating in catalysis. Only substitution of H287 renders the enzyme catalytically almost inactive with a residual activity of approx. 4% compared to wild-type DFPase. The other histidine residues do not significantly influence the enzymatic activity, but H181 and H274 seem to have a stabilizing function. These results are indicative of a catalytic mechanism in which H287 acts as a general base catalyst activating a nucleophilic water molecule by the abstraction of a proton.

Role of calcium ions in the structure and function of the di-isopropylfluorophosphatase from Loligo vulgaris

Di-isopropylfluorophosphatase (DFPase) is shown to contain two high-affinity Ca(2+)-binding sites, which are required for catalytic activity and stability. Incubation with chelating agents results in the irreversible inactivation of DFPase. From titrations with Quin 2 [2-([2-[bis(carboxymethyl)amino]-5-methylphenoxy]-methyl)-6-methoxy-8-[bis(carboxymethyl)-amino]quinoline], a lower-affinity site with dissociation constants of 21 and 840 nM in the absence and the presence of 150 mM KCl respectively was calculated. The higher-affinity site was not accessible, indicating a dissociation constant of less than 5.3 nM. Stopped-flow experiments have shown that the dissociation of bound Ca(2+) occurs in two phases, with rates of approx. 1.1 and 0.026 s(-1) corresponding to the dissociation from the low-affinity and high-affinity sites respectively. Dissociation rates depend strongly on temperature but not on ionic strength, indicating that Ca(2+) dissociation is connected with conformational changes. Limited proteolysis, CD spectroscopy, dynamic light scattering and the binding of 8-anilino-1-naphthalenesulphonic acid have been combined to give a detailed picture of the conformational changes induced on the removal of Ca(2+) from DFPase. The Ca(2+) dissociation is shown to result in a primary, at least partly reversible, step characterized by a large decrease in DFPase activity and some changes in enzyme structure and shape. This step is followed by an irreversible denaturation and aggregation of the apo-enzyme. From the temperature dependence of Ca(2+) dissociation and the denaturation results we conclude that the higher-affinity Ca(2+) site is required for stabilizing DFPase's structure, whereas the lower-affinity site is likely to fulfil a catalytic function.

High-yield expression, purification, and characterization of the recombinant diisopropylfluorophosphatase from Loligo vulgaris

Organophosphate degrading enzymes are of great interest in light of their ability to detoxify chemical warfare agents. The diisopropylfluorophosphatase (DFPase) from Loligo vulgaris is characterized by its high stability and broad substrate specifity. Here we report the production of large amounts of active, recombinant DFPase using an Escherichia coli expression system. The enzyme was purified to homogeneity using a combination of immobilized metal affinity and ion exchange chromatography. CD-spectroscopy indicates a well folded protein with a high amount of beta-sheet structure. Limited proteolysis was used to gain a deeper insight into the structural organization of the protein. DFPase possesses an internal protease-sensitive region located between amino acids 146 and 149. The two proteolytic fragments remain as a tight complex retaining a DFPase activity comparable to the intact enzyme. Overexpression clones for each fragment were constructed with the expression resulting in the formation of inclusion bodies. Upon isolation and refolding active protein is only formed when both fragments are present. Thus, the two proteolytic fragments are probably part of a stable single-domain protein with multiple contacts between them and only one protease accessible surface loop.

Crystallization and preliminary X-ray crystallographic analysis of DFPase from Loligo vulgaris

'Squid-type' diisopropylfluorophosphatases (DFPases), a subclass of the phosphotriesterases, are enzymes capable of hydrolysing organophosphorus nerve agents. To date, no three-dimensional structure of a 'squid-type' DFPase is known. Here, the crystallization of the DFPase originally isolated from head ganglion of the squid Loligo vulgaris is reported. The protein has been heterologously expressed in Escherichia coli, purified to homogeneity and subsequently crystallized. The protein crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 43.1, b = 82.1, c = 86.6 A and one monomer per asymmetric unit. Under cryoconditions (120 K) the crystals diffracted beyond 2.0 A using a Cu rotating-anode X-ray generator.

HNCAN pulse sequences for sequential backbone resonance assignment across proline residues in perdeuterated proteins

A TROSY-based triple-resonance pulse scheme is described which correlates backbone 1H and 15N chemical shifts of an amino acid residue with the 15N chemical shifts of both the sequentially preceding and following residues. The sequence employs 1J(NC alpha) and 2J(NC alpha) couplings in two sequential magnetization transfer steps in an 'out-and-back' manner. As a result, N,N connectivities are obtained irrespective of whether the neighbouring amide nitrogens are protonated or not, which makes the experiment suitable for the assignment of proline resonances. Two different three-dimensional variants of the pulse sequence are presented which differ in sensitivity and resolution to be achieved in one of the nitrogen dimensions. The new method is demonstrated with two uniformly 2H/13C/15N-labelled proteins in the 30-kDa range.

Protein A is the von Willebrand factor binding protein on Staphylococcus aureus

Endovascular infection is a highly critical complication of invasive Staphylococcus aureus disease. For colonization, staphylococci must first adhere to adhesive endovascular foci. Von Willebrand factor (vWF) is a large, multimeric glycoprotein mediating platelet adhesion at sites of endothelial damage. Earlier it was demonstrated that vWF binds to and promotes the surface adhesion of S. aureus, prompting this effort to identify the vWF adhesin. In Western ligand assays of S. aureus lysates, staphylococcal protein A (SPA) was recognized by purified vWF. Surface plasmon resonance demonstrated the binding of soluble vWF to immobilized recombinant protein A with a K(d) of 1.49 x 10(-8) mol/L. Using flow cytometry, the binding of fluorescein isothiocyanate-labeled vWF to S. aureus was found to be saturable and inhibitable by unlabeled vWF, antiprotein-A antibodies, or IgG. Isogenic Deltaspa::Tc(r) mutants were constructed by the insertion of a tetracycline resistance cassette into spa using allelic replacement, and it exhibited decreased binding of soluble vWF and decreased adhesion to vWF-adsorbed surfaces. The interaction was restored on complementation of the mutants with spa-containing plasmid pSPA7235. In conclusion, protein A confers interaction of S. aureus with soluble and immobilized vWF in a newly discovered function characterizing protein A as a novel member of the staphylococcal surface protein adhesin superfamily and suggesting its potential role in the pathogenesis of endovascular staphylococcal disease.

Interaction of von Willebrand factor with Staphylococcus aureus

Intravascular infection due to Staphylococcus aureus requires colonization of subendothelium in the presence of shear forces. von Willebrand factor (VWF) is a large multimeric glycoprotein playing a key role in platelet adhesion to subendothelium. To determine whether VWF may also play a role in adhesion of S. aureus to endovascular sites, binding of VWF to S. aureus and adhesion of S. aureus to VWF-adsorbed substrates was examined. Binding isotherms revealed a dose-dependent reaction of purified VWF with S. aureus Cowan 1 as well as VWF binding to other S. aureus strains. On solid phase, VWF showed saturable adsorption kinetics to polymethylmethacrylate and promoted S. aureus adhesion up to 67-fold in a trypsin-sensitive reaction. Similar adhesion promotion was observed when recombinant VWF was used. These results show that VWF interacts with S. aureus in suspension and promotes S. aureus adhesion to surfaces, suggesting a role of VWF in the pathogenesis of intravascular S. aureus infections.