Michael Przybylski

Therapeutically effective antibodies against amyloid-β peptide target amyloid-β residues 4−10 and inhibit cytotoxicity and fibrillogenesis

Immunization of transgenic mouse models of Alzheimer disease using amyloid-β peptide (Aβ) reduces both the Alzheimer disease–like neuropathology and the spatial memory impairments of these mice. However, a therapeutic trial of immunization with Aβ42 in humans was discontinued because a few patients developed significant meningo-encephalitic cellular inflammatory reactions. Here we show that beneficial effects in mice arise from antibodies selectively directed against residues 4–10 of Aβ42, and that these antibodies inhibit both Aβ fibrillogenesis and cytotoxicity without eliciting an inflammatory response. These findings provide the basis for improved immunization antigens as well as attempts to design small-molecule mimics as alternative therapies.

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.

SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA.

ABSTRACT SARs (scaffold attachment regions) are candidate DNA elements for partitioning eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to specific DNA binding proteins that recognize SARs by a mechanism not yet understood. We describe a novel, evolutionarily conserved protein domain that specifically binds to SARs but is not related to SAR binding motifs of other proteins. This domain was first identified in human scaffold attachment factor A (SAF-A) and was thus designated SAF-Box. The SAF-Box is present in many different proteins ranging from yeast to human in origin and appears to be structurally related to a homeodomain. We show here that SAF-Boxes from four different origins, as well as a synthetic SAF-Box peptide, bind to natural and artificial SARs with high specificity. Specific SAR binding of the novel domain is achieved by an unusual mass binding mode, is sensitive to distamycin but not to chromomycin, and displays a clear preference for long DNA fragments. This is the first characterization of a specific SAR binding domain that is conserved throughout evolution and has DNA binding properties that closely resemble that of the unfractionated nuclear scaffold.

Implications of the serine protease HtrA1 in amyloid precursor protein processing

The defining features of the widely conserved HtrA (high temperature requirement) family of serine proteases are the combination of a catalytic protease domain with one or more C-terminal PDZ domains and reversible zymogen activation. Even though HtrAs have previously been implicated in protein quality control and various diseases, including cancer, arthritis, and neuromuscular disorder, the biology of the human family members is not well understood. Our data suggest that HtrA1 is directly involved in the β-amyloid pathway as it degrades various fragments of amyloid precursor protein while an HtrA1 inhibitor causes accumulation of Aβ in astrocyte cell culture supernatants. Furthermore, HtrA1 colocalizes with β-amyloid deposits in human brain samples. Potential implications in Alzheimers disease are discussed.

Immunoproteasomes Down-Regulate Presentation of a Subdominant T Cell Epitope from Lymphocytic Choriomeningitis Virus

The cytotoxic T cell response to pathogens is usually directed against a few immunodominant epitopes, while other potential epitopes are either subdominant or not used at all. In C57BL/6 mice, the acute cytotoxic T cell response against lymphocytic choriomeningitis virus is directed against immunodominant epitopes derived from the glycoprotein (gp33–41) and the nucleoprotein (NP396–404), while the gp276–286 epitope remains subdominant. Despite extensive investigations, the reason for this hierarchy between epitopes is not clear. In this study, we show that the treatment of cells with IFN-γ enhanced the presentation of gp33–41, whereas presentation of the gp276–286 epitope from the same glycoprotein was markedly reduced. Because proteasomes are crucially involved in epitope generation and because IFN-γ treatment in vitro and lymphocytic choriomeningitis virus infection in vivo lead to a gradual replacement of constitutive proteasomes by immunoproteasomes, we investigated the role of proteasome composition on epitope hierarchy. Overexpression of the active site subunits of immunoproteasomes LMP2, LMP7, and MECL-1 as well as overexpression of LMP2 alone suppressed the presentation of the gp276–286 epitope. The ability to generate gp276–286-specific CTLs was enhanced in LMP2- and LMP7-deficient mice, and macrophages from these mice showed an elevated presentation of this epitope. In vitro digests demonstrated that fragmentation by immunoproteasomes, but not constitutive proteasomes led to a preferential destruction of the gp276 epitope. Taken together, we show that LMP2 and LMP7 can at least in part determine subdominance and shape the epitope hierarchy of CTL responses in vivo.

Elucidation of O-Glycosylation Structures of the beta-Amyloid Precursor Protein by Liquid Chromatography-Mass Spectrometry Using Electron Transfer Dissociation and Collision Induced Dissociation

Accumulation and deposition of beta-amyloid peptide, a major constituent in neuritic plaques are hallmarks of Alzheimers disease (AD) and AD-related neurodegenerative diseases. beta-Amyloid (Abeta) is derived from the proteolytic cleavage of amyloid precursor protein (APP), a transmembrane protein present in three major isoforms in brain comprising 695, 751 and 770 amino acids, respectively. Among other post-translational modifications, APP is modified during maturation by N- and O-glycosylation, which are thought to be responsible for its expression and secretion. Unlike N-glycosylation, no sites of O-glycosylation of APP have previously been reported. We report here the identification of three specific O-glycosylation sites of the secreted APP695 (sAPP695) produced in CHO cells, using a combination of high-performance liquid chromatography and electrospray-tandem mass spectrometry. With the use of electron transfer dissociation and collision induced dissociation (ETD and CID), we identified type, composition and structures of the Core 1 type O-linked glycans attached at the residues Thr 291, Thr 292 and Thr 576 of the full-length APP695. The glycosylations comprise multiple short glycans, containing N-acetyl galactosamine (GalNAc), Gal-GalNAc and sialic acid terminated structures. The presence of the glycopeptides in the tryptic mixture was identified using the CID-generated sugar oxonium ions. ETD proved to be valuable for the unambiguous identification of the modified sites as ETD fragmentation occurred along the peptide backbone with little or no cleavage of the glycans. Thus, the combination of the CID and ETD techniques in LC-MS is shown here, as a powerful tool for de novo identification of O-glycosylations at unknown modification sites in proteins.

Matrix-assisted Laser Desorption/Ionization Mass Spectrometric Peptide Mapping of the Neural Cell Adhesion Protein Neurolin Purified by Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis or Acidic Precipitation

Neurolin is a cell surface protein involved in the neural regeneration and neogenesis of the central nervous system of goldfish. Its theoretical molecular mass, based on the amino acid sequence translated from the cDNA, is 58 kDa, but in SDS-PAGE it shows an apparent MW of 86 kDa. Neurolin is stated to be a glycoprotein and it contains five potential N- and 96 potential O-glycosylation sites. The complete characterization of the primary structure and initial investigations on the postulated glycosylation of neurolin, immunopurified from goldfish brains, are described. The protein was either digested in situ in the sodium dodecyl sulfate polyacrylamide gel matrix or digested after trichloroacetic acid precipitation. Trypsin and endoprotease Glu-C were used as proteases and matrix-assisted laser desorption/ionization mass spectrometry was applied for direct peptide mapping analysis of the proteolytic mixtures. Various sample preparation techniques were performed and the mass spectra were recorded in both positive- and negative-ion modes.

Phosphorylation by Protein Kinase CK2 Changes the DNA Binding Properties of the Human Chromatin Protein DEK

ABSTRACT We have examined the posttranslational modification of the human chromatin protein DEK and found that DEK is phosphorylated by the protein kinase CK2 in vitro and in vivo. Phosphorylation sites were mapped by quadrupole ion trap mass spectrometry and found to be clustered in the C-terminal region of the DEK protein. Phosphorylation fluctuates during the cell cycle with a moderate peak during G1 phase. Filter binding assays, as well as Southwestern analysis, demonstrate that phosphorylation weakens the binding of DEK to DNA. In vivo, however, phosphorylated DEK remains on chromatin. We present evidence that phosphorylated DEK is tethered to chromatin throughout the cell cycle by the un- or underphosphorylated form of DEK.

Determination of phosphorus and metals in human brain proteins after isolation by gel electrophoresis by laser ablation inductively coupled plasma source mass spectrometry

Phosphorus, sulfur, silicon and metal concentrations (Al, Cu and Zn) were determined in human brain proteins by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) after separation of protein mixtures by two dimensional (2-D) gel electrophoresis. The analysis of phosphorus, silicon and metals in single protein spots in the gel was performed with an optimized microanalytical method using a double-focusing sector field inductively coupled plasma mass spectrometer coupled to a commercial laser ablation system (LA-ICP-MS). Relative ion intensities for P, Si and metals with respect to sulfur in protein spots were determined by LA-ICP-MS. The detection limits for phosphorus and sulfur in protein spots with a silver staining procedure on the 2-D gels were compared with the Coomassie staining technique described previously.

Structural identification and quantification of protein phosphorylations after gel electrophoretic separation using Fourier transform ion cyclotron resonance mass spectrometry and laser ablation inductively coupled plasma mass spectrometry

Abstract In the present work mass spectrometric approaches are described for the identification of phosphorylated protein structures, and the direct quantification of protein–phosphorus contents, using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). An ultrahigh resolution FT-ICR-MS method was developed and applied for the structural identification of phosphorylations in proteins, using direct peptide mapping analysis with high mass accuracy of tryptic phosphorylated fragments. The application of this method to human tau proteins, one of the key proteins for the formation of neurofibrillary tangles in Alzheimer’s disease, provided the identification of 17 phosphorylation sites. A high-sensitivity inorganic mass spectrometric technique has been developed for the direct determination of phosphor and sulfur concentrations in proteins separated by two-dimensional (2D) gel electrophoresis. Quantitative P and S determination in protein gel spots was performed with an optimized method using a double-focusing sector field ICP mass spectrometer coupled to a laser ablation chamber (LA-ICP-MS). Two different quantification strategies were applied: (i) determination of P and S in gel spots by LA-ICP-MS, following the determination of these elements in blank gel after trypsin and HNO 3 digestion using ICP-SFMS; (ii) a new quantification procedure by LA-ICP-MS was developed for the direct microlocal analysis in small protein spots from 2D gels. A solution-based calibration strategy in LA-ICP-MS was proposed for the quantification procedure using an ultrasonic nebulizer for introduction of calibration standard solutions coupled to the laser ablation chamber. Cobalt was used as an internal standard element, and was added to the gel at a defined concentration. The quality of phosphor determination by LA-ICP-MS was ascertained with β-casein as reference material. In a first application to the multi-phosphorylated tau protein, an average phosphorus content of ca. 20% was determined. The present results demonstrate the analytical merit of the combination of high resolution FT-ICR-MS and LA-ICP-MS for the molecular characterization of phosphorylated protein structures and determination of phosphorus and sulfur from 2D gels.