Phenylpiperidine-type γ-secretase modulators target the transmembrane domain 1 of presenilin 1.

Amyloid-ß peptide ending at the 42nd residue (Aß42) is implicated in the pathogenesis of Alzheimer's disease (AD). Small compounds that exhibit selective lowering effects on Aß42 production are termed γ-secretase modulators (GSMs) and are deemed as promising therapeutic agents against AD, although the molecular target as well as the mechanism of action remains controversial. Here, we show that a phenylpiperidine-type compound GSM-1 directly targets the transmembrane domain (TMD) 1 of presenilin 1 (PS1) by photoaffinity labelling experiments combined with limited digestion. Binding of GSM-1 affected the structure of the initial substrate binding and the catalytic sites of the γ-secretase, thereby decreasing production of Aß42, possibly by enhancing its conversion to Aß38. These data indicate an allosteric action of GSM-1 by directly binding to the TMD1 of PS1, pinpointing the target structure of the phenylpiperidine-type GSMs.

Experimental detection of proteolytic activity in a signal peptide peptidase of Arabidopsis thaliana.

BACKGROUND: Signal peptide peptidase (SPP) is a multi-transmembrane aspartic protease involved in intramembrane-regulated proteolysis (RIP). RIP proteases mediate various key life events by releasing bioactive peptides from the plane of the membrane region. We have previously isolated Arabidopsis SPP (AtSPP) and found that this protein is expressed in the ER. An AtSPP-knockout plant was found to be lethal because of abnormal pollen formation; however, there is negligible information describing the physiological function of AtSPP. In this study, we have investigated the proteolytic activity of AtSPP to define the function of SPPs in plants. RESULTS: We found that an n-dodecyl-ß-maltoside (DDM)-solubilized membrane fraction from Arabidopsis cells digested the myc-Prolactin-PP-Flag peptide, a human SPP substrate, and this activity was inhibited by (Z-LL)2-ketone, an SPP-specific inhibitor. The proteolytic activities from the membrane fractions solubilized by other detergents were not inhibited by (Z-LL)2-ketone. To confirm the proteolytic activity of AtSPP, the protein was expressed as either a GFP fusion protein or solely AtSPP in yeast. SDS-PAGE analysis showed that migration of the fragments that were cleaved by AtSPP were identical in size to the fragments produced by human SPP using the same substrate. These membrane-expressed proteins digested the substrate in a manner similar to that in Arabidopsis cells. CONCLUSIONS: The data from the in vitro cell-free assay indicated that the membrane fraction of both Arabidopsis cells and AtSPP recombinantly expressed in yeast actually possessed proteolytic activity for a human SPP substrate. We concluded that plant SPP possesses proteolytic activity and may be involved in RIP.

Regional medical inter-institutional cooperation in medical provider network constructed using patient claims data from Japan.

The aging world population requires a sustainable and high-quality healthcare system. To examine the efficiency of medical cooperation, medical provider and physician networks were constructed using patient claims data. Previous studies have shown that these networks contain information on medical cooperation. However, the usage patterns of multiple medical providers in a series of medical services have not been considered. In addition, these studies used only general network features to represent medical cooperation, but their expressive ability was low. To overcome these limitations, we analyzed the medical provider network to examine its overall contribution to the quality of healthcare provided by cooperation between medical providers in a series of medical services. This study focused on: i) the method of feature extraction from the network, ii) incorporation of the usage pattern of medical providers, and iii) expressive ability of the statistical model. Femoral neck fractures were selected as the target disease. To build the medical provider networks, we analyzed the patient claims data from a single prefecture in Japan between January 1, 2014 and December 31, 2019. We considered four types of models. Models 1 and 2 use node strength and linear regression, with Model 2 also incorporating patient age as an input. Models 3 and 4 use feature representation by node2vec with linear regression and regression tree ensemble, a machine learning method. The results showed that medical providers with higher levels of cooperation reduce the duration of hospital stay. The overall contribution of the medical cooperation to the duration of hospital stay extracted from the medical provider network using node2vec is approximately 20%, which is approximately 20 times higher than the model using strength.

The mechanism of poly-NEDD8 chain formation in vitro.

NEDD8 is a small ubiquitin-like protein that modifies target proteins in a reaction similar to ubiquitination. In this reaction, three enzymes are required and sufficient: NEDD8 activating E1-like enzyme (APP-BP1/Uba3), NEDD8-specific E2 enzyme (Ubc12) and RING-finger protein ROC1 (NEDD8 E3 ligase). Unlike ubiquitin, which is well known to form poly-ubiquitin chain, little is known about the formation of poly-NEDD8 chain. Here we show the mechanism of poly-NEDD8 chain formation on Cullin-1 using a complete in vitro reconstituted NEDD8 conjugation system. Intriguingly, poly-NEDD8 chain was build up on catalytic Cysteine residue of Ubc12. Furthermore, Ubc12 formed poly-NEDD8 chain without the activity of ROC1. Rather ROC1 mutant, defective for ubiquitin ligase activity, dramatically enhanced the poly-NEDD8 chain formation. In turn, ROC1 was essential for the transfer of poly-NEDD8 chain from Ubc12 to Cul-1. These results suggest the important regulatory role of ROC1 for poly-NEDD8 chain formation.

Perturbation-Based Proteomic Correlation Profiling as a Target Deconvolution Methodology.

Molecular target identification of small molecules, so-called target deconvolution, is a major obstacle to phenotype-based drug discovery. Here, we developed an approach called perturbation-based proteomic correlation profiling (PPCP) utilizing the correlation between protein quantity and binding activity of compounds under cellular perturbation by gene silencing and successfully identified lanosterol synthase as a molecular target of TGF-ß pathway inhibitor. This PPCP concept was extended to the use of a cell line panel and provides a new option for target deconvolution.

Glycine-alanine dipeptide repeat protein contributes to toxicity in a zebrafish model of C9orf72 associated neurodegeneration.

BACKGROUND: The most frequent genetic cause of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) is the expansion of a GGGGCC hexanucleotide repeat in a non-coding region of the chromosome 9 open reading frame 72 (C9orf72) locus. The pathological hallmarks observed in C9orf72 repeat expansion carriers are the formation of RNA foci and deposition of dipeptide repeat (DPR) proteins derived from repeat associated non-ATG (RAN) translation. Currently, it is unclear whether formation of RNA foci, DPR translation products, or partial loss of C9orf72 predominantly drive neurotoxicity in vivo. By using a transgenic approach in zebrafish we address if the most frequently found DPR in human ALS/FTLD brain, the poly-Gly-Ala (poly-GA) protein, is toxic in vivo. METHOD: We generated several transgenic UAS responder lines that express either 80 repeats of GGGGCC alone, or together with a translation initiation ATG codon forcing the translation of GA80-GFP protein upon crossing to a Gal4 driver. The GGGGCC repeat and GA80 were fused to green fluorescent protein (GFP) lacking a start codon to monitor protein translation by GFP fluorescence. RESULTS: Zebrafish transgenic for the GGGGCC repeat lacking an ATG codon showed very mild toxicity in the absence of poly-GA. However, strong toxicity was induced upon ATG initiated expression of poly-GA, which was rescued by injection of an antisense morpholino interfering with start codon dependent poly-GA translation. This morpholino only interferes with GA80-GFP translation without affecting repeat transcription, indicating that the toxicity is derived from GA80-GFP. CONCLUSION: These novel transgenic C9orf72 associated repeat zebrafish models demonstrate poly-GA toxicity in zebrafish. Reduction of poly-GA protein rescues toxicity validating this therapeutic approach to treat C9orf72 repeat expansion carriers. These novel animal models provide a valuable tool for drug discovery to reduce DPR associated toxicity in ALS/FTLD patients with C9orf72 repeat expansions.

Two Novel Mutations in the First Transmembrane Domain of Presenilin1 Cause Young-Onset Alzheimer's Disease.

BACKGROUND: The presenilin-1 protein (PS1) is the catalytic unit of γ-secretase implicated in the production of abnormally long forms of amyloid-ß (Aß), including Aß42, proteins thought critical in the pathogenesis of Alzheimer's disease (AD). In AD of autosomal dominant inheritance, the majority of pathogenic mutations have been found in the PSEN1 gene within which the location of the mutation can provide clues as to the mechanism of pathogenesis. OBJECTIVE: To describe clinical features of two novel mutations in the transmembrane portion 1 (TMD-1) of PSEN1 as well as biochemical features in one and neuropathological findings in the other. METHODS: Two index patients with young onset AD with an autosomal dominant pattern of inheritance underwent clinical and imaging assessments, as well as PSEN1 sequencing. Postmortem examination was completed in one patient. An artificial construct in which the P88L mutation was introduced was created to examine its effects on γ-secretase cleavage. RESULTS: Two novel variants in TMD-1 (P88L and V89L) were identified in affected probands. The neuropathological findings of AD were confirmed in the V89L mutation. Both patients presented around age 40 with early short-term memory deficits followed by seizures and corticospinal tract signs. The P88L mutation additionally featured early myoclonus followed by Parkinsonism. The causal role of the P88L mutation is supported by demonstration that this mutation dramatically increased Aß42 and decreased APP and Notch intracellular domain production in vitro. CONCLUSION: Changes in a single amino acid in codons 88 and 89 of TMD-1 can result in young-onset AD. The TMD-1 of PS1 is a region important for the γ-secretase cleavage of Aß.

Binding of longer Aß to transmembrane domain 1 of presenilin 1 impacts on Aß42 generation.

BACKGROUND: Amyloid-ß peptide ending at 42nd residue (Aß42) is believed as a pathogenic peptide for Alzheimer disease. Although γ-secretase is a responsible protease to generate Aß through a processive cleavage, the proteolytic mechanism of γ-secretase at molecular level is poorly understood. RESULTS: We found that the transmembrane domain (TMD) 1 of presenilin (PS) 1, a catalytic subunit for the γ-secretase, as a key modulatory domain for Aß42 production. Aß42-lowering and -raising γ-secretase modulators (GSMs) directly targeted TMD1 of PS1 and affected its structure. A point mutation in TMD1 caused an aberrant secretion of longer Aß species including Aß45 that are the precursor of Aß42. We further found that the helical surface of TMD1 is involved in the binding of Aß45/48 and that the binding was altered by GSMs as well as TMD1 mutation. CONCLUSIONS: Binding between PS1 TMD1 and longer Aß is critical for Aß42 production.

Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.

Drp35 is a protein induced by cell wall-affecting antibiotics or detergents; it possesses calcium-dependent lactonase activity. To determine the molecular basis of the lactonase activity, we first solved the crystal structures of Drp35 with and without Ca(2+); these showed that the molecule has a six-bladed beta-propeller structure with two calcium ions bound at the center of the beta-propeller and surface region. Mutational analyses of evolutionarily conserved residues revealed that the central calcium-binding site is essential for the enzymatic activity of Drp35. Substitution of some other amino acid residues for the calcium-binding residues demonstrated the critical contributions of Glu(48), Asp(138), and Asp(236) to the enzymatic activity. Differential scanning calorimetric analysis revealed that the loss of activity of E48Q and D236N, but not D138N, was attributed to their inability to hold the calcium ion. Further structural analysis of the D138N mutant indicates that it lacks a water molecule bound to the calcium ion rather than the calcium ion itself. Based on these observations and structural information, a possible catalytic mechanism in which the calcium ion and its binding residues play direct roles was proposed for the lactonase activity of Drp35.