Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins

We present a comprehensive workflow for large scale (>1000 transitions/run) label‐free LC‐MRM proteome assays. Innovations include automated MRM transition selection, intelligent retention time scheduling that improves S/N by twofold, and automatic peak modeling. Improvements to data analysis include a novel Q/C metric, normalized group area ratio, MLR normalization, weighted regression analysis, and data dissemination through the Yale protein expression database. As a proof of principle we developed a robust 90 min LC‐MRM assay for mouse/rat postsynaptic density fractions which resulted in the routine quantification of 337 peptides from 112 proteins based on 15 observations per protein. Parallel analyses with stable isotope dilution peptide standards (SIS), demonstrate very high correlation in retention time (1.0) and protein fold change (0.94) between the label‐free and SIS analyses. Overall, our method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC‐MRM assay.     

Evidence from 13C solid-state NMR spectroscopy for a lamella structure in an alanine-glycine copolypeptide: a model for the crystalline domain of Bombyx mori silk fiber

13C high-resolution solid-state NMR coupled with selective 13C isotope-labeling of different Ala one methyl carbons was used to clarify the structure of (AG)15 peptide in the silk II structure as a model for the crystalline domain of Bombyx mori silk fiber. At the inner part of the peptide, the fraction of the peak at 16.6 ppm of the Ala Cbeta resonance assigned to beta-turn structure increased at 11th and 19th positions. These data indicate the appearance of the most probable lamellar structure having a turn structure at these two positions, although the position of turn was distributed along the chain.     

A Dimeric PINK1-containing Complex on Depolarized Mitochondria Stimulates Parkin Recruitment

Parkinsonism typified by sporadic Parkinson disease is a prevalent neurodegenerative disease. Mutations in PINK1 (PTEN-induced putative kinase 1), a mitochondrial Ser/Thr protein kinase, or PARKIN, a ubiquitin-protein ligase, cause familial parkinsonism. The accumulation and autophosphorylation of PINK1 on damaged mitochondria results in the recruitment of Parkin, which ultimately triggers quarantine and/or degradation of the damaged mitochondria by the proteasome and autophagy. However, the molecular mechanism of PINK1 in dissipation of the mitochondrial membrane potential (ΔΨm) has not been fully elucidated. Here we show by fluorescence-based techniques that the PINK1 complex formed following a decrease in ΔΨm is composed of two PINK1 molecules and is correlated with intermolecular phosphorylation of PINK1. Disruption of complex formation by the PINK1 S402A mutation weakened Parkin recruitment onto depolarized mitochondria. The most disease-relevant mutations of PINK1 inhibit the complex formation. Taken together, these results suggest that formation of the complex containing dyadic PINK1 is an important step for Parkin recruitment onto damaged mitochondria.     

7-azabicyclo[2.2.1]heptane as a structural motif to block mutagenicity of nitrosamines

Nitrosamines are potent carcinogens and toxicants in the rat and potential genotoxins in humans. They are metabolically activated by hydroxylation at an α-carbon atom with respect to the nitrosoamino group, catalyzed by cytochrome P450. However, there has been little systematic investigation of the structure-mutagenic activity relationship of N-nitrosamines. Herein, we evaluated the mutagenicity of a series of 7-azabicyclo[2.2.1]heptane N-nitrosamines and related monocyclic nitrosamines by using the Ames assay. Our results show that the N-nitrosamine functionality embedded in the bicyclic 7-azabicylo[2.2.1]heptane structure lacks mutagenicity, that is, it is inert to α-hydroxylation, which is the trigger of mutagenic events. Further, the calculated α-C-H bond dissociation energies of the bicyclic nitrosamines are larger in magnitude than those of the corresponding monocyclic nitrosamines and N-nitrosodimethylamine by as much as 20-30 kcal/mol. These results are consistent with lower α-C-H bond reactivity of the bicyclic nitrosamines. Thus, the 7-azabicyclo[2.2.1]heptane structural motif may be useful for the design of nongenotoxic nitrosamine compounds with potential biological/medicinal applications.     

Phosphorylated ubiquitin chain is the genuine Parkin receptor

PINK1 selectively recruits Parkin to depolarized mitochondria for quarantine and removal of damaged mitochondria via ubiquitylation. Dysfunction of this process predisposes development of familial recessive Parkinson’s disease. Although various models for the recruitment process have been proposed, none of them adequately explain the accumulated data, and thus the molecular basis for PINK1 recruitment of Parkin remains to be fully elucidated. In this study, we show that a linear ubiquitin chain of phosphomimetic tetra-ubiquitin(S65D) recruits Parkin to energized mitochondria in the absence of PINK1, whereas a wild-type tetra-ubiquitin chain does not. Under more physiologically relevant conditions, a lysosomal phosphorylated polyubiquitin chain recruited phosphomimetic Parkin to the lysosome. A cellular ubiquitin replacement system confirmed that ubiquitin phosphorylation is indeed essential for Parkin translocation. Furthermore, physical interactions between phosphomimetic Parkin and phosphorylated polyubiquitin chain were detected by immunoprecipitation from cells and in vitro reconstitution using recombinant proteins. We thus propose that the phosphorylated ubiquitin chain functions as the genuine Parkin receptor for recruitment to depolarized mitochondria.     

Cellular uptake mechanisms and responses to NO transferred from mono- and poly-S-nitrosated human serum albumin

Endogenous S-nitrosated human serum albumin (E-Mono-SNO-HSA) is a large molecular weight nitric oxide (NO) carrier in human plasma, which has shown many beneficial effects in different animal models. To construct more efficient SNO-HSA preparations, SNO-HSA with many conjugated SNO groups has been prepared using chemical modification (CM-Poly-SNO-HSA). We have compared the properties of such a preparation to those of E-Mono-SNO-HSA. Cellular uptake of NO from E-Mono-SNO-HSA partly takes place via low molecular weight thiol, and it results in cytoprotective effects by induction of heme oxygenase-1. By contrast, transfer of NO from CM-Poly-SNO-HSA into the cells is faster and more pronounced. The influx mainly takes place by cell-surface protein disulfide isomerase. The considerable NO inflow results in apoptotic cell death by ROS induction and caspase-3 activation. Thus, increasing the number of SNO groups on HSA does not simply intensify the cellular responses to the product but can also result in very different effects.     

Nicorandil Prevents Gαq-Induced Progressive Heart Failure and Ventricular Arrhythmias in Transgenic Mice

Background

Beneficial effects of nicorandil on the treatment of hypertensive heart failure (HF) and ischemic heart disease have been suggested. However, whether nicorandil has inhibitory effects on HF and ventricular arrhythmias caused by the activation of G protein alpha q (Gα_q) -coupled receptor (GPCR) signaling still remains unknown. We investigated these inhibitory effects of nicorandil in transgenic mice with transient cardiac expression of activated Gα_q (Gα_q-TG).

Methodology/Principal Findings

Nicorandil (6 mg/kg/day) or vehicle was chronically administered to Gα_q-TG from 8 to 32 weeks of age, and all experiments were performed in mice at the age of 32 weeks. Chronic nicorandil administration prevented the severe reduction of left ventricular fractional shortening and inhibited ventricular interstitial fibrosis in Gα_q-TG. SUR-2B and SERCA2 gene expression was decreased in vehicle-treated Gα_q-TG but not in nicorandil-treated Gα_q-TG. eNOS gene expression was also increased in nicorandil-treated Gα_q-TG compared with vehicle-treated Gα_q-TG. Electrocardiogram demonstrated that premature ventricular contraction (PVC) was frequently (more than 20 beats/min) observed in 7 of 10 vehicle-treated Gα_q-TG but in none of 10 nicorandil-treated Gα_q-TG. The QT interval was significantly shorter in nicorandil-treated Gα_q-TG than vehicle-treated Gα_q-TG. Acute nicorandil administration shortened ventricular monophasic action potential duration and reduced the number of PVCs in Langendorff-perfused Gα_q-TG mouse hearts. Moreover, HMR1098, a blocker of cardiac sarcolemmal K_ATP channels, significantly attenuated the shortening of MAP duration induced by nicorandil in the Gα_q-TG heart.

Conclusions/Significance

These findings suggest that nicorandil can prevent the development of HF and ventricular arrhythmia caused by the activation of GPCR signaling through the shortening of the QT interval, action potential duration, the normalization of SERCA2 gene expression. Nicorandil may also improve the impaired coronary circulation during HF.     

Synthesis and structure-activity relationships of benzophenone-bearing diketopiperazine-type anti-microtubule agents

KPU-105 (4), a potent anti-microtubule agent that contains a benzophenone was derived from the diketopiperazine-type vascular disrupting agent (VDA) plinabulin 3, which displays colchicine-like tubulin depolymerization activity. To develop derivatives with more potent anti-microtubule and cytotoxic activities, we further modified the benzophenone moiety of 4. Accordingly, we obtained a 4-fluorobenzophenone derivative 16j that inhibited tumor cell growth in vitro with a subnanomolar IC(50) value against HT-29 cells (IC(50)=0.5 nM). Next, the effect of 16j on mitotic spindles was evaluated in HeLa cells. Treatment with 3nM of 16j partially disrupted the interphase microtubule network. By contrast, treatment with the same concentration of CA-4 barely affected the microtubule network, indicating that 16j exhibited more potent anti-mitotic effects than did CA-4.     

Localization and Targeting of an Unusual Pyridine Nucleotide Transhydrogenase in Entamoeba histolytica

Pyridine nucleotide transhydrogenase (PNT) catalyzes the direct transfer of a hydride-ion equivalent between NAD(H) and NADP(H) in bacteria and the mitochondria of eukaryotes. PNT was previously postulated to be localized to the highly divergent mitochondrion-related organelle, the mitosome, in the anaerobic/microaerophilic protozoan parasite Entamoeba histolytica based on the potential mitochondrion-targeting signal. However, our previous proteomic study of isolated phagosomes suggested that PNT is localized to organelles other than mitosomes. An immunofluorescence assay using anti-E. histolytica PNT (EhPNT) antibody raised against the NADH-binding domain showed a distribution to the membrane of numerous vesicles/vacuoles, including lysosomes and phagosomes. The domain(s) required for the trafficking of PNT to vesicles/vacuoles was examined by using amoeba transformants expressing a series of carboxyl-terminally truncated PNTs fused with green fluorescent protein or a hemagglutinin tag. All truncated PNTs failed to reach vesicles/vacuoles and were retained in the endoplasmic reticulum. These data indicate that the putative targeting signal is not sufficient for the trafficking of PNT to the vesicular/vacuolar compartments and that full-length PNT is necessary for correct transport. PNT displayed a smear of >120 kDa on SDS-PAGE gels. PNGase F and tunicamycin treatment, chemical degradation of carbohydrates, and heat treatment of PNT suggested that the apparent aberrant mobility of PNT is likely attributable to its hydrophobic nature. PNT that is compartmentalized to the acidic compartments is unprecedented in eukaryotes and may possess a unique physiological role in E. histolytica.Pyridine nucleotide transhydrogenase (PNT) participates in the bioenergetic processes of the cell. PNT generally resides on the cytoplasmic membranes of bacteria and the inner membrane of mammalian mitochondria (3, 16) and utilizes the electrochemical proton gradient across the membrane to drive NADPH formation from NADH (14, 15, 39) according to the reaction H⁺out + NADH + NADP⁺↔H⁺in + NAD⁺ + NADPH, where “out” and “in” denote the cytosol and the matrix of the mitochondria, or the periplasmic space and the cytosol of bacteria, respectively.PNT has been identified in several protozoan parasites, including Entamoeba histolytica (8, 51), Eimeria tenella (17, 47), Mastigamoeba balamuthi (11) Plasmodium falciparum (10), Plasmodium yoelii (6), and Plasmodium berghei (12). In general, PNT contains conserved structural units consisting of three domains, the NAD(H)-binding domain (domain I [dI]) and the NADP(H)-binding domain (domain III [dIII]), both of which face the matrix side of the eukaryotic mitochondria or the cytoplasmic side in bacteria, and the hydrophobic domain (domain II [dII]), containing 11 to 13 transmembrane regions. PNT from E. tenella and E. histolytica exists as a single polypeptide in an unusual configuration consisting of dIIb-dIII-dI-dIIa, with a 38-amino-acid-long linker region between dIII and dI (48).E. histolytica, previously considered an “amitochondriate” protist, is currently considered to possess a mitochondrion-related organelle with reduced and divergent functions, the mitosome (1, 21, 23a, 26, 42). Our recent proteomic study of isolated mitosomes identified about 20 new constituents (26), together with four proteins previously demonstrated in E. histolytica mitosomes: Cpn60 (8, 19, 21, 42), Cpn10 (46), mitochondrial Hsp70 (2, 44), and mitochondrion carrier family (MCF) (ADP/ATP transporter) (7). Despite the early presumption of PNT being localized in mitosomes (8), based on the amino-terminal region rich in hydroxylated (five serines and threonines) and acidic (three glutamates) amino acids, which slightly resembles known mitochondrion- and hydrogenosome-targeting sequences (8, 35), PNT was not discovered in the mitosome proteome. We also doubted this premise because PNT was one of the major proteins identified in isolated phagosomes (32, 33). Thus, the intracellular localization and trafficking of PNT remain unknown.In this report, we showed that E. histolytica PNT (EhPNT) is localized to various vesicles and vacuoles, including lysosomes and phagosomes, using wild-type amoebae and antiserum raised against recombinant EhPNT and an E. histolytica line expressing EhPNT with a carboxyl-terminal hemagglutinin (HA) epitope tag and anti-HA antibody. We also showed that all domains of EhPNT are required for its trafficking to the acidic compartment by using amoeba transformants expressing the HA tag or green fluorescent protein (GFP) fused with a region containing various domains of EhPNT.     

Mitochondria and apicoplast of Plasmodium falciparum: behaviour on subcellular fractionation and the implication

The mitochondrion and the apicoplast of the malaria parasite, Plasmodium spp. is microscopically observed in a close proximity to each other. In this study, we tested the suitability of two different separation techniques--Percoll density gradient centrifugation and fluorescence-activated organelle sorting--for improving the purity of mitochondria isolated from the crude organelle preparation of Plasmodium falciparum. To our surprise, the apicoplast was inseparable from the plasmodial mitochondrion by each method. This implies these two plasmodial organelles are bound each other. This is the first experimental evidence of a physical binding between the two organelles in Plasmodium.