C-Terminal Protein Characterization by Mass Spectrometry: Isolation of C-Terminal Fragments from Cyanogen Bromide-Cleaved Protein

A sample preparation method for protein C-terminal peptide isolation from cyanogen bromide (CNBr) digests has been developed. In this strategy, the analyte was reduced and carboxyamidomethylated, followed by CNBr cleavage in a one-pot reaction scheme. The digest was then adsorbed on ZipTip_C18 pipette tips for conjugation of the homoserine lactone-terminated peptides with 2,2′-dithiobis (ethylamine) dihydrochloride, followed by reductive release of 2-aminoethanethiol from the derivatives. The thiol-functionalized internal and N-terminal peptides were scavenged on activated thiol sepharose, leaving the C-terminal peptide in the flow-through fraction. The use of reversed-phase supports as a venue for peptide derivatization enabled facile optimization of the individual reaction steps for throughput and completeness of reaction. Reagents were replaced directly on the support, allowing the reactions to proceed at minimal sample loss. By this sequence of solid-phase reactions, the C-terminal peptide could be recognized uniquely in mass spectra of unfractionated digests by its unaltered mass signature. The use of the sample preparation method was demonstrated with low-level amounts of a whole, intact model protein. The C-terminal fragments were retrieved selectively and efficiently from the affinity support. The use of covalent chromatography for C-terminal peptide purification enabled recovery of the depleted material for further chemical and/or enzymatic manipulation. The sample preparation method provides for robustness and simplicity of operation and is anticipated to be expanded to gel-separated proteins and in a scaled-up format to high-throughput protein profiling in complex biological mixtures.     

Molecular Determinants of the Interaction Between the C-Terminal Domain of Alzheimer's β-Amyloid Peptide and Apolipoprotein E α-Helices

In a previous work, we predicted and demonstrated that the 29-42-residue fragment of beta-amyloid peptide (Abeta peptide) has in vitro capacities close to those of the tilted fragment of viral fusion proteins. We further demonstrated that apolipoprotein E2 and E3 but not apolipoprotein E4 can decrease the fusogenic activity of Abeta(29-42) via a direct interaction. Therefore, we suggested that this fragment is implicated in the neurotoxicity of Abeta and in the protective effects of apolipoprotein E in Alzheimer's disease. Because structurally related apolipoproteins do not interact with the Abeta C-terminal domain but inhibit viral fusion, we suggested that interactions existing between fusogenic peptides and apolipoproteins are selective and responsible for the inhibition of fusion. In this study, we simulated interactions of all amphipathic helices of apolipoproteins E and A-I with Abeta and simian immunodeficiency virus (SIV) fusogenic fragments by molecular modeling. We further calculated cross-interactions that do not inhibit fusion in vitro. The results suggest that interactions of hydrophobic residues are the major event to inhibit the fusogenic capacities of Abeta(29-42) and SIV peptides. Selectivity of those interactions is due to the steric complementarity between bulky hydrophobic residues in the fusogenic fragments and hydrophobic residues in the apolipoprotein C-terminal amphipathic helices.     

Immunolocalization of an Amino-Terminal Fragment of Apolipoprotein E in the Pick's Disease Brain

Although the risk factor for apolipoprotein E (apoE) polymorphism in Alzheimer''s disease (AD) has been well described, the role that apoE plays in other neurodegenerative diseases, including Pick''s disease, is not well established. To examine a possible role of apoE in Pick''s disease, an immunohistochemical analysis was performed utilizing a novel site-directed antibody that is specific for an amino-terminal fragment of apoE. Application of this antibody, termed the amino-terminal apoE cleavage fragment (nApoECF) antibody, consistently labeled Pick bodies within area CA1 of the hippocampus in 4 of the 5 cases examined. Co-localization of the nApoECF antibody with PHF-1, a general marker for Pick bodies, as well as with an antibody to caspase-cleaved tau (TauC3) was evident within the hippocampus. While staining of the nApoECF antibody was robust in area CA1, little co-localization with PHF-1 in Pick bodies within the dentate gyrus was observed. A quantitative analysis indicated that approximately 86% of the Pick bodies identified in area CA1 labeled with the nApoECF antibody. The presence of truncated apoE within Pick bodies suggests a broader role of apoE beyond AD and raises the question as to whether this protein contributes to pathogenesis associated with Pick''s disease.     

Mass Spectrometry Defines the C-Terminal Dimerization Domain and Enables Modeling of the Structure of Full-Length OmpA

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Apolipoprotein E and cholesterol metabolism in the pathogenesis and treatment of Alzheimer's disease

There is much evidence suggesting that there is a strong relationship between the deterioration of brain lipid homeostasis, vascular changes and the pathogenesis of Alzheimer's disease (AD). These associations include: (1). recognition that a key cholesterol transporter, apolipoprotein E type 4, acts a major genetic risk factor for both familial and sporadic AD; (2). epidemiological studies linking cardiovascular risk factors, such as hypertension and high plasma cholesterol, to dementia; (3). the discovery that small strokes can precipitate clinical dementia in cognitively normal elderly subjects; (4). the modulation of degradation of the amyloid precursor protein by cholesterol administration in cell culture and in animal models of beta-amyloid overproduction; and (5). the beneficial effect of cholesterol-lowering drugs, such as Probucol and statins, in combating common AD. The recent finding that there is a genetic association between the HMGR gene locus and sporadic AD further suggests that brain cholesterol metabolism is central to AD pathophysiology, and a potential therapeutic target for disease stabilization and primary disease prevention.     

Quantification of Histone Deacetylase Isoforms in Human Frontal Cortex,Human Retina,and Mouse Brain

Histone deacetylase (HDAC) inhibition has promise as a therapy for Alzheimer’s disease (AD) and other neurodegenerative diseases. Currently, therapeutic HDAC inhibitors target many HDAC isoforms, a particularly detrimental approach when HDAC isoforms are known to have different and specialized functions. We have developed a multiple reaction monitoring (MRM) mass spectrometry assay using stable isotope-labeled QconCATs as internal standards to quantify HDAC isoforms. We further determined a quantitative pattern of specific HDACs expressed in various human and mouse neural tissues. In human AD frontal cortex, HDAC1,2 decreased 32%, HDAC5 increased 47%, and HDAC6 increased 31% in comparison to age-matched controls. Human neural retina concentrations of HDAC1, 2, HDAC5, HDAC6, and HDAC7 decreased in age-related macular degeneration (AMD)-affected donors and exhibited a greater decrease in AD-affected donors in comparison to age-matched control neural retinas. Additionally, HDAC concentrations were measured in whole hemisphere of brain of 5XFAD mice, a model of β-amyloid deposition, to assess similarity to AD in human frontal cortex. HDAC profiles of human frontal cortex and mouse hemisphere had noticeable differences and relatively high concentrations of HDAC3 and HDAC4 in mice, which were undetectable in humans. Our method for quantification of HDAC isoforms is a practical and efficient technique to quantify isoforms in various tissues and diseases. Changes in HDAC concentrations reported herein contribute to the understanding of the pathology of neurodegeneration.     

Gonadal Steroids do not Affect Apolipoprotein E Expression in Aging Mouse Cerebral Cortex

The allelic variant of apolipoprotein (Apo) E4 is a known risk factor for the development of most common late onset form of Alzheimer’s disease (AD). As aging is associated with reduced circulating level of gonadal steroid hormones, hormone replacement therapies have been used for the possible treatment of AD. Both estrogen and testosterone have beneficial effects on brain due to interaction with apoE, but the underlying mechanism is still not clear. In this article, we report the effects of gonadectomy and hormone supplementation on apoE protein level in male and female mouse cerebral cortex during normal aging. We could not get any effect of gonadectomy and estradiol or testosterone treatment in adult and old mice of either sex. This suggests that during normal aging apoE protein level is not affected due to steroid hormone withdrawal or supplementation in the mouse cerebral cortex.     

Multi-Kinase Phosphorylation of the APC/C Activator Cdh1 Revealed by Mass Spectrometry

by activating a large ubiquitin ligase called the anaphase-promoting complex, or cyclosome (APC/C). At the end of G1, APC/CCdh1 is inhibited by cyclin-dependent kinase (CDK) phosphorylation of Cdh1. The specific Cdh1 phosphorylation sites used to regulate APC/CCdh1 activity have not been directly identified. Here, we used a mass spectrometric approach to identify the in vivo phosphorylation sites on yeast Cdh1. Surprisingly, in addition to several expected CDK phosphorylation sites, we discovered numerous non-CDK phosphorylation sites. In total, at least 19 serine and threonine residues on Cdh1 are phosphorylated in vivo. Seventeen of these sites are located in the N-terminal half of Cdh1, outside the highly conserved WD40 repeats. The pattern of phosphorylation was the same when Cdh1 was purified from yeast cultures arrested in S, early M and late M. Mutation of CDK consensus sequences eliminated detectable phosphorylation at many of the non-CDK sites. In contrast, mutation of non-CDK sites had no significant effect on CDK phosphorylation. We conclude that phosphorylation of CDK sites promotes the subsequent recognition of Cdh1 by at least one additional kinase. The function of non-CDK phosphorylation may differ from CDK phosphorylation because mutation of non-CDK sites did not result in constitutive activation of APC and consequent cell cycle arrest. These results suggest that phosphoregulation of APC/CCdh1 activity is much more complex than previously thought.     

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

There is a great need for quantitative assays in measuring proteins. Traditional sandwich immunoassays, largely considered the gold standard in quantitation, are associated with a high cost, long lead time, and are fraught with drawbacks (e.g. heterophilic antibodies, autoantibody interference, ''hook-effect'').¹ An alternative technique is affinity enrichment of peptides coupled with quantitative mass spectrometry, commonly referred to as SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies).² In this technique, affinity enrichment of peptides with stable isotope dilution and detection by selected/multiple reaction monitoring mass spectrometry (SRM/MRM-MS) provides quantitative measurement of peptides as surrogates for their respective proteins. SRM/MRM-MS is well established for accurate quantitation of small molecules ^{3, 4} and more recently has been adapted to measure the concentrations of proteins in plasma and cell lysates.^5-7 To achieve quantitation of proteins, these larger molecules are digested to component peptides using an enzyme such as trypsin. One or more selected peptides whose sequence is unique to the target protein in that species (i.e. "proteotypic" peptides) are then enriched from the sample using anti-peptide antibodies and measured as quantitative stoichiometric surrogates for protein concentration in the sample. Hence, coupled to stable isotope dilution (SID) methods (i.e. a spiked-in stable isotope labeled peptide standard), SRM/MRM can be used to measure concentrations of proteotypic peptides as surrogates for quantification of proteins in complex biological matrices. The assays have several advantages compared to traditional immunoassays. The reagents are relatively less expensive to generate, the specificity for the analyte is excellent, the assays can be highly multiplexed, enrichment can be performed from neat plasma (no depletion required), and the technique is amenable to a wide array of proteins or modifications of interest.^8-13 In this video we demonstrate the basic protocol as adapted to a magnetic bead platform.     

Apolipoprotein E and presenilin-1 allelic variation and Alzheimer's disease in India

As part of a larger epidemiological survey to study the prevalence of dementia in a suburb of Mumbai, Western India, we identified 78 cases with a Clinical Dementia Rating (CDR) > or = 1.0. Of these, 49 Alzheimer's disease (AD) cases were analyzed for risk association with APOE E*4 allele at apolipoprotein E gene (APOE) and presenilin-1 (PS-1) intron-8 polymorphism and were compared with 100 age- and sex-matched nondemented controls. Genotype analysis confirmed the association of APOE E*4 allele with AD as has been reported by various studies. We report a low frequency of APOE E*4 allele, consistent with a low prevalence of AD in this study. Comparisons with other similar studies on APOE from India suggest common risk factors for AD in the Indian population, which is diverse in its ethnic and racial characteristics. The frequency for allele 1 at PS-1 intron-8 polymorphism is the highest among all studies reported. This first report of PS-1 intron-8 polymorphism and AD from India demonstrates no significant association.     

Activation of AMP-Activated Protein Kinase Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry

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Changes of the cortex proteome and Apolipoprotein E in transgenic mouse models of Alzheimer's Disease

Transgenic mice carrying human Amyloid Precursor Protein mutations present amyloid plaque deposition in the brain upon aging. In this study, we characterized the changes of cortex proteome and endogenous Apolipoprotein E in these mice. Differential analysis of two-dimensional electrophoresis images revealed spots altered upon aging, transgene addition and plaque deposition. Alpha-synuclein and cytochrome oxidase polypeptide Va were up-regulated in transgenic mice. Upon aging, expression of ATP synthase alpha, alpha enolase, UMP-CMP kinase, and dihydropyrimidinase like-2 protein was modified. These proteins and their modification probably play a role in the amyloid aggregate formation in these mice.     

Changes in Cancer Cell Metabolism Revealed by Direct Sample Analysis with MALDI Mass Spectrometry

Biomarker discovery using mass spectrometry (MS) has recently seen a significant increase in applications, mainly driven by the rapidly advancing field of metabolomics. Instrumental and data handling advancements have allowed for untargeted metabolite analyses which simultaneously interrogate multiple biochemical pathways to elucidate disease phenotypes and therapeutic mechanisms. Although most MS-based metabolomic approaches are coupled with liquid chromatography, a few recently published studies used matrix-assisted laser desorption (MALDI), allowing for rapid and direct sample analysis with minimal sample preparation. We and others have reported that prostaglandin E₃ (PGE₃), derived from COX-2 metabolism of the omega-3 fatty acid eicosapentaenoic acid (EPA), inhibited the proliferation of human lung, colon and pancreatic cancer cells. However, how PGE₃ metabolism is regulated in cancer cells, particularly human non-small cell lung cancer (NSCLC) cells, is not fully understood. Here, we successfully used MALDI to identify differences in lipid metabolism between two human non-small-cell lung cancer (NSCLC) cell lines, A549 and H596, which could contribute to their differential response to EPA treatment. Analysis by MALDI-MS showed that the level of EPA incorporated into phospholipids in H596 cells was 4-fold higher than A549 cells. Intriguingly, H596 cells produced much less PGE₃ than A549 cells even though the expression of COX-2 was similar in these two cell lines. This appears to be due to the relatively lower expression of cytosolic phospholipase A₂ (cPLA₂) in H596 cells than that of A549 cells. Additionally, the MALDI-MS approach was successfully used on tumor tissue extracts from a K-ras transgenic mouse model of lung cancer to enhance our understanding of the mechanism of action of EPA in the in vivo model. These results highlight the utility of combining a metabolomics workflow with MALDI-MS to identify the biomarkers that may regulate the metabolism of omega-3 fatty acids and ultimately affect their therapeutic potentials.     

Neurotransmitter and Depolarization-Stimulated Accumulation of Inositol 1,3,4,5-Tetrakisphosphate Mass in Rat Cerebral Cortex Slices

[32P]Inositol 1,3,4,5-tetrakisphosphate ([32P]Ins(1,3,4,5)P4) binds to a rat cerebellar membrane site with high affinity (KD = 2.8 +/- 0.6 nM) and low capacity (Bmax = 176 +/- 34 fmol/mg of protein). Evidence for a low-affinity site (KD = 164 +/- 48 nM) was also apparent. The high-affinity site displayed marked specificity for the Ins(1,3,4,5)P4 isomer, compared with several other inositol polyphosphates, and has been used as the basis of a radioreceptor assay for Ins(1,3,4,5)P4 in extracts of rat cerebral cortex slices. The resting Ins(1,3,4,5)P4 concentration (1.89 +/- 0.11 pmol/mg of protein) in the slices was rapidly and dramatically increased by carbachol and quisqualate. K+ depolarization of cerebral cortex slices also stimulated Ins(1,3,4,5)P4 accumulation, with at least 50% of the response being sensitive to atropine, a result indicating that muscarinic receptor stimulation by released acetylcholine contributes significantly to the K+ effect.     

基于质谱的蛋白质N末端乙酰化程度定量方法的研究

随着质谱技术及各种定量方法的不断完善和发展,定量蛋白质组学的方法不断地被应用到各类生物学研究中。蛋白质组学定性定量数据的处理主要通过一些多功能的商业化或者开源软件来进行,如常用的数据分析软件Proteome Discoverer和Maxquant。但是在通过化学标记对蛋白质N末端乙酰化程度进行定量这一方面,Proteome Discoverer和Maxquant在一定程度上存在准确性不高和完整度不够的问题。于是本研究针对自己的实验特点,通过Java算法编写了相应的定量程序Acequant来完成N末端乙酰化程度的相对定量。本研究将该程序在已有相关报道的He La cell上进行了验证,Acequant共定量到1 587个蛋白质N末端,而Proteome Discoverer和Maxquant分别只定量到42个和306个N末端。同时,手动验证原始图谱也证实了Acequant定量的准确性更好。于是,本研究将此方法进一步应用到秀丽隐杆线虫N末端乙酰化的研究中,并初步发现了线虫整体的N末端乙酰化状态,为进一步的N末端研究提供了支持。     

Serotonergic Regulation of Acetylcholine Release in Rat Frontal Cortex

Abstract: The extent to which serotonin regulates the activity of cortically projecting cholinergic neurons was studied using in vivo microdialysis to monitor interstitial concentrations of acetylcholine in the frontal cortex of freely moving rats. Systemic administration of the serotonin release-inducing agent fenfluramine (3 or 10 mg/kg, i.p.) increased acetylcholine release by 110–130%. The fenfluramine-induced increase in acetylcholine release was significantly attenuated by pretreatment with the selective serotonin uptake inhibitor fluoxetine (10 mg/kg, i.p.). Pretreatment with the selective dopamine D₁ receptor antagonist SCH-23390 (0.3 mg/kg, s.c.) failed to prevent the fenfluramine-induced increase in acetylcholine release. In contrast, the serotonin 5-HT_2A receptor antagonist ketanserin (5 mg/kg, i.p.) blocked fenfluramine-induced increases in acetylcholine release. In contrast to previous studies that have concluded that serotonin has inhibitory actions on cortical acetylcholine release, the present results indicate that fenfluramine increases cortical acetylcholine release in vivo by its ability to enhance serotonin transmission and that serotonin produces these effects at least in part via actions at serotonin 5-HT_2A receptors.