Emulsified BMVC derivative induced filtration for G-quadruplex DNA structural separation

A novel method based on emulsion/filtration is introduced for G-quadruplex DNA structural separation. We first synthesized a lipophilic analogue of BMVC, 3,6-Bis(1-methyl-4-vinylpyridinium)-9-(12′-bromododecyl) carbazole diiodide (BMVC-12C-Br), which can form an oil-in-water (o/w) phase emulsion. Due to the binding preferences of BMVC-12C-Br emulsion to some specific DNA structures, the large emulsion (∼2 µm) bound DNA was separated from the small free DNA in the filtrate by a 0.22 µm pore size MCE membrane. This method is able to isolate the non-parallel G-quadruplexes from the parallel G-quadruplexes and the linear duplexes from both G-quadruplexes. In addition, this method allows us not only to determine the absence of the parallel G-quadruplexes of d(T2AG3)4 and the presence of the parallel G-quadruplexes of d(T2AG3)2 in K+ solution, but also to verify structural conversion from antiparallel to parallel G-quadruplexes of d[AG3(T2AG3)3] in K+ solution under molecular PEG condition. Moreover, this emulsion can separate the non-parallel G-quadruplexes of d(G3CGCG3AGGAAG5CG3) monomer from the parallel G-quadruplexes of its dimer in K+ solution. Together with NMR spectra, one can simplify the spectra for both the free DNA and the bound DNA to establish a spectrum-structure correlation for further structural analysis

A randomized trial and novel SPR technique identifies altered lipoprotein-LDL receptor binding as a mechanism underlying elevated LDL-cholesterol in APOE4s

At a population level APOE4 carriers (~25% Caucasians) are at higher risk of cardiovascular diseases. The penetrance of genotype is however variable and influenced by dietary fat composition, with the APOE4 allele associated with greater LDL-cholesterol elevation in response to saturated fatty acids (SFA). The etiology of this greater responsiveness is unknown. Here a novel surface plasmon resonance technique (SPR) is developed and used, along with hepatocyte (with the liver being the main organ modulating lipoprotein metabolism and plasma lipid levels) uptake studies to establish the impact of dietary fatty acid composition on, lipoprotein-LDL receptor (LDLR) binding, and hepatocyte uptake, according to APOE genotype status. In men prospectively recruited according to APOE genotype (APOE3/3 common genotype, or APOE3/E4), triglyceride-rich lipoproteins (TRLs) were isolated at fasting and 4-6 h following test meals rich in SFA, unsaturated fat and SFA with fish oil. In APOE4s a greater LDLR binding affinity of postprandial TRL after SFA, and lower LDL binding and hepatocyte internalization, provide mechanisms for the greater LDL-cholesterol raising effect. The SPR technique developed may be used for the future study of the impact of genotype, and physiological and behavioral variables on lipoprotein metabolism

Crowding Alone Cannot Account for Cosolute Effect on Amyloid Aggregation

Amyloid fiber formation is a specific form of protein aggregation, often resulting from the misfolding of native proteins. Aimed at modeling the crowded environment of the cell, recent experiments showed a reduction in fibrillation halftimes for amyloid-forming peptides in the presence of cosolutes that are preferentially excluded from proteins and peptides. The effect of excluded cosolutes has previously been attributed to the large volume excluded by such inert cellular solutes, sometimes termed “macromolecular crowding”. Here, we studied a model peptide that can fold to a stable monomeric β-hairpin conformation, but under certain solution conditions aggregates in the form of amyloid fibrils. Using Circular Dichroism spectroscopy (CD), we found that, in the presence of polyols and polyethylene glycols acting as excluded cosolutes, the monomeric β-hairpin conformation was stabilized with respect to the unfolded state. Stabilization free energy was linear with cosolute concentration, and grew with molecular volume, as would also be predicted by crowding models. After initiating the aggregation process with a pH jump, fibrillation in the presence and absence of cosolutes was followed by ThT fluorescence, transmission electron microscopy, and CD spectroscopy. Polyols (glycerol and sorbitol) increased the lag time for fibril formation and elevated the amount of aggregated peptide at equilibrium, in a cosolute size and concentration dependent manner. However, fibrillation rates remained almost unaffected by a wide range of molecular weights of soluble polyethylene glycols. Our results highlight the importance of other forces beyond the excluded volume interactions responsible for crowding that may contribute to the cosolute effects acting on amyloid formation

The molecular lifecycle of amyloid – Mechanism of assembly, mesoscopic organisation, polymorphism, suprastructures, and biological consequences

The formation of a diverse range of amyloid structures from normally soluble proteins and peptides is a hallmark of devastating human disorders as well as biological functions. The current molecular understanding of the amyloid lifecycle reveals four processes central to their growth and propagation: primary nucleation, elongation, secondary nucleation and division. However, these processes result in a wide range of cross-β packing and filament arrangements, including diverse assemblies formed from identical monomeric precursors with the same amino acid sequences. Here, we review current structural and mechanistic understanding of amyloid self-assembly, and discuss how mesoscopic, i.e. micrometre to nanometre, organisation of amyloid give rise to suprastructural features that may be the key link between the polymorphic amyloid structures and the biological response they elicit. A greater understanding of the mechanisms governing suprastructure formation will guide future strategies to combat amyloid associated disorders and to use and control the amyloid quaternary structure in synthetic biology and materials applications

Size analysis of polyglutamine protein aggregates using fluorescence detection in an analytical ultracentrifuge.

Defining the aggregation process of proteins formed by poly-amino acid repeats in cells remains a challenging task due to a lack of robust techniques for their isolation and quantitation. Sedimentation velocity methodology using fluorescence detected analytical ultracentrifugation is one approach that can offer significant insight into aggregation formation and kinetics. While this technique has traditionally been used with purified proteins, it is now possible for substantial information to be collected with studies using cell lysates expressing a GFP-tagged protein of interest. In this chapter, we describe protocols for sample preparation and setting up the fluorescence detection system in an analytical ultracentrifuge to perform sedimentation velocity experiments on cell lysates containing aggregates formed by poly-amino acid repeat proteins

Imaging brain metabolism in a mouse model of Huntington's disease

Introduction: Huntington's disease (HD) is a neurodegenerative disease, whose key pathological signature is the formation of intracellular inclusions. However, the exact role of inclusions in driving HD pathology remains to be clearly understood. Our lab has previously shown that the formation of huntingtin inclusions correlates with neuroblastoma cells becoming functionally quiescent and undergoing a slow death by necrosis. We hypothesize that inclusion formation establishes cellular quiescence in vivo. Our goal is to assess the extent to which neurons in vivo are metabolically quiescent and how this relates to the presence of inclusions in a transgenic mouse model (R6/1) of HD.Methods: We have studied the metabolic turnover of neuronal membrane lipids by feeding wild-type (WT) and HD mice with deuterated water at asymptomatic, pre-symptomatic &fully symptomatic ages of the disease. The left hemisphere of the brain was used for determining the spatial distribution and the abundance of neuronal lipids using MALDI-TOF imaging mass spectrometry (MALDI-IMS), while the right hemisphere was reserved for cross-validation using Liquid-Chromatography mass spectrometry (LC-MS). Results: Our data points towards alterations in neuronal lipids that play a critical role in neurotransmission, synaptic plasticity, myelination, and Endoplasmic reticulum (ER)- stress, thus providing lipid correlates for hippocampal-dependent cognitive deficits observed in HD pathology. Moreover, we found a remodeling of lipid synthesis in hippocampal areas that are densely populated by inclusions, detected using EM48-immunohistochemistry. We have also developed a novel bioinformatics tool to study in vivo kinetics using stable isotope labelling (Deuterium) coupled with a spatial metabolic approach.Conclusion: Collectively, this data reveals age-specific changes in brain lipids, providing mechanistic insights into the progressive changes observed in HD. Accelerated lipid synthesis observed in asymptomatic HD mice, hints at its possible role as an adaptive stress response to cope with ER-stress, thus providing an early biomarker for identification of HD

A Platform to View Huntingtin Exon 1 Aggregation Flux in the Cell Reveals Divergent Influences from Chaperones hsp40 and hsp70

Our capacity for tracking how misfolded proteins aggregate inside a cell and how different aggregation states impact cell biology remains enigmatic. To address this, we built a new toolkit that enabled the high throughput tracking of individual cells enriched with polyglutamine-expanded Htt exon 1 (Httex1) monomers, oligomers, and inclusions using biosensors of aggregation state and flow cytometry pulse shape analysis. Supplemented with gel filtration chromatography and fluorescence-adapted sedimentation velocity analysis of cell lysates, we collated a multidimensional view of Httex1 aggregation in cells with respect to time, polyglutamine length, expression levels, cell survival, and overexpression of protein quality control chaperones hsp40 (DNAJB1) and hsp70 (HSPA1A). Cell death rates trended higher for Neuro2a cells containing Httex1 in inclusions than with Httex1 dispersed through the cytosol at time points of expression over 2 days. hsp40 stabilized monomers and suppressed inclusion formation but did not otherwise change Httex1 toxicity. hsp70, however, had no major effect on aggregation of Httex1 but increased the survival rate of cells with inclusions. hsp40 and hsp70 also increased levels of a second bicistronic reporter of Httex1 expression, mKate2, and increased total numbers of cells in culture, suggesting these chaperones partly rectify Httex1-induced deficiencies in quality control and growth rates. Collectively, these data suggest that Httex1 overstretches the protein quality control resources and that the defects can be partly rescued by overexpression of hsp40 and hsp70. Importantly, these effects occurred in a pronounced manner for soluble Httex1, which points to Httex1 aggregation occurring subsequently to more acute impacts on the cell