Chemistry, Department of

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G-Quadruplex Structures Formed by Expanded Hexanucleotide Repeat RNA and DNA from the Neurodegenerative Disease-Linked C9orf72 Gene Efficiently Sequester and Activate Heme

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014-09-10
Abstract: 

The expansion of a (G4C2)n repeat within the human C9orf72 gene has been causally linked to a number of neurodegenerative diseases, most notably familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent studies have shown that the repeat expansion alters gene function in four ways, disrupting the gene's normal cellular roles and introducing toxic gain of function at the level of both DNA and RNA. (G4C2)n DNA, as well as the RNA transcribed from it, are found to fold into four-stranded G-quadruplex structures. It has been shown that the toxicity of the RNA G-quadruplexes, often localized in intracellular RNA foci, lies in their ability to sequester many important RNA binding proteins. Herein we propose that a distinct toxic property of such RNA and DNA G-quadruplexes from the C9orf72 gene may arise from their ability to bind and oxidatively activate cellular heme. We show that G-quadruplexes formed by both (G4C2)4 RNA and DNA not only complex tightly with heme but also enhance its intrinsic peroxidase and oxidase propensities. By contrast, the antisense (C4G2)4 RNA and DNA neither bind heme nor influence its oxidative activity. Curiously, the ability of C9orf72 DNA and transcripts to bind and activate heme mirror similar properties that have been reported for the Aβ peptide and its oligomers in Alzheimer's disease neurons. It is therefore conceivable that C9orf72 RNA G-quadruplex tangles play roles in sequestering intracellular heme and promoting oxidative damage in ALS and FTD analogous to those proposed for Aβ peptide and its tangles in Alzheimer's Disease. Given that neurodegenerative diseases in general are characterized by mitochondrial and respiratory malfunctions, the role of C9orf72 DNA and RNA in heme sequestration as well as its inappropriate activation in ALS and FTD neurons may warrant examination.

Document type: 
Article
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Human Lactate Dehydrogenase A Inhibitors: A Molecular Dynamics Investigation

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014-01-17
Abstract: 

Lactate dehydrogenase A (LDHA) is an important enzyme in fermentative glycolysis, generating most energy for cancer cells that rely on anaerobic respiration even under normal oxygen concentrations. This renders LDHA a promising molecular target for the treatment of various cancers. Several efforts have been made recently to develop LDHA inhibitors with nanomolar inhibition and cellular activity, some of which have been studied in complex with the enzyme by X-ray crystallography. In this work, we present a molecular dynamics (MD) study of the binding interactions of selected ligands with human LDHA. Conventional MD simulations demonstrate different binding dynamics of inhibitors with similar binding affinities, whereas steered MD simulations yield discrimination of selected LDHA inhibitors with qualitative correlation between the in silico unbinding difficulty and the experimental binding strength. Further, our results have been used to clarify ambiguities in the binding modes of two well-known LDHA inhibitors.

Document type: 
Article
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Pharmacological Inhibition of O-GlcNAcase (OGA) Prevents Cognitive Decline and Amyloid Plaque Formation in Bigenic Tau/APP Mutant Mice

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Background

Amyloid plaques and neurofibrillary tangles (NFTs) are the defining pathological hallmarks of Alzheimer’s disease (AD). Increasing the quantity of the O-linked N-acetylglucosamine (O-GlcNAc) post-translational modification of nuclear and cytoplasmic proteins slows neurodegeneration and blocks the formation of NFTs in a tauopathy mouse model. It remains unknown, however, if O-GlcNAc can influence the formation of amyloid plaques in the presence of tau pathology.

Results

We treated double transgenic TAPP mice, which express both mutant human tau and amyloid precursor protein (APP), with a highly selective orally bioavailable inhibitor of the enzyme responsible for removing O-GlcNAc (OGA) to increase O-GlcNAc in the brain. We find that increased O-GlcNAc levels block cognitive decline in the TAPP mice and this effect parallels decreased β-amyloid peptide levels and decreased levels of amyloid plaques.

Conclusions

This study indicates that increased O-GlcNAc can influence β-amyloid pathology in the presence of tau pathology. The findings provide good support for OGA as a promising therapeutic target to alter disease progression in Alzheimer disease.

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Article
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The Influence of 150-Cavity Binders on the Dynamics of Influenza A Neuraminidases as Revealed by Molecular Dynamics Simulations and Combined Clustering

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2013
Abstract: 

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations – the structures of which are provided to facilitate future molecular docking studies – and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed.

Document type: 
Article
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Water Oxidation by a Cytochrome P450: Mechanism and Function of the Reaction

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2013
Abstract: 

P450cam (CYP101A1) is a bacterial monooxygenase that is known to catalyze the oxidation of camphor, the first committed step in camphor degradation, with simultaneous reduction of oxygen (O2). We report that P450cam catalysis is controlled by oxygen levels: at high O2 concentration, P450cam catalyzes the known oxidation reaction, whereas at low O2 concentration the enzyme catalyzes the reduction of camphor to borneol. We confirmed, using 17O and 2H NMR, that the hydrogen atom added to camphor comes from water, which is oxidized to hydrogen peroxide (H2O2). This is the first time a cytochrome P450 has been observed to catalyze oxidation of water to H2O2, a difficult reaction to catalyze due to its high barrier. The reduction of camphor and simultaneous oxidation of water are likely catalyzed by the iron-oxo intermediate of P450cam, and we present a plausible mechanism that accounts for the 1:1 borneol:H2O2 stoichiometry we observed. This reaction has an adaptive value to bacteria that express this camphor catabolism pathway, which requires O2, for two reasons: 1) the borneol and H2O2 mixture generated is toxic to other bacteria and 2) borneol down-regulates the expression of P450cam and its electron transfer partners. Since the reaction described here only occurs under low O2 conditions, the down-regulation only occurs when O2 is scarce.

Document type: 
Article
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Synthesis of Ag Nanostructures by Photochemical Reduction Using Citrate-Capped Pt Seeds

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

A simple synthesis of Ag nanostructures such as nanorods and nanowires has been demonstrated with citrate-capped Pt seeds. UV-visible spectra and photographs of the synthesized solutions at different UV exposure times showed that the citrate-capped Pt seed played a crucial role in the growth of Ag nanostructures. After UV exposure of the colloidal solution for 60 min, the average diameter, length, and aspect ratio of the Ag nanostructures were about 95 nm, 2.1 nm, and 22, respectively. The photochemical reduction is hypothesized to result from photoelectron transfer from adsorbed citrate to Pt nanoparticle seed allowing Ag ions to form Ag nanostructures. Based on X-ray diffraction spectra and transmission electron microscope images, the synthesized Ag nanostructures were a face-centered cubic single crystal with good purity. These results suggest that the photochemical reduction method can provide Ag nanostructures in the presence of citrate-capped Pt seeds at room temperature for anisotropic Ag products.

Document type: 
Article

New Insights into Honey Bee (Apis mellifera) Pheromone Communication. Is the Queen Mandibular Pheromone Alone in Colony Regulation?

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: In social insects, the queen is essential to the functioning and homeostasis of the colony. This influencehas been demonstrated to be mediated through pheromone communication. However, the only social insect forwhich any queen pheromone has been identified is the honey bee (Apis mellifera) with its well-known queenmandibular pheromone (QMP). Although pleiotropic effects on colony regulation are accredited to the QMP, thispheromone does not trigger the full behavioral and physiological response observed in the presence of the queen,suggesting the presence of additional compounds. We tested the hypothesis of a pheromone redundancy in honeybee queens by comparing the influence of queens with and without mandibular glands on worker behavior andphysiology.Results: Demandibulated queens had no detectable (E)-9-oxodec-2-enoic acid (9-ODA), the major compound in QMP,yet they controlled worker behavior (cell construction and queen retinue) and physiology (ovary inhibition) asefficiently as intact queens.Conclusions: We demonstrated that the queen uses other pheromones as powerful as QMP to control the colony. Itfollows that queens appear to have multiple active compounds with similar functions in the colony (pheromoneredundancy). Our findings support two hypotheses in the biology of social insects: (1) that multiple semiochemicalswith synonymous meaning exist in the honey bee, (2) that this extensive semiochemical vocabulary exists because itconfers an evolutionary advantage to the colony.

Document type: 
Article