Characterization of Phosphorylated Tau-Microtubule complex with Molecular Dynamics (MD) simulation

Alzheimer's Disease (AD), a neurodegenerative disorder, is reported as one of the most severe health and socioeconomic problems in current public health. Tau proteins are assumed to be a crucial driving factor of AD that detach from microtubules (MT) and accumulate as neurotoxic aggregates in the brains of AD patients. Extensive experimental and computational research has observed that phosphorylation at specific tau residues enhances aggregation, but the exact mechanisms underlying this phenomenon remain unclear. In this study, we employed molecular dynamics (MD) simulations on pseudo-phosphorylated tau-MT complex (residue 199 ~ 312), incorporating structural data from recent cryo-electron microscopy studies. Simulation results have revealed altered tau conformations after applying pseudo-phosphorylation. Additionally, root-mean-square deviation (RMSD) analyses and dimensionality reduction of dihedral angles revealed key residues responsible for these conformational shiftsComment: 27pages, 12 figur

The role of BIP and PDI in the secretion of foreign proteins in the yeast Saccharomyces cerevisiae

As a single-celled microbial eucaryotic host for protein expression, the yeast Saccharomyces cerevisiae offers some of the advantages of bacterial systems, such as ease of fermentation, and of eucaryotic systems, such as post-translational modifications of secreted proteins. One disadvantage, however, is that secretion of foreign proteins is generally inefficient.The limiting step in protein secretion is often protein folding in the lumen of the endoplasmic reticulum (ER), a process assisted by accessory factors resident in this compartment. Chaperones, such as the hsp70 homolog binding protein (BiP), bind reversibly to the unfolded conformation of proteins, preventing irreversible aggregation. Foldases, such as protein disulfide isomerase (PDI), catalyze the formation and rearrangement of bonds which stabilize the folded conformation of proteins. I have examined the role of BiP and PDI in determining the efficiency of foreign protein secretion in the yeast Saccharomyces cerevisiae.I have found that high-level expression of foreign genes does not always lead to increased production of foreign proteins. In fact, prolonged constitutive expression of foreign secreted proteins reduces soluble BiP and PDI protein to levels undetectable by Western immunoassay. Fifteen-fold overexpression of PDI from a strong glycolytic promoter results in significant enhancement of secretion for some foreign proteins. Improved secretion is correlated with decreased ER retention, indicative of accelerated folding. When the chromosomal copy of BiP is deleted, and BiP levels are tightly regulated from a plasmid-borne copy of the gene controlled by the CUP1 promoter, both secretion and growth are decreased significantly when BiP falls below wild type levels. A mechanistic model can account for the behavior of BiP experimentally, and predictions have been made for altering cellular properties to increase protein secretion.U of I OnlyETDs are only available to UIUC Users without author permissio

Nonnative Interactions between Cysteines Direct Productive Assembly of P22 Tailspike Protein

Nonnative disulfide bond formation can play a critical role in the assembly of disulfide bonded proteins. During the folding and assembly of the P22 tailspike protein, nonnative disulfide bonds form both in vivo and in vitro. However, the mechanism and identity of cysteine disulfide pairs remains elusive, particularly for P22 tailspike, which contains no disulfide bonds in its native, functional form. Understanding the interactions between cysteine residues is important for developing a mechanistic model for the role of nonnative cysteines in P22 tailspike assembly. Prior in vivo studies have suggested that cysteines 496, 613, and 635 are the most likely site for sulfhydryl reactivity. Here we demonstrate that these three cysteines are critical for efficient assembly of tailspike trimers, and that interactions between cysteine pairs lead to productive assembly of native tailspike

Critical Molecular and Cellular Contributors to Tau Pathology

Tauopathies represent a group of neurodegenerative diseases including Alzheimer’s disease (AD) that are characterized by the deposition of filamentous tau aggregates in the brain. The pathogenesis of tauopathies starts from the formation of toxic ‘tau seeds’ from hyperphosphorylated tau monomers. The presence of specific phosphorylation sites and heat shock protein 90 facilitates soluble tau protein aggregation. Transcellular propagation of pathogenic tau into synaptically connected neuronal cells or adjacent glial cells via receptor-mediated endocytosis facilitate disease spread through the brain. While neuroprotective effects of glial cells—including phagocytotic microglial and astroglial phenotypes—have been observed at the early stage of neurodegeneration, dysfunctional neuronal-glial cellular communication results in a series of further pathological consequences as the disease progresses, including abnormal axonal transport, synaptic degeneration, and neuronal loss, accompanied by a pro-inflammatory microenvironment. Additionally, the discovery of microtubule-associated protein tau (MAPT) gene mutations and the strongest genetic risk factor of tauopathies—an increase in the presence of the ε2 allele of apolipoprotein E (ApoE)—provide important clues to understanding tau pathology progression. In this review, we describe the crucial signaling pathways and diverse cellular contributors to the progression of tauopathies. A systematic understanding of disease pathogenesis provides novel insights into therapeutic targets within altered signaling pathways and is of great significance for discovering effective treatments for tauopathies

The Interplay between GSK3β and Tau Ser262 Phosphorylation during the Progression of Tau Pathology

Tau hyperphosphorylation has been linked directly to the formation of toxic neurofibrillary tangles (NFTs) in tauopathies, however, prior to NFT formation, the sequence of pathological events involving tau phosphorylation remains unclear. Here, the effect of glycogen synthase kinase 3β (GSK3β) on tau pathology was examined independently for each step of transcellular propagation; namely, tau intracellular aggregation, release, cellular uptake and seeding activity. We find that overexpression of GSK3β-induced phosphorylated 0N4R tau led to a higher level of tau oligomerization in SH-SY5Y neuroblastoma cells than wild type 0N4R, as determined by several orthogonal assays. Interestingly, the presence of GSK3β also enhanced tau release. Further, we demonstrated that cells endocytosed more monomeric tau protein when pre-phosphorylated by GSK3β. Using an extracellular vesicle (EVs)-assisted tau neuronal delivery system, we show that exosomal GSK3β-phosphorylated tau, when added to differentiated SH-SY5Y cells, induced more efficient tau transfer, showing much higher total tau levels and increased tau aggregate formation as compared to wild type exosomal tau. The role of a primary tau phosphorylation site targeted by microtubule-affinity regulating kinases (MARKs), Ser262, was tested by pseudo-phosphorylation using site-directed mutagenesis to aspartate (S262D). S262D tau overexpression significantly enhanced tau release and intracellular tau accumulation, which were concurrent with the increase of pathological states of tau, as determined by immunodetection. Importantly, phosphorylation-induced tau accumulation was augmented by co-transfecting S262D tau with GSK3β, suggesting a possible interplay between Ser262 phosphorylation and GSK3β activity in tau pathology. Lastly, we found that pre-treatment of cells with amyloid-β (Aβ) further tau phosphorylation and accumulation when Ser262 pre-phosphorylation was present, suggesting that S262 may be a primary mediator of Aβ-induced tau toxicity. These findings provide a potential therapeutic target for treating tau-related disorders by targeting specific phospho-tau isoforms and further elucidate the GSK3β-mediated pathological seeding mechanisms

A Top-Down Approach to Mechanistic Biological Modeling: Application to the Single-Chain Antibody Folding Pathway

A top-down approach to mechanistic modeling of biological systems is presented and exemplified with the development of a hypothesis-driven mathematical model for single-chain antibody fragment (scFv) folding in Saccharomyces cerevisiae by mediators BiP and PDI. In this approach, model development starts with construction of the most basic mathematical model—typically consisting of predetermined or newly-elucidated biological behavior motifs—capable of reproducing desired biological behaviors. From this point, mechanistic detail is added incrementally and systematically, and the effects of each addition are evaluated. This approach follows the typical progression of experimental data availability in that higher-order, lumped measurements are often more prevalent initially than specific, mechanistic ones. It also necessarily provides the modeler with insight into the structural requirements and performance capabilities of the resulting detailed mechanistic model, which facilitates further analysis. The top-down approach to mechanistic modeling identified three such requirements and a branched dependency-degradation competition motif critical for the scFv folding model to reproduce experimentally observed scFv folding dependencies on BiP and PDI and increased production when both species are overexpressed and promoted straightforward prediction of parameter dependencies. It also prescribed modification of the guiding hypothesis to capture BiP and PDI synergy