Formation Of Helical Filaments Research Articles

Structural basis for the helical filament formation of Escherichia coli glutamine synthetase.

Escherichia coli glutamine synthetase (EcGS) spontaneously forms a dodecamer that catalytically converts glutamate to glutamine. EcGS stacks with other dodecamers to create a filament-like polymer visible under transmission electron microscopy. Filamentous EcGS is induced by environmental metal ions. We used cryo-electron microscopy (cryo-EM) to decipher the structure of metal ion (nickel)-induced EcGS helical filament at a sub-3Å resolution. EcGS filament formation involves stacking of native dodecamers by chelating nickel ions to residues His5 and His13 in the first N-terminal helix (H1). His5 and His13 from paired parallel H1 helices provide salt bridges and hydrogen bonds to tightly stack two dodecamers. One subunit of the EcGS filament hosts two nickel ions, whereas the dodecameric interface and the ATP/Mg-binding site both host a nickel ion each. We reveal that upon adding glutamate or ATP for catalytic reactions, nickel-induced EcGS filament reverts to individual dodecamers. Such tunable filament formation is often associated with stress responses. Our results provide detailed structural information on the mechanism underlying reversible and tunable EcGS filament formation.

Epigallocatechin-3-gallate modulates Tau Post-translational modifications and cytoskeletal network.

Background: Alzheimer’s disease is a type of dementia denoted by progressive neuronal death due to the accumulation of proteinaceous aggregates of Tau. Post-translational modifications like hyperphosphorylation, truncation, glycation, etc. play a pivotal role in Tau pathogenesis. Glycation of Tau aids in paired helical filament formation and abates its microtubule-binding function. The chemical modulators of Tau PTMs, such as kinase inhibitors and antibody-based therapeutics, have been developed, but natural compounds, as modulators of Tau PTMs are not much explored.Materials and Methods: We applied biophysical and biochemical techniques like fluorescence kinetics, oligomerization analysis and transmission electron microscopy to investigate the impact of EGCG on Tau glycation in vitro. The effect of glycation on cytoskeleton instability and its EGCG-mediated rescue were studied by immunofluorescence microscopy in neuroblastoma cells.Results: EGCG inhibited methyl glyoxal (MG)-induced Tau glycation in vitro. EGCG potently inhibited MG-induced advanced glycation endproducts formation in neuroblastoma cells as well modulated the localization of AT100 phosphorylated Tau in the cells. In addition to preventing the glycation, EGCG enhanced actin-rich neuritic extensions and rescued actin and tubulin cytoskeleton severely disrupted by MG. EGCG maintained the integrity of the Microtubule Organizing Center (MTOC) stabilized microtubules by Microtubule-associated protein RP/EB family member 1 (EB1).Conclusions: We report EGCG, a green tea polyphenol, as a modulator of in vitro methylglyoxal-induced Tau glycation and its impact on reducing advanced glycation end products in neuroblastoma cells. We unravel unprecedented function of EGCG in remodeling neuronal cytoskeletal integrity.

Microfluidic Protein Imaging Platform: Study of Tau Protein Aggregation and Alzheimer's Drug Response.

Tau protein aggregation is identified as one of the key phenomena associated with the onset and progression of Alzheimer’s disease. In the present study, we performed on-chip confocal imaging of tau protein aggregation and tau–drug interactions using a spiral-shaped passive micromixing platform. Numerical simulations and experiments were performed in order to validate the performance of the micromixer design. We performed molecular modeling of adenosine triphosphate (ATP)-induced tau aggregation in order to successfully validate the concept of helical tau filament formation. Tau aggregation and native tau restoration were realized using an immunofluorescence antibody assay. The dose–response behavior of an Alzheimer’s drug, methylthioninium chloride (MTC), was monitored on-chip for defining the optimum concentration of the drug. The proposed device was tested for reliability and repeatability of on-chip tau imaging. The amount of the tau protein sample used in our experiments was significantly less than the usage for conventional techniques, and the whole protein–drug assay was realized in less than two hours. We identified that intensity-based tau imaging could be used to study Alzheimer’s drug response. In addition, it was demonstrated that cell-free, microfluidic tau protein assays could be used as potential on-chip drug evaluation tools for Alzheimer’s disease.

Formation of solid helical filaments at temperatures of superfluid helium as self-organization phenomena in ultracold dusty plasma

A multimodal dusty plasma formed in a positive column of the direct current glow discharge at superfluid helium temperatures has been studied for the first time. Formation of a liquid-like dusty plasma structure occurred after injection of polydisperse cerium oxide particles in the glow discharge. The coupling parameter ~10 determined for the dusty plasma structure corresponds very well to its liquid-like type. The cloud of nanoparticles and non-linear waves within the cloud were observed at T < 2 K. Solid helical filaments with length up to 5 mm, diameter up to 22 μm, total charges ~106е, levitating in the gas discharge at the temperature ~2 K and pressure 4 Pa have been observed for the first time. Analysis of the experimental conditions and the filament composition allows us to conclude that the filaments and nanoclusters were formed due to ion sputtering of dielectric material during the experiments.

Bilateral Implantation of Shear Stress Modifier in ApoE Knockout Mouse Induces Cognitive Impairment and Tau Abnormalities.

Vascular cognitive impairment (VCI) encompasses all causes of cerebrovascular disease that lead to cognitive decline, or overt dementia, atherosclerotic disease being the most common contributor. However, few rodent models that mimic the pathology of VCI replicated the clinical cerebrovascular atherosclerosis. Here we aimed to investigate the mechanism underlying VCI in an Apolipoprotein E knockout (ApoE-KO) mouse model fed with western style food with implantation of bilateral shear stress modifiers. We established a cognitive decline in spatial learning and memory developed in the bilateral modifier treated mice. Brain imaging and pathological examinations demonstrated reduced glucose intake and neuronal loss in hippocampus. Although no amyloid plaques or neurofibrillary tangles (NFTs) were observed, tau pathology including hyperphosphorylation, paired helical filament formation and pathologic truncation were found at considerable higher extent in the bilateral modifier group 8 weeks post the procedure. In addition, gliosis and microglia activation were confirmed in corpus callosum (CC) and ventral striatum. Thus, this ApoE-KO mouse model faithfully replicates the stenosis of common carotid artery (CCA) and cognitive impairment following atherosclerotic deposition and global cerebral hypoperfusion. The close correlation of cognitive decline and tau pathology indicates the toxic tau species could be at least partially responsible for the neurodegenerative changes induced by the chronic hypoxia/ischemia.

The Bacterial Flagellar Filament Re-Examined at High Resolution

The bacterial flagellar filament has been an important model system in structural biology. Current models are based upon the notion that subunits can switch between two stable states, one forming left-handed 11-start protofilaments and the other forming right-handed ones (Calladine, 1975; Kamiya et al., 1980). Pioneering work on the structure of two flagellin mutants came from the Namba lab, studying the Salmonella filament (Maki-Yonekura et al., 2010; Samatey et al., 2001). We have been using cryo-EM to study the structure of a gram-positive bacterium, Bacillus subtilis. We have now reconstructed five mutants, all at a better resolution than obtained for Salmonella. For one mutant, we have reached ∼ 3.6 A, which allows for a full atomic model to be built with a high-degree of confidence. These results are being combined into a new model for how structural polymorphism is dictated by the switching between two states, only possible with the recent advances allowing for near-atomic resolution reconstructions of these filaments.Calladine, C.R. (1975). Construction of bacterial flagella. Nature 255, 121-124.Kamiya, R., Asakura, S., and Yamaguchi, S. (1980). Formation of helical filaments by copolymerization of two types of ’straight‘ flagellins. Nature 286, 628-630.Maki-Yonekura, S., Yonekura, K., and Namba, K. (2010). Conformational change of flagellin for polymorphic supercoiling of the flagellar filament. NatStructMolBiol 17, 417-422.Samatey, F.A., Imada, K., Nagashima, S., Vonderviszt, F., Kumasaka, T., Yamamoto, M., and Namba, K. (2001). Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature 410, 331-337.

Pittsburgh Compound-B (PiB) binds amyloid β-protein protofibrils.

The neuropathology of Alzheimer's disease (AD) includes amyloid plaque formation by the amyloid β-protein (Aβ) and intracellular paired helical filament formation by tau protein. These neuropathogenetic features correlate with disease progression and have been revealed in brains of AD patients using positron emission tomography (PET). One of the most useful positron emission tomography imaging agents has been Pittsburgh Compound-B (PiB). However, since its introduction in 2002, substantial evidence has accumulated suggesting that Aβ oligomerization and protofibril formation, rather than fibril formation per se, may be the more important pathogenetic event in AD. Detecting protofibrils and oligomeric forms of Aβ thus may be of value. We report here the results of experiments to determine whether PiB binds to oligomers or protofibrils formed by Aβ40 and Aβ42. We observed strong binding to Aβ42 fibrils, significant binding to protofibrils, and weaker binding to Aβ42 oligomers. PiB also binds Aβ40 fibrils, but its binding to Aβ40 protofibrils and oligomers is substantially lower than for that observed for Aβ42.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Without Binding ATP, Human Rad51 Does Not Form Helical Filaments on ssDNA.

Construction of the presynaptic filament (PSF) of proper helical structure by Rad51 recombinases is a prerequisite of the progress of homologous recombination repair. We studied the contribution of ATP-binding to this structure of wt human Rad51 (hRad51). We exploited the protein-dissociation effect of high hydrostatic pressure to determine the free energy of dissociation of the protomer interfaces in hRad51 oligomer states and used electron microscopy to obtain topological parameters. Without cofactors ATP and Ca(2+) and template DNA, hRad51 did not exist in monomer form, but it formed rodlike long filaments without helical order. ΔG(diss) indicated a strong inherent tendency of aggregation. Binding solely ssDNA left the filament unstructured with slightly increased ΔG(diss). Adding only ATP and Ca(2+) to the buffer disintegrated the self-associated rods into rings and short helices of further increased ΔG(diss). Rad51 binding to ssDNA only with ATP and Ca bound could lead to ordered helical filament formation of proper pitch size with interface contacts of K(d) ∼ 2 × 10(-11) M, indicating a structure of outstanding stability. ATP/Ca binding increased the ΔG(diss) of protomer contacts in the filament by 16 kJ/mol. The results emphasize that ATP-binding in the PSF of hRad51 has an essential, yet purely structural, role.

Tau accumulation in the nucleus accumbens in tangle-predominant dementia

BackgroundTangle-predominant dementia (TPD) is characterized neuropathologically by numerous neurofibrillary tangles in the limbic areas with no or occasional senile plaques throughout the brain. TPD is an under-recognized disease, while it is a common cause of dementia in those over 80 years of age. In the present study, we describe hyperphosphorylated tau (tau) accumulation in the nucleus accumbens (Acb) in patients with TPD.ResultsWe investigated immunohistochemically the brain tissues from 7 patients with TPD, 22 with Alzheimer disease (AD) and 11 non-demented aged subjects. In the Acb of all 7 TPD patients, a considerable number of tau positive neurons were found together with many neuropil threads. The tau deposits in the Acb were labeled with all the anti-tau antibodies used in the present study. They included conformational change-specific, phosphorylation-specific and phosphorylation-independent antibodies. The Acb consists of the predominant medium-sized neurons with a small number of large neurons. Both the cell types were affected by tau pathology in TPD. Tau accumulation in the majority of such neurons appeared to be pretangle-like, diffuse deposits with only occasional paired helical filament formation. Tau positive neurons were also found in the Acb in some AD and non-demented aged subjects but much fewer in the majority of cases. The immunoblot analyses of fresh frozen samples of the Acb and parahippocampal cortex from 3 TPD and 3 AD patients revealed that the insoluble tau in the Acb was a mixture of the 3- and 4-repeat isoforms.ConclusionsTo our knowledge, this is the first report on the occurrence of tau accumulation in the Acb in TPD. The Acb receives direct and massive projections from the hippocampal CA1 and subiculum where neurofibrillary tangles are known to occur more frequently in TPD than in AD. The prevalence of abnormal tau accumulation in the Acb in TPD may support the idea that abnormal tau aggregation propagates via neural circuits. In all but one TPD cases used in this study, delusion was a consistent clinical feature. Whether the Acb tau accumulation is related to the psychiatric symptoms in TPD may be an issue for further investigation.

A ring-like model for ASC self-association via the CARD domain

AbstractInflammasomes are molecular platforms controlling the innate immune response to pathogens and cellular stress. ASC is an adaptor protein common to most NLR (nucleotide-binding domain and leucine-rich repeat containing receptor) inflammasome complexes as its N-terminal PYD and C-terminal CARD interact with the homologous domains in NLR and procaspase-1. Although inflammasome activation depends on ASC oligomerization, the molecular basis of ASC self-association and the protein interactions mediating the inflammatory signaling pathway remain unknown. Both CARD and PYD domains are involved in the oligomerization process of ASC. Based on our previous structural and dynamics data on ASC we propose a model for its oligomerization consisting of a 7-member ring. In this model, CARD monomers associate via type I homotypic interactions leaving the remaining binding site of each monomer free for further oligomerization and thus ring formation. A second more open PYD ring is accommodated on top of the CARDs. Our model is discussed in light of previous work evidencing the formation of helical filaments and large globular structures by ASC. The double-ring model can help in the understanding of inflammasome assembly, nevertheless, ASC oligomerization has to be envisaged as a complex process that might include molecular organizations with structurally different features.

Magnetic topology changes induced by lower hybrid waves and their profound effect on edge-localized modes in the EAST tokamak.

Strong mitigation of edge-localized modes has been observed on Experimental Advanced Superconducting Tokamak, when lower hybrid waves (LHWs) are applied to H-mode plasmas with ion cyclotron resonant heating. This has been demonstrated to be due to the formation of helical current filaments flowing along field lines in the scrape-off layer induced by LHW. This leads to the splitting of the outer divertor strike points during LHWs similar to previous observations with resonant magnetic perturbations. The change in the magnetic topology has been qualitatively modeled by considering helical current filaments in a field-line-tracing code.

Structural Stability of Rad51 Filaments of Self-Aggregates and of Presynaptic Complexes Studied by Electron Microscopy and Pressure Tuning Fluorescence Spectroscopy

The maintenance and stability of the genetic material of cells is of vital significance. This task is fulfilled by complex mechanisms involving the associates of specific proteins that through several steps recognize and repair DNA damages. In this study we focus our attention on an early step in the process of homologous recombination of human cells that is related to the function of the protein Rad51. The repair action of the protein is initiated by a supposedly unspecific helical filament formation of its monomers around single stranded DNA overhangs at double strand breaks. We study the conditions that regulate the structure and thus the biological activity of this, presynaptic” filament. Now we report results of pressure tuning fluorescence spectroscopy (Schay et al.(2006) JBC, 281, 25972) concerning the strength of interaction at the monomer-monomer interfaces in the filament structures and results of electronmicroscopy concerning their topology and structural parameters. The fluorescence signal is based on the dye ANS that we show being bound near the monomer interfaces. The measurements yield new data concerning the role of ATP, Mg, and Ca as cofactors of the presynaptic filament formation and show the unique effect of bound K-ions significantly influencing both the stability and the topology of the presynaptic as well as of the self-aggregate filaments.Acknowledgements: the authors are grateful to Prof. Kovacs of Eotvos University for help and valuable advices in electron microscopy. The work was supported by the Hungarian grant OTKA K 84271.

Helical deformation of the filament of a scroll wave

In three-dimensional excitable systems scroll waves may lose their originally straight shape through different instabilities. In experiments, the formation of zigzag-shaped or helical filaments is often observed. Such a deformation may be due to either a twist-induced instability or a 3D meandering instability. We performed a systematic study using a Belousov-Zhabotinsky (BZ) system with a vertical gradient of excitability and determined the necessary twist for the onset of undulation in the filament. Thus, we demonstrate that in the case of a BZ system with a gradient parallel to the filament, the deformation of the filament is induced by a twist-induced instability.

Various mechanisms of flagella helicity formation in haloarchaea

The genome of a halophilic archaeon Haloarcula marismortui carries two flagellin genes, flaA2 and flaB. Previously, we demonstrated that the helical flagellar filaments of H. marismortui were composed primarily of flagellin FlaB molecules, while the other flagellin (FlaA2) was present in minor amounts. Mutant H. marismortui strains with either flagellin gene inactivated were obtained. It was shown that inactivation of the flaA2 gene did not lead to changes in cell motility and helicity of the filaments, while the cells with inactivated flaB lost their motility and flagella synthesis was stopped. Two FlaB flagellin forms having different sensitivities to proteolysis were found in the flagellar filament structure. It is speculated that these flagellin forms may ensure the helical filament formation. Moreover, the flagella of a psychrotrophic haloarchaeon Halorubrum lacusprofundi were isolated and characterized for the first time. H. lacusprofundi filaments were helical and exhibited morphological polymorphism, although the genome contained a single flagellin gene. These results suggest that the mechanisms of flagellar helicity may differ in different halophilic archaea, and sometimes the presence of two flagellin genes, in contrast to Halobacterium salinarum, is not necessary for the formation of a functional helical flagellum.

Modulation of oxidative stress and tau phosphorylation by the mTOR activator phosphatidic acid in SH-SY5Y cells

The mammalian target of rapamycin complex 1 (mTORC1) pathway including p70S6K (the 70-kDa p70 S6 kinase) and S6, controls protein synthesis, has anti-apoptotic functions and can phosphorylate tau protein. mTORC1 is triggered by nutrients such as phosphatidic acid (PA). Previous experimental studies have shown that oxidative stress may down-regulate this pathway leading to neuronal death. Our results showed that in human neuroblastoma cells, PA exposure can reduce H2O2-induced apoptosis and can increase tau protein phosphorylation on Ser214 via p70S6K activation. These findings reveal that PA, via the mTOR kinase, can trigger tau phosphorylation on a site known to reduce paired helical filament (PHF) formation.

D-Ribosylated Tau forms globular aggregates with high cytotoxicity.

Although the glycation of Tau that is involved in paired helical filament formation in Alzheimer's disease has been widely studied, little attention has been paid to the role of D-ribose in the glycation of Tau. Here, we show that Tau is rapidly glycated in the presence of D-ribose, resulting in oligomerization and polymerization. Glycated derivatives appeared after 24 h incubation. Western blotting indicated the formation of advanced glycation end-products (AGEs) during initial stages of glycation. Thioflavin T-positive (ThT-positive) aggregations that appeared from day 4 indicated the globular-like features. Atomic force microscopy revealed that the surface morphology of ribosylated Tau40 was globular-like. Kinetic studies suggested that D-ribosylated Tau is slowly oligomerized and rapidly polymerized with ThT-positive features. Moreover, D-ribosylated Tau aggregates were highly toxic to SHSY5Y cells and resulted in both apoptosis and necrosis. This work has demonstrated that D-ribose reacted with Tau protein rapidly, producing ThT-positive aggregations which had high cytotoxicity.

The Damage Signals Hypothesis of Alzheimer's Disease Pathogenesis

Virtually none of the hypotheses on Alzheimer's disease (AD) pathogenesis address the earliest events that trigger the molecular alterations that precede cerebral degeneration and account for the diversity of risk factors that converge on a well-defined disease phenotype. We propose that long-term activation of the innate immune system by an individual array of risk factors constitutes a unifying mechanism leading to the triggering of an inflammatory cascade that converges in cytoskeletal alterations (tau aggregation, paired helical filament formation) as a previously hypothesized final common pathway in AD. The key pathogenic phenomena consist in the long-term, maladaptive activation of innate immunity-triggering receptors--such as the toll-like and advanced glycation end-products receptors, and others located in the microglial membrane--by seemingly heterogeneous risk factors such as hyperlipidemia, hyperglycemia, oxidative stress, head injury, amyloid oligomers, etc. Our hypothesis provides a unifying mechanism that explains both the diversity of risk factors acting over long periods of time and the individual response to such insults. This formulation is amenable to both empirical testing and implementation into therapeutic strategies that may lead to effective prevention of AD as well as other disorders in which impaired regulation of the innate immunity is the unifying cause of the condition.

Linkage‐dependent contribution of repeat peptides to self‐aggregation of three‐ or four‐repeat microtubule‐binding domains in tau protein

Although one of the priorities in Alzheimer's research is to clarify the filament formation mechanism for the tau protein, it is still unclear how it is transformed from a normal structure in a neuron. To examine the linkage-dependent contribution of each repeat peptide (R1-R4) to filament formation of the three- or four-repeat microtubule-binding domain (MBD) in the tau protein, four two-repeat peptides (R12, R13, R23 and R34) and two three-repeat peptides (R123 and R234) were prepared, and their in vitro self-aggregation was investigated by thioflavin S fluorescence and circular dichroism measurements, and by electron microscopy in neutral buffer (pH 7.6). Comparison of these aggregation behaviors with previous results for single-repeat peptides and wild-type 3RMBD (R134) and 4RMBD (R1234) indicated that (a) the two-repeat R23, not the R2 or R3 single repeat, forms the core structure in self-aggregation of 4RMBD, whereas that of 3RMBD comprises the R3 single repeat, (b) co-existence of R1 and R4 repeats is necessary for the aggregation behavior inherent in 3RMBD and 4RMBD, whereas the R1 or R4 repeat alone functions as a repressor or modifier of the filament formation, (c) 4RMBD aggregation is accompanied by R1-driven transition from random and alpha-helix structures to a beta-sheet structure, whereas 3RMBD aggregation involves three-repeat R134-specific transition from a random structure to an alpha-helix structure without the participation of a beta-sheet structure, and (d) the peptides that include the R1 repeat form a long filament irrespective of the absence or presence of the R4 repeat, whereas those that include the R4 repeat, but not the R1 repeat, form a relatively short filament. To the best of our knowledge, a systematic study of the linkage-dependent contribution of each repeat peptide to the paired helical filament formation of tau MBD has not been carried out previously, and thus the present information is useful for understanding the essence of the filament formation of tau MBD.

Structural and Microtubule Binding Properties of Tau Mutants of Frontotemporal Dementias

Several mutations in the gene encoding the microtubule-associated protein tau are responsible for the formation of neurofibrillary inclusions in frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17). Here we present the high-resolution characterization of the conformational properties of two FTDP-17 mutants of the four-repeat domain of tau, P301L and DeltaK280, and their properties for binding to polyanions and microtubules. Multidimensional NMR spectroscopy shows that the mutations do no lead to a significant increase in the level of beta-structure in their monomeric state, even though the mutations strongly promote beta-structure during aggregation. However, local structural changes are induced in the second repeat. These changes only weakly affect the binding to the polyanion heparin, which promotes paired helical filament formation. The extent of binding to microtubules, however, is strongly decreased. Our results demonstrate that the reversible binding of tau to microtubules involves specific interactions, which are not essential for binding to polyanions.