Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2

Molecular mechanism of the effect of ZnCl2 and MgCl2 solution on the conformation of the tau267-312 monomer

Alzheimer's disease is generally believed to be caused by abnormal aggregation of tau protein; however, there remains a lack of understanding about the aggregation process of tau protein in a solution environment. To explore the conformational properties of the tau protein monomer (tau267-312) in the presence of zinc and magnesium ions, we performed all-atom molecular dynamics simulations of tau267-312 in solutions of zinc chloride and magnesium chloride at different concentrations and compared these results with those obtained in pure water. The calculation results show that the β-sheet content increases significantly in the presence of zinc and magnesium ions, which causes a more compact structure for the tau protein monomers. Furthermore, it was found that stronger interactions between residues, as well as alterations in hydrophilic and hydrophobic interactions, are molecular mechanisms driving structural changes within the tau protein monomers. These findings suggest that zinc and magnesium ions facilitate a more stable conformation and promote the aggregation of tau protein monomers, which is important for understanding the aggregation and folding process of tau protein in the environment of saline solution.

Impact of Phosphorylation and O-GlcNAcylation on the Binding Affinity of R4 Tau Peptide to Microtubule and Its Conformational Preference upon Dissociation

Tau is a microtubule (MT)-associated protein that binds to and stabilizes the MTs of neurons. Due to its intrinsically disordered nature, it undergoes several post-translational modifications (PTMs) that are intricately linked to both the physiological and pathophysiological roles of Tau. Prior research has shown phosphorylation and O-GlcNAcylation to have contrasting effects on Tau aggregation; however, the precise molecular mechanisms and potential synergistic effects of these modifications remain elusive. In this article, we study the impact of phosphorylation at S352, and S356, as well as the phosphorylation of O-GlcNAcylation at S356, individually and in combination, on the binding of the R4 (336-367) peptide with MTs by performing classical molecular dynamics (MD) simulations. By analyzing the binding free energies of the Tau-MT complex, we found that both individual and combined phosphorylation at S352 and S356 sites decreased the affinity of the R4 peptide toward MT. Surprisingly, O-GlcNAcylation, a likely neuroprotective modification, at S356 also decreased the binding affinity of Tau to MT similar to the single phosphorylation systems (pS352 or pS356) but was observed to maintain major interactions with MT comparable to unmodified R4. Additionally, we investigated the impact of phosphorylation at both sites and the interplay between phosphorylation at S352 and O-GlcNAcylation at S356, which showed that the latter preserved the interactions and affinity of the Tau with MT better than dual phosphorylation, though still not as effectively as single phosphorylation. These findings suggest that O-GlcNAcylation at residue S356 has a moderate destabilizing effect. We also performed replica-exchange MD simulations of the R4 peptide to understand the changes in conformational preferences upon phosphorylation, O-GlcNAcylation, and a combination of both modifications. Both individual and combined phosphorylation of R4 peptide at S352, and S356, sites induced salt-bridge interactions with positively charged side chains of lysine and arginine amino acids. However, O-GlcNAcylation at S356 induced secondary structural changes on the R4 peptide, leading to the formation of a β-sheet structure, consistent with previous experimental observations. Interestingly, simultaneous phosphorylation at S352 and the phosphorylation of O-GlcNAcylation at S356 resulted in conformations promoting salt-bridges and β-sheets. Thus, our study provides atomistic insights into the impact of PTMs on the binding of Tau peptide to MT and its conformational preferences upon dissociation.

Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer

To propose new mechanism-based therapeutics for Alzheimer's disease (AD), it is crucial to study the kinetics and oligomerization/aggregation mechanisms of the hallmark tau proteins, which have various isoforms and are intrinsically disordered. In this study, multiple all-atom (AA) and coarse-grained (CG) force fields (FFs) have been benchmarked on molecular dynamics (MD) simulations of K18 tau (M243-E372), which is a truncated form (130 residues) of full-length tau (441 residues). FF19SB is first excluded because the dynamics are too slow, and the conformations are too stable. All other benchmarked AAFFs (Charmm36m, FF14SB, Gromos54A7, and OPLS-AA) and CGFFs (Martini3 and Sirah2.0) exhibit a trend of shrinking K18 tau into compact structures with the radius of gyration (ROG) around 2.0 nm, which is much smaller than the experimental value of 3.8 nm, within 200 ns of AA-MD or 2000 ns of CG-MD. Gromos54A7, OPLS-AA, and Martini3 shrink much faster than the other FFs. To perform meaningful postanalysis of various properties, we propose a strategy of selecting snapshots with 2.5 < ROG < 4.5 nm, instead of using all sampled snapshots. The calculated chemical shifts of all C, CA, and CB atoms have very good and close root-mean-square error (RMSE) values, while Charmm36m and Sirah2.0 exhibit better chemical shifts of N than other FFs. Comparing the calculated distributions of the distance between the CA atoms of CYS291 and CYS322 with the results of the FRET experiment demonstrates that Charmm36m is a perfect match with the experiment while other FFs exhibit limitations. In summary, Charmm36m is recommended as the best AAFF, and Sirah2.0 is recommended as an excellent CGFF for simulating tau K18.

Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation

RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of the CTD affects clustering are not entirely known. In this work, we studied the concentrated solutions of two heptapeptide repeat (2CTD) models at different phosphorylation patterns and protein and ion concentrations using all-atom molecular dynamics simulations to investigate clustering behavior and molecular interactions driving the cluster formation. Our results show that salt concentration and phosphorylation patterns play an important role in determining the clustering pattern, specifically at low protein concentrations. The balance between inter- and intrapeptide interactions and counterion coordination together impact the clustering behavior upon phosphorylation.

nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat

Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.

True or false? Alzheimer's disease is type 3 diabetes: Evidences from bench to bedside

Globally, Alzheimer's disease (AD) is the most widespread chronic neurodegenerative disorder, leading to cognitive impairment, such as aphasia and agnosia, as well as mental symptoms, like behavioral abnormalities, that place a heavy psychological and financial burden on the families of the afflicted. Unfortunately, no particular medications exist to treat AD, as the current treatments only impede its progression.The link between AD and type 2 diabetes (T2D) has been increasingly revealed by research; the danger of developing both AD and T2D rises exponentially with age, with T2D being especially prone to AD. This has propelled researchers to investigate the mechanism(s) underlying this connection. A critical review of the relationship between insulin resistance, Aβ, oxidative stress, mitochondrial hypothesis, abnormal phosphorylation of Tau protein, inflammatory response, high blood glucose levels, neurotransmitters and signaling pathways, vascular issues in AD and diabetes, and the similarities between the two diseases, is presented in this review. Grasping the essential mechanisms behind this detrimental interaction may offer chances to devise successful therapeutic strategies.

Advanced computational approaches to understand protein aggregation

Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.

Ginkgo biloba and Its Chemical Components in the Management of Alzheimer's Disease

The pathogenesis of Alzheimer's disease (AD), a degenerative disease of the central nervous system, remains unclear. The main manifestations of AD include cognitive and behavioral disorders, neuropsychiatric symptoms, neuroinflammation, amyloid plaques, and neurofibrillary tangles. However, current drugs for AD once the dementia stage has been reached only treat symptoms and do not delay progression, and the research and development of targeted drugs for AD have reached a bottleneck. Thus, other treatment options are needed. Bioactive ingredients derived from plants are promising therapeutic agents. Specifically, Ginkgo biloba (Gb) extracts exert anti-oxidant, anticancer, neuroplastic, neurotransmitter-modulating, blood fluidity, and anti-inflammatory effects, offering alternative options in the treatment of cardiovascular, metabolic, and neurodegenerative diseases. The main chemical components of Gb include flavonoids, terpene lactones, proanthocyanidins, organic acids, polysaccharides, and amino acids. Gb and its extracts have shown remarkable therapeutic effects on various neurodegenerative diseases, including AD, with few adverse reactions. Thus, high-quality Gb extracts are a well-established treatment option for AD. In this review, we summarize the insights derived from traditional Chinese medicine, experimental models, and emerging clinical trials on the role of Gb and its chemical components in the treatment of the main clinical manifestations of AD.

Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats

Aggregation of tau protein into intracellular fibrillary inclusions is characterized as the hallmark of tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. The microtubule-binding (MTB) domain of tau, containing either three or four repeats with sequence similarities, plays an important role in determining tau's aggregation. Previous studies have reported that abnormal acetylation of lysine residues displays a distinct effect on the formation of pathological tau aggregates. However, the underlying molecular mechanism remains mostly elusive. In this study, we performed extensive replica exchange molecular dynamics (REMD) simulations of 144 μs in total to systematically investigate the dimerization of four tau MTB repeats and explore the impacts of Lys280 (K280) or Lys321 (K321) acetylation on the conformational ensembles of the R2 or R3 dimer. Our results show that R3 is the most prone to aggregation among the four repeats, followed by R2 and R4, while R1 displays the weakest aggregation propensity with a disordered structure. Acetylation of K280 could promote the aggregation of R2 peptides by increasing the formation of β-sheet structures and strengthening the interchain interaction. However, K321 acetylation decreases the β-sheet content of the R3 dimer, reduces the ability of R3 peptides to form long β-strands, and promotes the stable helix structure formation. The salt bridge and Y310-Y310 π-π stacking interactions of the R3 dimer are greatly weakened by K321 acetylation, resulting in the inhibition of dimerization. This study uncovers the structural ensembles of tau MTB repeats and provides mechanistic insights into the influences of acetylation on tau aggregation, which may deepen the understanding of the pathogenesis of tauopathies.

Evaluating p-tau217 and p-tau231 as Biomarkers for Early Diagnosis and Differentiation of Alzheimer's Disease: A Narrative Review

The escalating prevalence of Alzheimer's disease (AD) highlights the urgent need to develop reliable biomarkers for early diagnosis and intervention. AD is characterized by the pathological accumulation of amyloid-beta plaques and tau neurofibrillary tangles. Phosphorylated tau (p-tau) proteins, particularly p-tau217 and p-tau231, have been identified as promising biomarker candidates to differentiate the disease progression from preclinical stages. This narrative review is devoted to a critical evaluation of the diagnostic accuracy, sensitivity, and specificity of p-tau217 and p-tau231 levels in the detection of AD, measured in plasma, serum, and cerebrospinal fluid, compared to established biomarkers. Additionally, the efficacy of these markers in distinguishing AD from other neurodegenerative disorders is examined. The significant advances offered by p-tau217 and p-tau231 in AD diagnostics are highlighted, demonstrating their unique utility in early detection and differential diagnosis. This comprehensive analysis not only confirms the excellent diagnostic capabilities of these markers, but also deepens the understanding of the molecular dynamics of AD, contributing to the broader scientific discourse on neurodegenerative diseases. This review is aimed to provide key information for researchers and clinicians across disciplines, filling interdisciplinary gaps and highlighting the role of p-tau proteins in revolutionizing AD research and clinical practice.

Current and future therapeutic strategies for Alzheimer's disease: an overview of drug development bottlenecks

Alzheimer's disease (AD) is the most common chronic neurodegenerative disease worldwide. It causes cognitive dysfunction, such as aphasia and agnosia, and mental symptoms, such as behavioral abnormalities; all of which place a significant psychological and economic burden on the patients' families. No specific drugs are currently available for the treatment of AD, and the current drugs for AD only delay disease onset and progression. The pathophysiological basis of AD involves abnormal deposition of beta-amyloid protein (Aβ), abnormal tau protein phosphorylation, decreased activity of acetylcholine content, glutamate toxicity, autophagy, inflammatory reactions, mitochondria-targeting, and multi-targets. The US Food and Drug Administration (FDA) has approved five drugs for clinical use: tacrine, donepezil, carbalatine, galantamine, memantine, and lecanemab. We have focused on the newer drugs that have undergone clinical trials, most of which have not been successful as a result of excessive clinical side effects or poor efficacy. Although aducanumab received rapid approval from the FDA on 7 June 2021, its long-term safety and tolerability require further monitoring and confirmation. In this literature review, we aimed to explore the possible pathophysiological mechanisms underlying the occurrence and development of AD. We focused on anti-Aβ and anti-tau drugs, mitochondria-targeting and multi-targets, commercially available drugs, bottlenecks encountered in drug development, and the possible targets and therapeutic strategies for future drug development. We hope to present new concepts and methods for future drug therapies for AD.

Dissecting how ALS-associated D290V mutation enhances pathogenic aggregation of hnRNPA2286-291 peptides: Dynamics and conformational ensembles

The aggregation of RNA binding proteins, including hnRNPA1/2, TDP-43 and FUS, is heavily implicated in causing or increasing disease risk for a series of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). A recent experimental study demonstrated that an ALS-related D290V mutation in the low complexity domain (LCD) of hnRNPA2 can enhance the aggregation propensity of wild type (WT) hnRNPA2_286-291 peptide. However, the underlying molecular mechanisms remain elusive. Herein, we investigated effects of D290V mutation on aggregation dynamics of hnRNPA2_286-291 peptide and the conformational ensemble of hnRNPA2_286-291 oligomers by performing all-atom molecular dynamic and replica-exchange molecular dynamic simulations. Our simulations demonstrate that D290V mutation greatly reduces the dynamics of hnRNPA2_286-291 peptide and that D290V oligomers possess higher compactness and β-sheet content than WT, indicative of mutation-enhanced aggregation capability. Specifically, D290V mutation strengthens inter-peptide hydrophobic, main-chain hydrogen bonding and side-chain aromatic stacking interactions. Those interactions collectively lead to the enhancement of aggregation capability of hnRNPA2_286-291 peptides. Overall, our study provides insights into the dynamics and thermodynamic mechanisms underlying D290V-induced disease-causing aggregation of hnRNPA2_286-291, which could contribute to better understanding of the transitions from reversible condensates to irreversible pathogenic aggregates of hnRNPA2 LCD in ALS-related diseases.