Aggregation Pathway Research Articles

Fluid flow and amyloid transport and aggregation in the Brain Interstitial Space

Abstract The driving mechanisms at the base of the clearance of biological wastes in the Brain Interstitial Space are still poorly understood and an actively debated subject. A complete comprehension of the processes that lead to the aggregation of amyloid proteins in such environment, hallmark of the onset and progression of Alzheimer's disease, is of crucial relevance. Here we employ combined computational fluid dynamics and molecular dynamics techniques to uncover the role of fluid flow and proteins transport in the Brain Interstitial Space. Our work identifies diffusion as the principal mechanism for amyloid-β proteins clearance, whereas fluid advection may lead transport for larger molecular bodies, like amyloid-β aggregates or extracellular vesicles. We also clearly quantify the impact of large nascent prefibrils on the fluid flowing and shearing. Finally, we show that, even in the irregular Brain Interstitial Space, hydrodynamic interactions enhance amyloid-β aggregation at all stages of the aggregation pathway. Our results are key to understand the role of fluid flow and solvent-solute interplay on therapeutics like antibodies acting in the Brain Interstitial Space.

Drug-herb Synergistic Interactions between Clopidogrel and Natural Medicine.

Natural medicine (NM) has been used since ancient times for therapeutic purposes worldwide. Presently, the combination of clopidogrel and NM with a reasonable synergistic effect has gained increasing acceptance in clinical therapeutics. Here, we have performed a comprehensive retrieval of literature published in both English and Chinese databases until August 1, 2022, studying the synergistic interactions of clopidogrel and NM through pharmacokinetic/pharmacodynamic (PK-PD) analyses. We retrieved 7, 3, and 5 studies on PK analysis and 3, 3, and 8 studies on PD analysis for the interaction of clopidogrel with single herbal medicines, bioactive compounds, and herbal prescriptions, respectively. Most studies on NM have been found to mainly focus on preclinical observations, and there have been fewer clinical PK analyses. A potential drug-herb interaction has been observed to occur when clopidogrel and NM were metabolized by an enzyme network comprising P-gp, CES1, and CYP450. In contrast, most PD studies have focused on clinical observations, and few preclinical findings have been reported. Some cases have suggested that the combination of the two types of drugs would alter the antiplatelet efficacy and adverse effects. Studies on PK, however, have shown significant or slightly varying results for the drug prototype and its metabolites. In the combination therapies, the interaction between clopidogrel and NM was found to alter antiplatelet aggregation pathways and P2Y12 receptor function.

Synergistic Multi-Pronged Interactions Mediate the Effective Inhibition of Alpha-Synuclein Aggregation by the Chaperone HtrA1.

PD and other synucleinopathies are marked by misfolding and aggregation of α-Syn, forming higher-order species that propagate aggregation in a prion-like manner. Understanding how chaperone proteins inhibit α-Syn aggregation and spread is essential for therapeutic development against neurodegeneration. Through an integrative approach of solution-based NMR, AFM, aggregation kinetics, and computational analysis, we reveal how a catalytically inactive variant of the chaperone HtrA1 effectively disrupts aggregation pathways. We find that the inactive Protease and PDZ domains of HtrA1 synergistically bind to key intrinsically disordered sites on both α-Syn monomers and fibrils, thereby effectively inhibiting both aggregation and templated seeding. Our work provides a natural and unique blueprint for designing inhibitors to prevent the formation and seeding of aggregates in neurodegenerative diseases.

The Impact of Soil Dry–Wet Cycles on the Mineralization of Soil Organic Carbon and Total Nitrogen in Check Dams of the Loess Plateau

Frequent soil drying and wetting cycles significantly affect the mineralization processes of soil organic carbon (SOC) and total nitrogen (STN), impacting soil quality and contributing to nutrient loss. However, the effects of these dry–wet cycles on SOC and STN mineralization in dam soil are not well understood. This study simulated four consecutive wet–dry cycles under five soil moisture gradients of 0% (CK), 5%, 10%, 15%, and 100%, and 100%, across four cycles of 7, 14, 21, and 28 days, to investigate the effects on soil aggregates, enzyme activities, and the mineralization of SOC and STN. The results indicated that soil enzyme activity peaked after two dry–wet cycles and then began to decline. The dry–wet cycles reduced the proportion of soil macro-aggregates while also decreasing the proportions of small and micro-aggregates. In contrast, the 100% treatment conditions exhibited the opposite effect. Dry–wet cycles enhanced the mineralization rates of SOC and STN, with the average mineralization rates under the 10% soil moisture content being the highest—1.78 and 2.38 times greater than the CK treatment for SOC and STN, respectively. The impact of dry–wet cycles on SOC and STN mineralization through the enzyme pathway was greater than through the aggregate pathway. These research findings provide theoretical insights and scientific references for the efficient operation and ecological protection of sedimentation dams in the Loess Plateau.

TMET-31. OXIDATIVE STRESS INDUCED PROTEIN AGGREGATION VIA GGCT PRODUCED PYROGLUTAMIC ACID IN DRUG RESISTANT GLIOBLASTOMA

Abstract Drug resistance is a major barrier to cancer therapies and remains poorly understood. Recently, non-mutational mechanisms of drug resistance have been proposed where a more plastic metabolic response can play a major role. Here, we show that upon drug resistance, glioblastoma (GBM) cells have increased oxidative stress, mitochondria function, and protein aggregation. Gamma (y)-glutamylcyclotranserase (GGCT), an enzyme in the y-glutamyl cycle for glutathione production, located on chromosome 7 which is commonly amplified in GBM is also increased upon resistance. We further observe that the byproduct of GGCT – pyroglutamic acid – can bind aggregating proteins and that genetic and pharmacological inhibition of GGCT prevents protein aggregation. Finally, we found increased protein aggregation, GGCT expression, and pyroglutamic acid staining in recurrent GBM patient samples, as well as adjacent normal brain. These findings suggest a new pathway for protein aggregation within drug resistant brain cancer that should be further studied in other brain disorders.

Aggregation Dynamics of a 150 kDa Aβ42 Oligomer: Insights from Cryo Electron Microscopy and Multimodal Analysis

Protein misfolding is a widespread phenomenon that can result in the formation of protein aggregates, which are markers of various disease states, including Alzheimer's disease (AD). In AD, amyloid beta (Aβ) peptides are key players in the disease's progression, particularly the 40- and 42 residue variants, Aβ40 and Aβ42. These peptides aggregate to form amyloid plaques and contribute to neuronal toxicity. Recent research has shifted attention from solely Aβ fibrils to also include Aβ protofibrils and oligomers as potentially critical pathogenic agents. Particularly, oligomers demonstrate more significant toxicity compared to other Aβ specie. Hence, there is an increased interest in studying the correlation between toxicity and their structure and aggregation pathway. The present study investigates the aggregation of a 150kDa Aβ42 oligomer that does not lead to fibril formation. Using negative stain transmission electron microscopy (TEM), size exclusion chromatography (SEC), dynamic light scattering (DLS), and cryo-electron microscopy (cryo-EM), we demonstrate that 150kDa Aβ42 oligomers form higher-order string-like assemblies over time. These strings are unique from the classical Aβ fibrils. The significance of our work lies in elucidating molecular behavior of a novel non-fibrillar form of Aβ42 aggregate.

Evaluation of Anti-Alzheimer's Potential of Azo-Stilbene-Thioflavin-T derived Multifunctional Molecules: Synthesis, Metal and Aβ Species Binding and Cholinesterase Activity.

Inhibition of amyloid β (Aβ) aggregation and cholinesterase activity are two major therapeutic targets for Alzheimer's disease (AD). Multifunctional Molecules (MFMs) specifically designed to address other contributing factors, such as metal ion induced abnormalities, oxidative stress, toxic Ab aggregates etc. are very much required. Several multifunctional molecules have been developed using different molecular scaffolds. Reported herein is a new series of four MFMs based on ThT, Azo-stilbene and metal ion chelating pockets. The synthesis, characterization, and metal chelation ability for [Cu(II) and Zn(II)] are presented herein. Furthermore, we explored their multifunctionality w.r.t. to their (i) recognition of Aβ aggregates and monomeric form, (ii) utility in modulating the aggregation pathways of both metal-free and metal-bound amyloid-β, (iii) ex-vivo staining of amyloid plaques in 5xFAD mice brain sections, (iv) ability to scavenge free radicals and (v) ability to inhibit cholinesterase activity. Molecular docking studies were also performed with Aβ peptides and acetylcholinesterase enzyme to understand the observed inhibitory effect on activity. Overall, the studies presented here establish the multifunctional nature of these molecules and qualify them as promising candidates for furthermore investigation in the quest for finding Alzheimer's disease treatment.

Effect of the aggregation state of amyloid-beta (25-35) on the brain oxidative stress in vivo

Aggregation pathway of amyloid-β (25-35) in water affects the oxidative stress in the brain observed after administration of aggregated peptide in animals in vivo. Our studies on peptide aggregation ex situ prior to injection suggest that from the onset of peptide incubation in aqueous media, all samples exhibit the formation of fibril-like aggregates, characterized by a significant amount of β-sheets. This induces significant oxidative stress in vivo as observed for up to 60 min of peptide aggregation time. As the aggregation advances, the fibril-like aggregates become longer and intertwined, while the amount of β-sheets does not change significantly. An injection of such large, thick, and entangled aggregates in the animal brain results in a drastic increase in oxidative stress. This may be related to the number of activated microglia that initiate a sequence of inflammatory responses in the presence of large, highly interconnected fibrils.

High-Throughput Single-Particle Characterization of Aggregation Pathways and the Effects of Inhibitors for Large (Megadalton) Protein Oligomers.

Protein aggregation is involved in many human diseases, but characterizing the sizes and shapes of intermediate oligomers (∼10-100 nm) that are important to the formation of macroscale aggregates like amyloid fibrils is a significant analytical challenge. Here, charge detection mass spectrometry (CDMS) is used to characterize individual conformational states of bovine serum albumin oligomers with up to ∼225 molecules (15 MDa). Elongated, partially folded, and globular conformational families for each oligomer can be readily distinguished based on the extent of charging. The abundances of individual conformers vary with changes in the monomer concentration or by adding aggregation inhibitors, such as SDS, heparin, or MgCl2. These results show the potential of CDMS for investigating intermediate oligomers in protein aggregation processes that are important for understanding aggregate formation and inhibition mechanisms and could accelerate formulation buffer development to prevent the aggregation of biotherapeutics.

Unfolding Mechanism and Fibril Formation Propensity of Human Prion Protein in the Presence of Molecular Crowding Agents.

The pathological process of prion diseases implicates that the normal physiological cellular prion protein (PrPC) converts into misfolded abnormal scrapie prion (PrPSc) through post-translational modifications that increase β-sheet conformation. We recently demonstrated that HuPrP(90-231) thermal unfolding is partially irreversible and characterized by an intermediate state (β-PrPI), which has been revealed to be involved in the initial stages of PrPC fibrillation, with a seeding activity comparable to that of human infectious prions. In this study, we report the thermal unfolding characterization, in cell-mimicking conditions, of the truncated (HuPrP(90-231)) and full-length (HuPrP(23-231)) human prion protein by means of CD and NMR spectroscopy, revealing that HuPrP(90-231) thermal unfolding is characterized by two successive transitions, as in buffer solution. The amyloidogenic propensity of HuPrP(90-231) under crowded conditions has also been investigated. Our findings show that although the prion intermediate, structurally very similar to β-PrPI, forms at a lower temperature compared to when it is dissolved in buffer solution, in cell-mimicking conditions, the formation of prion fibrils requires a longer incubation time, outlining how molecular crowding influences both the equilibrium states of PrP and its kinetic pathways of folding and aggregation.

Membrane-assisted Aβ40 aggregation pathways.

Alzheimer's disease (AD) is caused by the assembly of amyloid-beta (Aβ) peptides into oligomers and fibrils. Endogenous Aβ aggregation may be assisted by cell membranes, which can accelerate the nucleation step enormously, but knowledge of membrane-assisted aggregation is still very limited. Here we used extensive MD simulations to structurally and energetically characterize key intermediates along the membrane-assisted aggregation pathways of Aβ40. Reinforcing experimental observations, the simulations reveal unique roles of GM1 ganglioside and cholesterol in stabilizing membrane-embedded β-sheets and of Y10 and K28 in the ordered release of a small oligomeric seed into solution. The same seed leads to either an open-shaped or R-shaped fibril, with significant stabilization provided by inter- or intra-subunit interfaces between a straight β-sheet (residues Q15-D23) and a bent β-sheet (residues A30-V36). This work presents the first comprehensive picture of membrane-assisted aggregation of Aβ40, with broad implications for developing AD therapies and rationalizing disease-specific polymorphisms of amyloidogenic proteins.

A Peptide Strategy for Inhibiting Different Protein Aggregation Pathways.

Protein aggregation correlates with many human diseases. Protein aggregates differ in structure and shape. Strategies to develop effective aggregation inhibitors that reach the clinic failed so far. Here, we developed a family of peptides targeting early aggregation stages for both amorphous and fibrillar aggregates of proteins unrelated in sequence and structure. They act on dynamic precursors before mechanistic differentiation takes place. Using peptide arrays, we first identified peptides inhibiting the amorphous aggregation of a molten globular, aggregation-prone mutant of the Axin tumor suppressor. Optimization revealed that the peptides activity did not depend on their sequences but rather on their molecular determinants: a composition of 20-30 % flexible, 30-40 % aliphatic and 20-30 % aromatic residues, a hydrophobicity/hydrophilicity ratio close to 1, and an even distribution of residues of different nature throughout the sequence. The peptides also suppressed fibrillation of Tau, a disordered protein that forms amyloids in Alzheimer's disease, and slowed down that of Huntingtin Exon1, an amyloidogenic protein in Huntington's disease, both entirely unrelated to Axin. Our compounds thus target early stages of different aggregation mechanisms, inhibiting both amorphous and amyloid aggregation. Such cross-mechanistic, multi-targeting aggregation inhibitors may be lead compounds for developing drug candidates against various protein aggregation diseases.

Abstract P452: Cell Populations and Transcriptomes Differ Across Blood Pressure and Sex in Perivascular Adipose Tissue: A Single-Nuclei RNA Sequencing Study

The perivascular adipose tissue (PVAT), fat that surrounds many blood vessels, is capable of modulating vascular tone through multiple modalities. Despite increasing research interest, PVAT remains less understood compared to other vascular layers. We hypothesized that the transcriptome and cell population of thoracic aorta PVAT (taPVAT) differ between hypertensive and normotensive rats. To test this hypothesis, we performed single-nucleus RNA-sequencing (snRNA-seq) on twenty-five taPVAT samples from male and female Dahl SS rats, fed either control (Con) chow or a high-fat diet (HFD) for 8 or 24 weeks. Mean arterial pressure (MAP) measurements showed elevated values in female rats fed a HFD for 24 weeks with a trend towards increasing blood pressure in male rats (Fig. 1a). Our analysis included at least three taPVAT samples per treatment group, resulting in 71,813 high-quality sequenced nuclei, representing eight major cell types (Fig. 1b) and twenty-eight cell sub-types. Within each cell type, the differences in population and gene expression across diet, diet duration, and sex were examined. The most substantial population proportion differences were observed across diet duration, with fewer differences noted across diet and sex (Fig. 1c). The total number of differentially expressed genes (DEGs) (adjusted p-value ≤ 0.05, |log 2 (fold change)| ≥ 1) across diet, diet duration, and sex were 191, 424, and 119, respectively. Interestingly, in the taPVAT from HFD fed rats, the gene Csmd1 (CUB and Sushi multiple domains 1) was consistently upregulated across nearly all cell types. Whereas Scd (stearoyl-CoA desaturase), which is involved in fatty acid biosynthesis, was frequently the most downregulated gene. Pathway enrichment analysis revealed that the DEGs related to the HFD were associated with a decrease in lipid and fatty acid biosynthetic processes. DEGs related to rats fed a HFD for twenty-four weeks versus eight weeks were linked to an enrichment in inflammatory response and extracellular matrix organization pathways, and in HFD fed male rats compared to females, there was enrichment for leukocyte aggregation and peptidyl-cysteine modification pathways. In conclusion, our findings help paint a more detailed picture of the molecular and cellular changes in taPVAT associated with hypertension.

Unraveling the Structure and Dynamics of Ac-PHF6-NH2 Tau Segment Oligomers.

The aggregation of the proteins tau and amyloid-β is a salient feature of Alzheimer's disease, the most common form of neurodegenerative disorders. Upon aggregation, proteins transition from their soluble, monomeric, and functional state into insoluble, fibrillar deposits through a complex process involving a variety of intermediate species of different morphologies, including monomers, toxic oligomers, and insoluble fibrils. To control and direct peptide aggregation, a complete characterization of all species present and an understanding of the molecular processes along the aggregation pathway are essential. However, this is extremely challenging due to the transient nature of oligomers and the complexity of the reaction networks. Therefore, we have employed a combined approach that allows us to probe the structure and kinetics of oligomeric species, following them over time as they form fibrillar structures. Targeting the tau protein peptide segment Ac-PHF6-NH2, which is crucial for the aggregation of the full protein, soft nano-electrospray ionization combined with ion mobility mass spectrometry has been employed to study the kinetics of heparin-induced intact oligomer formation. The oligomers are identified and characterized using high-resolution ion mobility mass spectrometry, demonstrating that the addition of heparin does not alter the structure of the oligomeric species. The kinetics of fibril formation is monitored through a Thioflavin T fluorescence assay. Global fitting of the kinetic data indicates that secondary nucleation plays a key role in the aggregation of the Ac-PHF6-NH2 tau segment, while the primary nucleation rate is greatly accelerated by heparin.

TAGLN2 induces resistance signature ISGs by activating AKT-YBX1 signal with dual pathways and mediates the IFN-related DNA damage resistance in gastric cancer

Recently, various cancer types have been identified to express a distinct subset of Interferon-stimulated genes (ISGs) that mediate therapy resistance. The mechanism through which cancer cells maintain prolonged Interferon stimulation effects to coordinate resistance remains unclear. Our research demonstrated that aberrant upregulation of TAGLN2 is associated with gastric cancer progression, and inhibiting its expression renders gastric cancer cells more susceptible to chemotherapy and radiation. We uncovered a novel role for TAGLN2 in the upregulation of resistance signature ISGs by enhancing YBX1-associated ssDNA aggregation and cGAS-STING pathway activation. TAGLN2 modulates YBX1 by recruiting c-Myc and SOX9 to YBX1 promoter region and directly interacting with AKT-YBX1, thereby enhancing YBX1 phosphorylation and nuclear translocation. Significantly, targeted downregulation of key proteins, inhibition of the TAGLN2-YBX1-AKT interaction (using Fisetin or MK2206) or disruption of the cGAS-STING pathway substantially reduced ssDNA accumulation, subsequent ISGs upregulation, and therapy resistance. The combination of Cisplatin with MK2206 displayed a synergistic effect in the higher TAGLN2-expressing xenograft tumors. Clinical analysis indicated that a derived nine-gene set effectively predicts therapeutic sensitivity and long-term prognosis in gastric cancer patients. These findings suggest that TAGLN2, YBX1 and induced ISGs are novel predictive markers for clinical outcomes, and targeting this axis is an attractive therapeutic sensitization strategy.

The role of biomolecular condensates in protein aggregation.

There is an increasing amount of evidence that biomolecular condensates are linked to neurodegenerative diseases associated with protein aggregation, such as Alzheimer's disease and amyotrophic lateral sclerosis, although the mechanisms underlying this link remain elusive. In this Review, we summarize the possible connections between condensates and protein aggregation. We consider both liquid-to-solid transitions of phase-separated proteins and the partitioning of proteins into host condensates. We distinguish five key factors by which the physical and chemical environment of a condensate can influence protein aggregation, and we discuss their relevance in studies of protein aggregation in the presence of biomolecular condensates: increasing the local concentration of proteins, providing a distinct chemical microenvironment, introducing an interface wherein proteins can localize, changing the energy landscape of aggregation pathways, and the presence of chaperones in condensates. Analysing the role of biomolecular condensates in protein aggregation may be essential for a full understanding of amyloid formation and offers a new perspective that can help in developing new therapeutic strategies for the prevention and treatment of neurodegenerative diseases.

Key charged residues influence the amyloidogenic propensity of the helix-1 region of serum amyloid A

Increased plasma levels of serum amyloid A (SAA), an acute-phase protein that is secreted in response to inflammation, may lead to the accumulation of amyloid in various organs thereby obstructing their functions. Severe cases can lead to a systemic disorder called AA amyloidosis. Previous studies suggest that the N-terminal helix is the most amyloidogenic region of SAA. Moreover, computational studies implicated a significant role for Arg-1 and the residue-specific interactions formed during the fibrillization process. With a focus on the N-terminal region of helix-1, SAA1–13, mutational analysis was employed to interrogate the roles of the amino acid residues, Arg-1, Ser-5, Glu-9, and Asp-12. The truncated SAA1–13 fragment was systematically modified by substituting the key residues with alanine or uncharged but structurally similar amino acids. We monitored the changes in the amyloidogenic propensities, associated conformational markers, and morphology of the amyloids resulting from the mutation of SAA1–13. Mutating out Arg-1 resulted in much reduced aggregation propensity and a lack of detectable β-structures alluding to the importance of salt-bridge interactions involving Arg-1. Our data revealed that by systematically mutating the key amino acid residues, we can modulate the amyloidogenic propensity and alter the time-dependent conformational variation of the peptide. When the behaviors of each mutant peptide were analyzed, they provided evidence consistent with the aggregation pathway predicted by MD simulation studies. Here, we detail the important temporal molecular interactions formed by Arg-1 with Ser-5, Glu-9, and Asp-12 and discuss its mechanistic implications on the self-assembly of the helix-1 region of SAA.

Aggregation Dynamics of a 150 kDa Aβ42 Oligomer: Insights from Cryo Electron Microscopy and Multimodal Analysis.

Protein misfolding is a widespread phenomenon that can result in the formation of protein aggregates, which are markers of various disease states, including Alzheimer's disease (AD). In AD, amyloid beta (Aβ) peptides, particularly Aβ40 and Aβ42, are key players in the disease's progression, as they aggregate to form amyloid plaques and contribute to neuronal toxicity. Recent research has shifted attention from solely Aβ fibrils to also include Aβ protofibrils and oligomers as potentially critical pathogenic agents. Particularly, oligomers demonstrate greater toxicity compared to other Aβ specie. Hence, there is an increased interest in studying the correlation between toxicity and their structure and aggregation pathway. The present study investigates the aggregation of a 150 kDa Aβ42 oligomer that does not lead to fibril formation over time. Using negative stain transmission electron microscopy (TEM), size exclusion chromatography (SEC), dynamic light scattering (DLS), and cryo-electron microscopy (cryo-EM), we demonstrate that 150 kDa Aβ42 oligomers form higher-order string-like assemblies over time. The strings are unique from the classical Aβ fibril structures. The significance of our work lies in elucidating molecular behavior of a novel non-fibrillar form of Aβ42 aggregate.

Allosteric Activation of SIRT1 by 2,4-Dihydroxy-azaflavanone Averts MPP+-Mediated Dysfunction in Mitochondrial Biogenesis and Bioenergetics: Implications for Parkinson's Disease.

Parkinson's disease (PD) is a complex neurodegenerative disorder that affects dopamine neurons of the substantia nigra pars compacta (SNpc), resulting in motor dysfunction. Among the pathways examined, mitochondria and α-synuclein were found to play a major role in the disease progression. Hence, several attempts are being made to restore mitochondrial bioenergetics or protein aggregation pathways as disease-modifying strategies. Our earlier studies reported the protective effect of 2,4-dihydroxy-azaflavanone (azaflavanone) in a transgenic Drosophila fly model of PD. In the present study, we found that azaflavanone acts as an allosteric activator of SIRT1 in both cell-free and cell-based systems and the effects were more pronounced as compared to resveratrol. Also, azaflavanone appears to interact selectively with SIRT1 as other SIRTs such as SIRT3 and SIRT6 did not exhibit any gross changes in cellular thermal shift assay (CETSA). Molecular docking studies depicted a higher docking score with azaflavanone than with resveratrol. Further, N27 cells treated with azaflavanone exhibited a dose-dependent increase in the mitotracker staining, mtDNA/nuclear DNA ratio, and also mitochondrial bioenergetics. The observed effects appear to be due to the activation of SIRT1, as evidenced by an increase in the expression of PGC-1α and TFAM, which are the downstream targets of SIRT1. Lastly, the Parkinsonian mimic MPP+-induced disturbance in the mitochondrial membrane potential, mitochondrial bioenergetics, and biogenesis were ameliorated by azaflavanone. Overall, our findings indicate that azaflavanone, being an antioxidant and an allosteric activator of SIRT1, is a promising compound for ameliorating the pathophysiology of PD.

Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study.

α-Synuclein (α-syn) is a 140 amino acid intrinsically disordered protein (IDP) and the primary component of cytotoxic oligomers implicated in the etiology of Parkinson's disease (PD). While IDPs lack a stable three-dimensional structure, they sample a heterogeneous ensemble of conformations that can, in principle, be assessed through molecular dynamics simulations. However, describing the structure and aggregation of large IDPs is challenging due to force field (FF) accuracy and sampling limitations. To cope with the latter, coarse-grained (CG) FFs emerge as a potential alternative at the expense of atomic detail loss. Whereas CG models can accurately describe the structure of the monomer, less is known about aggregation. The latter is key for assessing aggregation pathways and designing aggregation inhibitor drugs. Herein, we investigate the structure and dynamics of α-syn using different resolution CG (Martini3 and Sirah2) and all-atom (Amber99sb and Charmm36m) FFs to gain insight into the differences and resemblances between these models. The dependence of the magnitude of protein-water interactions and the putative need for enhanced sampling (replica exchange) methods in CG simulations are analyzed to distinguish between force field accuracy and sampling limitations. The stability of the CG models of an α-syn fibril was also investigated. Additionally, α-syn aggregation was studied through umbrella sampling for the CG models and CG/all-atom models for an 11-mer peptide (NACore) from an amyloidogenic domain of α-syn. Our results show that despite the α-syn structures of Martini3 and Sirah2 with enhanced protein-water interactions being similar, major differences exist concerning aggregation. The Martini3 fibril is not stable, and the binding free energy of α-syn and NACore is positive, opposite to Sirah2. Sirah2 peptides in a zwitterionic form, in turn, display termini interactions that are too strong, resulting in end-to-end orientation. Sirah2, with enhanced protein-water interactions and neutral termini, provides, however, a peptide aggregation free energy profile similar to that found with all-atom models. Overall, we find that Sirah2 with enhanced protein-water interactions is suitable for studying protein-protein and protein-drug aggregation.