Computational insights into the cross-talk between medin and Aß: implications for age-related vascular risk factors in Alzheimer's disease.

The aggregation of medin forming aortic medial amyloid is linked to arterial wall degeneration and cerebrovascular dysfunction. Elevated levels of arteriolar medin are correlated with an increased presence of vascular amyloid-ß (Aß) aggregates, a hallmark of Alzheimer's disease (AD) and vascular dementia. The cross-interaction between medin and Aß results in the formation of heterologous fibrils through co-aggregation and cross-seeding processes both in vitro and in vivo. However, a comprehensive molecular understanding of the cross-interaction between medin and Aß-two intrinsically disordered proteins-is critically lacking. Here, we employed atomistic discrete molecular dynamics simulations to systematically investigate the self-association, co-aggregation and also the phenomenon of cross-seeding between these two proteins. Our results demonstrated that both Aß and medin were aggregation prone and their mixture tended to form ß-sheet-rich hetero-aggregates. The formation of Aß-medin hetero-aggregates did not hinder Aß and medin from recruiting additional Aß and medin peptides to grow into larger ß-sheet-rich aggregates. The ß-barrel oligomer intermediates observed in the self-aggregations of Aß and medin were also present during their co-aggregation. In cross-seeding simulations, preformed Aß fibrils could recruit isolated medin monomers to form elongated ß-sheets. Overall, our comprehensive simulations suggested that the cross-interaction between Aß and medin may contribute to their pathological aggregation, given the inherent amyloidogenic tendencies of both medin and Aß. Targeting medin, therefore, could offer a novel therapeutic approach to preserving brain function during aging and AD by improving vascular health.

An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity.

Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible control over their activity for various biotechnological applications. Here, we apply a rational, computation-guided methodology to design and test a transferase-class enzyme allosterically regulated by light-oxygen-voltage 2 sensing domain. We utilize computational techniques to determine the intrinsic allosteric networks within N-acyltransferase (Orf11/∗Dbv8) and identify potential allosteric sites on the protein's surface. We insert light-oxygen-voltage 2 sensing domain at the predicted allosteric site, exerting reversible control over enzymatic activity. We demonstrate blue-light regulation of N-acyltransferase (Orf11/∗Dbv8) function. Our study for the first time demonstrates optogenetic regulation of a transferase-class enzyme as a proof-of-concept for controllable transferase design. This successful design opens the door for many future applications in metabolic engineering and cellular programming.

Probing the polyphenolic flavonoid, morin as a highly efficacious inhibitor against amyloid(A4V) mutant SOD1 in fatal amyotrophic lateral sclerosis.

Deposition of misfolded protein aggregates in key areas of human brain is the quintessential trait of various pertinent neurodegenerative disorders including amyotrophic lateral sclerosis (ALS). Genetic point mutations in Cu/Zn superoxide dismutase (SOD1) are found to be the most important contributing factor behind familial ALS. Especially, single nucleotide polymorphism (SNP) A4V is the most nocuous since it substantially decreases life expectancy of patients. Besides, the use of naturally occurring polyphenolic flavonoids is profoundly being advocated for palliating amyloidogenic behavior of proteopathic proteins. In the present analysis, through proficient computational tools, we have attempted to ascertain a pharmacodynamically promising flavonoid compound that effectively curbs the pathogenic behavior of A4V SOD1 mutant. Initial screening of flavonoids that exhibit potency against amyloids identified morin, myricetin and epigallocatechin gallate as promising leads. Further, with the help of feasible and yet adept protein-ligand interaction studies and stalwart molecular simulation analyses, we were able to observe that aforementioned flavonoids were able to considerably divert mutant A4V SOD1 from its distinct pathogenic behavior. Among which, morin showed the most curative potential against A4V SOD1. Therefore, morin holds a great therapeutic potential in contriving highly efficacious inhibitors in mitigating fatal and insuperable ALS.

The folding space of proteinß2-microglobulin is modulated by a single disulfide bridge.

Protein beta-2-microglobulin (ß2m) is classically considered the causative agent of dialysis related amyloidosis, a conformational disorder that affects patients undergoing long-term hemodialysis. The wild type (WT) form, the ΔN6 structural variant, and the D76N mutant have been extensively used as model systems ofß2m aggregation. In all of them, the native structure is stabilized by a disulfide bridge between the sulphur atoms of the cysteine residues 25 (at B strand) and 80 (at F strand), which has been considered fundamental inß2m fibrillogenesis. Here, we use extensive discrete molecular dynamics simulations of a full atomistic structure-based model to explore the role of this disulfide bridge as a modulator of the folding space ofß2m. In particular, by considering different models for the disulfide bridge, we explore the thermodynamics of the folding transition, and the formation of intermediate states that may have the potential to trigger the aggregation cascade. Our results show that the dissulfide bridge affects folding transition and folding thermodynamics of the considered model systems, although to different extents. In particular, when the interaction between the sulphur atoms is stabilized relative to the other intramolecular interactions, or even locked (i.e. permanently established), the WT form populates an intermediate state featuring a well preserved core and two unstructured termini, which was previously detected only for the D76N mutant. The formation of this intermediate state may have important implications in our understanding ofß2m fibrillogenesis.

Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel.

The epithelial sodium channel (ENaC) mediates sodium absorption in lung, kidney, and colon epithelia. Channels in the ENaC/degenerin family possess an extracellular region that senses physicochemical changes in the extracellular milieu and allosterically regulates the channel opening. Proteolytic cleavage activates the ENaC opening, by the removal of specific segments in the finger domains of the α- and γ ENaC-subunits. Cleavage causes perturbations in the extracellular region that propagate to the channel gate. However, it is not known how the channel structure mediates the propagation of activation signals through the extracellular sensing domains. Here, to identify the structure-function determinants that mediate allosteric ENaC activation, we performed MD simulations, thiol modification of residues substituted by cysteine, and voltage-clamp electrophysiology recordings. Our simulations of an ENaC heterotetramer, α1ßα2γ, in the proteolytically cleaved and uncleaved states revealed structural pathways in the α-subunit that are responsible for ENaC proteolytic activation. To validate these findings, we performed site-directed mutagenesis to introduce cysteine substitutions in the extracellular domains of the α-, ß-, and γ ENaC-subunits. Insertion of a cysteine at the α-subunit Glu557 site, predicted to stabilize a closed state of ENaC, inhibited ENaC basal activity and retarded the kinetics of proteolytic activation by 2-fold. Our results suggest that the lower palm domain of αENaC is essential for ENaC activation. In conclusion, our integrated computational and experimental approach suggests key structure-function determinants for ENaC proteolytic activation and points toward a mechanistic model for the allosteric communication in the extracellular domains of the ENaC/degenerin family channels.

Structural complexity and functional diversity of plant NADPH oxidases.

Plant NADPH oxidases also known as respiratory burst oxidase homologs (Rbohs) are a family of membrane-bound enzymes that play diverse roles in the defense response and morphogenetic processes via regulated generation of reactive oxygen species. Rbohs are associated with a variety of functions, although the reason for this is not clear. To evaluate using bioinformatics, the possible mechanisms for the observed functional diversity within the plant kingdom, 127 Rboh protein sequences representing 26 plant species were analyzed. Multiple clusters were identified with gene duplications that were both dicot as well as monocot-specific. The N-terminal sequences were observed to be highly variable. The conserved cysteine (equivalent of Cys890) in C-terminal of AtRbohD suggested that the redox-based modification like S-nitrosylation may regulate the activity of other Rbohs. Three-dimensional models corresponding to the N-terminal domain for Rbohs from Arabidopsis thaliana and Oryza sativa were constructed and molecular dynamics studies were carried out to study the role of Ca2+ in the folding of Rboh proteins. Certain mutations indicated possibly affect the structure and function of the plant NADPH oxidases, thereby providing the rationale for further experimental validation.

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase.

Prolyl hydroxylase domain-containing protein 2 (PHD2), as one of the most important regulators of angiogenesis and metastasis of cancer cells, is a promising target for cancer therapy drug design. Progressive studies imply that abnormality in PHD2 function may be due to misfolding. Therefore, study of the PHD2 unfolding pathway paves the way for a better understanding of the influence of PHD2 mutations and cancer cell metabolites on the protein folding pathway. We study the unfolding of the PHD2 catalytic domain using differential scanning calorimetry (DSC), fluorescence spectroscopy, and discrete molecular dynamics simulations (DMD). Using computational and experimental techniques, we find that PHD2 undergoes four transitions along the thermal unfolding pathway. To illustrate PHD2 unfolding events in atomic detail, we utilize DMD simulations. Analysis of computational results indicates an intermediate species in the PHD2 unfolding pathway that may enhance aggregation propensity, explaining mutation-independent PHD2 malfunction.

Inhibition of hIAPP Amyloid Aggregation and Pancreatic ß-Cell Toxicity by OH-Terminated PAMAM Dendrimer.

Human islet amyloid polypeptide (hIAPP, or amylin) forms amyloid deposits in the islets of Langerhans, a phenomenon that is associated with type-2 diabetes impacting millions of people worldwide. Accordingly, strategies against hIAPP aggregation are essential for the prevention and eventual treatment of the disease. Here, it is shown that generation-3 OH-terminated poly(amidoamine) dendrimer, a polymeric nanoparticle, can effectively halt the aggregation of hIAPP and shut down hIAPP toxicity in pancreatic MIN6 and NIT-1 cells as well as in mouse islets. This finding is supported by high-throughput dynamic light scattering experiment and thioflavin T assay, where the rapid evolution of hIAPP nucleation and elongation processes is halted by the addition of the dendrimer up to 8 h. Discrete molecular dynamics simulations further reveal that hIAPP residues bound strongly with the dendrimer near the c-terminal portion of the peptide, where the amyloidogenic sequence (residues 22-29) locates. Furthermore, simulations of hIAPP dimerization reveal that binding with the dendrimer significantly reduces formation of interpeptide contacts and hydrogen bonds, thereby prohibiting peptide self-association and amyloidosis. This study points to a promising nanomedicinal strategy for combating type-2 diabetes and may have broader implications for targeting neurological disorders whose distinct hallmark is also amyloid fibrillation.

Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid ß-Protein.

Alzheimer's disease (AD) is a neurological disorder associated with amyloid ß-protein (Aß) assembly into toxic oligomers. In addition to the two predominant alloforms, Aß1-40 and Aß1-42, other C-terminally truncated Aß peptides, including Aß1-38 and Aß1-43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aß1-38, Aß1-40, Aß1-42, and Aß1-43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aß1-38 and Aß1-40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aß1-42 and Aß1-43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aß1-42) or octamers and pentadecamers (for Aß1-43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aß1-42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure-function paradigm governing oligomers formed by various Aß isoforms.

Structural and dynamic insights into α-synuclein dimer conformations.

Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed ß-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.

Defensin-based therapeutic peptide design in attenuating V30M TTR-induced Familial Amyloid Polyneuropathy.

In the present study, we aimed to formulate an effective therapeutic candidate against V30M mutant transthyretin (TTR) protein to hinder its pathogenic misfolding. Nicotiana alata Defensin 1 (NaD1) Antimicrobial Peptide (AMP) was availed due to its tendency to aggregate, which may compete for aggregation-prone regions of pathogenic TTR protein. Based on NaD1's potential to bind to V30M TTR, we proposed NaD1-derived tetra peptides: CKTE and SKIL to be initial therapeutic candidates. Based on their association with mutant TTR protein, CKTE tetra peptide showed considerable interaction and curative potential as compared to SKIL tetra peptide. Further analyses from discrete molecular dynamics simulation corroborate CKTE tetra peptide's effectiveness as a 'beta-sheet breaker' against V30M TTR. Various post-simulation trajectory analyses suggested that CKTE tetra peptide alters the structural dynamics of pathogenic V30M TTR protein, thereby potentially attenuating its beta-sheets and impeding its aggregation. Normal mode analysis simulation corroborated that V30M TTR conformation is altered upon its interaction with CKTE peptide. Moreover, simulated thermal denaturation findings suggested that CKTE-V30M TTR complex is more susceptible to simulated denaturation, relative to pathogenic V30M TTR; further substantiating CKTE peptide's potential to alter V30M TTR's pathogenic conformation. Moreover, the residual frustration analysis augmented CKTE tetra peptide's proclivity in reorienting the conformation of V30M TTR. Therefore, we predicted that the tetra peptide, CKTE could be a promising therapeutic candidate in mitigating the amyloidogenic detrimental effects of V30M TTR-mediated familial amyloid polyneuropathy (FAP). Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03646-4.

Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology.

Precise RNA tertiary structure prediction can aid in the design of RNA nanoparticles. However, most existing RNA tertiary structure prediction methods are limited to small RNAs with relatively simple secondary structures. Large RNA molecules usually have complex secondary structures, including multibranched loops and pseudoknots, allowing for highly flexible RNA geometries and multiple stable states. Various experiments and bioinformatics analyses can often provide information about the distance between atoms (or residues) in RNA, which can be used to guide the prediction of RNA tertiary structure. In this chapter, we will introduce a platform, iFoldNMR, that can incorporate non-exchangeable imino protons resonance data from NMR as restraints for RNA 3D structure prediction. We also introduce an algorithm, DVASS, which optimizes distance restraints for better RNA 3D structure prediction.

Molecular simulation unravels the amyloidogenic misfolding of nascent ApoA1 protein, driven by deleterious point mutations occurring in between 170-178 hotspot region.

Protein ApoA1 is extensively studied for its role in lipid metabolism. Its seedy dark side of amyloid formulation remains relatively understudied yet. Due to genetic mutations, the protein pathologically misshapes into its amyloid form that gets accumulated in various organs, including the heart. To contrive effective therapeutics against this debilitating congenital disorder, it is imperative to comprehend the structural ramifications induced by mutations in APoA1's dynamic conformation. Till now, several point mutations have been implicated in ApoA1's amyloidosis, although only a handful has been examined considerably. Especially, the single nucleotide polymorphisms (SNPs) that occur in-between 170-178 mutation hotspot site of APoA1 needs to be investigated, since most of them are culpable of amyloid deposition in the heart. To that effect, in the present study, we have computationally quantified and studied the ApoA1's biomolecular modifications fostered by SNPs in the 170-178 mutation hotspot. Findings from discrete molecular dynamics simulation studies indicate that the SNPs have noticeably steered the ApoA1's behaviour from its native structural dynamics. Analysis of protein's secondary structural changes exhibits a considerable change upon mutations. Further, subjecting the protein structures to simulated thermal denaturation shows increased resistance to denaturation among mutants when compared to native. Further, normal mode analysis of protein's dynamic motion also shows discrepancy in its dynamic structural change upon SNP. These structural digressions induced by SNPs can very well be the biomolecular incendiary that drives ApoA1 into its amyloidogenesis. And, understanding these structural modifications initiates a better understanding of SNP's amyloidogenic pathology on APoA1.Communicated by Ramaswamy H. Sarma.

Different Forms of Disorder in NMDA-Sensitive Glutamate Receptor Cytoplasmic Domains Are Associated with Differences in Condensate Formation.

The N-methyl-D-aspartate (NMDA)-sensitive glutamate receptor (NMDAR) helps assemble downstream signaling pathways through protein interactions within the postsynaptic density (PSD), which are mediated by its intracellular C-terminal domain (CTD). The most abundant NMDAR subunits in the brain are GluN2A and GluN2B, which are associated with a developmental switch in NMDAR composition. Previously, we used single molecule fluorescence resonance energy transfer (smFRET) to show that the GluN2B CTD contained an intrinsically disordered region with slow, hop-like conformational dynamics. The CTD from GluN2B also undergoes liquid-liquid phase separation (LLPS) with synaptic proteins. Here, we extend these observations to the GluN2A CTD. Sequence analysis showed that both subunits contain a form of intrinsic disorder classified as weak polyampholytes. However, only GluN2B contained matched patterning of arginine and aromatic residues, which are linked to LLPS. To examine the conformational distribution, we used discrete molecular dynamics (DMD), which revealed that GluN2A favors extended disordered states containing secondary structures while GluN2B favors disordered globular states. In contrast to GluN2B, smFRET measurements found that GluN2A lacked slow conformational dynamics. Thus, simulation and experiments found differences in the form of disorder. To understand how this affects protein interactions, we compared the ability of these two NMDAR isoforms to undergo LLPS. We found that GluN2B readily formed condensates with PSD-95 and SynGAP, while GluN2A failed to support LLPS and instead showed a propensity for colloidal aggregation. That GluN2A fails to support this same condensate formation suggests a developmental switch in LLPS propensity.

Substoichiometric Inhibition of Insulin against IAPP Aggregation Is Attenuated by the Incompletely Processed N-Terminus of proIAPP.

Substoichiometric aggregation inhibition of human islet amyloid polypeptide (IAPP), the hallmark of type 2 diabetes impacting millions of people, is crucial for developing clinic therapies, yet it remains challenging given that many candidate inhibitors require high doses. Intriguingly, insulin, the key regulatory polypeptide on blood glucose levels that are cosynthesized, costored, and cosecreted with IAPP by pancreatic ß cells, has been identified as a potent inhibitor that can suppress IAPP amyloid aggregation at substoichiometric concentrations. Here, we computationally investigated the molecular mechanisms of the substoichiometric inhibition of insulin against the aggregation of IAPP and the incompletely processed IAPP (proIAPP) using discrete molecular dynamics simulations. Our results suggest that the amyloid aggregations of both IAPP and proIAPP might be disrupted by insulin through its binding with the shared amyloidogenic core sequences. However, the N-terminus of proIAPP competed with the amyloidogenic core sequences for the insulin interactions, resulting in attenuated inhibition by insulin. Moreover, insulin preferred to bind the elongation surfaces of IAPP seeds with fibril-like structure, with a stronger affinity than that of IAPP monomers. The capping of elongation surfaces by a small amount of insulin sterically prohibited the seed growth via monomer addition, achieving the substoichiometric inhibition. Together, our computational results provided molecular insights for the substoichiometric inhibition of insulin against IAPP aggregation, also the weakened effect on proIAPP. The uncovered substoichiometric inhibition by capping the elongation of amyloid seeds or fibrils may guide the rational designs of new potent inhibitors effective at low doses.

Investigating the pernicious effects of heparan sulfate in serum amyloid A1 protein aggregation: a structural bioinformatics approach.

Amyloid-A mediated (AA) amyloidosis is the pathogenic byproduct of body's prolonged exposure to inflammatory conditions. It is described by the aggregation of mutated/misfolded serum amyloid A1 (SAA1) protein in various tissues and organs. Genetic polymorphism G90D is suspected to cause AA amyloidosis, although the causal mechanism remains cryptic. Recent experimental findings insinuate that heparan sulphate (HS), a glycosaminoglycans, exhibits binding with SAA1 to promote its aggregation. To foster the enhanced binding of HS, we computationally determined the pernicious modifications in G90D mutant SAA1 protein. Also, we examined the influence of HS on the dynamic conformation of mutant SAA1 that could potentially succor amyloidosis. Accordingly, the protein-ligand binding studies indicate that upon SNP G90D, SAA1 protein exhibited an augmented association with HS. Further, the simulation of HS bound mutant SAA1 complex delineates an increase in RMSD, Rg, and RMSF. Also, both RMSD and Rg evinced a fluctuating trajectory. Further, the complex showed increase of beta turn in its secondary structural composition. Additionally, the free energy landscape of mutant SAA1-HS complex posits the occurrence of multiple global minima conformers as opposed to the presence of a single global energy minima conformation in native SAA1 protein. In conclusion, the aforementioned conformational ramifications induced by HS on SAA1 could potentially be the proteopathic incendiary behind AA amyloidosis; this incendiary will need to be considered in future studies for developing effective therapeutics against AA amyloidosis.Communicated by Ramaswamy H. Sarma.

Fuzzy supertertiary interactions within PSD-95 enable ligand binding.

The scaffold protein PSD-95 links postsynaptic receptors to sites of presynaptic neurotransmitter release. Flexible linkers between folded domains in PSD-95 enable a dynamic supertertiary structure. Interdomain interactions within the PSG supramodule, formed by PDZ3, SH3, and Guanylate Kinase domains, regulate PSD-95 activity. Here we combined discrete molecular dynamics and single molecule Förster resonance energy transfer (FRET) to characterize the PSG supramodule, with time resolution spanning picoseconds to seconds. We used a FRET network to measure distances in full-length PSD-95 and model the conformational ensemble. We found that PDZ3 samples two conformational basins, which we confirmed with disulfide mapping. To understand effects on activity, we measured binding of the synaptic adhesion protein neuroligin. We found that PSD-95 bound neuroligin well at physiological pH while truncated PDZ3 bound poorly. Our hybrid structural models reveal how the supertertiary context of PDZ3 enables recognition of this critical synaptic ligand.

In silico characterization of mutations circulating in SARS-CoV-2 structural proteins.

SARS-CoV-2 has recently emerged as a pandemic that has caused more than 2.4 million deaths worldwide. Since the onset of infections, several full-length sequences of viral genome have been made available which have been used to gain insights into viral dynamics. We utilised a meta-data driven comparative analysis tool for sequences (Meta-CATS) algorithm to identify mutations in 829 SARS-CoV-2 genomes from around the world. The algorithm predicted sixty-one mutations among SARS-CoV-2 genomes. We observed that most of the mutations were concentrated around three protein coding genes viz nsp3 (non-structural protein 3), RdRp (RNA-directed RNA polymerase) and Nucleocapsid (N) proteins of SARS-CoV-2. We used various computational tools including normal mode analysis (NMA), C-α discrete molecular dynamics (DMD) and all-atom molecular dynamic simulations (MD) to study the effect of mutations on functionality, stability and flexibility of SARS-CoV-2 structural proteins including envelope (E), N and spike (S) proteins. PredictSNP predictor suggested that four mutations (L37H in E, R203K and P344S in N and D614G in S) out of seven were predicted to be neutral whilst the remaining ones (P13L, S197L and G204R in N) were predicted to be deleterious in nature thereby impacting protein functionality. NMA, C-α DMD and all-atom MD suggested some mutations to have stabilizing roles (P13L, S197L and R203K in N protein) where remaining ones were predicted to destabilize mutant protein. In summary, we identified significant mutations in SARS-CoV-2 genomes as well as used computational approaches to further characterize the possible effect of highly significant mutations on SARS-CoV-2 structural proteins.Communicated by Ramaswamy H. Sarma.

Hydroxylated single-walled carbon nanotube inhibits ß2m21-31 fibrillization and disrupts pre-formed proto-fibrils.

Pathological aggregation of amyloid polypeptides is associated with numerous degenerative diseases. Preventing aggregation and clearing amyloid deposits are considered as promising strategies against amyloidosis. With the capacity of crossing the blood-brain barrier and good biocompatibility, the hydroxylated single-walled carbon nanotube (SWCNT-OH) has been shown with excellent anti-amyloid properties. Here, we systematically studied the SWCNT-OH effects on the fibrillization of the ß2m21-31 peptides utilizing all-atom discrete molecular dynamics (DMD) simulation. Our results demonstrated the isolated ß2m21-31 peptides first nucleated into unstructured oligomers followed by coil-to-sheet conformational conversions in oligomers with at least six peptides. The elongation and lateral surfaces of the preformed ß-sheet could catalyze the other unstructured monomers and small oligomers converted into ß-sheet formations via dock-lock fibril growth and secondary nucleation processes. Eventually, the ß2m21-31 peptides would self-assemble into well-ordered cross-ß structures. Regardless of isolated monomers or well-defined cross-ß assemblies, the ß2m21-31 would attach on the surfaces of SWCNT-OH adopting unstructured formations indicating the SWCNT-OH not only inhibited the fibrillization of ß2m21-31 but also destroyed pre-formed proto-fibrils. Overall, our study displays a complete picture of the fibrillization mechanism of ß2m21-31 and the amyloid inhibitory mechanism of SWCNT-OH, offering new insight into the de-novo design of anti-amyloid inhibitors.

Spontaneous Formation of ß-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta.

Soluble low-molecular-weight oligomers formed during the early aggregation of amyloid peptides have been hypothesized as a major toxic species of amyloidogenesis. Herein, we performed the first synergic in silico, in vitro and in vivo validations of the structure, dynamics and toxicity of Aß42 oligomers. Aß peptides readily assembled into ß-rich oligomers comprised of extended ß-hairpins and ß-strands. Nanosized ß-barrels were observed with certainty with simulations, transmission electron microscopy and Fourier transform infrared spectroscopy, corroborated by immunohistochemistry, cell viability, apoptosis, inflammation, autophagy and animal behavior assays. Secondary and tertiary structural proprieties of these oligomers, such as the sequence regions with high ß-sheet propensities and inter-residue contact frequency patterns, were similar to the properties known for Aß fibrils. The unambiguous spontaneous formation of ß-barrels in the early aggregation of Aß42 supports their roles as the common toxic intermediates in Alzheimer's pathobiology and a target for Alzheimer's therapeutics.