Structures and dynamics of ß-barrel oligomer intermediates of amyloid-beta16-22 aggregation.

Accumulating evidence suggests that soluble oligomers are more toxic than final fibrils of amyloid aggregations. Among the mixture of inter-converting intermediates with continuous distribution of sizes and secondary structures, oligomers in the ß-barrel conformation - a common class of protein folds with a closed ß-sheet - have been postulated as the toxic species with well-defined three-dimensional structures to perform pathological functions. A common mechanism for amyloid toxicity, therefore, implies that all amyloid peptides should be able to form ß-barrel oligomers as the aggregation intermediates. Here, we applied all-atom discrete molecular dynamics (DMD) simulations to evaluate the formation of ß-barrel oligomers and characterize their structures and dynamics in the aggregation of a seven-residue amyloid peptide, corresponding to the amyloid core of amyloid-ß with a sequence of 16KLVFFAE22 (Aß16-22). We carried out aggregation simulations with various numbers of peptides to study the size dependence of aggregation dynamics and assembly structures. Consistent with previous computational studies, we observed the formation of ß-barrel oligomers in all-atom DMD simulations. Using a network-based approach to automatically identify ß-barrel conformations, we systematically characterized ß-barrels of various sizes. Our simulations revealed the conformational inter-conversion between ß-barrels and double-layer ß-sheets due to increased structural strains upon forming a closed ß-barrel while maximizing backbone hydrogen bonds. The potential of mean force analysis further characterized the free energy barriers between these two states. The obtained structural and dynamic insights of ß-barrel oligomers may help better understand the molecular mechanism of oligomer toxicities and design novel therapeutics targeting the toxic ß-barrel oligomers. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.

Star Polymers Reduce Islet Amyloid Polypeptide Toxicity via Accelerated Amyloid Aggregation.

Protein aggregation into amyloid fibrils is a ubiquitous phenomenon across the spectrum of neurodegenerative disorders and type 2 diabetes. A common strategy against amyloidogenesis is to minimize the populations of toxic oligomers and protofibrils by inhibiting protein aggregation with small molecules or nanoparticles. However, melanin synthesis in nature is realized by accelerated protein fibrillation to circumvent accumulation of toxic intermediates. Accordingly, we designed and demonstrated the use of star-shaped poly(2-hydroxyethyl acrylate) (PHEA) nanostructures for promoting aggregation while ameliorating the toxicity of human islet amyloid polypeptide (IAPP), the peptide involved in glycemic control and the pathology of type 2 diabetes. The binding of PHEA elevated the ß-sheet content in IAPP aggregates while rendering a new morphology of "stelliform" amyloids originating from the polymers. Atomistic molecular dynamics simulations revealed that the PHEA arms served as rodlike scaffolds for IAPP binding and subsequently accelerated IAPP aggregation by increased local peptide concentration. The tertiary structure of the star nanoparticles was found to be essential for driving the specific interactions required to impel the accelerated IAPP aggregation. This study sheds new light on the structure-toxicity relationship of IAPP and points to the potential of exploiting star polymers as a new class of therapeutic agents against amyloidogenesis.

Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide.

A direct observation of amyloid aggregation from isolated peptides to cross-ß fibrils is crucial for understanding the nucleation-dependence process, but the corresponding macroscopic timescales impose a major computational challenge. Using rapid all-atom discrete molecular dynamics simulations, we capture the oligomerization and fibrillization dynamics of the amyloid core sequences of amyloid-ß (Aß) in Alzheimer's disease and islet amyloid polypeptide (IAPP) in type-2 diabetes, namely Aß16-22 and IAPP22-28. Both peptides and their mixture spontaneously assemble into cross-ß aggregates in silico, but follow distinct pathways. Aß16-22 is highly aggregation-prone with a funneled free energy basin toward multi-layer ß-sheet aggregates. IAPP22-28, on the other hand, features the accumulation of unstructured oligomers before the nucleation of ß-sheets and growth into double-layer ß-sheet aggregates. In the presence of Aß16-22, the aggregation of IAPP22-28 is promoted by forming co-aggregated multi-layer ß-sheets. Our study offers a detailed molecular insight to the long-postulated oligomerization-nucleation process in the amyloid aggregations.

A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface.

It has been under debate if a self-assembled monolayer (SAM) with two immiscible ligands of different chain lengths and/or bulkiness can form a stripe-like pattern on a nanoparticle (NP) surface. The entropic gain upon such pattern formation due to difference in chain lengths and/or bulkiness has been proposed as the driving force in literature. Using atomistic discrete molecular dynamics simulations it is shown that stripe-like pattern could indeed emerge, but only for a subset of binary SAM systems. In addition to entropic contributions, the formation of a striped pattern also strongly depends upon interligand interactions governed by the physicochemical properties of the ligand constituents. Due to the interplay between entropy and enthalpy, a binary SAM system can be categorized into three different types depending on whether and under what condition a striped pattern can emerge. The results help clarify the ongoing debate and our proposed principle can aid in the engineering of novel binary SAMs on a NP surface.

Loss of Phosphomannose Isomerase Impairs Growth, Perturbs Cell Wall Integrity, and Reduces Virulence of Fusarium oxysporum f. sp. cubense on Banana Plants.

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes Fusarium wilt of banana, necessitating urgent measures to control this disease. However, the molecular mechanisms underlying Foc TR4 virulence remain elusive. Phosphomannose isomerase is a key enzyme involved in the biosynthesis of GDP mannose, an important precursor of fungal cell walls. In this study, two phosphomannose isomerases were identified in the Foc TR4 genome, of which only Focpmi1 was highly expressed throughout all developmental stages. Generated null mutants in Foc TR4 showed that only the ΔFocpmi1 mutant required exogenous mannose for growth, indicating that Focpmi1 is the key enzyme involved in GDP mannose biosynthesis. The Focpmi1 deficient strain was unable to grow without exogenous mannose and exhibited impaired growth under stress conditions. The mutant had reduced chitin content in its cell wall, rendering it vulnerable to cell wall stresses. Transcriptomic analysis revealed up- and down-regulation of several genes involved in host cell wall degradation and physiological processes due to the loss of Focpmi1. Furthermore, Focpmi1 was also found to be crucial for Foc TR4 infection and virulence, making it a potential antifungal target to address the threats posed by Foc TR4.

Islet Amyloid Polypeptide Promotes Amyloid-Beta Aggregation by Binding-Induced Helix-Unfolding of the Amyloidogenic Core.

Amyloid aggregation of amyloid-beta (Aß) and islet amyloid polypeptide (IAPP) is associated with Alzheimer's disease (AD) and type-2 diabetes (T2D), respectively. With T2D being the risk factor for AD and the ability of IAPP to cross the blood-brain barrier, the coaggregation of Aß and IAPP has been explored to understand the cross-talk between the two diseases. Recent studies demonstrated that soluble IAPP could significantly accelerate the aggregation of Aß while preformed amyloids of IAPP were poor "seeds" for Aß aggregation. Here, we apply all-atom discrete molecular dynamics simulations to investigate possible molecular mechanisms for the accelerated coaggregation of IAPP and Aß42 comparing to Aß42 aggregation alone, which was confirmed by the complementary thioflavin-T fluorescence assay. Our simulation results suggest that peptides in the mixture tend to form heterodimers as the first step toward their coaggregation. Strong interpeptide interactions with IAPP in the heterodimer shift the helical conformation of Aß42 in its amyloidogenic central hydrophobic core, residues 16-22 (Aß16-22), to the extended conformation ready to form ß-sheets. Our study suggests that the unfolding of Aß16-22 helix contributes to the aggregation free-energy barrier and corresponds to the rate-limiting conformational change for Aß42 aggregation. Therefore, we propose that soluble IAPP promotes the aggregation of Aß42 by binding-induced conformational change of Aß42 in its amyloidogenic core and thus reduced aggregation free-energy barrier.

ß-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-ß Aggregates.

Oligomers populated during the early amyloid aggregation process are more toxic than mature fibrils, but pinpointing the exact toxic species among highly dynamic and heterogeneous aggregation intermediates remains a major challenge. ß-barrel oligomers, structurally-determined recently for a slow-aggregating peptide derived from αB crystallin, are attractive candidates for exerting amyloid toxicity due to their well-defined structures as therapeutic targets and compatibility to the "amyloid-pore" hypothesis of toxicity. To assess whether ß-barrel oligomers are common intermediates to amyloid peptides - a necessary step toward associating ß-barrel oligomers with general amyloid cytotoxicity, we computationally studied the oligomerization and fibrillization dynamics of seven well-studied fragments of amyloidogenic proteins with different experimentally-determined aggregation morphologies and cytotoxicity. In our molecular dynamics simulations, ß-barrel oligomers were only observed in five peptides self-assembling into the characteristic cross-ß aggregates, but not the other two that formed polymorphic ß-rich aggregates as reported experimentally. Interestingly, the latter two peptides were previously found nontoxic. Hence, the observed correlation between ß-barrel oligomers formation and cytotoxicity supports the hypothesis of ß-barrel oligomers as the common toxic intermediates of amyloid aggregation.

Nanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules.

Understanding how small molecules interface amyloid fibrils on the nanoscale is of importance for developing therapeutic treatment against amyloid-based diseases. Here we show, for the first time, that human islet amyloid polypeptide (IAPP) in the fibrillar form is polymorphic and ambidextrous possessing multiple periodicities. Upon interfacing with small molecule epigallocatechin gallate (EGCG), IAPP aggregation was rendered off pathway assuming the form of soft and disordered clusters, while mature IAPP fibrils displayed kinks and branching but conserved the twisted fibril morphology. These nanoscale phenomena resulted from competitive interactions between EGCG and the IAPP amyloidogenic region, as well as end capping of the fibrils by the small molecule. This information is crucial to delineating IAPP toxicity implicated in type 2 diabetes and developing new inhibitors against amyloidogenesis.

Zinc-coordination and C-peptide complexation: a potential mechanism for the endogenous inhibition of IAPP aggregation.

Aggregation of the highly amyloidogenic IAPP is endogenously inhibited inside beta-cell granules at millimolar concentrations. Combining in vitro experiments and computer simulations, we demonstrated that the stabilization of IAPP upon the formation of zinc-coordinated ion molecular complex with C-peptide might be important for the endogenous inhibition of IAPP aggregation.

Brushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding.

To provide a molecular insight for guiding polymer coating in surface science and nanotechnology, here we examined the structures of brushed polyethylene glycol(bPEG)- and phosphorylcholine(bPC)-grafted iron oxide nanoparticles and analyzed their protein avoiding properties. We show bPC as an advantageous biomimetic alternative to PEG in rendering stealth nanostructures.