Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation

Sterol-activated amyloid beta fibril formation

The metabolic processes that link Alzheimer's disease (AD) to elevated cholesterol levels in the brain are not fully defined. Amyloid beta (Aβ) plaque accumulation is believed to begin decades prior to symptoms and to contribute significantly to the disease. Cholesterol and its metabolites accelerate plaque formation through as-yet-undefined mechanisms. Here, the mechanism of cholesterol (CH) and cholesterol 3-sulfate (CS) induced acceleration of Aβ42 fibril formation is examined in quantitative ligand binding, Aβ42 fibril polymerization, and molecular dynamics studies. Equilibrium and pre-steady-state binding studies reveal that monomeric Aβ42•ligand complexes form and dissociate rapidly relative to oligomerization, that the ligand/peptide stoichiometry is 1-to-1, and that the peptide is likely saturated in vivo. Analysis of Aβ42 polymerization progress curves demonstrates that ligands accelerate polymer synthesis by catalyzing the conversion of peptide monomers into dimers that nucleate the polymerization reaction. Nucleation is accelerated ∼49-fold by CH, and ∼13,000-fold by CS - a minor CH metabolite. Polymerization kinetic models predict that at presumed disease-relevant CS and CH concentrations, approximately half of the polymerization nuclei will contain CS, small oligomers of neurotoxic dimensions (∼12-mers) will contain substantial CS, and fibril-formation lag times will decrease 13-fold relative to unliganded Aβ42. Molecular dynamics models, which quantitatively predict all experimental findings, indicate that the acceleration mechanism is rooted in ligand-induced stabilization of the peptide in non-helical conformations that readily form polymerization nuclei.

Antibody binding modulates the dynamics of the membrane-bound prion protein

Misfolding of the cellular prion protein (PrP^C) is associated with lethal neurodegeneration. PrP^C consists of a flexible tail (residues 23-123) and a globular domain (residues 124-231) whose C-terminal end is anchored to the cell membrane. The neurotoxic antibody POM1 and the innocuous antibody POM6 recognize the globular domain. Experimental evidence indicates that POM1 binding to PrP^C emulates the influence on PrP^C of the misfolded prion protein (PrP^Sc) while the binding of POM6 has the opposite biological response. Little is known about the potential interactions between flexible tail, globular domain, and the membrane. Here, we used atomistic simulations to investigate how these interactions are modulated by the binding of the Fab fragments of POM1 and POM6 to PrP^C and by interstitial sequence truncations to the flexible tail. The simulations show that the binding of the antibodies restricts the range of orientations of the globular domain with respect to the membrane and decreases the distance between tail and membrane. Five of the six sequence truncations influence only marginally this distance and the contact patterns between tail and globular domain. The only exception is a truncation coupled to a charge inversion mutation of four N-terminal residues, which increases the distance of the flexible tail from the membrane. The interactions of the flexible tail and globular domain are modulated differently by the two antibodies.

Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation

Alzheimer’s disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) simulation studies of Aβ peptides and Aβ fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aβ, a β-hairpin structure promotes the formation of intermolecular β-sheet structures. Aβ peptides tend to exist at hydrophilic/hydrophobic interfaces and form more β-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aβ peptides, interact with Aβ. An MD simulation study of the Aβ amyloid fibrils in equilibrium is also presented: the Aβ amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer’s disease using MD simulations.

SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence

It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low-complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, was required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.

Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions

Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in biology and human diseases. It is now also recognized that many IDPs remain dynamic even in specific complexes and functional assemblies. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for a mechanistic understanding of IDPs in biology, diseases, and therapeutics. Here, we provide an in-depth review of recent advances in the multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs. These techniques are critical for adequate sampling of the manifold functionally relevant conformational spaces of IDPs. Together with dramatically improved protein force fields, these advanced simulation approaches have achieved substantial success and demonstrated significant promise towards the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also discuss important challenges remaining in the atomistic simulation of larger systems and how various coarse-grained approaches may help to bridge the remaining gaps in the accessible time- and length-scales of IDP simulations.

Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg

Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.

Amyloid-Like Peptide Aggregates

Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.

Curcumin Inhibits the Primary Nucleation of Amyloid-Beta Peptide: A Molecular Dynamics Study

The amyloid plaques are a key hallmark of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease. Amyloidogenesis is a complex long-lasting multiphase process starting with the formation of nuclei of amyloid peptides: a process assigned as a primary nucleation. Curcumin (CU) is a well-known inhibitor of the aggregation of amyloid-beta (Aβ) peptides. Even more, CU is able to disintegrate preformed Aβ firbils and amyloid plaques. Here, we simulate by molecular dynamics the primary nucleation process of 12 Aβ peptides and investigate the effects of CU on the process. We found that CU molecules intercalate among the Aβ chains and bind tightly to them by hydrogen bonds, hydrophobic, π–π, and cation–π interactions. In the presence of CU, the Aβ peptides form a primary nucleus of a bigger size. The peptide chains in the nucleus become less flexible and more disordered, and the number of non-native contacts and hydrogen bonds between them decreases. For comparison, the effects of the weaker Aβ inhibitor ferulic acid (FA) on the primary nucleation are also examined. Our study is in good agreement with the observation that taken regularly, CU is able to prevent or at least delay the onset of neurodegenerative disorders.

Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) contribute to a multitude of functions. De novo design of IDPs should open the door to modulating functions and phenotypes controlled by these systems. Recent design efforts have focused on compositional biases and specific sequence patterns as the design features. Analysis of the impact of these designs on sequence-function relationships indicates that individual sequence/compositional parameters are insufficient for describing sequence-function relationships in IDPs. To remedy this problem, we have developed information theoretic measures for sequence–ensemble relationships (SERs) of IDPs. These measures rely on prior availability of statistically robust conformational ensembles derived from all atom simulations. We show that the measures we have developed are useful for comparing sequence-ensemble relationships even when sequence is poorly conserved. Based on our results, we propose that de novo designs of IDPs, guided by knowledge of their SERs, should provide improved insights into their sequence–ensemble–function relationships.

Tau Inclusions in Alzheimer's, Chronic Traumatic Encephalopathy and Pick's Disease. A Speculation on How Differences in Backbone Polarization Underlie Divergent Pathways of Tau Aggregation

Tau-related dementias appear to involve specific to each disease aggregation pathways and morphologies of filamentous tau assemblies. To understand etiology of these differences, here we elucidate molecular mechanism of formation of tau PHFs based on the PMO theory of misfolding and aggregation of pleiomorphic proteins associated with neurodegenerative diseases. In this model, fibrillization of tau is initiated by the coupled binding and folding of the MTB domains that yields antiparallel homodimers, in analogy to folding of split inteins. The free energy of binding is minimized when the antiparallel alignment brings about backbone-backbone H-bonding between the MTBD segments of similar "strand" propensities. To assess these propensities, a function of the NMR shielding tensors of the Cα atoms is introduced as the folding potential function FP i ; the Cα tensors are obtained by the quantum mechanical modeling of protein secondary structure (GIAO//B3LYP/D95**). The calculated FP i plots show that the "strand" propensities of the MBTD segments, and hence the homodimer's register, can be affected by the relatively small changes in the environment's pH, as a result of protonation of MBTD's conserved histidines. The assembly of the antiparallel tau dimers into granular aggregates and their subsequent conversion into the parallel cross-β structure of paired helical filaments is expected to follow the same path as the previously described fibrillization of Aβ. Consequently, the core structure of the nascent tau fibril is determined by the register of the tau homodimer. This model accounts for the reported differences in (i) fibril-core structure of in vivo and in vitro filaments, (ii) cross-seeding of isoforms, (iii) effects of reducing/non-reducing conditions, (iv) effects of PHF6 mutations, and (v) homologs' aggregation properties. The proposed model also suggests that in contrast to Alzheimer's and chronic traumatic encephalopathy disease, the assembly of tau prions in Pick's disease would be facilitated by a moderate drop in pH that accompanies e.g., transit in the endosomal system, inflammation response or an ischemic injury.

Significantly different contact patterns between Aβ40 and Aβ42 monomers involving the N-terminal region

Aβ42 peptide, with two additional residues at C-terminus, aggregates much faster than Aβ40. We performed equilibrium replica-exchange molecular dynamics simulations of their monomers using our residue-specific force field. Simulated ³ J_{HNH α} -coupling constants agree excellently with experimental data. Aβ40 and Aβ42 have very similar local conformational features, with considerable β-strand structures in the segments: A2-H6 (A), L17-A21 (B), A30-V36 (C) of both peptides and V39-I41 (D) of Aβ42. Both peptides have abundant A-B and B-C contacts, but Aβ40 has much more contacts between A and C than Aβ42, which may retard its aggregation. Only Aβ42 has considerable A-B-C-D topology. Decreased probability of A-C contact in Aβ42 relates to the competition from C-D contact. Increased A-C contact probability may also explain the slower aggregation of A2T and A2V mutants of Aβ42.

Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study

We present a simulation study of the early events of peptide dissociation from a fibril of the Alzheimer's Aβ42 peptide. The fibril consists of layers of two adjacent Aβ42 peptides each folded in an S-shaped structure which has been determined by solid state NMR spectroscopy of a monomorphic disease-relevant species. Multiple molecular dynamics runs (16 at 310 K and 15 at 370 K) were carried out starting from an 18-peptide protofibril for a cumulative sampling of about 15 μs. The simulations show structural stability of the fibrillar core and an overall increase in the twist to about 3 degrees. The N-terminal segment 1-14 is disordered in all peptides. At both ends of the fibril, the central segment 21-29, which includes part of the β₂ strand, dissociates in some of the simulations. The β₁ and β₃ strands, residues 15-20 and 35-41, respectively, are structurally stable. The transient binding of the N-terminal stretch to the β₃ strand of the adjacent peptide at the tip is likely to contribute to the arrest phase of the stop-and-go mechanism.

Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions

Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures. This ability to decouple collapse from folding is determined by the sequence details of proteins. In this review, we highlight insights gleaned from studies over the past decade. Using a polymer physics framework, we explain how the interplay among sidechains, backbone units, and solvent determines the driving forces for collapsed versus expanded states in aqueous solvents.

Energy Landscapes for the Aggregation of Aβ17-42

The aggregation of the Aβ peptide (Aβ_1-42) to form fibrils is a key feature of Alzheimer's disease. The mechanism is thought to be a nucleation stage followed by an elongation process. The elongation stage involves the consecutive addition of monomers to one end of the growing fibril. The aggregation process proceeds in a stop-and-go fashion and may involve off-pathway aggregates, complicating experimental and computational studies. Here we present exploration of a well-defined region in the free and potential energy landscapes for the Aβ_17-42 pentamer. We find that the ideal aggregation process agrees with the previously reported dock-lock mechanism. We also analyze a large number of additional stable structures located on the multifunnel energy landscape, which constitute kinetic traps. The key contributors to the formation of such traps are misaligned strong interactions, for example the stacking of F19 and F20, as well as entropic contributions. Our results suggest that folding templates for aggregation are a necessity and that aggregation studies could employ such species to obtain a more detailed description of the process.

Dynamic micellar oligomers of amyloid beta peptides play a crucial role in their aggregation mechanisms

Aβ40 and Aβ42 peptides form micellar precursors of amyloid nuclei contributing to important differences in their aggregation pathways.

Force field development and simulations of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) play important roles in many physiological processes such as signal transduction and transcriptional regulation. Computer simulations that are based on empirical force fields have been increasingly used to understand the biophysics of disordered proteins. In this review, we focus on recent improvement of protein force fields, including polarizable force fields, concerning their accuracy in modeling intrinsically disordered proteins. Some recent benchmarks and applications of these force fields are also overviewed.

Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip

The growth of amyloid fibrils from Aβ_1-42 peptide, one of the key pathogenic players in Alzheimer's disease, is believed to follow a nucleation-elongation mechanism. Fibril elongation is often described as a "dock-lock" procedure, where a disordered monomer adsorbs to an existing fibril in a relatively fast process (docking), followed by a slower conformational transition toward the ordered state of the template (locking). Here, we use molecular dynamics simulations of an ordered pentamer of Aβ42 at fully atomistic resolution, which includes solvent, to characterize the elongation process. We construct a Markov state model from an ensemble of short trajectories generated by an advanced sampling algorithm that efficiently diversifies a subset of the system without any bias forces. This subset corresponds to selected dihedral angles of the peptide chain at the fibril tip favored to be the fast growing one experimentally. From the network model, we extract distinct locking pathways covering time scales in the high microsecond regime. Slow steps are associated with the exchange of hydrophobic contacts, between nonnative and native intermolecular contacts as well as between intra- and intermolecular ones. The N-terminal segments, which are disordered in fibrils and typically considered inert, are able to shield the lateral interfaces of the pentamer. We conclude by discussing our findings in the context of a refined dock-lock model of Aβ fibril elongation, which involves structural disorder for more than one monomer at the growing tip.

Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions

Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the C^α atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrP^C, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrP^Sc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.

Envisaging the Structural Elevation in the Early Event of Oligomerization of Disordered Amyloid β Peptide

In Alzheimer's disease (AD), amyloid β (Aβ) protein plays a detrimental role in neuronal injury and death. Recent in vitro and in vivo studies suggest that soluble oligomers of the Aβ peptide are neurotoxic. Structural properties of the oligomeric assembly, however, are largely unknown. Our present investigation established that the 40-residue-long Aβ peptide (Aβ40) became more helical, ordered, and compact in the oligomeric state, and both the helical and β-sheet components were found to increase significantly in the early event of oligomerization. The band-selective two-dimensional NMR analysis suggested that majority of the residues from sequence 12 to 22 gained a higher-ordered secondary structure in the oligomeric condition. The presence of a significant amount of helical conformation was confirmed by Raman bands at 1650 and 1336 cm^-1. Other residues remained mostly in the extended polyproline II (PPII) and less compact β-conformation space. In the event of maturation of the oligomers into an amyloid fiber, both the helical content and the PPII-like structural components declined and ∼72% residues attained a compact β-sheet structure. Interestingly, however, some residues remained in the collagen triple helix/extended 2.5₁-helix conformation as evidenced by the amide III Raman signature band at 1272 cm^-1. Molecular dynamics analysis using an optimized potential for liquid simulation force field with the peptide monomer indicated that some of the residues may have preferences for helical conformation and this possibly contributed in the event of oligomer formation, which eventually became a β-sheet-rich amyloid fiber.

Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors

Alzheimer’s disease (AD) is characterized by deposition of amyloid beta (Aβ) peptides into senile plaques in the brain. While most familial mutations are associated with early-onset AD, recent studies report the AD-protective nature of two genetic human Aβ variants, i.e. A2T and A2V, in the heterozygous state. The mixture of A2V Aβ1-6 (Aβ₆) hexapeptide and WT Aβ1–42 (Αβ₄₂) is also found neuroprotective. Motivated by these findings, in this study we investigate the effects of WT, A2V, and A2T Aβ₆ hexapeptide binding on the monomeric WT Aβ₄₂ landscape. For this purpose, we have performed extensive atomistic Replica Exchange Molecular Dynamics simulations, elucidating preferential binding of Aβ₄₂ with the A2V and A2T hexapeptides compared to WT Aβ₆. A notable reorganization of the Aβ₄₂ landscape is revealed due to hexapeptide association, as manifested by lowering of transient interactions between the central and C-terminal hydrophobic patches. Concurrently, Aβ₆-bound Aβ₄₂ monomer exhibits alternative structural features that are strongly dependent on the hexapeptide sequence. For example, a central helix is more frequently populated within the A2T-bound monomer, while A2V-bound Aβ₄₂ is often enhanced in overall disorder. Taken together, the present simulations offer novel molecular insights onto the effect of the N-terminal hexapeptide binding on the Aβ₄₂ monomer structure, which might help in explaining their reported amyloid inhibition properties.

Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent?

By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 ³J_HNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of ³J_HNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the differences in the conformational ensembles of Aβ10-40 and Aβ1-40 are small and the former can be used as proxy of the full-length peptide. Based on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most accurate representation of Aβ10-40 conformational ensemble.

Dependence of protein conformational ensembles on force field parameterizations limits the predictive power of molecular dynamics simulations. To address this problem, we evaluated five all-atom force fields for their consistency in reproducing the conformational ensemble of Alzheimer’s Aβ10-40 peptide. To generate conformational ensembles, we have used replica exchange molecular dynamics and computed Aβ10-40 secondary and tertiary structures. We found that, although all force fields predict Aβ10-40 unfolded structure, they strongly disagree on helix and β propensities and tertiary structure distributions. We have also calculated Aβ10-40 J-coupling and residual dipolar coupling constants and compared them with the experimental data for the full-length Aβ1-40 peptide. Unexpectedly, we determined that in silico Aβ10-40 and experimental Aβ1-40 constants are in better agreement than these quantities computed and measured previously for identical peptides, such as Aβ1-40 or Aβ1-42. We then concluded that the conformational ensembles of Aβ10-40 and Aβ1-40 are similar and on this basis argue that CHARMM36 force field with standard TIP3P water model provides the most accurate description of Aβ10-40. Although our objective was not to evaluate the biomolecular force fields in general, our study is expected to facilitate their proper selection for the simulations of Alzheimer’s peptides.

Effects of Intrinsic and Extrinsic Factors on Aggregation of Physiologically Important Intrinsically Disordered Proteins

Misfolding and aggregation of proteins and peptides play an important role in a number of diseases as well as in many physiological processes. Many of the proteins that misfold and aggregate in vivo are intrinsically disordered. Protein aggregation is a complex multistep process, and aggregates can significantly differ in morphology, structure, stability, cytotoxicity, and self-propagation ability. The aggregation process is influenced by both intrinsic (e.g., mutations and expression levels) and extrinsic (e.g., polypeptide chain truncation, macromolecular crowding, posttranslational modifications, as well as interaction with metal ions, other small molecules, lipid membranes, and chaperons) factors. This review examines the effect of a variety of these factors on aggregation of physiologically important intrinsically disordered proteins.

Molecular Dynamics Study on the Inhibition Mechanisms of Drugs CQ1-3 for Alzheimer Amyloid-β40 Aggregation Induced by Cu(2.)

The aggregation of amyloid-β (Aβ) peptide induced by Cu(2+) is a key factor in development of Alzheimer's disease (AD), and metal ion chelation therapy enables treatment of AD. Three CQi (i = 1, 2, and 3 with R = H, Cl, and NO2, respectively) drugs had been verified experimentally to be much stronger inhibitors than the pioneer clioquinol (CQ) in both disaggregation of Aβ40 aggregate and reduction of toxicity induced by Cu(2+) binding at low pH. Due to the multiple morphologies of Cu(2+)-Aβ40 complexes produced at different pH states, we performed a series of molecular dynamics simulations to explain the structural changes and morphology characteristics as well as intrinsic disaggregation mechanisms of three Cu(2+)-Aβ40 models in the presence of any of the three CQi drugs at both low and high pH states. Three inhibition mechanisms for CQi were proposed as "insertion", "semi-insertion", and "surface" mechanisms, based on the morphologies of CQi-model x (CQi-x, x = 1, 2, and 3) and the strengths of binding between CQi and the corresponding model x. The insertion mechanism was characterized by the morphology with binding strength of more than 100 kJ/mol and by CQi being inserted or embedded into the hydrophobic cavity of model x. In those CQi-x morphologies with lower binding strength, CQi only attaches on the surface or inserts partly into Aβ peptide. Given the evidence that the binding strength is correlated positively with the effectiveness of drug to inhibit Aβ aggregation and thus to reduce toxicity, the data of binding strength presented here can provide a reference for one to screen drugs. From the point of view of binding strength, CQ2 is the best drug. Because of the special role of Asp23 in both Aβ aggregation and stabilizing the Aβ fibril, the generation of a H-bond between CQ3 and Asp23 of the Aβ40 peptide is believed to be responsible for CQ3 having the strongest disaggregation capacity. Therefore, besides strong binding, stronger propensity to H-bond with Asp23 would be another key factor to be taken seriously into account in drug screens. Meanwhile, the structural characteristics of drug CQi itself are also worthy of attention. First, the increasing polarity from CQ1 and CQ2 to CQ3 in turn results in increasing probability and strength of the interaction between the drug and the N-terminal (NT) region of Aβ40, which obviously inhibits Aβ peptide aggregation induced by Cu(2+) binding. Second, both the benzothiazole ring and phenol ring of CQi can overcome the activation energy barrier (∼16 kJ/mol) to rotate flexibly around the intramolecular C7-N14 bond to achieve the maximum match and interaction with the ambient Aβ40 residues. Such a structural feature of CQi paves the new way for ones in selection and modification of a drug.

Interaction of the amyloid β peptide with sodium dodecyl sulfate as a membrane-mimicking detergent

The amyloid β (A β) peptide is important in the context of Alzheimer’s disease, since it is one of the major components of the fibrils that constitute amyloid plaques. Agents that can influence fibril formation are important, and of those, membrane mimics are particularly relevant, because the hydrophobic part of A β suggests a possible membrane activity of the peptide. We employed spin-label EPR to investigate the aggregation process of A β1–40 in the presence of the sodium dodecyl sulfate (SDS) detergent as a membrane-mimicking agent. In this work, the effect of SDS on A β is studied using two positions of spin label, the N-terminus and position 26. By comparing the two label positions, the effect of local mobility of the spin label is eliminated, revealing A β aggregation in the SDS concentration regime below the critical micelle concentration (CMC). We demonstrate that, at low SDS concentrations, the N-terminus of A β participates in the solubilization, most likely by being located at the particle–water interface. At higher SDS concentrations, an SDS-solubilized state that is a precursor to the one A β/micelle state above the CMC of SDS prevails. We propose that A β is membrane active and that aggregates include SDS. This study reveals the unique potential of EPR in studying A β aggregation in the presence of detergent.

A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences

The aggregation of proteins with expanded polyglutamine (polyQ) tracts is directly relevant to the formation of neuronal intranuclear inclusions in Huntington's disease. In vitro studies have uncovered the effects of flanking sequences as modulators of the driving forces and mechanisms of polyQ aggregation in sequence segments associated with HD. Specifically, a seventeen-residue amphipathic stretch (N17) that is directly N-terminal to the polyQ tract in huntingtin decreases the overall solubility, destabilizes nonfibrillar aggregates, and accelerates fibril formation. Published results from atomistic simulations showed that the N17 module reduces the frequency of intermolecular association. Our reanalysis of these simulation results demonstrates that the N17 module also reduces interchain entanglements between polyQ domains. These two effects, which are observed on the smallest lengthscales, are incorporated into phenomenological pair potentials and used in coarse-grained Brownian dynamics simulations to investigate their impact on large-scale aggregation. We analyze the results from Brownian dynamics simulations using the framework of diffusion-limited cluster aggregation. When entanglements prevail, which is true in the absence of N17, small spherical clusters and large linear aggregates form on distinct timescales, in accord with in vitro experiments. Conversely, when entanglements are quenched and a barrier to intermolecular associations is introduced, both of which are attributable to N17, the timescales for forming small species and large linear aggregates become similar. Therefore, the combination of a reduction of interchain entanglements through homopolymeric polyQ and barriers to intermolecular associations appears to be sufficient for providing a minimalist phenomenological rationalization of in vitro observations regarding the effects of N17 on polyQ aggregation.

Varied Probability of Staying Collapsed/Extended at the Conformational Equilibrium of Monomeric Aβ40 and Aβ42

In present study, we set out to investigate the conformation dynamics of Aβ40 and Aβ42 through exploring the impact of intra-molecular interactions on conformation dynamics using equilibrium molecular dynamics simulations. Our 40 microsecond-scale simulations reveal heterogeneous conformation ensembles of Aβ40 and Aβ42 that encompass ~35% β-strand and ~60% unstructured coils. Two conformational states were identified in both alloforms: a collapsed state (CS) that resembles the structural motif of face-to-face hydrophobic clustering in amyloid fibrils, and an extended state (ES) that features the structural characteristics of anti-parallel β-sheets in amyloid oligomers. In Aβ40, the C-terminus remains unstructured and rarely interacts with other parts, thereof the hydrophobic clustering is in loose contact and the peptide assumes ES with high probability. In contrast, the C-terminus of Aβ42 adopts a β-strand structure that strongly interacts with segments E3-R5 and V18-A21. The active association leads to a more compact hydrophobic collapse and refrain the alloform from ES. Based on the structural characterization, we propose that the fibril and oligomer assembly pathways could respectively take off from CS and ES, and their aggregation propensity may be governed by the probability of visiting the corresponding conformational states at the equilibrium.

Anti-amyloidogenic properties of some phenolic compounds

A family of 21 polyphenolic compounds consisting of those found naturally in danshen and their analogues were synthesized and subsequently screened for their anti-amyloidogenic activity against the amyloid beta peptide (Aβ₄₂) of Alzheimer’s disease. After 24 h incubation with Aβ₄₂, five compounds reduced thioflavin T (ThT) fluorescence, indicative of their anti-amyloidogenic propensity (p < 0.001). TEM and immunoblotting analysis also showed that selected compounds were capable of hindering fibril formation even after prolonged incubations. These compounds were also capable of rescuing the yeast cells from toxic changes induced by the chemically synthesized Aβ₄₂. In a second assay, a Saccharomyces cerevisiae AHP1 deletant strain transformed with GFP fused to Aβ₄₂ was treated with these compounds and analyzed by flow cytometry. There was a significant reduction in the green fluorescence intensity associated with 14 compounds. We interpret this result to mean that the compounds had an anti-amyloid-aggregation propensity in the yeast and GFP-Aβ₄₂ was removed by proteolysis. The position and not the number of hydroxyl groups on the aromatic ring was found to be the most important determinant for the anti-amyloidogenic properties.

Neuropathology and biochemistry of Aβ and its aggregates in Alzheimer's disease

Alzheimer's disease (AD) is characterized by β-amyloid plaques and intraneuronal τ aggregation usually associated with cerebral amyloid angiopathy (CAA). Both β-amyloid plaques and CAA deposits contain fibrillar aggregates of the amyloid β-peptide (Aβ). Aβ plaques and CAA develop first in neocortical areas of preclinical AD patients and, then, expand in a characteristic sequence into further brain regions with end-stage pathology in symptomatic AD patients. Aβ aggregates are not restricted to amyloid plaques and CAA. Soluble and several types of insoluble non-plaque- and non-CAA-associated Aβ aggregates have been described. Amyloid fibrils are products of a complex self-assembly process that involves different types of transient intermediates. Amongst these intermediate species are protofibrils and oligomers. Different variants of Aβ peptides may result from alternative processing or from mutations that lead to rare forms of familial AD. These variants can exhibit different self-assembly and aggregation properties. In addition, several post-translational modifications of Aβ have been described that result, for example, in the production of N-terminal truncated Aβ with pyroglutamate modification at position 3 (AβN3pE) or of Aβ phosphorylated at serine 8 (pSer8Aβ). Both AβN3pE and pSer8Aβ show enhanced aggregation into oligomers and fibrils. However, the earliest detectable soluble and insoluble Aβ aggregates in the human brain exhibit non-modified Aβ, whereas AβN3pE and pSer8Aβ are detected in later stages. This finding indicates the existence of different biochemical stages of Aβ aggregate maturation with pSer8Aβ being related mainly to cases with symptomatic AD. The conversion from preclinical to symptomatic AD could thereby be related to combined effects of increased Aβ concentration, maturation of aggregates and spread of deposits into additional brain regions. Thus, the inhibition of Aβ aggregation and maturation before entering the symptomatic stage of the disease as indicated by the accumulation of pSer8Aβ may represent an attractive treatment strategy for preventing disease progression.

Direct evidence for self-propagation of different amyloid-β fibril conformations

BACKGROUND

Amyloid fibrils formed by amyloid-β (Aβ) peptides are associated with Alzheimer's disease and can occur in a range of distinct morphologies that are not uniquely determined by the Aβ sequence. Whether distinct conformations of Aβ fibrils can be stably propagated over multiple cycles of seeding and fibril growth has not been established experimentally.

OBJECTIVE

The ability of the 40-residue peptide Aβ1-40 to assemble into fibrils with the conformation of the mutant Aβ1-40 peptide containing the 'Osaka' mutation E22Δ was investigated.

METHODS

Fibril formation of highly pure, recombinant Aβ1-40 in the presence of distinct, preformed seeds in vitro was recorded with thioflavin T fluorescence, and distinct fibrillar structures were identified and distinguished by fluorescence spectroscopy and electron microscopy.

RESULTS

We propagated the specific quaternary structure of Aβ1-40 E22Δ fibrils with wild-type Aβ1-40 over up to seven cycles of seeding and fibril elongation. As a result of a 10(7)-fold dilution of the initially present Aβ1-40 E22Δ seeds, the vast majority of fibrils formed after the seventh propagation cycle with Aβ1-40 did not contain a single molecule of Aβ1-40 E22Δ, but still retained the conformation of the initial Aβ1-40 E22Δ seeds. Increased critical concentrations of Aβ1-40 fibrils formed in the presence of Aβ1-40 E22Δ nuclei suggest that these fibrils are less stable than homologously seeded Aβ1-40 fibrils, consistent with a kinetically controlled mechanism of fibril formation.

CONCLUSION

The propagation of a distinct Aβ fibril conformation over multiple cycles of seeded fibril growth demonstrates the basic ability of the Aβ peptide to form amyloid strains that in turn may cause phenotypes in Alzheimer's disease.

Amyloid-β peptide-specific DARPins as a novel class of potential therapeutics for Alzheimer disease

Passive immunization with anti-amyloid-β peptide (Aβ) antibodies is effective in animal models of Alzheimer disease. With the advent of efficient in vitro selection technologies, the novel class of designed ankyrin repeat proteins (DARPins) presents an attractive alternative to the immunoglobulin scaffold. DARPins are small and highly stable proteins with a compact modular architecture ideal for high affinity protein-protein interactions. In this report, we describe the selection, binding profile, and epitope analysis of Aβ-specific DARPins. We further showed their ability to delay Aβ aggregation and prevent Aβ-mediated neurotoxicity in vitro. To demonstrate their therapeutic potential in vivo, mono- and trivalent Aβ-specific DARPins (D23 and 3×D23) were infused intracerebroventricularly into the brains of 11-month-old Tg2576 mice over 4 weeks. Both D23 and 3×D23 treatments were shown to result in improved cognitive performance and reduced soluble Aβ levels. These findings demonstrate the therapeutic potential of Aβ-specific DARPins for the treatment of Alzheimer disease.

Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins

There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.

Design and application of implicit solvent models in biomolecular simulations

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Implicit solvent replaces explicit water by a potential of mean force.

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Popular models are SASA, VOL and Generalized Born.

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Implicit solvent is used in MD, protein modelling, folding, design, prediction and drug screening.

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Large-scale simulations allow for parametrisation via force matching.

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Application to nucleic acids and membranes is challenging.

We review implicit solvent models and their parametrisation by introducing the concepts and recent devlopments of the most popular models with a focus on parametrisation via force matching. An overview of recent applications of the solvation energy term in protein dynamics, modelling, design and prediction is given to illustrate the usability and versatility of implicit solvation in reproducing the physical behaviour of biomolecular systems. Limitations of implicit modes are discussed through the example of more challenging systems like nucleic acids and membranes.

Differences in β-strand populations of monomeric Aβ40 and Aβ42

Using homonuclear (1)H NOESY spectra, with chemical shifts, (3)JH(N)H(α) scalar couplings, residual dipolar couplings, and (1)H-(15)N NOEs, we have optimized and validated the conformational ensembles of the amyloid-β 1-40 (Aβ40) and amyloid-β 1-42 (Aβ42) peptides generated by molecular dynamics simulations. We find that both peptides have a diverse set of secondary structure elements including turns, helices, and antiparallel and parallel β-strands. The most significant difference in the structural ensembles of the two peptides is the type of β-hairpins and β-strands they populate. We find that Aβ42 forms a major antiparallel β-hairpin involving the central hydrophobic cluster residues (16-21) with residues 29-36, compatible with known amyloid fibril forming regions, whereas Aβ40 forms an alternative but less populated antiparallel β-hairpin between the central hydrophobic cluster and residues 9-13, that sometimes forms a β-sheet by association with residues 35-37. Furthermore, we show that the two additional C-terminal residues of Aβ42, in particular Ile-41, directly control the differences in the β-strand content found between the Aβ40 and Aβ42 structural ensembles. Integrating the experimental and theoretical evidence accumulated over the last decade, it is now possible to present monomeric structural ensembles of Aβ40 and Aβ42 consistent with available information that produce a plausible molecular basis for why Aβ42 exhibits greater fibrillization rates than Aβ40.

Comparative studies of disordered proteins with similar sequences: application to Aβ40 and Aβ42

Quantitative comparisons of intrinsically disordered proteins (IDPs) with similar sequences, such as mutant forms of the same protein, may provide insights into IDP aggregation-a process that plays a role in several neurodegenerative disorders. Here we describe an approach for modeling IDPs with similar sequences that simplifies the comparison of the ensembles by utilizing a single library of structures. The relative population weights of the structures are estimated using a Bayesian formalism, which provides measures of uncertainty in the resulting ensembles. We applied this approach to the comparison of ensembles for Aβ40 and Aβ42. Bayesian hypothesis testing finds that although both Aβ species sample β-rich conformations in solution that may represent prefibrillar intermediates, the probability that Aβ42 samples these prefibrillar states is roughly an order of magnitude larger than the frequency in which Aβ40 samples such structures. Moreover, the structure of the soluble prefibrillar state in our ensembles is similar to the experimentally determined structure of Aβ that has been implicated as an intermediate in the aggregation pathway. Overall, our approach for comparative studies of IDPs with similar sequences provides a platform for future studies on the effect of mutations on the structure and function of disordered proteins.

Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide

The aggregation of intrinsically disordered peptides and proteins is associated with a wide range of highly debilitating neurological and systemic disorders. In this work we explored the potential of a structure-based drug discovery procedure to target one such system, the soluble monomeric form of the Aβ42 peptide. We utilised for this purpose a set of structures of the Aβ42 peptide selected from clusters of conformations within an ensemble generated by molecular dynamics simulations. Using these structures we carried out fragment mapping calculations to identify binding "hot spots" on the monomeric form of the Aβ42 peptide. This procedure provided a set of hot spots with ligand efficiencies comparable to those observed for structured proteins, and clustered into binding pockets. Such binding pockets exhibited a propensity to bind small molecules known to interact with the Aβ42 peptide. Taken together these results provide an initial indication that fragment-based drug discovery may represent a potential therapeutic strategy for diseases associated with the aggregation of intrinsically disordered proteins.

Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide

All-atom explicit solvent model and replica exchange molecular dynamics were used to investigate binding of Alzheimer's biomarker FDDNP to the Aβ(10-40) monomer. At low and high concentrations, FDDNP binds with high affinity to two sites in the Aβ(10-40) monomer located near the central hydrophobic cluster and in the C-terminal. Analysis of ligand- Aβ(10-40) interactions at both concentrations identifies hydrophobic effect as a main binding factor. However, with the increase in ligand concentration the interactions between FDDNP molecules also become important due to strong FDDNP self-aggregation propensity and few specific binding locations. As a result, FDDNP ligands partially penetrate the core of the Aβ(10-40) monomer, forming large self-aggregated clusters. Ligand self-aggregation does not affect hydrophobic interactions as a main binding factor or the location of binding sites in Aβ(10-40). Using the Aβ(10-40) conformational ensemble in ligand-free water as reference, we show that FDDNP induces minor changes in the Aβ(10-40) secondary structure at two ligand concentrations studied. At the same time, FDDNP significantly alters the peptide tertiary fold in a concentration-dependent manner by redistributing long-range, side-chain interactions. We argue that because FDDNP does not change Aβ(10-40) secondary structure, its antiaggregation effect is likely to be weak. Our study raises the possibility that FDDNP may serve as a biomarker of not only Aβ fibril species, but of monomers as well.

Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation

Aggregation of amyloid beta (Aβ) is the hallmark of Alzheimer's disease (AD). Small molecules inhibiting Aβ can be valuable therapeutics for AD. We have previously reported that 1,4-naphthoquinon-2-yl-l-tryptophan (NQTrp), reduces aggregation and oligomerization of Aβ in vitro and in vivo. In silico analysis further showed that certain functional groups of NQTrp, not in the aromatic rings, are also involved in binding and inhibiting Aβ. To better understand the exact mode of action and identify the groups crucial for NQTrp inhibitory activity, we conducted structure-activity analysis. Four derivatives of NQTrp were studied in silico: a D-isomer, two single-methylated and one double-methylated derivative. In silico results showed that the NQTrp groups involved in hydrogen bonds are the anilinic NH (i.e., the NH linker between the quinone and tryptophan moieties), the quinonic carbonyls, and the carboxylic acid. These predictions were supported by in vitro results. Our results should aid in designing improved small-molecule inhibitors of Aβ aggregation for treating AD.

Describing sequence-ensemble relationships for intrinsically disordered proteins

Intrinsically disordered proteins participate in important protein-protein and protein-nucleic acid interactions and control cellular phenotypes through their prominence as dynamic organizers of transcriptional, post-transcriptional and signalling networks. These proteins challenge the tenets of the structure-function paradigm and their functional mechanisms remain a mystery given that they fail to fold autonomously into specific structures. Solving this mystery requires a first principles understanding of the quantitative relationships between information encoded in the sequences of disordered proteins and the ensemble of conformations they sample. Advances in quantifying sequence-ensemble relationships have been facilitated through a four-way synergy between bioinformatics, biophysical experiments, computer simulations and polymer physics theories. In the present review we evaluate these advances and the resultant insights that allow us to develop a concise quantitative framework for describing the sequence-ensemble relationships of intrinsically disordered proteins.