1H NMR of A beta amyloid peptide congeners in water solution. Conformational changes correlate with plaque competence

Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance

Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.

Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study

The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.

Designing multi-target-directed flavonoids: a strategic approach to Alzheimer's disease

The underlying causes of Alzheimer's disease (AD) remain a mystery, with multiple pathological components, including oxidative stress, acetylcholinesterase, amyloid-β, and metal ions, all playing a role. Here we report a strategic approach to designing flavonoids that can effectively tackle multiple pathological elements involved in AD. Our systematic investigations revealed key structural features for flavonoids to simultaneously target and regulate pathogenic targets. Our findings led to the development of a highly promising flavonoid that exhibits a range of functions, based on a complete structure-activity relationship analysis. Furthermore, our mechanistic studies confirmed that this flavonoid's versatile reactivities are driven by its redox potential and direct interactions with pathogenic factors. This work highlights the potential of multi-target-directed flavonoids as a novel solution in the fight against AD.

Stability of the Aβ42 Peptide in Mixed Solutions of Denaturants and Proline

Amyloid β-peptide (Aβ) is responsible for the neuronal damage and death of a patient with Alzheimer's disease (AD). Aβ42 oligomeric forms are dominant neurotoxins and are related to neurodegeneration. Their different forms are related to various pathological conditions in the brain. We investigated Aβ42 peptides in different environments of proline, urea, and GdmCl solutions (in pure and mixed binary forms) through atomistic molecular dynamics simulations. Preferential exclusion from the protein surface and facile formation of a large number of weak molecular interactions are the driving forces for the osmolyte's action. We have focused on these interactions between peptide monomers and pure/mixed osmolytes and denaturants. Urea, as usual, denatures the peptide strongly compared to the GdmCl by accumulation around the peptide. GdmCl shows lesser build-up around protein in contrast to urea but is involved in destabilizing the salt bridge formation of Asp23 and Lys28. Proline as an osmolyte protects the peptide from aggregation when mixed with urea and GdmCl solutions. In mixed solutions of two denaturants and osmolyte plus denaturant, the peptide shows enhanced stability as compared to pure denaturant urea solution. The enhanced stability of peptides in proline may be attributed to its exclusion from the peptide surface and favoring salt bridge formation.

Rational design of photoactivatable metal complexes to target and modulate amyloid-β peptides

The accumulation of amyloid-β (Aβ) aggregates is found in the brains of Alzheimer's disease patients. Thus, numerous efforts have been made to develop chemical reagents capable of targeting Aβ peptides and controlling their aggregation. In particular, tunable coordination and photophysical properties of transition metal complexes, with variable oxidation and spin states on the metal centers, can be utilized to probe Aβ aggregates and alter their aggregation profiles. In this review, we illustrate some rational strategies for designing photoactivatable metal complexes as chemical sensors for Aβ peptides or modulators against their aggregation pathways, with some examples.

Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation

Intrinsically disordered peptides, such as amyloid β42 (Aβ42), lack a well-defined structure in solution. Aβ42 can undergo abnormal aggregation and amyloidogenesis in the brain, forming fibrillar plaques, a hallmark of Alzheimer's disease. The insoluble fibrillar forms of Aβ42 exhibit well-defined, cross β-sheet structures at the molecular level and are less toxic than the soluble, intermediate disordered oligomeric forms. However, the mechanism of initial interaction of monomers and subsequent oligomerization is not well understood. The structural disorder of Aβ42 adds to the challenges of determining the structural properties of its monomers, making it difficult to understand the underlying molecular mechanism of pathogenic aggregation. Certain regions of Aβ42 are known to exhibit helical propensity in different physiological conditions. NMR spectroscopy has shown that the Aβ42 monomer at lower pH can adopt an α-helical conformation and as the pH is increased, the peptide switches to β-sheet conformation and aggregation occurs. CD spectroscopy studies of aggregation have shown the presence of an initial spike in the amount of α-helical content at the start of aggregation. Such an increase in α-helical content suggests a mechanism wherein the peptide can expose critical non-polar residues for interaction, leading to hydrophobic aggregation with other interacting peptides. We have used molecular dynamics simulations to characterize in detail the conformational landscape of monomeric Aβ42 in solution to identify molecular properties that may mediate the early stages of oligomerization. We hypothesized that conformations with α-helical structure have a higher probability of initiating aggregation because they increase the hydrophobicity of the peptide. Although random coil conformations were found to be the most dominant, as expected, α-helical conformations are thermodynamically accessible, more so than β-sheet conformations. Importantly, for the first time α-helical conformations are observed to increase the exposure of aromatic and hydrophobic residues to the aqueous solvent, favoring their hydrophobically driven interaction with other monomers to initiate aggregation. These findings constitute a first step toward characterizing the mechanism of formation of disordered, low-order oligomers of Aβ42.

In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

The role of the environment in amyloid formation based on the fuzzy oil drop model (FOD) is discussed here. This model assumes that the hydrophobicity distribution within a globular protein is consistent with a 3D Gaussian (3DG) distribution. Such a distribution is interpreted as the idealized effect of the presence of a polar solvent-water. A chain with a sequence of amino acids (which are bipolar molecules) determined by evolution recreates a micelle-like structure with varying accuracy. The membrane, which is a specific environment with opposite characteristics to the polar aquatic environment, directs the hydrophobic residues towards the surface. The modification of the FOD model to the FOD-M form takes into account the specificity of the cell membrane. It consists in "inverting" the 3DG distribution (complementing the Gaussian distribution), which expresses the exposure of hydrophobic residues on the surface. It turns out that the influence of the environment for any protein (soluble or membrane-anchored) is the result of a consensus factor expressing the participation of the polar environment and the "inverted" environment. The ratio between the proportion of the aqueous and the "reversed" environment turns out to be a characteristic property of a given protein, including amyloid protein in particular. The structure of amyloid proteins has been characterized in the context of prion, intrinsically disordered, and other non-complexing proteins to cover a wider spectrum of molecules with the given characteristics based on the FOD-M model.

Molecular dynamics study of conformation transition from helix to sheet of Aβ42 peptide

Aβ42 peptides can form helix and sheet structure under different conditions. The conformational conversion is closely associated with Aβ peptides aggregation and their neurotoxicity. But the transition from helix to sheet is not be clearly understood. In this study we performed microsecond timescale MD simulations of Aβ42 peptide to investigate the conformation transition from α-helix to β-sheet. Markov state model (MSM) was built to facilitate identification of crucial intermediate states and possible transition pathway. Based on the analysis, we found that the region Y10-A21 in the middle of Aβ42 peptide plays an initial role in this transition. MSM model revealed that the collapse of helical structure in this region might trigger the formation of sheet structure. Moreover, we further simulated the aggregation of Aβ42 peptides with different conformations. We found that the Aβ42 peptides forming sheet structure have higher aggregation potential compared with peptides with helix structure. These results demonstrate that we can prevent the aggregation of Aβ42 peptides by stabilizing the helix structure in the region of Y10-A21. In addition, this study provides new insight into better understanding the conformational transition and aggregation of Aβ42 peptides.

Structure Analysis of Amyloid Aggregates at Lipid Bilayers by Supercritical Angle Raman Microscopy

The amyloid-β peptide is correlated with Alzheimer's disease and is assumed to cause toxicity by its interaction with the neuron membrane. A custom-made microscope objective based on the supercritical angle technique was developed by our group, which allows investigation of interfacial events by performing surface-sensitive and low-invasive spectroscopy. Applied to Raman spectroscopy, this technique was used to collect information about the structure of polypeptides that interact with a supported lipid bilayer. Notably, the conformation used by amyloid-β(1-40) and amyloid-β(1-42) when interacting directly with or next to the supported lipid bilayer was characterized. We observed two distinct secondary structures, α-helix and β-sheet, which were exhibited by the peptide. These two structures were detected simultaneously. The propensity of the peptide to fold into these structures seemed dependent on both their number of amino acids and their proximity with the supported lipid bilayer. The α-helix structure was observed for amyloid-β(1-42) fragments that were closer to the lipid bilayer. Peptides that were located further away from the bilayer favored the β-sheet structure. Amyloid-β(1-40) was less prone to adopt the α-helix secondary structure.

Cyanidin-3-O-glucoside inhibits Aβ40 fibrillogenesis, disintegrates preformed fibrils, and reduces amyloid cytotoxicity

Alzheimer's disease (AD) is mainly caused by the fibrillogenesis of amyloid-β protein (Aβ). Therefore, the development of effective inhibitors against Aβ fibrillogenesis offers great hope for the treatment of AD. Cyanidin-3-O-glucoside (Cy-3G) is a commonly found anthocyanin that is mainly present in fruits, with established neuroprotective effects in situ. However, it remains unknown if Cy-3G can prevent Aβ fibrillogenesis and alleviate the corresponding cytotoxicity. In this study, extensive biochemical, biophysical, biological and computational experiments were combined to address this issue. It was found that Cy-3G significantly inhibits Aβ40 fibrillogenesis and disintegrates mature Aβ fibrils, and its inhibitory capacity is dependent on the Cy-3G concentration. The circular dichroism results showed that Cy-3G and Aβ40 at a molar ratio of 3 : 1 slightly prevents the structural transformation of Aβ40 from its initial random coil to the β-sheet-rich structure. Co-incubation of Aβ40 with Cy-3G significantly reduced the production of intracellular reactive oxygen species induced by Aβ40 fibrillogenesis and thus reduced Aβ40-induced cytotoxicity. Molecular dynamics simulations revealed that Cy-3G disrupted the β-sheet structure of the Aβ40 trimer. Cy-3G was found to mainly interact with the N-terminal region, the central hydrophobic cluster and the β-sheet region II via hydrophobic and electrostatic interactions. The ten hot spot residues D7, Y10, E11, F19, F20, E22, I31, I32, M35 and V40 were also identified. These findings not only enable a comprehensive understanding of the inhibitory effect of Cy-3G on Aβ40 fibrillogenesis, but also allow the identification of a valuable dietary ingredient that possesses great potential to be developed into functional foods to alleviate AD.

Amyloid-β Peptide-Lipid Bilayer Interaction Investigated by Supercritical Angle Fluorescence

The understanding of the interaction between the membrane of neurons and amyloid-β peptides is of crucial importance to shed light on the mechanism of toxicity in Alzheimer's disease. This paper describes how supercritical angle fluorescence spectroscopy was applied to monitor in real-time the interaction between a supported lipid bilayer (SLB) and the peptide. Different forms of amyloid-β (40 and 42 amino acids composition) were tested, and the interfacial fluorescence was measured to get information about the lipid integrity and mobility. The results show a concentration-dependent damaging process of the lipid bilayer. Prolonged interaction with the peptide up to 48 h lead to an extraction and clustering of lipid molecules from the surface and a potential disruption of the bilayer, correlated with the formation of peptide aggregates. The natural diffusion of the lipid was slightly hindered by the interaction with amyloid-β(1-42) and closely related to the oligomerization of the peptide. The adsorption and desorption of Amyloid-β was also characterized in terms of affinity. Amyloid-β(1-42) exhibited a slightly higher affinity than amyloid-β(1-40). The former was also more prone to aggregate and to adsorb on the bilayer as oligomer.

Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation

Structural characterization of amyloid (A)β peptides implicated in Alzheimer's disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. Only limited information is currently available from experiments on conformational properties and aggregation pathways of the peptides in cellular environments. In silico modeling complements experimental information, providing atomistic insight into structure and dynamics of different Aβ species. All-atom explicit solvent molecular dynamics (MD) simulations with a properly selected force field can deliver reliable structural and dynamic information. In the case of intrinsically disordered Aβ peptides, enhanced sampling simulations beyond the nanosecond time scale are required to obtain statistically meaningful results even for simple solvent conditions. To overcome the challenges of conformational sampling in crowded cellular environments, alternative approaches have to be used, including postprocessing of MD data. In this study, we employ the statistical-mechanical, three-dimensional reference interaction site model with the Kovalenko-Hirata closure integral equation molecular theory of solvation to describe solvent composition effects on the conformational equilibrium in a structural ensemble of the Aβ42 (covering residues 1-42) monomer based on a statistical reweighting technique. The methodology enables a computationally efficient prediction on how different factors in the cellular environment, such as solvent composition, nonpolar solvation, and macromolecular crowding, affect the structural properties of the monomer. Similarities have been identified between changes in the structural ensemble caused by nonpolar solvation and crowded environments modeled by ionic solution with large negative ions. In particular, both solvent conditions reduce the random coil content and enhance the helical structure content of the monomer. In contrast to the previous studies, which reported increased α-helical content of peptides in crowded environments, this work attributes these structural features to the difference in solvent exposure of hydrophilic residues of the monomer for different secondary structure elements, rather than to (entropic) excluded volume effects.

Strategies Employing Transition Metal Complexes To Modulate Amyloid-β Aggregation

Aggregation of amyloid-β (Aβ) peptides is implicated in the development of Alzheimer's disease (AD), the most common type of dementia. Thus, numerous efforts to identify chemical tactics to control the aggregation pathways of Aβ peptides have been made. Among them, transition metal complexes as a class of chemical modulators against Aβ aggregation have been designed and utilized. Transition metal complexes are able to carry out a variety of chemistry with Aβ peptides (e.g., coordination chemistry and oxidative and proteolytic reactions for peptide modifications) based on their tunable characteristics, including the oxidation state of and coordination geometry around the metal center. This Viewpoint illustrates three strategies employing transition metal complexes toward modulation of Aβ aggregation pathways (i.e., oxidation and hydrolysis of Aβ as well as coordination to Aβ), along with some examples of such transition metal complexes. In addition, proposed mechanisms for three reactivities of transition metal complexes with Aβ peptides are discussed. Our greater understanding of how transition metal complexes have been engineered and used for alteration of Aβ aggregation could provide insight into the new discovery of chemical reagents against Aβ peptides found in AD.

Nonproductive Binding Modes as a Prominent Feature of Aβ40 Fiber Elongation: Insights from Molecular Dynamics Simulation

The formation of amyloid fibers has been implicated in a number of neurodegenerative diseases. The growth of amyloid fibers is strongly thermodynamically favorable, but kinetic traps exist where the incoming monomer binds in an incompatible conformation that blocks further elongation. Unfortunately, this process is difficult to follow experimentally at the atomic level. It is also too complex to simulate in full detail and to date has been explored either through coarse-grained simulations, which may miss many important interactions, or full atomic simulations, in which the incoming peptide is constrained to be near the ideal fiber geometry. Here we use an alternate approach starting from a docked complex in which the monomer is from an experimental NMR structure of one of the major conformations in the unbound ensemble, a largely unstructured peptide with the central hydrophobic region in a 3₁₀ helix. A 1000 ns full atomic simulation in explicit solvent shows the formation of a metastable intermediate by sequential, concerted movements of both the fiber and the monomer. A Markov state model shows that the unfolded monomer is trapped at the end of the fiber in a set of interconverting antiparallel β-hairpin conformations. The simulation here may serve as a model for the binding of other non-β-sheet conformations to amyloid fibers.

Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations

Experimental characterization of the molecular structure of small amyloid (A)β oligomers that are currently considered as toxic agents in Alzheimer's disease is a formidably difficult task due to their transient nature and tendency to aggregate. Such structural information is of importance because it can help in developing diagnostics and an effective therapy for the disease. In this study, molecular simulations and protein-protein docking are employed to explore a possible connection between the structure of Aβ monomers and the properties of the intermonomer interface in the Aβ42 dimer. A structurally diverse ensemble of conformations of the monomer was sampled in microsecond timescale implicit solvent replica exchange molecular dynamics simulations. Representative structures with different solvent exposure of hydrophobic residues and secondary structure content were selected to build structural models of the dimer. Analysis of these models reveals that formation of an intramonomer salt bridge (SB) between Asp23 and Lys28 residues can prevent the building of a hydrophobic interface between the central hydrophobic clusters (CHCs) of monomers upon dimerization. This structural feature of the Aβ42 dimer is related to the difference in packing of hydrophobic residues in monomers with the Asp23-Lys28 SB in on and off states, in particular, to a lower propensity to form hydrophobic contacts between the CHC domain and C-terminal residues in monomers with a formed SB. These findings could have important implications for understanding the difference between aggregation pathways of Aβ monomers leading to neurotoxic oligomers or inert fibrillar structures.

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

Molecular dynamics studies of a β-sheet blocking peptide with the full-length amyloid beta peptide of Alzheimer’s disease

The region encompassing residues 13–23 of the amyloid beta peptide (Aβ(13–23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization. A number of pseudopeptides have been designed to bind to Aβ(13–23) and been computationally shown to do so with high affinity. More interactions are available in full-length Aβ than are available in the shorter peptide. We describe herein a study by molecular dynamics (MD) of nine distinct complexes formed by one such pseudopeptide, SGA1, with full-length beta amyloid, Aβ(1–42). The relative stabilities of the Aβ–SGA1 complexes were estimated by a combination of MD and ab initio methods. The most stable complex, designated AB1, was found to be one in which SGA1 is bound to the self-recognition site of Aβ(1–42) in an antiparallel β-sheet fashion. Another complex, designated AB3, also involved SGA1 binding to the self-recognition region of Aβ(1–42), albeit with lower affinity. In both AB1 and AB3, SGA1 formed antiparallel β-sheets but to opposite edges of Aβ. A complex, AB4, with similar stability to AB3, was found with a parallel β-sheet in the self-recognition site. A fourth complex, AB7, also with similar stability, formed a parallel β-sheet in the hydrophobic central region of Aβ. In all cases, complexation of SGA1 induced extensive β-sheet structure in Aβ(1–42).

Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation

Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.

Molecular Structure of Aggregated Amyloid-β: Insights from Solid-State Nuclear Magnetic Resonance

Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates.

Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo.

Conformational features of the Aβ42 peptide monomer and its interaction with the surrounding solvent

Heterogeneous conformational flexibility of the Aβ monomers has been found to be correlated with the corresponding non-uniform entropy gains.

Targeting protein aggregation for the treatment of degenerative diseases

The aggregation of specific proteins is hypothesized to underlie several degenerative diseases, which are collectively known as amyloid disorders. However, the mechanistic connection between the process of protein aggregation and tissue degeneration is not yet fully understood. Here, we review current and emerging strategies to ameliorate aggregation-associated degenerative disorders, with a focus on disease-modifying strategies that prevent the formation of and/or eliminate protein aggregates. Persuasive pharmacological and genetic evidence now supports protein aggregation as the cause of postmitotic tissue dysfunction or loss. However, a more detailed understanding of the factors that trigger and sustain aggregate formation and of the structure-activity relationships underlying proteotoxicity is needed to develop future disease-modifying therapies.

Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations

Interactions of the amyloid β-protein (Aβ) with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer’s disease. Natural mutations in Aβ₄₂, such as the Arctic mutation (E22G) have been shown to increase Aβ₄₂ aggregation and neurotoxicity, leading to the early-onset of Alzheimer’s disease. A correlation between the propensity of Aβ₄₂ to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ₄₂ peptide it was further revealed that the aggregation of different Aβ₄₂ mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ₄₂ mutation and peptide–membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ₄₂ variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants) as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ₄₂ stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ₄₂ peptide and a decreased stability for D23G compared to wild-type Aβ₄₂, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.

Use of a combination of the RDC method and NOESY NMR spectroscopy to determine the structure of Alzheimer's amyloid Aβ10-35 peptide in solution and in SDS micelles

The spatial structure of Alzheimer's amyloid Aβ10-35-NH2 peptide in aqueous solution at pH 7.3 and in SDS micelles was investigated by use of a combination of the residual dipolar coupling method and two-dimensional NMR spectroscopy (TOCSY, NOESY). At pH 7.3 Aβ10-35-NH2 adopts a compact random-coil conformation whereas in SDS micellar solutions two helical regions (residues 13-23 and 30-35) of Aβ10-35-NH2 were observed. By use of experimental data, the structure of "peptide-micelle" complex was determined; it was found that Aβ10-35-NH2 peptide binds to the micelle surface at two regions (residues 17-20 and 29-35).

Effects of confinement on the structure and dynamics of an intrinsically disordered peptide: a molecular-dynamics study

In vivo, proteins and peptides are exposed to radically different environments than those in bulk. Because of the abundance of other cellular components, proteins perform their function in crowded and confined spaces. Confinement has been shown to alter the structure, dynamics, and folding of proteins that possess a native fold. Little is known, however, of the effects of confinement on biologically important intrinsically disordered proteins or peptides (IDP). Here, we use extensive molecular dynamics simulations to investigate the effects of confinement in an IDP, the Aβ21-30, a central folding nucleus of the full length amyloid β-protein. In this study, we report results derived from 107 μs of molecular dynamics simulations that subjected the Aβ21-30 to two types of confinement: hydrophilic and hydrophobic pores. Results show that turn structures are enhanced as a function of decreasing pore size (increasing confinement) over other structures, including coils, β-hairpins, and bridges. However, the percentage occurrence of the dominant hydrogen bond between amino acids Asp23 and Ser26 shown to stabilize the turn in bulk simulations does not increase as a function of confinement signifying a disconnect between structure and internal hydrogen bonding. Differences in structure and dynamics of the decapeptide due to hydrophilic and hydrophobic confinement are more apparent at the extreme confinement conditions, where a reduction of the available phase space in hydrophilic confinement is explained in terms of interactions between the decapeptide and a layer of water at the interface between the decapeptide and the surface of the pore, and a smaller size of the decapeptide in the hydrophobic pores is rationalized in terms of peptide-surface interactions.

Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of plaque deposits in the human brain. The main component of these plaques consists of highly ordered structures called amyloid fibrils, formed by the amyloid β-peptide (Aβ). The mechanism connecting Aβ and AD is yet undetermined. In a previous study, a coarse-grained united-residue model and molecular dynamics simulations were used to model the growth mechanism of Aβ amyloid fibrils. On the basis of these simulations, a dock/lock mechanism was proposed, in which Aβ fibrils grow by adding monomers at either end of an amyloid fibril template. To examine the structures in the early time-scale formation and growth of amyloid fibrils, simulated two-dimensional ultraviolet spectroscopy is used. These early structures are monitored in the far ultraviolet regime (λ = 190-250 nm) in which the computed signals originate from the backbone nπ* and ππ* transitions. These signals show distinct cross-peak patterns that can be used, in combination with molecular dynamics, to monitor local dynamics and conformational changes in the secondary structure of Aβ-peptides. The protein geometry-correlated chiral xxxy signal and the non-chiral combined signal xyxy-xyyx were found to be sensitive to, and in agreement with, a dock/lock pathway.

Modulation of beta-amyloid aggregation by engineering the sequence connecting beta-strand forming domains

Aggregation of beta-amyloid (Aβ) into oligomers and fibrils is associated with the pathology of Alzheimer's disease. The major structural characteristics of Aβ fibrils include the presence of β sheet-loop-β sheet conformations. Several lines of study suggested a potentially important role of the Aβ loop forming sequence (referred to as the Aβ linker region) in Aβ aggregation. Effects of mutations in several charged residues within the Aβ linker region on aggregation have been extensively studied. However, little is known about oligomerization effects of sequence variation in other residues within the Aβ linker region. Moreover, modulation effects of the Aβ linker mutants on Aβ aggregation have yet to be characterized. Here, we created and characterized Aβ linker variants containing sequences preferentially found in specific β turn conformations. Our results indicate that a propensity to form oligomers may be changed by local sequence variation in the Aβ linker region without mutating the charged residues. Strikingly, one Aβ linker variant rapidly formed protofibrillar oligomers, which did not convert to fibrillar aggregates in contrast to Aβ aggregating to fibrils under similar incubation conditions. Moreover, our results suggest that molecular forces critical in oligomerization and fibrillization may differ at least for those involved in the linker region. When co-incubated with Aβ, some Aβ linker variants were found to induce accumulation of Aβ oligomers. Our results suggest that engineering of the Aβ linker region as described in this paper may represent a novel approach to control Aβ oligomerization and create Aβ oligomerization modulators.

Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer

The aggregation of amyloid beta (Aβ) peptides plays an important role in the development of Alzheimer's disease. Despite extensive effort, it has been difficult to characterize the secondary and tertiary structure of the Aβ monomer, the starting point for aggregation, due to its hydrophobicity and high aggregation propensity. Here, we employ extensive molecular dynamics simulations with atomistic protein and water models to determine structural ensembles for Aβ(42), Aβ(40), and Aβ(42)-E22K (the Italian mutant) monomers in solution. Sampling of a total of >700 microseconds in all-atom detail with explicit solvent enables us to observe the effects of peptide length and a pathogenic mutation on the disordered Aβ monomer structural ensemble. Aβ(42) and Aβ(40) have crudely similar characteristics but reducing the peptide length from 42 to 40 residues reduces β-hairpin formation near the C-terminus. The pathogenic Italian E22K mutation induces helix formation in the region of residues 20-24. This structural alteration may increase helix-helix interactions between monomers, resulting in altered mechanism and kinetics of Aβ oligomerization.

Dynamics of metastable β-hairpin structures in the folding nucleus of amyloid β-protein

The amyloid β-protein (Aβ), which is present predominately as a 40- or 42-residue peptide, is postulated to play a seminal role in the pathogenesis of Alzheimer's disease (AD). Folding of the Aβ(21-30) decapeptide region is a critical step in the aggregation of Aβ. We report results of constant temperature all-atom molecular dynamics simulations in explicit water of the dynamics of monomeric Aβ(21-30) and its Dutch [Glu22Gln], Arctic [Glu22Gly], and Iowa [Asp23Asn] isoforms that are associated with familial forms of cerebral amyloid angiopathy and AD. The simulations revealed a variety of loop conformers that exhibited a hydrogen bond network involving the Asp23 and Ser26 amino acids. A population of conformers, not part of the loop population, was found to form metastable β-hairpin structures with the highest probability in the Iowa mutant. At least three β-hairpin structures were found that differed in their hydrogen bonding register, average number of backbone hydrogen bonds, and lifetimes. Analysis revealed that the Dutch mutant had the longest β-hairpin lifetime (≥500 ns), closely followed by the Iowa mutant (≈500 ns). Aβ(21-30) and the Arctic mutant had significantly lower lifetimes (≈200 ns). Hydrophobic packing of side chains was responsible for enhanced β-hairpin lifetimes in the Dutch and Iowa mutants, whereas lifetimes in Aβ(21-30) and its Arctic mutant were influenced by the backbone hydrogen bonding. The data suggest that prolonged β-hairpin lifetimes may impact peptide pathogenicity in vivo.

A strategy for designing a peptide probe for detection of β-amyloid oligomers

Aggregation of β-amyloid (Aβ) is implicated in the pathology of Alzheimer's disease. Development of a robust strategy to detect Aβ oligomeric intermediates, which have been identified as significant toxic agents, would be highly beneficial in the screening of drug candidates as well as enhancing our understanding of Aβ oligomerization. Rapid, specific and quantitative detection, currently unavailable, would be highly preferred for accurate and reliable probing of transient Aβ oligomers. Here, we report the development of a novel peptide probe, PG46, based on the nature of Aβ self-assembly and the conformation-sensitive fluorescence of the biarsenical dye, FlAsH. PG46 was found to bind to Aβ oligomers and displayed an increase in FlAsH fluorescence upon binding. No such event was observed when PG46 was co-incubated with Aβ low-molecular-weight species or Aβ fibrils. Aβ oligomer detection was fast, and occurred within one hour without any additional sample incubation or preparation. We anticipate that the development of a strategy for detection of amyloid oligomers described in this study will be directly relevant to a host of other amyloidogenic proteins.

Secondary Structure Assignment of Amyloid-β Peptide Using Chemical Shifts

The distinct conformational dependence of chemical shifts caused by α-helices and β-sheets renders NMR chemical shift analysis a powerful tool for the structural determination of proteins. However, the time scale of NMR experiments can make a secondary structure assignment of highly flexible peptides or proteins, which may be converting between conformational substates, problematic. For instance the amyloid-β monomer, according to NMR chemical shifts, adopts a predominately random coil structure in aqueous solution (with <3% α-helical content). Molecular dynamics simulations, on the other hand, suggest that α-helical content can be significant (10-25%). In this paper, we explore the possible reasons for this discrepancy and show that the different results from experiments and theory are not necessarily mutually exclusive but may reflect a general problem of secondary structure assignment of conformationally flexible biomolecules.

Toward a molecular theory of early and late events in monomer to amyloid fibril formation

Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of transition from monomers to fibrils is needed to obtain insights into the growth of amyloid fibrils and more generally self-assembly multisubunit protein complexes. Significant advances using computations of protein aggregation in a number of systems have established generic and sequence-specific aspects of the early steps in oligomer formation. Theoretical considerations, which view oligomer and fibril growth as diffusion in a complex energy landscape, and computational studies, involving minimal lattice and coarse-grained models, have revealed general principles governing the transition from monomeric protein to ordered fibrillar aggregates. Detailed atomistic calculations have explored the early stages of the protein aggregation pathway for a number of amyloidogenic proteins, most notably amyloid β- (Aβ-) protein and fragments from proteins linked to various diseases. These computational studies have provided insights into the role of sequence, role of water, and specific interatomic interactions underlying the thermodynamics and dynamics of elementary kinetic steps in the aggregation pathway. Novel methods are beginning to illustrate the structural basis for the production of Aβ-peptides through interactions with secretases in the presence of membranes. We show that a variety of theoretical approaches, ranging from scaling arguments to minimal models to atomistic simulations, are needed as a complement to experimental studies probing the principles governing protein aggregation.

Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field

The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ(1-40) fibril, we placed an unstructured monomer at a distance of 20 Å from a fibril template and allowed it to interact freely with the latter. The monomer was not biased towards fibril conformation by either the force field or the MD algorithm. With the use of a coarse-grained model with replica-exchange molecular dynamics, a longer timescale was accessible, making it possible to observe how the monomers probe different binding modes during their search for the fibril conformation. Although different assembly pathways were seen, they all follow a dock-lock mechanism with two distinct locking stages, consistent with experimental data on fibril elongation. Whereas these experiments have not been able to characterize the conformations populating the different stages, we have been able to describe these different stages explicitly by following free monomers as they dock onto a fibril template and to adopt the fibril conformation (i.e., we describe fibril elongation step by step at the molecular level). During the first stage of the assembly ("docking"), the monomer tries different conformations. After docking, the monomer is locked into the fibril through two different locking stages. In the first stage, the monomer forms hydrogen bonds with the fibril template along one of the strands in a two-stranded β-hairpin; in the second stage, hydrogen bonds are formed along the second strand, locking the monomer into the fibril structure. The data reveal a free-energy barrier separating the two locking stages. The importance of hydrophobic interactions and hydrogen bonds in the stability of the Aβ fibril structure was examined by carrying out additional canonical MD simulations of oligomers with different numbers of chains (4-16 chains), with the fibril structure as the initial conformation. The data confirm that the structures are stabilized largely by hydrophobic interactions and show that intermolecular hydrogen bonds are highly stable and contribute to the stability of the oligomers as well.

Lipid-induced conformational transition of amyloid beta peptide fragments

Conformational transition of soluble monomeric amyloid beta-peptide (Abeta) into oligomeric and protofibrillar aggregates plays a key role in the pathogenesis of Alzheimer's disease (AD). One of the central questions surrounding the molecular pathophysiology of AD is how the soluble Abeta is converted into its aggregated toxic form. A more detailed understanding of the conformational transitions involved in the self-assembly of Abeta may facilitate the design of inhibitors of aggregation. In this study, we evaluated the wild-type (WT) Abeta 16-28 peptide (KLVFFAEDVGSNK) and its associated mutants, including A21G (Flemish), E22K (Italian), E22Q (Dutch), and E22G (Arctic) mutants, by examining, in particular, their aggregation kinetics in the presence and in the absence of negatively charged and zwitterionic lipids. Circular dichroic and thioflavin T fluorescence studies indicated that the WT peptide undergoes a rapid conformational transition into beta-sheet structure in solution, whereas the Arctic and Dutch variants show a markedly rapid transition into beta-sheet structure in the presence of negatively charged lipids. These results provide strong evidence suggesting that the reduction in net charge, with a concurrent increase in the net hydrophobicity of the peptide alone or when complexed with lipid in solution, determines the rate of aggregate formation.

Principles governing oligomer formation in amyloidogenic peptides

Identifying the principles that describe the formation of protein oligomers and fibrils with distinct morphologies is a daunting problem. Here we summarize general principles of oligomer formation gleaned from molecular dynamics simulations of Abeta-peptides. The spectra of high free energy structures sampled by the monomer provide insights into the plausible fibril structures, providing a rationale for the 'strain phenomenon.' Heterogeneous growth dynamics of small oligomers of Abeta(16-22), whose lowest free energy structures are like nematic droplets, can be broadly described using a two-stage dock-lock mechanism. In the growth process, water is found to play various roles depending on the oligomer size, and peptide length, and sequence. Water may be an explicit element of fibril structure linked to various fibril morphologies.

Structures and thermodynamics of Alzheimer's amyloid-beta Abeta(16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Abeta fibrillation

Many proteins display a strand-loop-strand motif in their amyloid fibrillar states. For instance, the amyloid beta-protein, Abeta1-40, associated with Alzheimer's disease, displays a loop at positions 22-28 in its amyloid fibril state. It has been suggested that this loop could appear early in the aggregation process, but quantitative information regarding its presence in small oligomers remains scant. Because residues 1-15 are disordered in Abeta1-42 fibrils and Abeta10-35 forms fibrils in vitro, we select the peptide Abeta16-35, centered on residues 22-28 and determine the structures and thermodynamics of the monomer and dimer using coarse-grained implicit solvent replica exchange molecular dynamics simulations. Our simulations totalling 5 mus for the monomer and 12 micros for the dimer show no sign of strong secondary structure signals in both instances and the significant impact of dimerization on the global structure of Abeta16-35. They reveal however that the loop 22-28 acts as a quasi-independent unit in both species. The loop structure ensemble we report in Abeta16-35 monomer and dimer has high similarity to the loop formed by the Abeta21-30 peptide in solution and, to a lesser extent, to the loop found in Abeta1-40 fibrils. We discuss the implications of our findings on the assembly of full-length Abeta.

Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences

Alloform-specific differences in structural dynamics between amyloid beta-protein (Abeta) 40 and Abeta42 appear to underlie the pathogenesis of Alzheimer's disease. To elucidate these differences, we performed microsecond timescale replica-exchange molecular dynamics simulations to sample the conformational space of the Abeta monomer and constructed its free-energy surface. We find that neither peptide monomer is unstructured, but rather that each may be described as a unique statistical coil in which five relatively independent folding units exist, comprising residues 1-5, 10-13, 17-22, 28-37, and 39-42, which are connected by four turn structures. The free-energy surfaces of both peptides are characterized by two large basins, comprising conformers with either substantial alpha-helix or beta-sheet content. Conformational transitions within and between these basins are rapid. The two additional hydrophobic residues at the Abeta42 C-terminus, Ile41 and Ala42, significantly increase contacts within the C-terminus, and between the C-terminus and the central hydrophobic cluster (Leu17-Ala21). As a result, the beta-structure of Abeta42 is more stable than that of Abeta40, and the conformational equilibrium in Abeta42 shifts towards beta-structure. These results suggest that drugs stabilizing alpha-helical Abeta conformers (or destabilizing the beta-sheet state) would block formation of neurotoxic oligomers. The atomic-resolution conformer structures determined in our simulations may serve as useful targets for this purpose. The conformers also provide starting points for simulations of Abeta oligomerization-a process postulated to be the key pathogenetic event in Alzheimer's disease.