Oligomerization of amyloid Abeta16-22 peptides using hydrogen bonds and hydrophobicity forces

Phase networks of cross-β peptide assemblies

Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.

Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations

To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

Spontaneous formation of twisted Aβ(16-22) fibrils in large-scale molecular-dynamics simulations

Protein aggregation is associated with fatal neurodegenerative diseases, including Alzheimer's and Parkinson's. Mapping out kinetics along the aggregation pathway could provide valuable insights into the mechanisms that drive oligomerization and fibrillization, but that is beyond the current scope of computational research. Here we trace out the full kinetics of the spontaneous formation of fibrils by 48 Aβ(16-22) peptides, following the trajectories in molecular detail from an initial random configuration to a final configuration of twisted protofilaments with cross-β-structure. We accomplish this by performing large-scale molecular-dynamics simulations based on an implicit-solvent, intermediate-resolution protein model, PRIME20. Structural details such as the intersheet distance, perfectly antiparallel β-strands, and interdigitating side chains analogous to a steric zipper interface are explained by and in agreement with experiment. Two characteristic fibrillization mechanisms - nucleation/templated growth and oligomeric merging/structural rearrangement - emerge depending on the temperature.

Molecular insight into conformational transition of amyloid β-peptide 42 inhibited by (-)-epigallocatechin-3-gallate probed by molecular simulations

Considerable experimental evidence indicates that (-)-epigallocatechin-3-gallate (EGCG) inhibits the fibrillogenesis of Aβ(42) and alleviates its associated cytotoxicity. However, the molecular mechanism of the inhibition effect of EGCG on the conformational transition of Aβ(42) remains unclear due to the limitations of current experimental techniques. In this work, molecular dynamics simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis were coupled to better understand the issue. It was found that the direct interactions between EGCG and the peptide are the origin of its inhibition effects. Specifically, EGCG molecules expel water from the surface of the Aβ(42), cluster with each other, and interact directly with the peptide. The results of free energy decomposition calculated by MM-PBSA indicate that the nonpolar term contributes more than 71% to the binding free energy of the EGCG-Aβ(42) complex, while polar interactions (i.e., hydrogen bonding) play a minor role. It was identified that there are 12 important residues of Aβ(42) that strongly interact with EGCG (Phe4, Arg5, Phe19, Phe20, Glu22, Lys28, Gly29, Leu34-Gly37, and Ile41), while nonpolar interactions are mainly provided by the side chains of some hydrophobic residues (Phe, Met and Ile) and the main chains of some nonhydrophobic residues (Lys28 and Gly29). On the contrary, polar interactions are mainly formed by the main chain of Aβ(42), of which the main chains of Gly29 and Gly37 contribute greatly. The work has thus elucidated the molecular mechanism of the inhibition effect of EGCG on the conformational transition of Aβ(42), and the findings are considered critical for exploring more effective agents for the inhibition of Aβ(42) fibrillogenesis.

Intrinsic determinants of Aβ(12-24) pH-dependent self-assembly revealed by combined computational and experimental studies

The propensity of amyloid- (A) peptide to self-assemble into highly ordered amyloid structures lies at the core of their accumulation in the brain during Alzheimer's disease. By using all-atom explicit solvent replica exchange molecular dynamics simulations, we elucidated at the atomic level the intrinsic determinants of the pH-dependent dimerization of the central hydrophobic segment A and related these with the propensity to form amyloid fibrils measured by experimental tools such as atomic force microscopy and fluorescence. The process of A dimerization was evaluated in terms of free energy landscape, side-chain two-dimensional contact probability maps, -sheet registries, potential mean force as a function of inter-chain distances, secondary structure development and radial solvation distributions. We showed that dimerization is a key event in A amyloid formation; it is highly prompted in the order of pH 5.02.98.4 and determines further amyloid growth. The dimerization is governed by a dynamic interplay of hydrophobic, electrostatic and solvation interactions permitting some variability of -sheets at each pH. These results provide atomistic insight into the complex process of molecular recognition detrimental for amyloid growth and pave the way for better understanding of the molecular basis of amyloid diseases.

Self-assembly of short aβ(16-22) peptides: effect of terminal capping and the role of electrostatic interaction

We report the characterization of self-assembly of two short β-amyloid (Aβ) peptides (16-22), KLVFFAE and Ac-KLVFFAE-NH2, focusing on examining the effect of terminal capping. At pH 2.0, TEM and AFM imaging revealed that the uncapped peptide self-assembled into long, straight, and unbranched nanofibrils with a diameter of 3.8 ± 1.0 nm while the capped one formed nanotapes with a width of 70.0 ± 25.0 nm. CD analysis indicated the formation of β-sheet structures in both aggregated systems, but the characteristic CD peaks were less intense and less red-shifted for the uncapped than the capped one, indicative of weaker hydrogen bonding and weaker π-π stacking. Fluorescence and rheological measurements also confirmed stronger intermolecular attraction associated with the capped nanotapes. At acidic pH 2, each uncapped KLVFFAE molecule carries two positive charges at the N-terminus, and the strong electrostatic repulsion favors interfacial curving and twisting within the β-sheet, causing weakening of hydrogen bonds and π-π stacking. In contrast, capping reduces the charge by half, and intermolecular electrostatic repulsion is drastically reduced. As a result, the lateral attraction of β-sheets favors stronger lamellar structuring, leading to the formation of rather flat nanotapes. Flat tapes with similar morphological structure were also formed by the capped peptide at pH 12.0 where the charge on the capping end was reversed. This study has thus demonstrated how self-assembled nanostructures of small peptides can be manipulated through simple molecular structure design and tuning of electrostatic interaction.

Impact on the replacement of Phe by Trp in a short fragment of Aβ amyloid peptide on the formation of fibrils

Aβ(16-22) (Ac-KLVFFAE-NH(2) ) is one of the shortest amyloid fibril-forming sequences identified in β-amyloid peptide. At neutral pH, the peptide forms fibrils in the concentration range of 0.2-2.0 mM after ≥ 10 days of incubation. Structures of the fibrils proposed based on solid-state NMR and MD simulations studies suggest antiparallel arrangement of β-strands and aromatic interactions between the Phe residues. In an effort to examine the role of aromatic interactions between two Phe residues in Aβ(16-22) , we have studied the self-assembly of Aβ(16-22) (AβFF) and two of its variants, Ac-KLVFWAE-NH(2) (AβFW) and Ac-KLVWFAE-NH(2) (AβWF). The peptides were dissolved in methanol (MeOH) at a concentration of 1 mM and in water (AβFW and AβWF, 1 mM; AβFF, 330 µM). Peptide solutions (100 µM) were prepared in 50 mM sodium phosphate buffer at pH 7 by diluting from MeOH and water stock solutions. AβFW forms amyloid-like fibrils immediately from MeOH, as indicated by atomic force microscopy. Dilution of AβFW into phosphate buffer from stock solution prepared in MeOH results in fibrils, but with different morphology and dimensions. The secondary structure potentiated by MeOH seems to be important for the self-assembly of AβFW, as fibrils are not formed from water where the peptide is unordered. On the other hand, AβFF and AβWF do not form amyloid fibrils rapidly from any of the solvents used for dissolution. However, drying of AβWF from MeOH on mica surface gives rod-like and fibrous structures. Our study indicates that positioning of the aromatic residues F and W has an important role to play in promoting self-assembly of the Aβ(16-22) peptides.

Extending the PRIME model for protein aggregation to all 20 amino acids

We extend PRIME, an intermediate-resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, to the description of the geometry and energetics of peptides containing all 20 amino acid residues. The 20 amino acid side chains are classified into 14 groups according to their hydrophobicity, polarity, size, charge, and potential for side chain hydrogen bonding. The parameters for extended PRIME, called PRIME 20, include hydrogen-bonding energies, side chain interaction range and energy, and excluded volume. The parameters are obtained by applying a perceptron-learning algorithm and a modified stochastic learning algorithm that optimizes the energy gap between 711 known native states from the PDB and decoy structures generated by gapless threading. The number of independent pair interaction parameters is chosen to be small enough to be physically meaningful yet large enough to give reasonably accurate results in discriminating decoys from native structures. The most physically meaningful results are obtained with 19 energy parameters.

Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: insights from all-atom simulations

Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

Probing the strand orientation and registry alignment in the propagation of amyloid fibrils

Detailed knowledge of the structure and growth mechanism of amyloid fibrils is important for understanding the disease process. Recently, solid-state NMR and other spectroscopic data have revealed the equilibrium organization of the tertiary structure of fibrils formed by various segments of beta-amyloid peptides. A three-step "dock-and-lock" mechanism for fibril growth has been proposed on the basis of the kinetic data. Here we use all-atom replica-exchange molecular dynamics simulations in generalized-Born implicit solvent to probe the mechanism of tertiary structure propagation in fibrils of Abeta(16-22) modeled as an oligomer consisting of two beta-sheets each having four strands. The data show that following association with the oligomer, but before being fully locked onto the existing beta-sheet, the added monomer predominantly samples states with the antiparallel strand orientation, but both in- and one-residue shifted backbone hydrogen bond alignments. The in-register state, which is the experimentally observed equilibrium alignment, is marginally more stable than the registry-shifted one. These results suggest that, following the fast docking step, the added monomer dynamically slides in the backbone registry, and stabilization of the preferential alignment must occur in the second locking step as the monomer becomes fully integrated with the fibril. We also delineate the electrostatic and hydrophobic effects in directing the registry alignment during monomer addition. Surprisingly, the in-register alignment provides both increased cross-strand electrostatic attraction and hydrophobic surface burial. Finally, our data support the notion that side chain hydrophobic burial is a major driving force for beta-sheet assembly.

Self-assembly of polypeptides into left-handedly twisted fibril-like structures

In this paper, we investigated the spontaneous formation of aggregation structures of amyloid-forming peptide (GGVVIA) using a coarse-grained model and Monte Carlo simulations. The effects of concentration and temperature on the formation of different aggregation structures were studied. Three types of aggregation structures, single-layer beta sheet, amorphous beta-sheet aggregate, and fibril-like structures, were observed in our simulations. The fibril-like structures obtained in simulations have a common cross-beta spine structure in which beta sheets twist in a left-handed fashion. The averaged twisting angle of the beta sheet in the fibril-like structures is 12 degrees +/-2 degrees. Moreover, it was found that the peptides in the same beta sheets prefer to arrange in a parallel way, which is consistent with the corresponding GGVVIA crystalline structure. On the other hand, it was found that there is a rich family of beta-sheet stacking patterns in the fibril-like structures suggesting that the fibril structures are more complex than the corresponding crystalline structure and there exist many local free-energy minima rather than a distinct global minimum.

Elongation dynamics of amyloid fibrils: a rugged energy landscape picture

Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained model of peptides. Our simulation results suggest that the elongation process is dominated by a series of local minimum due to frustration in monomer-fibril interactions. This rugged energy landscape picture indicates that the amount of recycling of monomers at the fibrils' ends before being fibrilized is substantially reduced in comparison to the conventional two-step elongation model. This picture, along with other predictions discussed, can be tested with current experimental techniques.

A coarse-grained protein force field for folding and structure prediction

We have revisited the protein coarse-grained optimized potential for efficient structure prediction (OPEP). The training and validation sets consist of 13 and 16 protein targets. Because optimization depends on details of how the ensemble of decoys is sampled, trial conformations are generated by molecular dynamics, threading, greedy, and Monte Carlo simulations, or taken from publicly available databases. The OPEP parameters are varied by a genetic algorithm using a scoring function which requires that the native structure has the lowest energy, and the native-like structures have energy higher than the native structure but lower than the remote conformations. Overall, we find that OPEP correctly identifies 24 native or native-like states for 29 targets and has very similar capability to the all-atom discrete optimized protein energy model (DOPE), found recently to outperform five currently used energy models.

Effect of dehydration on the aggregation kinetics of two amyloid peptides

It is well-known that water plays a crucial role in the folding, dynamics, and function of proteins. Here we provide further evidence showing that the aggregation kinetics of peptides also depend strongly on their hydration status. Using reverse micelles as a tool to modulate the accessible number of water molecules and infrared spectroscopy and transmission electron microscopy as means to monitor aggregate formation, we show that the rate of aggregation of two amyloid forming peptides increases significantly under conditions where limited hydration of the peptide molecule is expected to occur. These results not only are in accord with recent computer simulations indicating that the expulsion of interfacial water molecules is a key event in the dimerization/oligmerization of amyloid beta (Abeta) peptides but also have implications for amyloid formation in vivo where molecular crowding is expected to influence the solvation status of proteins.

Computational validation of protein nanotubes

We present a novel generic computational method to assess protein nanotubes with variable diameter sizes at the atomic level given their low resolution protomeric structures. The method is based on the symmetrical assembly of a repeating protein subunit into a nanotube. Given the protein unit-cell, and the tube diameter and helicity, we carry out all-atom molecular dynamics simulations, combined with a unique mathematical transformation. This allows us to mimic nanotubes of even huge sizes without end or edge effects. All our simulation setups attempt to explicitly adhere to the conditions under which the experiments were conducted. Thus, we are able to obtain high resolution atomic-scale structures at reasonable computational costs. We expect that our approach would prove useful in assessing protein nanotubes, as well as in silico constructions of novel nanobiomaterials.

Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition

The study of the molecular recognition and self-organization properties of peptides has emerged in recent years as a very active and diverse field of research, ranging from biomedicine to biotechnology and even to material sciences. In the case of biomedicine, peptides can be used as ligands of biological receptors to gain insights into the structural, dynamical, and chemical determinants underlying the formation of complexes and identify new effectors of biological processes of interest. In the case of biotechnology and material science, short sequences have been used to understand the sequence determinants of the formation of ordered supra-molecular structures of nanoscale dimensions. In this work, we will describe our research activities in these two areas of modern chemical biology. In the first part, we will describe the development of a new, specific, potent, and selective anticancer peptide and its use to obtain the information needed to identify a non-peptidic small molecular lead to be used as an inhibitor of cancer growth. In the second part, we will describe the introduction of a new method for the description of the self-organization process at the basis of the growth of ordered supra-molecular structures held together by weak, non-covalent, yet specific interactions.

Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment

Small oligomers formed early in the process of amyloid fibril formation may be the major toxic species in Alzheimer's disease. We investigate the early stages of amyloid aggregation for the tau fragment AcPHF6 (Ac-VQIVYK-NH2) using an implicit solvent all-atom model and extensive Monte Carlo simulations of 12, 24, and 36 chains. A variety of small metastable aggregates form and dissolve until an aggregate of a critical size and conformation arises. However, the stable oligomers, which are β-sheet-rich and feature many hydrophobic contacts, are not always growth-ready. The simulations indicate instead that these supercritical oligomers spend a lengthy period in equilibrium in which considerable reorganization takes place accompanied by exchange of chains with the solution. Growth competence of the stable oligomers correlates with the alignment of the strands in the β-sheets. The larger aggregates seen in our simulations are all composed of two twisted β-sheets, packed against each other with hydrophobic side chains at the sheet–sheet interface. These β-sandwiches show similarities with the proposed steric zipper structure for PHF6 fibrils but have a mixed parallel/antiparallel β-strand organization as opposed to the parallel organization found in experiments on fibrils. Interestingly, we find that the fraction of parallel β-sheet structure increases with aggregate size. We speculate that the reorganization of the β-sheets into parallel ones is an important rate-limiting step in the formation of PHF6 fibrils.

It is believed that the self association of certain protein molecules into aggregated structures, known as amyloid fibrils, plays an important role in a variety of human diseases, such as Alzheimer's disease and Parkinson's disease. Although the ability to form such amyloid fibrils is a common property for proteins, the process leading to these fibrils is incompletely understood. The early stages of the process involve small transient heterogeneous structures made of a few protein chains and are especially difficult to characterize. Here we use atomic-level simulations to explore the early part of the aggregation process for a fibril-forming fragment of the protein tau associated with Alzheimer's disease. We find that a multitude of small aggregates, rich in sheetlike structures, form through a nucleation process. Interestingly, a statistically preferred type of aggregate, consisting of two tightly packed sheets, emerges with increasing aggregate size. Growth of these larger aggregates seems to be a slow process that correlates with the emergence of more uniformly ordered sheets. We speculate that reorganization of the protein chains leading to that ordered arrangement is an important bottleneck to amyloid fibril formation for this peptide.

Probing the mechanisms of fibril formation using lattice models

Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature (T) and the number of chains (M). While these models are, at best, caricatures of peptides, we show that a number of generic features thought to govern fibril assembly are captured by the toy model. The monomer, which contains eight beads made from three letters (hydrophobic, polar, and charged), adopts a compact conformation in the native state. In both the single-layered protofilament (seen for M10) structures, the monomers are arranged in an antiparallel fashion with the "strandlike" conformation that is perpendicular to the fibril axis. Partial unfolding of the folded monomer that populates an aggregation prone conformation (N(*)) is required for ordered assembly. The contacts in the N(*) conformation, which is one of the four structures in the first "excited" state of the monomer, are also present in the native conformation. The time scale for fibril formation is a minimum in the T-range when the conformation N(*) is substantially populated. The kinetics of fibril assembly occurs in three distinct stages. In each stage there is a cascade of events that transforms the monomers and oligomers to ordered structures. In the first "burst" stage, highly mobile oligomers of varying sizes form. The conversion to the N(*) conformation occurs within the oligomers during the second stage in which a vast number of interchain contacts are established. As time progresses, a dominant cluster emerges that contains a majority of the chains. In the final stage, the aggregation of N(*) particles serve as a template onto which smaller oligomers or monomers can dock and undergo conversion to fibril structures. The overall time for growth in the latter stages is well described by the Lifshitz-Slyazov growth kinetics for crystallization from supersaturated solutions. The detailed analysis shows that elements of the three popular models, namely, nucleation and growth, templated assembly, and nucleated conformational conversion are present at various stages of fibril assembly.

The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations

Thioflavin T (ThT) is a fluorescent dye commonly used to stain amyloid plaques, but the binding sites of this dye onto fibrils are poorly characterized. We present molecular dynamics simulations of the binding of ThT and its neutral analog BTA-1 [2-(4'-methylaminophenyl)benzothiazole] to model protofibrils of the Alzheimer's disease Abeta(16-22) (amyloid beta) peptide. Our simulations reveal two binding modes located at the grooves of the beta-sheet surfaces and at the ends of the beta-sheet. These simulations provide new insight into recent experimental work and allow us to characterize the high-capacity, micromolar-affinity site seen in experiment as binding to the beta-sheet surface grooves and the low-capacity, nanomolar-affinity site seen as binding to the beta-sheet extremities of the fibril. The structure-activity relationship upon mutating charged ThT to neutral BTA-1 in terms of increased lipophilicity and binding affinity was studied, with calculated solvation free energies and binding energies found to be in qualitative agreement with the experimental measurements.

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments

The role of water in promoting the formation of protofilaments (the basic building blocks of amyloid fibrils) is investigated using fully atomic molecular dynamics simulations. Our model protofilament consists of two parallel beta-sheets of Alzheimer Amyloid-beta 16-22 peptides (Ac-K(16)-L(17)-V(18)-F(19)-F(20)-A(21)-E(22)-NH2). Each sheet presents a distinct hydrophobic and hydrophilic face and together self-assemble to a stable protofilament with a core consisting of purely hydrophobic residues (L(17), F(19), A(21)), with the two charged residues (K(16), E(22)) pointing to the solvent. Our simulations reveal a subtle interplay between a water mediated assembly and one driven by favorable energetic interactions between specific residues forming the interior of the protofilament. A dewetting transition, in which water expulsion precedes hydrophobic collapse, is observed for some, but not all molecular dynamics trajectories. In the trajectories in which no dewetting is observed, water expulsion and hydrophobic collapse occur simultaneously, with protofilament assembly driven by direct interactions between the hydrophobic side chains of the peptides (particularly between F-F residues). For those same trajectories, a small increase in the temperature of the simulation (on the order of 20 K) or a modest reduction in the peptide-water van der Waals attraction (on the order of 10%) is sufficient to induce a dewetting transition, suggesting that the existence of a dewetting transition in simulation might be sensitive to the details of the force field parametrization.

Finite size effects in simulations of protein aggregation

It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligomeric species are starting to make significant contributions to our understanding of the determinants of protein aggregation. We simulate different systems at constant concentration but with a different number of peptides and we study the how the finite number of proteins affects the underlying free energy of the system and therefore the relative stability of the species involved in the process. If not taken into account, this finite size effect can undermine the validity of theoretical predictions regarding the relative stability of the species involved and the rates of conversion from one to the other. We discuss the reasons that give rise to this finite size effect form both a probabilistic and energy fluctuations point of view and also how this problem can be dealt by a finite size scaling analysis.

Energy landscapes of the monomer and dimer of the Alzheimer's peptide Abeta(1-28)

The cytotoxicity of Alzheimer's disease has been linked to the self-assembly of the 4042 amino acid of the amyloid-beta (Abeta) peptide into oligomers. To understand the assembly process, it is important to characterize the very first steps of aggregation at an atomic level of detail. Here, we focus on the N-terminal fragment 1-28, known to form fibrils in vitro. Circular dichroism and NMR experiments indicate that the monomer of Abeta(1-28) is alpha-helical in a membranelike environment and random coil in aqueous solution. Using the activation-relaxation technique coupled with the OPEP coarse grained force field, we determine the structures of the monomer and of the dimer of Abeta(1-28). In agreement with experiments, we find that the monomer is predominantly random coil in character, but displays a non-negligible beta-strand probability in the N-terminal region. Dimerization impacts the structure of each chain and leads to an ensemble of intertwined conformations with little beta-strand content in the region Leu17-Ala21. All these structural characteristics are inconsistent with the amyloid fibril structure and indicate that the dimer has to undergo significant rearrangement en route to fibril formation.

The complex folding pathways of protein A suggest a multiple-funnelled energy landscape

Folding proteins into their native states requires the formation of both secondary and tertiary structures. Many questions remain, however, as to whether these form into a precise order, and various pictures have been proposed that place the emphasis on the first or the second level of structure in describing folding. One of the favorite test models for studying this question is the B domain of protein A, which has been characterized by numerous experiments and simulations. Using the activation-relaxation technique coupled with a generic energy model (optimized potential for efficient peptide structure prediction), we generate more than 50 folding trajectories for this 60-residue protein. While the folding pathways to the native state are fully consistent with the funnel-like description of the free energy landscape, we find a wide range of mechanisms in which secondary and tertiary structures form in various orders. Our nonbiased simulations also reveal the presence of a significant number of non-native beta and alpha conformations both on and off pathway, including the visit, for a non-negligible fraction of trajectories, of fully ordered structures resembling the native state of nonhomologous proteins.

The Alzheimer's beta amyloid (Abeta1-39) monomer in an implicit solvent

Results from replica-exchange and regular room temperature molecular dynamics simulations of the Alzheimer's beta amyloid (Abeta(1-39)) monomer in an implicit solvent are reported. Our data indicate that at room temperature, the monomer assumes random-coil and soluble conformations. No beta content is observed which therefore seems to be a product of oligomerization and aggregation of monomers.

Computational study on the structural diversity of amyloid Beta Peptide (abeta(10-35)) oligomers

We studied the oligomerization of Alzheimer amyloid beta peptide (Abeta) using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with Abeta(10-35) dimers, trimers, and tetramers. Extensive REMD simulations illustrated several possible oligomer conformations. As the size of the oligomer increased from a dimer to a tetramer, the number of possible configurations was reduced. We identified all the possible conformations for each oligomer and characterized their temperature dependence. It was found that the detailed structures of the oligomers, which may act as folding intermediates, are highly sensitive to the parameters of the simulation environment such as temperature and concentration. Structural diversities of Abeta oligomers suggest multiple pathways of the aggregation process.

Modeling amyloid fibril formation: a free-energy approach

Amyloid fibrils are structures consisting of many proteins with a well-defined conformation. The formation of these fibrils has been the subject of intense research, largely due to their connection to several diseases. We focus here on the computational studies and discuss these from a free-energy point of view. The fibrillogenic properties of many proteins can be predicted and understood by taking the relevant free energies into account in an appropriate way. This is because both the equilibrium and the kinetic properties of the protein system depend on its free-energy landscape. Advanced simulation techniques can be used to understand the relationship between the free-energy landscape of a protein and its three-dimensional structure and propensity to form amyloid fibrils. We give an overview of existing simulation techniques that operate at a molecular level of detail and that are capable of generating relevant free-energy values. The free energies obtained with these methods can be inserted into a statistical-mechanical or kinetic framework to predict mean fibril properties on length scales and time scales that are inaccessible by molecular-scale simulation methods.

Protofibril assemblies of the arctic, Dutch, and Flemish mutants of the Alzheimer's Abeta1-40 peptide

Using a coarse-grained model of the Abeta peptide, we analyze the Arctic (E22G), Dutch (E22Q), and Flemish (A21G) familial Alzheimer's disease (FAD) mutants for any changes in the stability of amyloid assemblies with respect to the wild-type (WT) sequence. Based on a structural reference state of two protofilaments aligned to create the "agitated" protofibril as determined by solid-state NMR, we determine free energy trends for Abeta assemblies for the WT and FAD familial sequences. We find that the structural characteristics and oligomer size of the critical nucleus vary dramatically among the hereditary mutants. The Arctic mutant's disorder in the turn region introduces new stabilizing interactions that better align the two protofilaments, yielding a well-defined protofibril axis at relatively small oligomer sizes with respect to WT. By contrast, the critical nucleus for the Flemish mutant is beyond the 20 chains characterized in this study, thereby showing a strong shift in the equilibrium toward monomers with respect to larger protofibril assemblies. The Dutch mutant forms more ordered protofilaments than WT, but exhibits greater disorder in protofibril structure that includes an alternative polymorph of the WT fibril. An important conclusion of this work is that the Dutch mutant does not support the agitated protofibril assembly. We discuss the implications of the structural ensembles and free energy profiles for the FAD mutants in regards to interpretation of the kinetics of fibril assembly using chromatography and dye-binding experiments.

Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils

Increasing evidence indicates that oligomeric protein assemblies may represent the molecular species responsible for cytotoxicity in a range of neurological disorders including Alzheimer and Parkinson diseases. We use all-atom computer simulations to reveal that the process of oligomerization can be divided into two steps. The first is characterised by a hydrophobic coalescence resulting in the formation of molten oligomers in which hydrophobic residues are sequestered away from the solvent. In the second step, the oligomers undergo a process of reorganisation driven by interchain hydrogen bonding interactions that induce the formation of beta sheet rich assemblies in which hydrophobic groups can become exposed. Our results show that the process of aggregation into either ordered or amorphous species is largely determined by a competition between the hydrophobicity of the amino acid sequence and the tendency of polypeptide chains to form arrays of hydrogen bonds. We discuss how the increase in solvent-exposed hydrophobic surface resulting from such a competition offers an explanation for recent observations concerning the cytotoxicity of oligomeric species formed prior to mature amyloid fibrils.

New insights into the mechanism of Alzheimer amyloid-beta fibrillogenesis inhibition by N-methylated peptides

Alzheimer's disease is a debilitating neurodegenerative disorder associated with the abnormal self-assembly of amyloid-beta (Abeta) peptides into fibrillar species. N-methylated peptides homologous to the central hydrophobic core of the Abeta peptide are potent inhibitors of this aggregation process. In this work, we use fully atomistic molecular dynamics simulations to study the interactions of the N-methylated peptide inhibitor Abeta16-20m (Ac-Lys(16)-(Me)Leu(17)-Val(18)-(Me)Phe(19)-Phe(20)-NH(2)) with a model protofilament consisting of Alzheimer Abeta16-22 peptides. Our simulations indicate that the inhibitor peptide can bind to the protofilament at four different sites: 1), at the edge of the protofilament; 2), on the exposed face of a protofilament layer; 3), between the protofilament layers; and 4), between the protofilament strands. The different binding scenarios suggest several mechanisms of fibrillogenesis inhibition: 1), fibril inhibition of longitudinal growth (in the direction of monomer deposition); 2), fibril inhibition of lateral growth (in the direction of protofilament assembly); and 3), fibril disassembly by strand removal and perturbation of the periodicity of the protofilament (disruption of fibril morphology). Our simulations suggest that the Abeta16-20m inhibitor can act on both prefibrillar species and mature fibers and that the specific mechanism of inhibition may depend on the structural nature of the Abeta aggregate. Disassembly of the fibril can be explained by a mechanism through which the inhibitor peptides bind to disaggregated or otherwise free Abeta16-22 peptides in solution, leading to a shift in the equilibrium from a fibrillar state to one dominated by inhibitor-bound Abeta16-22 peptides.

Improving an all-atom force field

Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability.

Structural and Pathway Complexity of β-Strand Reorganization within Aggregates of Human Transthyretin(105−115) Peptide

Interstrand conformational rearrangements of human transthyretin peptide (TTR(105-115)) within dimeric aggregates were simulated by means of molecular dynamics (MD) with implicit solvation model for a total length of 48 micros. The conformations sampled in the MD simulations were clustered to identify free energy minima without any projections of free energy surface. A connected graph was constructed with nodes (=clusters) and edges corresponding to free energy minima and transitions between nodes, respectively. This connected graph which reflects the complexity of the free energy surface was used to extract the transition disconnectivity graph, which reflects the overall free energy barriers between pairs of free energy minima but does not contain information on transition paths. The routes of transitions between important free energy minima were obtained by further processing the original graph and the MD data. We have found that both parallel and antiparallel aggregates are populated. The parallel aggregates with different alignment patterns are separated by nonnegligible free energy barriers. Multiroutes exist in the interstrand conformational reorganization. Most visited routes do not dominant the kinetics, while less visited routes contribute a little each but they are numerous and their total contributions are actually dominant. There are various kinds of reptation motions, including those through a beta-bulge, side-chain aided reptation, and flipping or rotation of a hairpin formed by one strand.

Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology

Self-assembly at the nanoscale is becoming increasingly important for the fabrication of novel supramolecular structures, with applications in the fields of nanobiotechnology and nanomedicine. Peptides represent the most favorable building blocks for the design and synthesis of nanostructures because they offer a great diversity of chemical and physical properties, they can be synthesized in large amounts, and can be modified and decorated with functional elements, which can be used in diverse applications. In this article, we review some of the most recent experimental advances in the use of nanoscale self-assembled peptide structures and the theoretical efforts aimed at understanding the microscopic determinants of their formation, stability and conformational properties. The combination of experimental observations and theoretical advances will be fundamental to fully realizing the biotechnological potential of peptide self-organization.

Aggregation of beta-amyloid fragments

The authors study the folding and aggregation of six chains of the beta-amyloid fragment 16-22 using Monte Carlo simulations. While the isolated fragment prefers a helical form at room temperature, in the system of six interacting fragments one observes both parallel and antiparallel beta sheets below a crossover temperature T(x) approximately equal to 420 K. The antiparallel sheets have lower energy and are therefore more stable. Above the nucleation temperature the aggregate quickly dissolves into widely separated, weakly interacting chains.

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations

Amyloid fibril formation, as observed in Alzheimer's disease and type II diabetes, is currently described by a nucleation-condensation mechanism, but the details of the process preceding the formation of the nucleus are still lacking. In this study, using an activation-relaxation technique coupled to a generic energy model, we explore the aggregation pathways of 12 chains of the hexapeptide NFGAIL. The simulations show, starting from a preformed parallel dimer and ten disordered chains, that the peptides form essentially amorphous oligomers or more rarely ordered beta-sheet structures where the peptides adopt a parallel orientation within the sheets. Comparison between the simulations indicates that a dimer is not a sufficient seed for avoiding amorphous aggregates and that there is a critical threshold in the number of connections between the chains above which exploration of amorphous aggregates is preferred.

The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

The conformational states sampled by the Alzheimer amyloid beta (10-35) (Abeta 10-35) peptide were probed using replica-exchange molecular dynamics (REMD) simulations in explicit solvent. The Abeta 10-35 peptide is a fragment of the full-length Abeta 40/42 peptide that possesses many of the amyloidogenic properties of its full-length counterpart. Under physiological temperature and pressure, our simulations reveal that the Abeta 10-35 peptide does not possess a single unique folded state. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is dominated by random coil and bend structures with insignificant presence of an alpha-helical or beta-sheet structure. The 3D structure of Abeta 10-35 is seen to be defined by a salt bridge formed between the side-chains of K28 and D23. This salt bridge is also observed in Abeta fibrils and our simulations suggest that monomeric conformations of Abeta 10-35 contain pre-folded structural motifs that promote rapid aggregation of this peptide.

Coarse-grained protein molecular dynamics simulations

A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

Computational simulations of the early steps of protein aggregation

There is strong evidence that the oligomers of key proteins, formed during the early steps of aggregation, could be the primary toxic species associated with human neuro-degenerative diseases, such as Alzheimer's and prion diseases. Here, we review recent progress in the development of computational approaches in order to understand the structures, dynamics and free energy surfaces of oligomers. We also discuss possible research directions for the coming years.

Molecular dynamics simulation suggests possible interaction patterns at early steps of beta2-microglobulin aggregation

Early events in aggregation of proteins are not easily accessible by experiments. In this work, we perform a 5-ns molecular dynamics simulation of an ensemble of 27 copies of beta(2)-microglobulin in explicit solvent. During the simulation, the formation of intermolecular contacts is observed. The simulation highlights the importance of apical residues and, in particular, of those at the N-terminus end of the molecule. The most frequently found pattern of interaction involves a head-to-head contact arrangement of molecules. Hydrophobic contacts appear to be important for the establishment of long-lived (on the simulation timescale) contacts. Although early events on the pathway to aggregation and fibril formation are not directly related to the end-state of the process, which is reached on a much longer timescale, simulation results are consistent with experimental data and in general with a parallel arrangement of intermolecular beta-strand pairs.

Microcanonical analyses of peptide aggregation processes

We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite length, we find that the microcanonical entropy behaves convex in the transition region, leading to a negative microcanonical specific heat. As this effect is also seen in first-order-like transitions of other finite systems, our results provide clear evidence for recent hints that the characterization of phase separation in first-order-like transitions of finite systems profits from this microcanonical view.

Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide

We use a coarse-grained protein model to characterize the critical nucleus, structural stability, and fibril elongation propensity of Abeta(1-40) oligomers for the C(2x) and C(2z) quaternary forms proposed by solid-state NMR. By estimating equilibrium populations of structurally stable and unstable protofibrils, we determine the shift in the dominant population from free monomer to ordered fibril at a critical nucleus of ten chains for the C(2x) and C(2z) forms. We find that a minimum assembly of 16 monomer chains is necessary to mimic a mature fibril, and show that its structural stability correlates with a plateau in the hydrophobic residue density and a decrease in the likelihood of losing hydrophobic interactions by rotating the fibril subunits. While Abeta(1-40) protofibrils show similar structural stability for both C(2x) and C(2z) quaternary structures, we find that the fibril elongation propensity is greater for the C(2z) form relative to the C(2x) form. We attribute the increased propensity for elongation of the C(2z) form as being due to a stagger in the interdigitation of the N-terminal and C-terminal beta-strands, resulting in structural asymmetry in the presented fibril ends that decreases the amount of incorrect addition to the N terminus on one end. We show that because different combinations of stagger and quaternary structure affect the structural symmetry of the fibril end, we propose that differences in quaternary structures will affect directional growth patterns and possibly different morphologies in the mature fiber.