In silico assembly of Alzheimer's Abeta16-22 peptide into beta-sheets

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.

A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided.

The formation of amyloid fibrils is associated with many neurodegenerative diseases such as Alzheimer's, Creutzfeld-Jakob, Parkinson's, the Prion disease and diabetes mellitus. In all cases, proteins misfold to form highly ordered insoluble aggregates called amyloid fibrils that deposit intra- and extracellularly and are resistant to proteases. All proteins are believed to have the instrinsic capability of forming amyloid fibrils that share common specific structural properties that have been observed by X-ray crystallography and by NMR. However, little is known about the aggregation dynamics of amyloid assemblies, and their toxicity mechanism is therefore poorly understood. It is believed that small amyloid oligomers, formed on the aggregation pathway of full amyloid fibrils, are the toxic species. A detailed atomic characterization of the oligomerization process is thus necessary to further our understanding of the amyloid oligomer's toxicity. Our approach here is to study the aggregation dynamics of a 7-residue amyloid peptide GNNQQNY through a combination of numerical techniques. Our results suggest that this amyloid sequence can form fibril-like structures and is polymorphic, which agrees with recent experimental observations. The ability to fully characterize and describe the aggregation pathway of amyloid sequences numerically is key to the development of future drugs to target amyloid oligomers.

The use of mass spectrometry to study amyloid-β peptides

Amyloid-β peptide (Aβ) varies in size from 39 to 43 amino acids and arises from sequential β- and γ-secretase processing of the amyloid precursor protein. Whereas the non-pathological role for Aβ is yet to be established, there is no disputing that Aβ is now widely regarded as central to the development of Alzheimer's disease (AD). The so named "amyloid cascade hypothesis" states that disease progression is the result of an increased Aβ burden in affected areas of the brain. To elucidate the Aβ role in AD, many analytical approaches have been proposed as suitable tools to investigate not only the total Aβ load but also many other issues that are considered crucial for AD, such as: (i) the aggregation state in which Aβ is present; (ii) its interaction with other species or metals; (iii) its ability to induce oxidative stress; and (iv) its degradative pathways. This review provides an insight into the use of mass spectrometry (MS) in the field of Aβ investigation aimed to assess its role in AD. In particular, the different MS-based approaches applied in vitro and in vivo that can provide detailed information on the above-mentioned issues are reviewed. Moreover, the advantages offered by the MS methods over all the other techniques are highlighted, together with the recent developments and uses of combined analytical approaches to detect and characterize Aβ.

Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations

Alzheimer's disease (AD) pathogenesis is associated with formation of amyloid fibrils caused by polymerization of the amyloid β-peptide (Aβ), which is a process that requires unfolding of the native helical structure of Aβ. According to recent experimental studies, stabilization of the Aβ central helix is effective in preventing Aβ polymerization into toxic assemblies. To uncover the fundamental mechanism of unfolding of the Aβ central helix, we performed molecular dynamics simulations for wild-type (WT), V18A/F19A/F20A mutant (MA), and V18L/F19L/F20L mutant (ML) models of the Aβ central helix. It was quantitatively demonstrated that the stability of the α-helical conformation of both MA and ML is higher than that of WT, indicating that the α-helical propensity of the three nonpolar residues (18, 19, and 20) is the main factor for the stability of the whole Aβ central helix and that their hydrophobicity plays a secondary role. WT was found to completely unfold by a three-step mechanism: 1) loss of α-helical backbone hydrogen bonds, 2) strong interactions between nonpolar sidechains, and 3) strong interactions between polar sidechains. WT did not completely unfold in cases when any of the three steps was omitted. MA and ML did not completely unfold mainly due to the lack of the first step. This suggests that disturbances in any of the three steps would be effective in inhibiting the unfolding of the Aβ central helix. Our findings would pave the way for design of new drugs to prevent or retard AD.

Effects of G33A and G33I mutations on the structures of monomer and dimer of the amyloid-β fragment 29-42 by replica exchange molecular dynamics simulations

The early formed oligomers of amyloid-β proteins with 40 and 42 amino acids are believed to be the culprits of Alzheimer's disease. Aβ1-42 peptides with alanine and isoleucine mutations of glycine 33 are known to be much less toxic than the wild-type Aβ1-42 and promote the aggregation process in vitro. The fragment Aβ29-42 has also been shown to form fibrils, disrupt Aβ1-42 oligomerization, and inhibit Aβ1-42-induced neurotoxicity. As a first step toward understanding the impact of G33A and G33I mutations on the earliest steps along the Aβ1-42 aggregation pathway, we have studied the structures of the monomer and dimer of Aβ29-42 and its two G33 variants using coarse-grained replica exchange molecular dynamics simulations. These simulations, totaling 15 μs, indicate that both substitutions impact the conformational ensemble of Aβ29-42. For the monomer, the population of the β-hairpin is high for wild-type Aβ29-42, but marginal for Aβ29-42 G33I mutant. The three dimers are also stabilized by different patterns of interaction. The data are discussed in terms of the differences in the aggregation characteristics between wild-type Aβ1-42 and its two G33A and G33I variants.

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.

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.

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.

Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations

The human islet amyloid polypeptide (hIAPP) or amylin is a 37-residue hormone found as amyloid deposits in pancreatic extracts of nearly all type 2 diabetes patients. The fragment 20-29 of sequence SNNFGAILSS (hIAPP20-29) has been shown to be responsible for the amyloidogenic propensities of the full length protein. Various polymorphic forms of hIAPP20-29 fibrils were described by using Fourier transform infrared (FTIR) and solid-state NMR experiments: unseeded hIAPP20-29 fibril with out-of-register antiparallel beta-strands, and two forms of seeded hIAPP20-29 fibril, with in-register antiparallel or in-register parallel beta-strands. As a first step toward understanding this polymorphism, we explore the equilibrium structures of the soluble hIAPP20-29 trimer, using multiple molecular dynamics (MD) simulations with the Optimized Potential for Efficient structure Prediction (OPEP) coarse-grained implicit solvent force field for a total length of 3.2 micros. Although, the trimer is found mainly random coil, consistent with the signal measured experimentally during the lag phase of hIAPP20-29 fibril formation, the central FGAIL residues have a relative high propensity to form interpeptide beta-sheets and antiparallel beta-strands are more probable than parallel beta-strands. One MD-predicted out-of-register antiparallel three-stranded beta-sheet matches exactly the FTIR-derived unseeded hIAPP20-29 fibril model. Our simulations, however, do not reveal any evidence of in-register parallel or in-register antiparallel beta-sheets as reported for seeded hIAPP20-29 fibrils. All these results indicate that fibril polymorphism is partially encoded in a trimer.

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.

Dynamics of locking of peptides onto growing amyloid fibrils

Sequence-dependent variations in the growth mechanism and stability of amyloid fibrils, which are implicated in a number of neurodegenerative diseases, are poorly understood. We have carried out extensive all-atom molecular dynamics simulations to monitor the structural changes that occur upon addition of random coil (RC) monomer fragments from the yeast prion Sup35 and Abeta-peptide onto a preformed fibril. Using the atomic resolution structures of the microcrystals as the starting points, we show that the RC --> beta-strand transition for the Sup35 fragment occurs abruptly over a very narrow time interval, whereas the acquisition of strand content is less dramatic for the hydrophobic-rich Abeta-peptide. Expulsion of water, resulting in the formation of a dry interface between 2 adjacent sheets of the Sup35 fibril, occurs in 2 stages. Ejection of a small number of discrete water molecules in the second stage follows a rapid decrease in the number of water molecules in the first stage. Stability of the Sup35 fibril is increased by a network of hydrogen bonds involving both backbone and side chains, whereas the marginal stability of the Abeta-fibrils is largely due to the formation of weak dispersion interaction between the hydrophobic side chains. The importance of the network of hydrogen bonds is further illustrated by mutational studies, which show that substitution of the Asn and Gln residues to Ala compromises the Sup35 fibril stability. Despite the similarity in the architecture of the amyloid fibrils, the growth mechanism and stability of the fibrils depend dramatically on the sequence.

Amyloidogenesis abolished by proline substitutions but enhanced by lipid binding

The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20-29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20-29 fragments aggregate into partially ordered beta-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel beta-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23-25 is found to stabilize the ordered beta-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20-29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides.

Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent

Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.

What can we learn from highly connected beta-rich structures for structural interface design?

Most hubs' binding sites are able to transiently interact with numerous proteins. We focus on beta-rich hubs with the goal of inferring features toward design. Since they are able to interact with many partners and association of beta-conformations may lead to amyloid fibrils, we ask whether there is some property that distinguishes them from low-connectivity beta-rich proteins, which may be more interaction specific. Identification of such features should be useful as they can be incorporated in interface design while avoiding polymerization into fibrils. We classify the proteins in the yeast interaction map according to the types of their secondary structures. The small number of the obtained beta-rich protein structures in the Protein Data Bank likely reflects their low occurrence in the proteome. Analysis of the obtained structures indicates that highly connected beta-rich proteins tend to have clusters of conserved residues in their cores, unlike beta-rich structures with low connectivity, suggesting that the highly packed conserved cores are important to the stability of proteins, which have residue composition and sequence prone to beta-structure and amyloid formation. The enhanced stability may hinder partial unfolding, which, depending on the conditions, is more likely to lead to polymerization of these sequences.

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.

Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association

Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel beta-sheets. The data show that GNNQQNY preference for parallel or antiparallel beta-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.

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.

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.

Thermodynamics and kinetics of aggregation for the GNNQQNY peptide

The energy landscape of the monomer and dimer are explored for the amyloidogenic heptapeptide GNNQQNY from the N-terminal prion-determining domain of the yeast protein Sup35. The peptide is modeled by a united-atom potential and an implicit solvent representation. Replica exchange molecular dynamics is used to explore the conformational space, and discrete path sampling is employed to investigate the pathways that interconvert the most populated minima on the free energy surfaces. For the monomer, we find a rapid fluctuation between four different conformations, where a geometry intermediate between compact and extended structures is the most thermodynamically favorable. The GNNQQNY dimer forms three stable sheet structures, namely in-register parallel, off-register parallel, and antiparallel. The antiparallel dimer is stabilized by strong electrostatic interactions resulting from interpeptide hydrogen bonds, which restrict its conformational flexibility. The in-register parallel dimer, which is close to the amyloid beta-sheet structure, has fewer interpeptide hydrogen bonds, making hydrophobic interactions more important and increasing the conformational entropy compared to the antiparallel sheet. The estimated two-state rate constants indicate that the formation of dimers from monomers is fast and that the dimers are kinetically stable against dissociation at room temperature. Interconversions between the different dimers are feasible processes and are more likely than dissociation.

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.

Synthesis, in vitro assay, and molecular modeling of new piperidine derivatives having dual inhibitory potency against acetylcholinesterase and Aβ1–42 aggregation for Alzheimer’s disease therapeutics

With the goal of developing Alzheimer's disease therapeutics, we have designed and synthesized new piperidine derivatives having dual action of acetylcholinesterase (AChE) and beta-amyloid peptide (Abeta) aggregation inhibition. For binding with the catalytic site of AChE, an ester with aromatic group was designed, and for the peripheral site, another aromatic group was considered. And for intercalating amyloid-beta oligomerization, long and linear conformation with a lipophilic group was considered. The synthetic methods employed for the structure with dual action depended on alcohols with an aromatic ring and the substituted benzoic acids, which are esterificated in the last step of the synthetic pathway. We screened these new derivatives through inhibition tests of acetylcholinesterase, butyrylcholinesterase (BChE), and Abeta(1-42) peptide aggregation, AChE-induced Abeta(1-42) aggregation. Our results displayed that compound 12 showed the best inhibitory potency and selectivity of AChE, and 29 showed the highest selectivity of BChE inhibition. Compounds 15 and 12 had inhibitory activities against Abeta(1-42) aggregation and AChE-induced Abeta aggregation. In the docking model, we confirmed that 4-chlorobenzene of 12 plays the parallel pi-pi stacking against the indole ring of Trp84 in the bottom gorge of AChE. Because the benzyhydryl moiety of 12 covered the peripheral site of AChE in a funnel-like shape, 12 showed good inhibitory potency against AChE and could inhibit AChE-induced Abeta(1-42) peptide aggregation.

Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations

Many human neurodegenerative diseases are associated with amyloid fibril formation. The human 99-residue beta(2)-microglobulin (beta2m) is one of the most intensively studied amyloid-forming proteins. Recent studies show that the C-terminal fragments 72-99, 83-89, and 91-96 form by themselves amyloid fibrils in vitro and play a significant role in fibrillization of the full-length beta2m protein under acidic pH conditions. In this work, we have studied the equilibrium structures of the 17-residue fragment 83-99 in solution, and investigated its dimerization process by multiple molecular dynamics simulations. We find that an intertwined dimer, with the positions of the beta-strands consistent with the results for the monomer, is a possible structure for two beta2m(83-89) peptides. Based on our molecular-dynamics-generated dimeric structure, a protofibril model is proposed for the full-length beta2m protein.

The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution

Alzheimer's disease has been linked to the self-assembly of the amyloid-beta protein of 40 and 42 residues. Although monomers are in equilibrium with higher-order species ranging from dimers to heptamers, structural knowledge of the monomeric amyloid-beta (Abeta) peptides is an important issue. Recent experimental data have shown that the fragment (21-30) is protease-resistant within full-length Abeta peptides and displays two structural families in solution. Because the details of the Abeta(21-30) structures found using distinct force fields and protocols differ at various degrees from those of the NMR structures, we revisit the conformational space of this peptide using the activation-relaxation technique (ART nouveau) coupled with a coarse-grained force field (OPEP v.3.0). We find that although Abeta(21-30) does not have a secondary structure, it dominantly populates three structural families, with a loop spanning residues Val24-Lys28. The first two families, which differ in the nature of the electrostatic interactions, satisfy the five interproton rotating frame nuclear Overhauser effect spectroscopy (ROESY) distances and superpose well onto the NMR structures. The third family, which cannot be seen by ROESY NMR experiments, displays a more open structure. This numeric study complements the experimental results by providing a much more detailed description of the dominant structures. Moreover, it provides further evidence of the capability of ART OPEP in providing a reliable conformational picture of peptides in solution.

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.

Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure

We present a detailed analysis of the structural properties of one monomer of Abeta(11-25) as well as of the aggregation mechanisms for four chains of Abeta(11-25) using the activation-relaxation technique coupled with a generic energy potential. Starting from a random distribution of these four chains, we find that the system assembles rapidly into a random globular state that evolves into three- and four-stranded antiparallel beta-sheets. The aggregation process is considerably accelerated by the presence of preformed dimers. We also find that the reptation mechanism already identified in shorter peptides plays a significant role here in allowing the structure to reorganize without having to fully dissociate.

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.

Following the aggregation of amyloid-forming peptides by computer simulations

There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer's disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys-phe-phe-glu (KFFE) peptides. This is the shortest peptide known to form amyloid fibrils in vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys-pro-gly-glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.

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.

Controlling amyloid growth in multiple dimensions

The great progress made in defining the structure of protein and peptide amyloid assemblies, particularly the arrangement of peptides in beta-sheets, is counterbalanced by the still poor understanding of the higher organization of beta-sheets within the fibril and overall fibril/fibril associations. The assembly pathway and basis of amyloid toxicity may well depend on these higher-order structural features. For example, significant evidence points to association between sheets as the rate limiting step in fibril assembly, and a critical metal binding site has now been identified that involves residues from different individual sheets. Here we review experiments that are identifying some of the issues associated with sheet-sheet association by investigating simple model peptides derived from the central core of the Abeta peptide implicated in Alzheimer's disease. These peptides transit between fibril/ribbon/nanotube morphologies in response to assembly conditions, laying the foundation for understanding the folding landscape for these higher order assemblies, revealing potential targets for therapeutic intervention, and opening strategies for the design of highly ordered peptide self-assembled microscale morphologies.

Structures of soluble amyloid oligomers from computer simulations

Alzheimer's, Parkinson's, and Creutzfeldt-Jakob's neurodegenerative diseases are all linked with the assembly of normally soluble proteins into amyloid fibrils. Because of experimental limitations, structural characterization of the soluble oligomers, which form early in the process of fibrillogenesis and are cytotoxic, remains to be determined. In this article, we study the aggregation paths of seven chains of the shortest amyloid-forming peptide, using an activitated method and a reduced atomic representation. Our simulations show that disordered KFFE monomers ultimately form three distinct topologies of similar energy: amorphous oligomers, incomplete rings with beta-barrel character, and cross-beta-sheet structures with the meridional but not the equatorial X-ray fiber reflections. The simulations also shed light on the pathways from misfolded aggregates to fibrillar-like structures. They also underline the multiplicity of building blocks that can lead to the formation of the critical nucleus from which rapid growth of the fibril occurs.

Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer

Several neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases are associated with amyloid fibrils formed by different polypeptides. We probe the structure and stability of oligomers of different sizes of the fragment Abeta(16-22) of the Alzheimer beta-amyloid peptide using atomic-detail molecular dynamics simulations with explicit solvent. We find that only large oligomers form a stable beta-sheet aggregate, the minimum nucleus size being of the order of 8-16 peptides. This effect is attributed to better hydrophobic contacts and a better shielding of backbone-backbone hydrogen bonds from the solvent in bigger assemblies. Moreover, the observed stability of beta-sheet aggregates with a different number of layers can be explained on the basis of their solvent-accessible surface area. Depending on the stacking interface between the sheets, we observe straight or twisted structures, which could be linked to the experimentally observed polymorphism of amyloid fibrils. To compare our 32-mer structure to experimental data, we calculate its x-ray diffraction pattern. Good agreement is found between experimentally and theoretically determined reflections, suggesting that our model indeed closely resembles the structures found in vitro.

Endogenous plastic composite material in the Alzheimer's brain

Accumulation of amyloid beta (Abeta) peptide in brain is the hallmark of Alzheimer's disease (AD). The resulting plaques though fibrous in nature may also consist of additional structures currently poorly defined. We hypothesize that plastic composite material contributes to plaque formation. This material is organized by polymers of acrolein, which is an oxidized lipid fragment found in AD. Acrolein, a 3-carbon compound, contains a carbonyl and a vinyl group that participate in polymerization via fundamental latex chemistry. The redox and surfactant properties of Abeta allow it to catalyze the polymerization of acrolein. We previously reported observations of thin plastic fragments of Abeta-polyacrolein. The current paper outlines the proposed steps in forming these plastic fragments. Endogenous plastic composite material may significantly contribute to the pathogenesis of AD.

Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm

Discretization of protein conformational space and fragment assembly methods simplify the search of native structures. These methods, mostly of Monte Carlo and genetic-type, do not exploit, however, the fact that short fragments describing consecutive parts of proteins are conformation-dependent. Yet, this information should be useful in improving ab initio and comparative protein structure modeling. In a preliminary study, we have assessed the possibility of using greedy algorithms for protein structure reconstruction based on the assembly of fragments of four-residue length. Greedy algorithms differ from Monte Carlo and genetic approaches in that they grow a polypeptide chain one fragment after another. Here, we move one step further in complexity, and provide strong evidence that the dependence between consecutive local conformations during assembly makes possible the reconstruction of protein structures from their secondary structures using a Go potential. Overall our procedure can reproduce 20 protein structures of 50-164 amino acids within 2.7 to 6.5 A RMSd and is able to identify native topologies for all proteins, although some targets are stabilized by very long-range interactions.

ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes

We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly.

Atomic-Level Description of Amyloid β-Dimer Formation

All-atom simulations have been carried out on a monomer and dimer of the aggregation-prone fragment (16-22) of amyloid beta peptide, which is implicated in Alzheimer's disease. The replica exchange molecular dynamics method, which has been successfully applied to peptide folding, is utilized as a means to sample the configurational space with proper Boltzmann weighting so that the structural, motional, and thermodynamic description of self-assembly can be obtained. The free energy landscape showing the delicate balance between different monomer and dimer conformations is mapped along carefully chosen reaction coordinates. The canonical ensembles at 38 different temperatures are used to describe the thermodynamics and the relative stabilities of at least six different dimer conformations including that of parallel and antiparallel orientations. We also delineate the nature of the molecular forces that activate and stabilize these different dimer conformations as a function of temperature, especially as related to secondary structural propensity of monomer. We identify parallel loop dimer conformations that are stabilized due to specific interactions with water molecules.