Modeling amyloid-beta as homogeneous dodecamers and in complex with cellular prion protein

Molecular interactions between monoclonal oligomer-specific antibody 5E3 and its amyloid beta cognates

Oligomeric amyloid β (Aβ) is currently considered the most neurotoxic form of the Aβ peptide implicated in Alzheimer’s disease (AD). The molecular structures of the oligomers have remained mostly unknown due to their transient nature. As a result, the molecular mechanisms of interactions between conformation-specific antibodies and their Aβ oligomer (AβO) cognates are not well understood. A monoclonal conformation-specific antibody, m5E3, was raised against a structural epitope of Aβ oligomers. m5E3 binds to AβOs with high affinity, but not to Aβ monomers or fibrils. In this study, a computational model of the variable fragment (Fv) of the m5E3 antibody (Fv5E3) is introduced. We further employ docking and molecular dynamics simulations to determine the molecular details of the antibody-oligomer interactions, and to classify the AβOs as Fv5E3-positives and negatives, and to provide a rationale for the low affinity of Fv5E3 for fibrils. This information will help us to perform site-directed mutagenesis on the m5E3 antibody to improve its specificity and affinity toward oligomeric Aβ species. We also provide evidence for the possible capability of the m5E3 antibody to disaggregate AβOs and to fragment protofilaments.

Stability analysis of a steady state of a model describing Alzheimer's disease and interactions with prion proteins

Alzheimer's disease (AD) is a neuro-degenerative disease affecting more than 46 million people worldwide in 2015. AD is in part caused by the accumulation of A[Formula: see text] peptides inside the brain. These can aggregate to form insoluble oligomers or fibrils. Oligomers have the capacity to interact with neurons via membrane receptors such as prion proteins ([Formula: see text]). This interaction leads [Formula: see text] to be misfolded in oligomeric prion proteins ([Formula: see text]), transmitting a death signal to neurons. In the present work, we aim to describe the dynamics of A[Formula: see text] assemblies and the accumulation of toxic oligomeric species in the brain, by bringing together the fibrillation pathway of A[Formula: see text] peptides in one hand, and in the other hand A[Formula: see text] oligomerization process and their interaction with cellular prions, which has been reported to be involved in a cell-death signal transduction. The model is based on Becker-Döring equations for the polymerization process, with delayed differential equations accounting for structural rearrangement of the different reactants. We analyse the well-posedness of the model and show existence, uniqueness and non-negativity of solutions. Moreover, we demonstrate that this model admits a non-trivial steady state, which is found to be globally stable thanks to a Lyapunov function. We finally present numerical simulations and discuss the impact of model parameters on the whole dynamics, which could constitute the main targets for pharmaceutical industry.

Probing oligomerization of amyloid beta peptide in silico

Aggregation of amyloid β (Aβ) peptide is implicated in fatal Alzheimer's disease, for which no cure is available. Understanding the mechanisms responsible for this aggregation is required in order for therapies to be developed. In an effort to better understand the molecular mechanisms involved in spontaneous aggregation of Aβ peptide, extensive molecular dynamics simulations are reported, and the results are analyzed through a combination of structural biology tools and a novel essential collective dynamics method. Several model systems composed of ten or twelve Aβ_17-42 chains in water are investigated, and the influence of metal ions is probed. The results suggest that Aβ monomers tend to aggregate into stable globular-like oligomers with 13-23% of β-sheet content. Two stages of oligomer formation have been identified: quick collapse within the first 40 ns of the simulation, characterized by a decrease in inter-chain separation and build-up of β-sheets, and the subsequent slow relaxation of the oligomer structure. The resulting oligomers comprise a stable, coherently moving sub-aggregate of 6-9 strongly inter-correlated chains. Cu²⁺ and Fe²⁺ ions have been found to develop coordination bonds with carboxylate groups of E22, D23 and A42, which remain stable during 200 ns simulations. The presence of Fe²⁺, and particularly Cu²⁺ ions, in negatively charged cavities has been found to cause significant changes in the structure and dynamics of the oligomers. The results indicate, in particular, that formation of non-fibrillar oligomers might be involved in early template-free aggregation of Aβ_17-42 monomers, with charged species such as Cu²⁺ or Fe²⁺ ions playing an important role.

Alzheimer's disease: analysis of a mathematical model incorporating the role of prions

We introduce a mathematical model of the in vivo progression of Alzheimer's disease with focus on the role of prions in memory impairment. Our model consists of differential equations that describe the dynamic formation of β-amyloid plaques based on the concentrations of Aβ oligomers, PrP(C) proteins, and the Aβ-x-Aβ-PrP(C)complex, which are hypothesized to be responsible for synaptic toxicity. We prove the well-posedness of the model and provided stability results for its unique equilibrium, when the polymerization rate of Aβ-amyloid is constant and also when it is described by a power law.

Hydrophobic core in domains of immunoglobulin-like fold

This work analyzes proteins which contain an immunoglobulin fold, focusing on their hydrophobic core structure. The "fuzzy oil drop" model was used to measure the regularity of hydrophobicity distribution in globular domains belonging to proteins which exhibit the above-mentioned fold. Light-chain IgG domains are found to frequently contain regular hydrophobic cores, unlike the corresponding heavy-chain domains. Enzymes and DNA binding proteins present in the data-set are found to exhibit poor accordance with the hydrophobic core model.

Characterizing affinity epitopes between prion protein and β-amyloid using an epitope mapping immunoassay

Cellular prion protein, a membrane protein, is expressed in all mammals. Prion protein is also found in human blood as an anchorless protein, and this protein form is one of the many potential sources of misfolded prion protein replication during transmission. Many studies have suggested that β-amyloid1-42 oligomer causes neurotoxicity associated with Alzheimer's disease, which is mediated by the prion protein that acts as a receptor and regulates the hippocampal potentiation. The prevention of the binding of these proteins has been proposed as a possible preventative treatment for Alzheimer's disease; therefore, a greater understanding of the binding hot-spots between the two molecules is necessary. In this study, the epitope mapping immunoassay was employed to characterize binding epitopes within the prion protein and complementary epitopes in β-amyloid. Residues 23-39 and 93-119 in the prion protein were involved in binding to β-amyloid1-40 and 1-42, and monomers of this protein interacted with prion protein residues 93-113 and 123-166. Furthermore, β-amyloid antibodies against the C-terminus detected bound β-amyloid1-42 at residues 23-40, 104-122 and 159-175. β-Amyloid epitopes necessary for the interaction with prion protein were not determined. In conclusion, charged clusters and hydrophobic regions of the prion protein were involved in binding to β-amyloid1-40 and 1-42. The 3D structure appears to be necessary for β-amyloid to interact with prion protein. In the future, these binding sites may be utilized for 3D structure modeling, as well as for the pharmaceutical intervention of Alzheimer's disease.