Aβ25-35 is a short, cytotoxic, and naturally occurring fragment of the Alzheimer's Aβ peptide. To map the molecular mechanism of Aβ25-35 binding to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer, we have performed replica exchange with solute tempering molecular dynamics simulations using all-atom explicit membrane and water models. Consequences of sequence truncation on the binding mechanism have been measured by utilizing as a control our previous simulations probing binding of the longer peptide Aβ10-40 to the same bilayer. The most intriguing feature of Aβ25-35 binding to the DMPC bilayer is a coexistence of two bound states with strikingly different characteristics: a dominant surface-bound state and a less stable inserted state. In the surface-bound state, the peptide samples extended conformations, in which its unbound C-terminal is pointed away from the bilayer. In contrast, in the inserted state, the C-terminal resides deep in the bilayer hydrophobic core. In both states, the N-terminal remains anchored to the bilayer. Free energy landscape analysis reveals that the two states are separated by a moderate barrier, suggesting that Aβ25-35 monomer may frequently interconvert between them. The net effect of Aβ25-35 binding is a minor impact on the bilayer structure, which contrasts with the considerable bilayer perturbations induced by a longer Aβ10-40 peptide penetrating deep into the bilayer core. Therefore, we conclude that the binding mechanisms of Aβ25-35 and Aβ10-40 peptides are different. Potential implications of our results for Aβ25-35 cytotoxicity are discussed. A comparison of experimental data with our findings reveals a good agreement.

We have applied replica exchange with solute tempering (REST) molecular dynamics to study a short fragment of the Aβ peptide, Aβ25-35, in water and a much larger system incorporating two Aβ10-40 peptides binding to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer. As a control, we used traditional replica exchange molecular dynamics (REMD) applied to the same systems. Our objective was to assess the practical utility of REST simulations. Taken together, our results suggest four conclusions. First, compared to REMD, the number of replicas in REST simulations can be reduced four to five times without affecting the temperature range or compromising an efficient random walk of REST replicas over temperatures. Second, although overall REST produces much fewer conformational states than REMD, there is no substantial difference in the collection of unique states for the wild-type replica in REST and REMD, especially for the system featuring Aβ peptides binding to the lipid bilayer. Third, we performed a thorough comparison of REST and REMD equilibrium conformational ensembles, including thermal averages and probability distributions. REST reproduces REMD data extremely well for the system of Aβ peptides binding to the DMPC lipid bilayer. The agreement between REST and REMD equilibrium sampling of Aβ25-35 in water is less perfect, but it improves with addition of new REST simulations. Surprisingly, REST demonstrates much better convergence for the system featuring ordered peptides binding to lipid bilayer rather than for a small unstructured peptide solvated in water. Fourth, REST delivers its full computational advantage over REMD when applied to peptides interacting with lipid bilayers. For peptides solvated in water, REST does not appear to offer computational gain but may make replica simulations practically feasible due to a lower requirement for parallel computing environments. Our study is expected to facilitate wider application of REST in biomolecular simulations.

A potential mechanism of cytotoxicity attributed to Alzheimer’s A β peptides postulates that their aggregation disrupts membrane structure causing uncontrollable permeation of Ca 2+ ions. To gain molecular insights into these processes, we have performed all-atom explicit solvent replica exchange with solute tempering molecular dynamics simulations probing aggregation of the naturally occurring A β fragment A β 25-35 within the DMPC lipid bilayer. To compare the impact produced on the bilayer by A β 25-35 oligomers and monomers, we used as a control our previous simulations, which explored binding of A β 25-35 monomers to the same bilayer. We found that compared to monomeric species aggregation results in much deeper insertion of A β 25-35 peptides into the bilayer hydrophobic core causing more pronounced disruption in its structure. A β 25-35 peptides aggregate by incorporating monomer-like structures with stable C-terminal helix. As a result the A β 25-35 dimer features unusual helix head-to-tail topology supported by a parallel off-registry interface. Such topology affords further growth of an aggregate by recruiting additional peptides. Free energy landscape reveals that inserted dimers represent the dominant equilibrium state augmented by two metastable states associated with surface bound dimers and inserted monomers. Using the free energy landscape we propose the pathway of A β 25-35 binding, aggregation, and insertion into the lipid bilayer.

Using all-atom explicit water replica-exchange molecular dynamics simulations, we examined the impact of three popular force fields (FF) on the equilibrium binding of Aβ10−40 peptide to the dimyristoylgylcerophosphocholine (DMPC) bilayer. The comparison included CHARMM22 protein FF with CHARMM36 lipid FF (C22), CHARMM36m protein FF with CHARMM36 lipid FF (C36), and Amber14SB protein FF with Lipid14 lipid FF (A14). Analysis of Aβ10−40 binding to the DMPC bilayer in three FFs revealed a consensus binding mechanism. Its main features include (i) a stable helical structure in the bound peptide, (ii) insertion of the C-terminus and, in part, the central hydrophobic cluster into the bilayer hydrophobic core, (iii) considerable thinning of the DMPC bilayer beneath the bound peptide coupled with significant drop in bilayer density, and (iv) a strong disordering in the DMPC fatty acid tails. Although the three FFs diverge on many details concerning Aβ and bilayer conformational ensembles, these discrepancies do not offset the features of the consensus binding mechanism. We compared our findings with other FF evaluations and proposed that an agreement between C22, C36, and A14 is a consequence of a strong ordering effect created by polar−apolar interface in the lipid bilayer. By comparing the consensus Aβ binding mechanism with experimental data, we surmise that the three tested FFs largely correctly capture the interactions of Aβ peptides with the DMPC lipid bilayer.

The consequences of phosphorylation of the Aβ25−35 peptide at the position Ser26 on its aggregation have not been examined. To investigate them, we performed all-atom replica exchange simulations probing the binding of phosphorylated Aβ25−35 (pAβ25−35) peptides to the dimyristoyl phosphatidylcholine (DMPC) bilayer and their subsequent aggregation. As a control, we used our previous study of unmodified peptides. We found that phosphorylation moderately reduces the helical propensity in pAβ25−35 and its binding affinity to the DMPC bilayer. Phosphorylation preserves the bimodal binding observed for unmodified Aβ25−35, which features a preferred inserted state and a less probable surface bound state. Phosphorylation also retains the inserted dimer with a head-to-tail helical aggregation interface as the most thermodynamically stable state. Importantly, this post-translation modification strengthens interpeptide interactions by adding a new aggregation "hot spot" created by cross-bridging phosphorylated Ser26 with water, cationic ions, or Lys28. The cross-bridging constitutes the molecular mechanism behind most structural phosphorylation effects. In addition, phosphorylation eliminates pAβ25−35 monomers and diversifies the pool of aggregated species. As a result, it changes the binding and aggregation mechanism by multiplying pathways leading to stable inserted dimers. These findings offer a plausible molecular rationale for experimental observations, including enhanced production of low molecular weight oligomers and cytotoxicity of phosphorylated Aβ peptides.