A theoretical study on the molecular determinants of the affibody protein ZAβ3 bound to an amyloid β peptide

Amyloid beta (Aβ) peptides are small cleavage products of the amyloid precursor protein. Aggregates of Aβ peptides are thought to be linked with Alzheimer's and other neurodegenerative diseases. Strategies aimed at inhibiting amyloid formation and promoting Aβ clearance have been proposed and investigated in in vitro experiments and in vivo therapies. A recent study indicated that a novel affibody protein ZAβ3, which binds to an Aβ40 monomer with a binding affinity of 17 nM, is able to prevent the aggregation of Aβ40. However, little is known about the energetic contribution of each residue in ZAβ3 to the formation of the (ZAβ3)2:Aβ complex. To address this issue, we carried out unbiased molecular dynamics simulations and molecular mechanics Poisson–Boltzmann surface area calculations. Through the per-residue decomposition scheme, we identified that the van der Waals interactions between the hydrophobic residues of (ZAβ3)2 and those at the exterior and interior faces of Aβ are the main contributors to the binding of (ZAβ3)2 to Aβ. Computational alanine scanning identified 5 hot spots, all residing in the binding interface and contributing to the binding of (ZAβ3)2 to Aβ through the hydrophobic effect. In addition, the amide hydrogen bonds in the 4-strand β-sheet and the π–π stacking were also analyzed. Overall, our study provides a theoretical basis for future experimental improvement of the ZAβ3 peptide binding to Aβ.