Computational Investigation Of The Binding Dynamics Of Oligo P-Phenylene Ethynylene Fluorescence Sensors And A Beta Oligomers

Amyloid protein aggregates are pathological hallmarks of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) diseases and are believed to be formed well before the onset of neurodegeneration and cognitive impairment. Monitoring the course of protein aggregation is thus vital to understanding and combating these diseases. We have recently demonstrated that a novel class of fluorescence sensors, oligomeric p-phenylene ethynylene (PE)-based electrolytes (OPEs) selectively bind to and detect prefibrillar and fibrillar aggregates of AD-related amyloid-beta (A beta) peptides over monomeric A beta. In this study, we investigated the binding between two OPEs, anionic OPE12- and cationic OPE24+, and to two different beta-sheet rich A beta oligomers using classical all-atom molecular dynamics simulations. Our simulations have revealed a number of OPE binding sites on A beta oligomer surfaces, and these sites feature hydrophobic amino acids as well as oppositely charged amino acids. Binding energy calculations show energetically favorable interactions between both anionic and cationic OPEs with A beta oligomers. Moreover, OPEs bind as complexes as well as single molecules. Compared to free OPEs, A beta protofibril bound OPEs show backbone planarization with restricted rotations and reduced hydration of the ethyl ester end groups. These characteristics, along with OPE complexation, align with known mechanisms of binding induced OPE fluorescence turn-on and spectral shifts from a quenched, unbound state in aqueous solutions. This study thus sheds light on the molecular-level details of OPE-A beta protofibril interactions and provides a structural basis for fluorescence turn-on sensing modes of OPEs.