Study of interaction between prefoldin nano actuator and amyloid beta dimeric pathogenetic cargo with MD simulation

Alzheimer is the most common form of dementia. Amyloid beta peptides play a key role in the pathology of Alzheimer and the recent surveys have demonstrated that amyloid beta oligomers are the most toxic component of them. Among oligomers, considering the high durability of dimer in comparison to other kinds, it has more toxic effects. Prefoldin is a molecular chaperone which prevents accumulation of misfolded proteins. Prefoldin is demonstrated that it can also operate as a nano actuator. In this article, we investigate the interaction between the prefoldin nano actuator and dimeric pathogenic nano cargo in molecular dimensions, hence the all-atom molecular dynamic simulation in explicit solvent were performed at physiological temperature. Visualizing the results and investigating the atomic distance between nano actuator and pathogenic nano cargo revealed that two arms of six arms of prefoldin nano actuator have been able to capture cargo and during the simulation they have made hydrogen bonds. Furthermore, investigating the hydrophobic effects between the hydrophobic amino acids in the cargo and nano actuator revealed that these effects have positively affected the stability of the binding between arms and the cargo. This article introduces the prefoldin as an inhibitor factor for dimeric oligomer from amyloid beta.