Adenosine triphosphate (ATP) is newly expected to be involved in the clearance of amyloid beta 1-42 (A beta(42)) fibril and its precursors, A beta(42 )oligomer. Meanwhile, the microscopic mechanism of the role in dissolving the protein aggregate still remains elusive. Aiming to elucidate the mechanism, we examined effects of ATP on the conformational change and thermodynamic stability of the protomer dimer of A beta(42) pentamer and tetramer, A beta(42) (9), by employing all-atom molecular dynamics simulations. We observed interprotomer twisting and intraprotomer peeling of A beta(42) (9). These conformational changes remarkably accelerate dissociation of the protomer dimer. However, the presence of ATP itself has no positive effect on dissociation processes of the protomer dimer and a monomer from the dimer, indicating its irrelevance to decomposition of the A beta(42) oligomer. Rather, it could be supposed that ATP prevents additional binding and rebinding of A beta(42) monomers to the A beta(42) oligomer and it then converts A beta(42) oligomer into an offpathway species which is excluded from A beta(42) fibril growth processes. Interestingly, hydrophobic adenosine in ATP makes contact with A beta(42)(9) on its backbone atoms, with respect to both A beta(42) monomers on the edge of A beta(42)(9) and dissociated Afi 42 monomers in A beta(42)(9). These roles of ATP would be applied without regard to the structural polymorphism of the A beta(42) fibril.