Journal of Physical Chemistry B, Vol.116, No.45, 13368-13373, 2012
Dynamical Stability and Assembly Cooperativity of beta-Sheet Amyloid Oligomers - Effect of Polarization
The soluble intermediate oligomers of amyloidogenic proteins are suspected to be more Cytotoxic than the mature fibrils in neurodegenerative disorders. Here, the dynamic Stability and assembly cooperativity of a model oligomer of human islet amyloid polypeptide (hIAPP) segments were explored by means of all-atom molecular dynamics (MD) simulations under different force fields including AMBER99SB, OPLS, and polarized protein-specific charge (PPC) model. Simulation results show that the dynamic stability of beta-sheet oligomers is seriously impacted by electrostatic polarization. Without inclusion of polarization (simulation under standard AMBER and OPLS force field), the beta sheet oligomers are dynamically unstable during MD simulation. For comparison, simulation results under PPC give significantly more stable dynamical structures of the oligomers. Furthermore, calculation of electrostatic interaction energy between the neighboring beta strands with an polarizable method produces energetic evidence for cooperative assembly of beta-strand oligomers. This result supports a picture of downhill-like cooperative assembly of beta strands during fibrillation process. The present study demonstrates the critical role of polarization in dynamic stability and assembly cooperativity of beta-sheet-rich amyloid oligomers.