SCRUTINIZING THE IAPP CONFORMATIONAL SPACE WITH REPLICA-EXCHANGE: A COMPARISON OF AMYLIN VARIANTS

Amylin (hIAPP, 37 residue peptide) is an intrinsic disordered protein (IDP) directly related to the Type-II Diabetes Melitus pathology. In diseased individuals, the molecule self-assembles, producing amyloid deposits. Investigating the monomeric energy landscape relates to the evidence of helical intermediates binding with phospholipid membranes, yet, the molecule interconversion mechanism and intermediates formation is poorly understood. Molecular Dynamics (MD) propagates the coordinates of molecular systems in time to infer their dynamics given an underlying forcefield. Proper sampling of the many shallow minima of an IDP molecule presents an enormous challenge for unbiased simulations. 

We investigate differences across sequences for four different amylin sequences utilizing Replica-Exchange Molecular Dynamics (REMD) in implicit solvent: The human, the S20G mutant, the rat and cat variants. The S20G is a mutation found in oriental populations related to early T2DM manifestation, the rat amylin is a non amyloidogenic sequence and the cat is amyloidogenic. REMD simulations initiated from the AlphaFold coordinates are propagated with exchanges attempted every 10ps, resulting in an exchange probability of approximately 30%. We utilized the Energy Landscape Visualization Method (ELViM) to visualize the relative Free Energies of which and to explore possible pathways for fiber formation. The implicit solvent simulations for the human sequence are validated by performing explicit solvent simulations with ff19SB+OPC forcefields using an hybrid REMD model. 

We verify that the amyloidogenic sequences consistently populate structures that form β-sheets, which are accordingly absent in the rat variant. Previous REMD simulations have suggested an equilibrium between coil and 𝛼-helix intermediates, which assumes that the helix element is a biological key element for ligand recognition and membrane binding. The S20G ensemble is more compact and with reduced helicity, populating both coil and β structures. The cat amylin favors an ensemble with β-sheet being formed by the C-terminus. Finally, rat amylin is devoid of β-sheet formation. Human amylin populate hairpin structures while sampling the helix-coil equilibrium, emphasizing the complexity of IDP’s energy landscape.