Understanding the atomistic resolution changes during the self-assembly of amyloid peptides or proteins is important to develop compounds or conditions to alter the aggregation pathways and suppress the toxicity, and potentially aid in the development of drugs. However, the complexity of protein aggregation and the transient order/disorder of oligomers along pathways to fibril are very challenging. In this perspective, we discuss computational studies of amyloid polypeptides carried out under various conditions, including conditions closely mimicking in vivo, and point out the challenges in obtaining physiologically-relevant results, focusing mainly on the amyloid-beta Aβ peptides.
1.IntroductionAmyloid fibril with a cross β-structure and intermolecular H-bonds parallel to the long fibril axis is a hallmark of many sequences differing in amino acid length and composition involved in neurogenerative diseases. These involve Aβ and tau proteins in Alzheimer's disease (AD), α-synuclein in Parkinson disease, superoxide dismutase 1 (SOD1) protein in amyotrophic lateral sclerosis, transthyretin protein in cardiac and systemic amyloidosis, prion protein in prion disease, and human islet amyloid polypeptide (hIAPP) in type 2 diabetes, among others.Fragments of these proteins form fibrils as well, which represent ideal systems for computational studies. 1 In this perspective, we mainly focus on the Aβ peptides.
Results and Discussion
Protein self-assembly under quiescent solution conditionsThe aggregation kinetics of amyloid proteins in aqueous solution, as measured by Thioflavin T (ThT) fluorescence assays, displays a sigmoidal curve with a lag-phase where monomers undergo conformational conversion and self-assemble into oligomers until the growth phase where the fibril elongates. This is followed by the saturation phase where the system is in equilibrium between fibrils and a low concentration of monomers. Aggregation is described by microscopic events involving primary nucleation, elongation and dissociation of a fibril by one monomer, and secondary (fibril fragmentation and fibril surface-catalyzed) nucleation. The rates of the different microscopic processes are obtained by fitting the experimental aggregation kinetic curves using multiple initial monomer concentrations. It was shown the aggregation kinetics is sensitive to variations in temperature, pH, protein concentration, ionic strength, and the presence of cofactors and preformed aggregates. 2 General questions probing amyloid fibril formation of short peptides adopting straight β-strands in the bulk solution were addressed by on-lattice models and Monte Carlo simulations. It was demonstrated that the energy difference between the monomeric native state and the fibril-prone (N*) state, and therefore the population of the ensemble of N* structures in the full spectrum of conformations, are the major determinants of the time for fibril formation. 3,4 Based on a cubic lattice that considers the formation of H-bonds and pairwise side chain interactions, 5 and replic...