Simulation de l’agrégation des protéines en fibres amyloides.

Laboratoire de Biochimie Théorique, UPR 9080

Alzheimer’s disease (AD) is the most common form of senile dementia, affecting more than 15 million people worldwide. AD is characterized by elevated numbers of amyloid deposits in the walls of cerebral blood vessels. A large body of evidence points to the aggregation of the amyloid-beta protein (Aβ) of 39-43 amino acids as a key player in the pathological process, and more precisely to the early Aβ oligomers as the primary toxic species. Structural characterization of these initial assemblies is very difficult using standard tools of biology, because they are transient and in dynamic equilibrium between various topologies.

One alternative is to use computer simulations to determine the thermodynamics and kinetics of protein aggregation. Using activation-relaxation technique (ART), molecular dynamics (MD) and replica exchange molecular dynamics (REMD) with a coarse-grained protein energy model (OPEP), we started to develop a thermodynamics and kinetics picture for several small amyloid-forming peptides.

Figure 1: Free energy surface (in kcal/mol) of the β2m (83-89) tetramer at 310 K from MD and REMD-OPEP. The surface is plotted as function of the radii of gyration (rg) of the backbone Cα atoms and side-chain beads. 

Figure 1 shows that the tetramer of b2m(83-89) is in dynamic equilibrium between various topologies and the amyloid-competent conformations consisting of states 2 and 6 are marginally populated at 310 K (only 17%). This emphasizes the role of additional monomers in stabilising the fibril. We also find that all the rates vary between 0.2 and 0.8 ns-1. Since an implicit solvent and a reduced side-chain representation accelerate the time scale by at least two orders of magnitude, these transitions will be observable by all-atom explicit solvent trajectories covering 100 - 500ns, i.e. a time scale not reachable using reasonable computer simulations.

Figure 2: A generic aggregation picture derived from ART- and MD-OPEP simulations. Starting from a randomly chosen state, the peptides form amorphous aggregates. From there, the outcome changes with the oligomer size (OS) and chain length (L). For OS <9 and L < 8, rapid aggregation proceeds directly to ordered b-sheets or indirectly through β-barrels. The double arrows indicate reversibility. For larger OS or L, aggregation into β-barrels and ordered b-sheets is very slow and rare.

Figure 2 shows a generic aggregation picture derived from ART and MD-OPEP simulations. Using MD-OPEP on seven β2m(83-89) chains, we find that the transition is more rapid from β-barrel to β-sheets than from β-sheets to β-barrel, and the estimated time scale for both reactions is on the order of the μs range in explicit solvent. Since this time increases with the oligomer size and the peptide length, only coarse-grained protein simulations can provide information of the assemblies associated with Alzheimer’s disease.

Selected References:

• S. Santini, G.-H. Wei,  N. Mousseau, P. Derreumaux,  Pathway complexity of Alzheimer's beta-amyloid Abeta16-22 peptide assembly. Structure 2004, 12, 1245-55.

• S. Santini, N. Mousseau, P. Derreumaux, In silico assembly of Alzheimer's Ab(16-22) peptide into beta-sheets, J. Am. Chem. Soc. 2004, 126, 11509-11516.

• N. Mousseau, P. Derreumaux, Exploring the early steps of amyloid peptide aggregation by computers. Acc Chem Res. 2005, 38(11):885-91.

• P. Derreumaux, N. Mousseau, Coarse-grained protein molecular dynamics simulations, J. Chem. Phys. 2007, 126(2) : 025101.

• G.H. Wei, N. Mousseau, P. Derreumaux, Computational simulations of the early steps of protein aggregation, Prion J. 2007 (in press)

• A. Melquiond, J-C. Gelly, N Mousseau, P. Derreumaux,  Probing amyloid-fibril formation of the NFGAIL peptide by computer simulations, J. Chem. Phys. 2007, In press