Computer Simulation of Protein Aggregation Kinetics Using an Intermediate Resolution Model
Erin M. Phelps and Carol K. Hall. Department of Chemical and Biomolecular Engineering, North Carolina State University, College of Engineering 1, Box 7905, 911 Partners Way, Raleigh, NC 27695
Protein aggregation into fibril structures is a symptom of over twenty known human neurodegenerative diseases including Alzheimer's, Huntington's, and the prion diseases. Computer simulations allow us to study aggregation behavior on a molecular level. Our group uses an intermediate resolution model, PRIME, to represent the protein in order to capture its essential physical features and interactions, such as hydrogen bonding and the hydrophobic effect. Discontinuous molecular dynamics is used in conjunction with PRIME so that we can obtain long time scale simulation results in a reasonable time frame (days) rather than the months it takes for all-atom representations using traditional molecular dynamics. This project focuses on the kinetics of fibril formation; it is an attempt to identify and quantify the reaction mechanism underlying the aggregation process. A mathematical model was constructed to represent a proposed nucleation reaction mechanism which includes reversible monomer addition, oligomer addition, and lateral association reactions. Multiple simulations of a system of 96 KA14K peptide chains were then performed covering a range of concentrations including 2.5, 5, 7.5, and 10 mM, and reduced temperatures of T* = 0.12, 0.13, and 0.14. The simulations produced population data which was used to determine kinetic rate constants in the mathematical model. Preliminary results indicate that the intermediate species, such as oligomers, exhibit nonlinear behavior, which is evidenced by the oscillatory nature of their population percentage over time during the simulation.