Protein Folding Pathways and Kinetics: Molecular Dynamics Simulations of β-Strand Motifs

AbstractThe folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel β-strand protein models interacting via a hybrid Go-type potential have been investigated using discontinuous molecular dynamics simulations. The kinetic study of protein folding was conducted by temperature quenching from a denatured or random coil state to a native state. The progress parameters used in the kinetic study include the squared radius of gyration Rg2, the fraction of native contacts within the protein as a whole Q, and between specific strands Qab. In the time series of folding, the denatured proteins undergo a conformational change toward the native state. The model proteins exhibit a variety of kinetic folding pathways that include a fast-track folding pathway without passing through an intermediate and multiple pathways with trapping into more than one intermediate. The kinetic folding behavior of the β-strand proteins strongly depends on the native-state geometry of the model proteins and the size of the bias gap g, an artificial measure of a model protein's preference for its native state