Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs.
The folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel beta-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 R(2)(g), the fraction of native contacts within the protein as a whole Q, and between specific strands Q(ab). 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 beta-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.
Department of Chemical Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA.
Hyunbum
H
Jang
Carol K
CK
Hall
Yaoqi
Y
Zhou
D020816:Amino Acid Motifs; D055592:Biophysical Phenomena; D001703:Biophysics; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013696:Temperature
D011506:Proteins