Universality classes in folding times of proteins.
Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes that are correlated with the types of structure: the alpha-, alpha-beta-, and beta- proteins have the scaling exponents of approximately 1.7, 2.5, and 3.2, respectively. The three classes merge into one when the contact range is truncated at a reasonable value. We elucidate the role of the potential associated with the chirality of a protein.
Cieplak
Marek
M
Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland. mc@decaf.ifpan.edu.pl
Hoang
Trinh Xuan
TX
D003198:Computer Simulation; D007536:Isomerism; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000145:classification*
D011506:Proteins