title: How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations.
abstract: How the Escherichia coli GroEL/ES chaperonin assists folding of a substrate protein remains to be uncovered. Recently, it was suggested that confinement into the chaperonin cage itself can significantly accelerate folding of a substrate. Performing comprehensive molecular simulations of eight proteins confined into various sizes L of chaperonin-like cage, we explore how and to what extent protein thermodynamics and folding mechanisms are altered by the cage. We show that a substrate protein is remarkably stabilized by confinement; the estimated increase in denaturation temperature DeltaTf is as large as approximately 60 degrees C. For a protein of size R0, the stabilization DeltaTf scales as (R0/L)nu, where nu approximately 3, which is consistent with a mean field theory of polymer. We also found significant free energy cost of confining a protein, which increases with R0/L, indicating that the confinement requires external work provided by the chaperonin system. In kinetic study, we show the folding is accelerated in a modestly well confined case, which is consistent with a recent experimental result on ribulose-1,5-bisphosphate carboxylase-oxygenase folding and simulation results of a beta hairpin. Interestingly, the acceleration of folding is likely to be larger for a protein with more complex topology, as quantified by the contact order. We also show how ensemble of folding pathways are altered by the chaperonin-like cage calculating a variant of value used in the study of spontaneous folding.
authors.affiliation: PRESTO, Japan Science and Technology Corporation, and Department of Chemistry, Faculty of Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan.
authors.forename: Fumiko
authors.initials: F
authors.lastname: Takagi
authors.forename: Nobuyasu
authors.initials: N
authors.lastname: Koga
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D018833:Chaperonins / Q000737:chemistry*; D007700:Kinetics; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins; D018833:Chaperonins