title: The cooperativity of burst phase reactions explored.
abstract: The denaturant-dependence of the major, observable relaxation rates for folding (kobs) of ribonuclease HI from Escherichia coli (RNase H) and phage T4 lysozyme (T4L) reveal that, for both proteins, folding begins with the rapid and transient accumulation of intermediate species in a "burst phase" which precedes the rate-limiting formation of the native state; this is evidenced by a "rollover" in the folding limb of the rate profiles (kobs versus denaturant, or chevron plot). These rate profiles are most simply described by a three-state mechanism (unfolded-to-intermediate-to-native), which implies that the burst phase represents a transition between two distinct thermodynamic states. It is shown here that the equilibrium properties of these burst phase reactions can be equally well modeled by a mechanism involving a continuum of states where the free energy of each state is linearly related to its m-value (the parameter describing the linear relationship between free energy and denaturant). A numerical model is also developed to describe the time evolution of such a system, which exhibits nearly perfect exponential behavior. Both models emphasize how a continuum of states operating under a linear free energy relationship may behave like a two state system. Such a scheme finds experimental justification from an interpretation of recent native state hydrogen exchange data. The analytical model described for a continuum can account for the observed kinetic profiles of several other model proteins. The results, however, appear context specific, suggesting that burst phase reactions are not entirely random and non-specific. The results reported in this study have important implications for the concept of cooperativity in protein folding reactions.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. martin@zebra.berkeley.edu
authors.forename: M J
authors.initials: MJ
authors.lastname: Parker
authors.forename: S
authors.initials: S
authors.lastname: Marqusee
mesh_terms: D017122:Bacteriophage T4 / Q000201:enzymology*; D003545:Cysteine / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology*; D019791:Guanidine; D006859:Hydrogen / Q000378:metabolism; D007700:Kinetics; D008962:Models, Theoretical; D009113:Muramidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D011489:Protein Denaturation; D017510:Protein Folding; D016914:Ribonuclease H / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000378:metabolism
chemical_list: D014867:Water; D006859:Hydrogen; D016914:Ribonuclease H; D009113:Muramidase; D019791:Guanidine; D003545:Cysteine