A statistical appraisal of native state hydrogen exchange data: evidence for a burst phase continuum?
For a number of proteins, folding occurs via the rapid accumulation of secondary and tertiary structural features in a so-called burst phase, preceding the relatively slow, highly activated transition leading to the native state. A fundamental question is: do these burst phase reactions comprise two phase-separated thermodynamic states or a continuum of states? Ribonuclease HI (RNase H) from Escherichia coli and phage T4 lysozyme (T4L) both exhibit such a phenomenon. Native-state hydrogen exchange (NHX) data have been collected for these proteins, providing residue-specific free energies and m-values (a measure of hydrocarbon solvation) for the manifold of partially unfolded, exchange-competent forms that are accessible from the native state (DeltaG(sg) and m(sg), where the sg subscript denotes sub-global). There is good evidence that these parameters pertain to exchange-competent species comprising the burst phase observed in the global folding kinetics. We combine the results from the global folding kinetics of these proteins with a statistical analysis of their NHX parameters to determine if the distribution of experimental (m(sg), DeltaG(sg)) values derive from a mechanism where the burst phase is two-state. For RNase H, this analysis demonstrates that the burst phase of this protein is not two-state; the results imply a distribution of states, m and DeltaG exhibiting a linear functional relationship consistent with the global folding parameters. For T4L, it is difficult to distinguish the observed distribution of m(sg), DeltaG(sg) values from that expected for a mechanism where the burst phase is two-state. The results for RNase H* lend support for the idea that the burst phase reaction of this protein comprises a continuum of states. This has important implications for how we model the process of structural acquisition in protein folding reactions.
Parker
M J
MJ
Department of Molecular and Cell Biology, University of California, 229 Stanley Hall, Berkeley, CA 94720, USA. martin@zebra.berkeley.edu
Marqusee
S
S
D017122:Bacteriophage T4 / Q000201:enzymology; D004926:Escherichia coli / Q000201:enzymology; D006859:Hydrogen / Q000378:metabolism*; D007700:Kinetics; D008956:Models, Chemical; D009113:Muramidase / Q000737:chemistry* / Q000378:metabolism*; D011489:Protein Denaturation; D017510:Protein Folding; D011522:Protons; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism*; D013223:Statistics as Topic; D013816:Thermodynamics
D011522:Protons; D006859:Hydrogen; D016914:Ribonuclease H; D009113:Muramidase