title: Transition-states in protein folding kinetics: the structural interpretation of Phi values.
abstract: Phi values are experimental measures of the effects of mutations on the folding kinetics of a protein. A central question is what structural information Phi values give about the transition-state of folding. Traditionally, a Phi value is interpreted as representing the "nativeness" of a mutated residue in the transition-state. However, this interpretation is often problematic. We present here a better structural interpretation of Phi values for mutations within a given helix. Our interpretation is based on a simple physical model that distinguishes between secondary and tertiary free energy contributions of helical residues. From a linear fit of the model to experimental data, we obtain two structural parameters: the extent of helix formation in the transition-state, and the nativeness of tertiary interactions in the transition-state. We apply the model to all proteins with well-characterized helices for which more than 10 Phi values are available: protein A, CI2, and protein L. The model is simple to apply to experimental data, captures nonclassical Phi values <0 or >1 in these helices, and explains how different mutations at a given site can lead to different Phi values.
authors.affiliation: Max Planck Institute of Colloids and Interfaces, Theory Department, 14424 Potsdam, Germany. thomas.weikl@mpikg.mpg.de
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Weikl
authors.forename: Ken A
authors.initials: KA
authors.lastname: Dill
mesh_terms: D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D009154:Mutation / Q000235:genetics; D017510:Protein Folding; D011498:Protein Precursors / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013205:Staphylococcal Protein A / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D011498:Protein Precursors; D011506:Proteins; D013205:Staphylococcal Protein A