title: The structure of the major transition state for folding of an FF domain from experiment and simulation.
abstract: We have analysed the transition state of folding of the four-helix FF domain from HYPA/FBP11 by high-resolution experiment and simulation as part of a continuing effort to understand the principles of folding and the refinement of predictive methods. The major transition state for folding was subjected to a Phi-value analysis utilising 50 mutants. The transition state contained a nucleus for folding centred around the end of helix 1 (H1) and the beginning of helix 2 (H2). Secondary structure in this region was fully formed (PhiF=0.9-1) and tertiary interactions were well developed. Interactions in the distal part of the native structure were weak (PhiF=0-0.2). The hydrophobic core and other parts of the protein displayed intermediate Phi-values, suggesting that interactions coalesce as the end of H1 and beginning of H2 are in the process of being formed. The distribution of Phi-values resembled that of barnase, which folds via an intermediate, rather than that of CI2 which folds by a concerted nucleation-condensation mechanism. The overall picture of the transition state structure identified in molecular dynamics simulations is in qualitative agreement, with the turn connecting H1 and H2 being formed, a loosened core, and H4 partially unfolded and detached from the core. There are some differences in the details and interpretation of specific Phi-values.
authors.affiliation: MRC Centre for Protein Engineering, Hills Road, CB2 2QH Cambridge, UK.
authors.forename: Per
authors.initials: P
authors.lastname: Jemth
authors.forename: Ryan
authors.initials: R
authors.lastname: Day
authors.forename: Stefano
authors.initials: S
authors.lastname: Gianni
authors.forename: Faaizah
authors.initials: F
authors.lastname: Khan
authors.forename: Mark
authors.initials: M
authors.lastname: Allen
authors.forename: Valerie
authors.initials: V
authors.lastname: Daggett
authors.forename: Alan R
authors.initials: AR
authors.lastname: Fersht
mesh_terms: D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D005998:Glycine / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D011489:Protein Denaturation; D015202:Protein Engineering; D017510:Protein Folding; D020673:Protein Renaturation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D002352:Carrier Proteins; C491404:PRPF40A protein, human; D005998:Glycine