Microsecond Barrier-Limited Chain Collapse Observed by Time-Resolved FRET and SAXS

• Published in: Journal of molecular biology 2014-05, Vol.426 (9), p.1980-1994
• Main Authors: Kathuria, Sagar V., Kayatekin, Can, Barrea, Raul, Kondrashkina, Elena, Graceffa, Rita, Guo, Liang, Nobrega, R. Paul, Chakravarthy, Srinivas, Matthews, C. Robert, Irving, Thomas C., Bilsel, Osman
• Format: Article
• Language: English
• Subjects: Cytochromes c - chemistry; Cytochromes c - metabolism; energy transfer; fluorescence; Fluorescence Resonance Energy Transfer; FRET; guanidinium; Kinetics; polypeptides; population growth; Protein Conformation; Protein Folding; Scattering, Small Angle; small-angle X-ray scattering; solvents; thermodynamics; unfolded state; X-radiation
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2014.02.020

It is generally held that random-coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59-to-heme distance was probed by time-resolved Förster resonance energy transfer in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59–heme distance close to that of the guanidinium hydrochloride (GdnHCl) denatured state is present after ~27μs of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET (Förster resonance energy transfer) state (efficiency>90%) show that the collapse is barrier limited. Small-angle X-ray scattering (SAXS) measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady-state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with the use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native-like conditions. [Display omitted] •Chain collapse in cytochrome c is compared using lifetime-resolved FRET and SAXS.•Trp59–heme FRET pair requires no extrinsic modifications for FRET or SAXS.•Collapse proceeds without population of distances between compact and random coil.•Minimizing dynamic averaging gives consistent results between FRET and SAXS.•Marginally stable states in dynamic equilibrium with U need to be considered.