Folding of Protein L with implications for collapse in the denatured state ensemble

Abstract

A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst-phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst-phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst-phase of folding, we find that FRET experiments overestimate radius of gyration, R_g, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract R_g from the FRET efficiency. FRET experiments estimate 6 \ decrease in R_g when the actual decrease is 3 \ on Guanidinium Chloride denaturant dilution from 7.5M to 1M, and thereby suggesting pronounced compaction in the protein dimensions in the burst-phase. The 3 \ decrease is close to the statistical uncertainties of the R_g data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the -analysis experiments. The results support the hypothesis that the TSE of single domain proteins depend on protein topology, and are not stabilised by local interactions alone.

Tasks

Reproductions