Folding of Protein L with implications for collapse in the denatured   state ensemble
  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 $\approx$ 6\AA \ decrease in $R_g$ when the actual decrease is $\approx$ 3\AA \ on Guanidinium Chloride denaturant dilution from 7.5M to 1M, and thereby suggesting pronounced compaction in the protein dimensions in the burst-phase. The $\approx$ 3\AA \ 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 $\Psi$-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. 
Hiranmay Maity and Govardhan Reddy
q-bio.BM