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

TL;DR

This study uses simulations to investigate Protein L folding, revealing that collapse and folding occur simultaneously, and clarifying discrepancies between FRET and SAXS experimental results regarding early protein compaction.

Contribution

The paper demonstrates through modeling that Protein L collapse coincides with folding and explains experimental overestimations of protein compaction during early folding stages.

Findings

Collapse occurs concomitantly with folding.

FRET overestimates radius of gyration during burst-phase.

Transition state ensemble is globular and topology-dependent.

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 $\approx$ 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.