How accurate are polymer models in the analysis of Forster resonanceenergy transfer experiments on proteins?

摘要

Single molecule Forster resonance energy transfer (FRET) experiments are used to infer theproperties of the denatured state ensemble (DSE) of proteins. From the measured average FRETefficiency, (E), the distance distribution P(R) is inferred by assuming that the DSE can be describedas a polymer. The single parameter in the appropriate polymer model (Gaussian chain, wormlikechain, or self-avoiding walk) for P(R) is determined by equating the calculated and measured (E).In order to assess the accuracy of this "standard procedure," we consider the generalized Rousemodel (GRM), whose properties [(E) and P(R)] can be analytically computed, and the Molecular Transfer Model for protein L for which accurate simulations can be carried out as a function ofguanadinium hydrochloride (GdmCl) concentration. Using the precisely computed (E) for the GRM and protein L, we infer P(R) using the standard procedure. We find that the mean end-to-enddistance can be accurately inferred (less than 10% relative error) using (E) and polymer models forP(R). However, the value extracted for the radius of gyration (R_g)and the persistence length(1p)areless accurate. For protein L, the errors in the inferred properties increase as the GdmCl concentrationincreases for all polymer models. The relative error in the inferred Rg and 1p, With respect to theexact values, can be as large as 25% at the highest GdmCl concentration. We propose aself-consistency test, requiring measurements of (E) by attaching dyes to different residues in theprotein, to assess the validity of describing DSE using the Gaussian model. Application of theself-consistency test to the GRM shows that even for this simple model, which exhibits an order→disorder transition, the GaussianP(R)is inadequate. Analysis of experimental data FRETefficiencies with dyes at several locations for the cold shock protein, and simulations results forprotein L, for which accurate FRET efficiencies between various locations were computed, showsthat at high GdmCl concentrations there are significant deviations in the DSE P(R) from theGaussian model.