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Single molecule Forster resonance energy transfer (FRET) experiments are usedto infer the properties of the denatured state ensemble (DSE) of proteins. Fromthe measured average FRET efficiency, <E>, the distance distribution P(R) isinferred by assuming that the DSE can be described as a polymer. The singleparameter in the appropriate polymer model (Gaussian chain, Wormlike chain, orSelf-avoiding walk) for P(R) is determined by equating the calculated andmeasured <E>. In order to assess the accuracy of this "standard procedure," weconsider the generalized Rouse model (GRM), whose properties [<E> and P(R)] canbe analytically computed, and the Molecular Transfer Model for protein L forwhich accurate simulations can be carried out as a function of guanadiniumhydrochloride (GdmCl) concentration. Using the precisely computed <E> for theGRM and protein L, we infer P(R) using the standard procedure. We find that themean end-to-end distance can be accurately inferred (less than 10% relativeerror) using <E> and polymer models for P(R). However, the value extracted forthe radius of gyration (Rg) and the persistence length (lp) are less accurate.The relative error in the inferred R-g and lp, with respect to the exactvalues, can be as large as 25% at the highest GdmCl concentration. We propose aself-consistency test, requiring measurements of <E> by attaching dyes todifferent residues in the protein, to assess the validity of describing DSEusing the Gaussian model. Application of the self-consistency test to the GRMshows that even for this simple model the Gaussian P(R) is inadequate. Analysisof experimental data of FRET efficiencies for the cold shock protein shows thatat there are significant deviations in the DSE P(R) from the Gaussian model.

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