Modeling of Multicolor Single-Molecule Forster Resonance Energy-Transfer Experiments on Protein Folding

Using a coarse-grained, C-alpha-model of BBL protein, a multicolor single-molecule Forster resonance energy transfer (FRET) experiment is modeled. Three fluorophores are introduced, which, for simplicity, are associated with C-alpha beads. Two fluorophores are placed at the ends of protein chain and the third one at the middle of the chain. The free-energy surfaces (FESs) depending on the interfluorophore distances and on the FRET efficiencies corresponding to these distances have been constructed and compared with the FESs depending on the conventional collective variables, such as the fraction of native contacts and radius of gyration. It has been found that multicolor experiments can successfully resolve all essential BBL states that are revealed by the conventional FESs. The resolution of these states with the FRET-efficiency histogram is found to be successful if the energy transfer is measured between the fluorophores at the BBL ends. We also show that, although the present model construct of BBL is very simple, it captures some characteristic features of the single-molecule FRET experiments, such as the pattern of the FRET efficiency histograms and their evolution with the denaturant concentration.