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

Area of Science:

• Biophysics
• Computational Biology
• Protein Dynamics

Background:

• Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for studying protein dynamics.
• Coarse-grained models simplify complex protein structures for computational efficiency.
• Understanding protein folding and conformational changes is crucial in molecular biology.

Purpose of the Study:

• To model a multicolor single-molecule Förster resonance energy transfer (FRET) experiment using a coarse-grained model of BBL protein.
• To compare free-energy surfaces (FESs) derived from FRET efficiencies with those from conventional collective variables.
• To assess the capability of multicolor FRET experiments in resolving protein conformational states.

Main Methods:

• Development of a coarse-grained Cα-model for BBL protein.
• Incorporation of three fluorophores at specific positions on the protein chain.
• Construction and analysis of free-energy surfaces based on interfluorophore distances and FRET efficiencies.
• Comparison with FESs derived from radius of gyration and fraction of native contacts.

Main Results:

• Multicolor FRET experiments successfully resolve essential BBL protein states, comparable to conventional methods.
• Optimal resolution of states is achieved when FRET is measured between fluorophores at the protein ends.
• The simplified model captures characteristic features of experimental FRET-efficiency histograms and their dependence on denaturant concentration.

Conclusions:

• Multicolor smFRET experiments offer a viable approach for characterizing protein conformational landscapes.
• Strategic placement of fluorophores is key to maximizing the information content of FRET measurements.
• Coarse-grained modeling, even with simplified representations, can provide valuable insights into experimental smFRET observations.