Extracting protein folding kinetics in single-pair fluorescence resonance energy transfer experiment based on wavelet analysis

Abstract

Dynamic structural changes of protein folding and biological macromolecules undergoing biochemical reactions can be monitored and studied using the single-pair fluorescence resonance energy transfer (sp-FRET) spectroscopy tool. In this work, we have simulated a single-pair FRET photoemission process as an illustrative model example, where a FRET pair resides on a folding protein that undergoes diffusion in water. And then we apply the wavelet analysis method, which is a widely used method in many fields, such as the digital signal processing, noise reduction and the data compression (JPEG2000), to deal with the case of fluorescence resonance energy transfer (FRET) experiment for protein folding. It is shown that the wavelet analysis filter facilitates the detection of various intermediate conformational states in a noisy trajectory. Thus it is finally suggested that it is particularly suitable for sp-FRET spectroscopy studies of protein folding and can be of use for directly extracting the folding energy landscape. Our study establishes potentially useful data analysis technique and theoretical guidelines for the study of sp-FRET spectroscopy experiments.