The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods

The simplest dynamic model for an unfolded protein is a statistical coil that continually undergoes substantial conformational fluctuations. A growing number of studies indicate that the unfolded protein is not a simple random coil but rather forms transient structures. We have directly measured the rate of conformational fluctuations of unfolded intestinal fatty acid binding protein (131aa, 15kDa) by using fluorescence self-quenching in combination with fluorescence correlation spectroscopy. The conformational fluctuations in this state have an apparent relaxation time,τ_R, of 1.6 μsec in 3 M guanidine-HCl at pH 7 and 20°C. The value of τ_R increases with increasing solution viscosity, suggesting a diffusive process. In the molten globule state at pH 2, τ_R is 2.5 μsec, increasing further with the formation of salt-induced secondary structure. These measurements, which should be widely applicable to other systems, can provide important information about the still incompletely understood conformational properties of unfolded proteins and the mechanism of protein folding.