Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation

Abstract

The Engrailed Homeodomain protein has the highest refolding and unfolding rate constants directly observed to date. Temperature jump relaxation measurements gave a refolding rate constant of 37,500 s ⁻¹ in water at 25°C, rising to 51,000 s ⁻¹ around 42°C. The unfolding rate constant was 1,100 s ⁻¹ in water at 25°C and 205,000 s ⁻¹ at 63°C. The unfolding half-life is extrapolated to be ≈7.5 ns at 100°C, which allows real-time molecular dynamics unfolding simulations to be tested on this system at a realistic temperature. Preliminary simulations did indeed conform to unfolding on this time scale. Further, similar transition states were observed in simulations at 100°C and 225°C, suggesting that high-temperature simulations provide results applicable to lower temperatures.