Simulating the peptide folding kinetic related spectra based on the Markov State Model

Optical spectroscopic tools are used to monitor protein folding/unfolding dynamics after a fast triggering such as the laser induced temperature jump. These techniques provide new opportunities for comparison between theory and simulations and atom-level understanding protein folding mechanism. However, the direct comparison still face two main challenges: a gap between folding relevant timescales (microseconds or above) and length of molecular dynamics simulations (typically tens to hundreds of nanoseconds), and difficulty in directly calculating spectroscopic observables from simulation configurations. Markov State Model (MSM) approach is one of the most powerful means which can increase simulations timescale up to microsecond or even millisecond. We address progress on modeling infrared and fluorescence spectroscopic signals of temperature jump induced unfolding dynamics for a few small proteins. The harmoniousness between experiment and theoretical can both improve our understanding of protein folding mechanisms and provide direct validation of those theoretical models.