Sampling the equilibrium kinetic network of Trp-cage in explicit solvent.
We employed the single replica multiple state transition interface sampling (MSTIS) approach to sample the kinetic (un)folding network of Trp-cage mini-protein in explicit water. Cluster analysis yielded 14 important metastable states in the network. The MSTIS simulation thus resulted in a full 14 × 14 rate matrix. Analysis of the kinetic rate matrix indicates the presence of a near native intermediate state characterized by a fully formed alpha helix, a slightly disordered proline tail, a broken salt-bridge, and a rotated arginine residue. This intermediate was also found in recent IR experiments. Moreover, the predicted rate constants and timescales are in agreement with previous experiments and simulations.