Protein folding is an important problem that is attracting scientists from a wide range of disciplines. One of the major challenges comes from the gap between the experimental and the theoretical studies. We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and 2DIR spectra using explicit solvent model based on the Markov State Model (MSM) and Nonlinear Exciton Propagation (NEP) methods. MSMs partition the conformation space into a set of non-overlapping metastable states, and we can calculate spectra signal for each of these states using NEP method. To further explore the potential for simulating the spectrum of larger protein systems, we also carried out a spectroscopic calculation of TrpZip2 peptide using implicit solvent, peptide conformational distribution was sampled using Integrated Tempering Sampling (ITS) method at a series of temperatures. The agreement of the simulation with the experiment provides a justification for our protocol as well as a physical insight underlying the spectroscopic observables.

Simulating protein folding spectra using explicit and implicit solvent models

244th National Meeting (2012)

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