Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First-Principles Simulation Study

The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first‐principles simulations of two‐dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant noninteracting aromatic residues. The π‐stacking and excitonic coupling effects are included through ab initio simulations based on multiconfigurational methods within a hybrid quantum mechanics/molecular mechanics scheme. It is shown that linear absorption spectroscopy in the ultraviolet (UV) region is unable to resolve the unstacking dynamics characterized by the three‐step process: T‐shaped→twisted offset stacking→unstacking. Conversely, pump–probe spectroscopy can be used to resolve aromatic interactions by probing in the visible region, the excited‐state absorptions (ESAs) that involve charge‐transfer states. 2D UV spectroscopy offers the highest sensitivity to the unfolding process, by providing the disentanglement of ESA signals belonging to different aromatic chromophores and high correlation between the conformational dynamics and the quartic splitting. On the right track: A quantum mechanics/molecular mechanics approach, coupled to the dominant reaction pathway dynamics method, is used to resolve aromatic interactions during protein folding/unfolding by means of simulations of nonlinear electronic spectra of a model system. Quartic splittings, which correlate to the interchromophore distance, are resolved.