Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics.

ABSTRACT: Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe grou

SUBMITTER: Macaluso V 

PROVIDER: S-EPMC8450903 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature