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 ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
Highlights
Photoreceptors are proteins that use photosensing chromophores to capture light signals from the environment
Multiscale methods, and in particular methods based on quantum mechanics/molecular mechanics (QM/MM), represent the method of choice to study such systems especially when used in combination with molecular dynamics (MD) simulations.[14−20] Within this framework, QM/MM results need to be averaged over various configurations extracted from the MD trajectories, which are usually performed within a fully classical description using MM force fields
We demonstrate that ground-state (GS) and excited-state (ES) Born−Oppenheimer molecular dynamics (BOMD) trajectories can be used to simulate transient IR spectra and gain insight into the ultrafast structural changes of a protein-embedded chromophore induced by the excitation
Summary
Photoreceptors are proteins that use photosensing chromophores to capture light signals from the environment. Multiscale methods, and in particular methods based on quantum mechanics/molecular mechanics (QM/MM), represent the method of choice to study such systems especially when used in combination with molecular dynamics (MD) simulations.[14−20] Within this framework, QM/MM results need to be averaged over various configurations extracted from the MD trajectories, which are usually performed within a fully classical description using MM force fields Such a strategy is generally accurate in many cases but can fail for properties deeply and finely connected to the coupling between structural fluctuations of the protein and the chromophore. We demonstrate that ground-state (GS) and excited-state (ES) BOMD trajectories can be used to simulate transient IR spectra and gain insight into the ultrafast structural changes of a protein-embedded chromophore induced by the excitation This is achieved by calculating the spectra through the autocorrelation dipole moment of the GS and ES trajectories and assigning the corresponding normal modes through a signal-processing technique. We could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing
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