研究目的
Assessing the structures and spectra of red fluorescent proteins, which are the most important labels for molecular processes in living systems, using the combined quantum mechanics/molecular mechanics approach.
研究成果
The DFTB method is suitable for estimating the equilibrium geometry configurations of fluorescent proteins but requires more accurate methods for the estimation of vertical transition energies.
研究不足
The DFTB method is suitable for estimating equilibrium geometry configurations but cannot be used for the subsequent estimation of vertical electronic transition energies.
1：Experimental Design and Method Selection:
The study used the combined quantum mechanics/molecular mechanics (QM/MM) approach with the quantum-mechanical subsystem described by the density functional tight-binding (DFTB) method.
2：Sample Selection and Data Sources:
The mCherry red fluorescent protein and its modifications (mRojoA, mRojoA-VYGV, and mRojoA-YChroY) were analyzed.
3：List of Experimental Equipment and Materials:
The Charmm force field was used for the molecular-mechanical part, and the CP2K software package was used for calculations.
4：Experimental Procedures and Operational Workflow:
The DFTB/MM method was used to optimize geometric parameters, and the vertical electronic transition energies were calculated using TDDFT, SOS-CIS(D), and XMCQDFT2 methods.
5：Data Analysis Methods:
The geometric parameters and vertical transition energies were compared with those obtained using the DFT/MM method and experimental data.
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