研究目的
Investigating the trans-to-cis photoisomerization mechanism in channelrhodopsin-2 (ChR2) to understand how different hydrogen bonding environments affect the excited states and photocycle, and to characterize the first photocycle intermediate P500.
研究成果
The RSBH+–E123 pattern is identified as the most productive for photoisomerization in ChR2, involving a two-state pathway with a small energy barrier, leading to a twisted 13-cis retinal configuration that matches experimental FTIR spectra. This suggests E123 as the proton acceptor, providing insights into the photocycle mechanism and highlighting the role of hydrogen bonding in modulating excited state dynamics.
研究不足
The study relies on computational models which may not fully capture all biological complexities; only three hydrogen bonding patterns were considered, and the RSBH+–D253 pattern was deemed less relevant due to high energy barriers. Experimental validation is limited to available data, and the focus is on the all-trans retinal isomer, excluding 13-cis contributions.
1：Experimental Design and Method Selection:
Applied quantum mechanics/molecular mechanics (QM/MM) methodology with CASPT2//CASSCF level for excited state calculations and SCC-DFTB for molecular dynamics. Used mechanical and electrostatic embedding schemes, microiteration for geometry optimization, and FTTCF method for FTIR spectrum simulation.
2：Sample Selection and Data Sources:
Built three models of ChR2-WT with different hydrogen bonding patterns (RSBH+ with E123, water, or D253) based on previous molecular dynamics simulations. Used protein structures from PDB and simulated systems.
3：List of Experimental Equipment and Materials:
Computational software including Molcas 8.0, Tinker 6.3.2, CHARMM37b1, SCC-DFTB program; Charmm22 force field; basis set 6-31G(d); no physical equipment mentioned.
4：0, Tinker 2, CHARMM37b1, SCC-DFTB program; Charmm22 force field; basis set 6-31G(d); no physical equipment mentioned.
Experimental Procedures and Operational Workflow:
4. Experimental Procedures and Operational Workflow: Steps include ground state optimization, vertical excitation energy calculation, relaxed scan along isomerization coordinate, optimization to cis conformer, and FTIR spectrum simulation via QM/MM molecular dynamics with 100 trajectories per pattern.
5：Data Analysis Methods:
Analyzed energy profiles, Mulliken charge distributions, bond lengths, torsions, and vibrational bands using CASPT2, CASSCF, and statistical averaging of spectra.
独家科研数据包，助您复现前沿成果，加速创新突破
获取完整内容
