Hybrid QM/MM study of FMO complex with polarized protein-specific charge

Abstract

The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point calculations have been employed to predict the energy transfer pathways utilizing the polarized protein-specific charge (PPC), which provides a more realistic description of Coulomb interaction potential in the protein than conventional mean-field charge scheme. The recently discovered eighth pigment has also been included in this study. Comparing with the conventional mean-field charges, more stable structures of FMO complex were found under PPC scheme during molecular dynamic simulation. Based on the electronic structure calculations, an exciton model was constructed to consider the couplings during excitation. The results show that pigments 3 and 4 dominate the lowest exciton levels whereas the highest exciton level are mainly constituted of pigments 1 and 6. This observation agrees well with the assumption based on the spatial distribution of the pigments. Moreover, the obtained spectral density in this study gives a reliable description of the diverse local environment embedding each pigment.

Excitation energy transfer pathways in light‐harvesting proteins: Modeling with PyFREC

“…The values of TDMs obtained from quantum chemical calculations average to 7.62 Debye (D) with minimal values for BCL407 (7.51 D) and 401 (7.52 D) and maximal for BCL403 (7.75 D) and 404 (7.73 D). Those values exceed previously reported by 20% ( μ = 6.12 D) as indicated by the consistently maintained for all fragments ratio . That consistent ratio likely indicates a systematic error of the computational method.…”

“…The excitation energies of BChl‐a pigments have previously been reported in multiple studies . Despite some discrepancies in absolute values of Q y excitation energies of FMO pigments, there is an agreement that BCL403 has the lowest excitation energy, BCL401, 402, 406, and 407 have higher energies than other FMO pigments.…”

“…In the first model, TDM is mechanistically defined as a vector aligned with the direction connecting atoms N B and N D (according to PDB notation) of the porphyrin ring (Fig. ) with a constant magnitude of 6.12 Debye, and the center of each fragment coincides with the positon of the Mg ion. In the second model, TDM is obtained from quantum chemical calculations (see above) and the center of a fragment is defined as the center of nuclear charge of a molecule .…”

“…Currently, such a full description is not feasible for many systems. Recently, significant progress in quantum dynamics simulations through application of the quantum master equation formalism and QM/MM approximations for protein‐solvent surrounding descriptions, as well as recent advances in the development of molecular fragmentation approaches were made …”

“…Found in green sulfur bacteria, FMO is commonly utilized as a model system to study pigment–protein interactions due to its relative stability compared to other structures . The molecular structure of FMO has been identified and thoroughly investigated using X‐ray crystallography, electronic spectroscopy, and computational techniques . The structure of the FMO protein complex is unique, such that a trimer of identical subunits containing seven or eight bacteriochlorophyll‐a ( BChl‐a ) molecules constitute a complex, located between a large peripheral antenna, and the reaction center, forming a bridge for efficient charge separation and energy use .…”