The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes.

摘要: Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and catalytic sites embedded in macrobiomolecules (eg, proteins nucleic acids). QM/MM methodologies highly efficient since they implement quantum chemistry modeling only portion system involving bond-breaking/forming processes (QM layer), as influenced by surrounding molecular environment described terms force fields (MM layer). Some limitations when polarization effects not explicitly considered include approximate treatment electrostatic interactions between QM MM layers. Here, we review recent advances development protocols that allow rigorous biomacromolecules structural refinement, beyond common methods. We focus on photosystem II (PSII) with emphasis description oxygen-evolving complex (OEC) its high-resolution extended X-ray absorption fine structure spectra (EXAFS) conjunction Monte Carlo refinement. Furthermore, refinement DNA G4 quadruplexes monovalent cations direct comparisons to NMR data.