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The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules

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Abstract

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).

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Abbreviations

BS:

Broken symmetry

DFT:

Density functional theory

DNA:

Deoxyribonucleic acid

EE:

Electronic-embedding

ESP:

Electrostatic potential

EXAFS:

Extended X-ray absorption fine structure

FTIR:

Fourier Transform Infrared Spectroscopy

MEP:

Minimum energy path

MoD-QM/MM:

Moving-domain QM/MM

OEC:

Oxygen-evolving complex

P-EXAFS:

Polarized extended X-ray absorption fine structure

PSII:

Photosystem II

QM/MM:

Quantum mechanics–molecular mechanics

SC-QM/MM:

Spectroscopically constrained QM/MM

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Acknowledgements

V. S. Batista acknowledges a generous allocation of DOE supercomputer time from the National Energy Research Scientific Computing Center (NERSC) and financial support from the Grants NSF ECCS # 0404191, DOE DE-FG02-07ER15909, NIH 2R01-GM043278 and the US-Israel BSF R08164. G. W. Brudvig acknowledges support from NIH GM32715.

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  1. José A. Gascón

    Present address: Department of Chemistry, University of Connecticut, Unit 3060, Storrs, CT, 06269, USA

Authors and Affiliations

  1. Department of Chemistry, Yale University, P. O. Box 208107, New Haven, CT, 06520-8107, USA

    Eduardo M. Sproviero, Michael B. Newcomer, José A. Gascón, Gary W. Brudvig & Victor S. Batista

  2. Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

    Enrique R. Batista

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  1. Eduardo M. Sproviero
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Sproviero, E.M., Newcomer, M.B., Gascón, J.A. et al. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. Photosynth Res 102, 455–470 (2009). https://doi.org/10.1007/s11120-009-9467-6

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