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

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

Research output: Contribution to journalArticle

28 Citations (Scopus)

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).

Original languageEnglish
Pages (from-to)455-470
Number of pages16
JournalPhotosynthesis Research
Volume102
Issue number2
DOIs
Publication statusPublished - Nov 2009

Fingerprint

Molecular mechanics
Photosystem II Protein Complex
Mechanics
Macromolecules
Quantum theory
photosystem II
mechanics
Coulomb interactions
electrostatic interactions
Static Electricity
methodology
Quantum chemistry
Exchange coupling
Chemical modification
X ray absorption
system optimization
Nucleic Acids
Charge transfer
Structural properties
Electrostatics

Keywords

  • EXAFS
  • MoD-QM/MM
  • Molecular mechanics
  • Photosystem II
  • Quantum mechanics

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology
  • Biochemistry

Cite this

The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. / Sproviero, Eduardo M.; Newcomer, Michael B.; Gascón, José A.; Batista, Enrique R.; Brudvig, Gary W; Batista, Victor S.

In: Photosynthesis Research, Vol. 102, No. 2, 11.2009, p. 455-470.

Research output: Contribution to journalArticle

Sproviero, Eduardo M. ; Newcomer, Michael B. ; Gascón, José A. ; Batista, Enrique R. ; Brudvig, Gary W ; Batista, Victor S. / The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. In: Photosynthesis Research. 2009 ; Vol. 102, No. 2. pp. 455-470.
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