Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis

Maria Gabriella Chiariello, Rubi Zarmiento-Garcia, Siewert Jan Marrink*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

As a critical step in advancing the simulation of photosynthetic complexes, we present the Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting (LHCII) proteins and the photosystem II (PSII) core complex. Our work focuses on the parametrization of beta-carotene, plastoquinone/quinol, violaxanthin, lutein, neoxanthin, chlorophyll A, chlorophyll B, and heme. We derived the CG parameters to match the all-atom reference simulations, while structural and thermodynamic properties of the cofactors were compared to experimental values when available. To further assess the reliability of the parameterization, we tested the behavior of these cofactors within their physiological environments, specifically in a lipid bilayer and bound to photosynthetic complexes. The results demonstrate that our CG models maintain the essential features required for realistic simulations. This work lays the groundwork for detailed simulations of the PSII-LHCII super-complex, providing a robust parameter set for future studies.

Original languageEnglish
Article number7947
Number of pages20
JournalInternational Journal of Molecular Sciences
Volume25
Issue number14
DOIs
Publication statusPublished - Jul-2024

Keywords

  • CG parametrization
  • coarse-graining (CG)
  • free energy calculations
  • light-harvesting cofactors
  • Martini 3
  • molecular dynamics simulations
  • photosystem II
  • protein dynamics

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