TY - JOUR
T1 - Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis
AU - Chiariello, Maria Gabriella
AU - Zarmiento-Garcia, Rubi
AU - Marrink, Siewert Jan
N1 - Publisher Copyright:
© 2024 by the authors.
PY - 2024/7
Y1 - 2024/7
N2 - 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.
AB - 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.
KW - CG parametrization
KW - coarse-graining (CG)
KW - free energy calculations
KW - light-harvesting cofactors
KW - Martini 3
KW - molecular dynamics simulations
KW - photosystem II
KW - protein dynamics
UR - http://www.scopus.com/inward/record.url?scp=85199789081&partnerID=8YFLogxK
U2 - 10.3390/ijms25147947
DO - 10.3390/ijms25147947
M3 - Article
C2 - 39063190
AN - SCOPUS:85199789081
SN - 1422-0067
VL - 25
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
IS - 14
M1 - 7947
ER -