PSII–LHCII Supercomplex Organizations in Photosynthetic Membrane by Coarse-Grained Simulation

Abstract

Green plant photosystem II (PSII) and light-harvesting complex II (LHCII) in the stacked grana regions of thylakoid membranes can self-organize into various PSII-LHCII supercomplexes with crystalline or fluid-like supramolecular structures to adjust themselves with external stimuli such as high/low light and temperatures, rendering tunable solar light absorption spectrum and photosynthesis efficiencies. However, the mechanisms controlling the PSII-LHCII supercomplex organizations remain elusive. In this work, we constructed a coarse-grained (CG) model of the thylakoid membrane including lipid molecules and a PSII-LHCII supercomplex considering association/dissociation of moderately bound-LHCIIs. The CG interaction between CG beads were constructed based on electron microscope (EM) experimental results, and we were able to simulate the PSII-LHCII supramolecular organization of a 500 × 500 nm(2) thylakoid membrane, which is compatible with experiments. Our CGMD simulations can successfully reproduce order structures of PSII-LHCII supercomplexes under various protein packing fractions, free-LHCII:PSII ratios, and temperatures, thereby providing insights into mechanisms leading to PSII-LHCII supercomplex organizations in photosynthetic membranes.

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale

“…Highly coarse-grained (DPD) models have been used recently to study the dynamic organization of PSII–LHCII supercomplexes in plant photosynthetic membranes [73]. These and related models, which address the dynamic organization of thylakoid membranes on a several-hundred nanometer lengthscale, can be used to model light harvesting mechanisms, thus enabling direct comparison with spectroscopic data on these processes [74 •• ].…”

Computational ‘microscopy’ of cellular membranes

“…However, when carefully parameterized from higher-resolution models, semi-quantitative predictions can be made (Dama et al, 2013). Recent examples of the supra-coarse-grained approach include simulations of large-scale membrane remodelling by Bin-amphiphysin-Rvs (BAR) domains (Cui et al, 2013;Simunovic et al, 2013;Yu and Schulten, 2013), the membrane-induced formation of peptide fibrils (Morriss-Andrews et al, 2014) and the supra-molecular organization of photosynthetic membranes (Lee et al, 2015). Furthermore, the supra-coarse-grained approach allows for a natural connection to the macroscopic scale using, for instance, field-theory-or fluid-dynamics-based descriptions of cell membranes (Ayton et al, 2009;Camley and Brown, 2014;Fedosov et al, 2014;Yolcu et al, 2014).…”

Atomic-level description of protein–lipid interactions using an accelerated membrane model

“…Coarse-grained models work by mapping groups of atoms into beads, e.g., four heavy atoms and their associated hydrogens are represented as a single bead, which increases simulation timescales by allowing for longer timesteps (due to the increased mass of each particle) that occur more frequently (due to the reduced number of particles) [50]. Coarse-grained approaches can handle mixed lipids and probe membrane complex formation [56, 62, 63]. Implicit membrane models work by reducing the membrane to a continuum representation, e.g., a spatial region within the system with a different dielectric constant [64].…”