Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

Abstract

The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.

Aggregation of chlorophylls on plant thylakoid membranes using coarse-grained simulations

“…16 Using molecular dynamics simulations, chains of interactions within the chlorophyll-LHCII protein have been identified which stabilize the trimeric form. 17 The role of LHCII aggregation in the NPQ is evident in vivo by isolating the trimeric and aggregated LHCII antenna. 18 Using high-resolution time-resolved fluorescence spectra, the photoprotection mechanism in vivo can be understood via an elusive change in the number of LHCIIs to the quenched state.…”

Interactive Visualization of Protein RINs using NetworKit in the Cloud

“…NETWORKIT implements two modules csbridge (2D graphs) and plotlybridge (2D and 3D graphs), which are based on ipywidget and act as such an adapter for embedded graph visualization. These widgets use external Python packages ipycytoscape and plotly, which has previously been used to visualize RINs [47]. For the scope of this paper and the requirements for RIN-exploration, we will focus on the module plotlybridge, while in principle csbridge follows a similar approach.…”

Thylakoid Composition Facilitates Chlorophyll a Dimerization through Stronger Interlipid Interactions

“…The configuration of chlorophylls is crucial to have maximum absorption of light, which increases the efficiency of photosynthesis. The LHCII trimer is stable in conjunction with the pigments and lipids by the synergistic effects of sequentially positioned hydrogen bonds and salt bridges within the monomer of the trimer . To understand the complex behavior of chlorophyll configuration in the plant LHCII complex, a thorough investigation of the interactions of CLA dimers and the driving force for the CLA association is required.…”

“…The LHCII trimer is stable in conjunction with the pigments and lipids by the synergistic effects of sequentially positioned hydrogen bonds and salt bridges within the monomer of the trimer. 5 To understand the complex behavior of chlorophyll configuration in the plant LHCII complex, a thorough investigation of the interactions of CLA dimers and the driving force for the CLA association is required. Using absorption and fluorescence spectra, the first CLA dimer is reported in saturated hydrocarbon in a concentrated solution.…”