Million-atom molecular dynamics simulations reveal the interfacial interactions and assembly of plant PSII-LHCII supercomplex

Abstract

Protein-protein interface interactions dictate efficient excitation energy transfer from light-harvesting antennas to the photosystem II (PSII) core. In this work, we construct a 1.2 million atom-scale model of plant C₂S₂-type PSII-LHCII supercomplex and perform microsecond-scale molecular dynamics (MD) simulations to explore the interactions and assembly mechanisms of the sizeable PSII-LHCII supercomplex. We optimize the nonbonding interactions of the PSII-LHCII cryo-EM structure using microsecond-scale MD simulations. Binding free energy calculations with component decompositions reveal that hydrophobic interactions predominantly drive antenna-core association and the antenna-antenna interactions are relatively weak. Despite the positive electrostatic interaction energies, hydrogen bonds and salt bridges mainly provide directional or anchoring forces for interface binding. Analysis of the roles of small intrinsic subunits of PSII suggests that LHCII and CP26 first interact with small intrinsic subunits and then bind to the core proteins, whereas CP29 adopts a one-step binding process to the PSII core without the assistance of other factors. Our study provides insights into the molecular underpinnings of the self-organization and regulation of plant PSII-LHCII. It lays the framework for deciphering the general assembly principles of photosynthetic supercomplexes and possibly other macromolecular structures. The finding also has implications for repurposing photosynthetic systems to enhance photosynthesis.

Fig. 1. Validation of the quality of MD simulation. (A) Stromal view on the PSII-LHCII dimer. For clarity, only the subunits of the right monomer are highlighted, and different subunits are colored and labeled differently (the four extrinsic subunits are not shown). Among them, the 4 large core subunits are shown using the surface model and the remaining parts are shown using the cartoon model. The positions of three antennae–core interfaces are indicated in the left monomer. (B and C) Ramachandran plots for cryo-EM and MD structures, respectively. (D and E) RMSD values of proteins associated with the antennae–core interfaces (for CP26 and PsbW, only the RMSDs of non-loop regions were considered due to the high volatility of the loop regions). The RMSDs are obtained using the average of the two monomers and are colored as in (A).

Fig. 2. RMSF fluctuations of the PSII-LHCII backbone. (A) Side view and (B) stromal view on the PSII-LHCII dimer. All protein residues were colored according to the RMSF values of C_α atoms capped at 2.5 Å: red represents a high RMSF value and blue represents a small RMSF value. (C–E) RMSF values of LHCII(A), CP29 and CP26 residues, respectively. Grey boxes and arrows indicate the regions with higher fluctuation values.

Fig. 3. Binding free energy and corresponding component contribution of hot spots on S_LHCII/core, S_CP26/core and S_CP29/core and their localization. (A and B) Localization of hot spots on LHCII and the core complex (at the S_LHCII/core), respectively. (C and D) Localization of hot spots on CP26 and the core complex (at the S_CP26/core), respectively. The protein surface map colored according to the free energy contribution of each hot spot. The yellow dotted lines in panels (B) and (D) correspond to the positions of the small intrinsic subunits PsbH and PsbZ, respectively. The unit of energy is kcal mol⁻¹. (E) Binding free energy and corresponding component contribution of hot spots, including hydrophobic (red), electrostatic (blue) and total (yellow) contribution. Color scheme is presented as the same as shown in Fig. 1A. The dotted box lines with different colors represent different subunits, which are CP43 (tan), PsbW (purple), LHCII (lime), PsbZ (silver) and CP26 (pink). Hot spots that participate in the formation of hydrogen bonds or salt bridges are marked with *. See Table S5 for more details. (F and H) Localization of CP29 and corresponding hot spots. (G and I) Are the localization of core complex (at the S_CP29/core) and corresponding hot spots. The yellow dotted lines in panel (i) correspond to the positions of the small intrinsic subunits PsbH. (J) Binding free energy and corresponding component contribution of hot spots. The dotted box lines with different colors represent different subunits, which are CP47 (ochre), D1 (ice blue), PsbH (mauve), PsbL (green), and CP29 (cyan), and the colors correspond to Fig. 1A. See Table S6 for more details.

Fig. 4. Hydrogen bond and salt bridge interactions at S_LHCII/core (a), S_CP26/core (b), and S_CP29/core (c). Hydrogen bonds and salt bridges are represented by yellow and orange dashed lines, respectively. Colour scheme is presented as the same as shown in Fig. 1A.

Fig. 5. Binding free energy changes caused by the deletion of key subunits and a schematic diagram of the inferred assembly process. (A) Display of the small intrinsic subunits PsbW, PsbZ, PsbH, and Motif II of the N-terminal loop region of CP29, the colors of protein subunits correspond to Fig. 1a, and the Motif II is shown in yellow. (B) Affinity changes of the antenna–core interface in the absence of PsbW, PsbZ, PsbH and Motif II.

Fig. 6. Schematic diagram of the antenna–core assembly process of the C₂S₂-type PSII-LHCII. LHCII is represented in green, CP26 in pink, CP29 in blue, PsbW in purple, and PsbZ in gray, these colors correspond to Fig. 1A. Motif II of CP29 is shown with a yellow coil. Brown and maroon show dimerized PSII cores. Arrows with numbers represent potential assembly steps.