Shedding Light on Primary Donors in Photosynthetic Reaction Centers

Abstract

Chlorophylls (Chl)s exist in a variety of flavors and are ubiquitous in both the energy and electron transfer processes of photosynthesis. The functions they perform often occur on the ultrafast (fs-ns) time scale and until recently, these have been difficult to measure in real time. Further, the complexity of the binding pockets and the resulting protein-matrix effects that alter the respective electronic properties have rendered theoretical modeling of these states difficult. Recent advances in experimental methodology, computational modeling, and emergence of new reaction center (RC) structures have renewed interest in these processes and allowed researchers to elucidate previously ambiguous functions of Chls and related pheophytins. This is complemented by a wealth of experimental data obtained from decades of prior research. Studying the electronic properties of Chl molecules has advanced our understanding of both the nature of the primary charge separation and subsequent electron transfer processes of RCs. In this review, we examine the structures of primary electron donors in Type I and Type II RCs in relation to the vast body of spectroscopic research that has been performed on them to date. Further, we present density functional theory calculations on each oxidized primary donor to study both their electronic properties and our ability to model experimental spectroscopic data. This allows us to directly compare the electronic properties of hetero- and homodimeric RCs.

Keywords: chlorophyll; density functional theory; electron paramagnetic resonance; heterodimer; homodimer; primary donor; reaction center.

FIGURE 1

Structure and orientation of early (B)Chl acceptors in Type I (top) and Type II (bottom) RCs viewed from different angles. (A,C) A parallel orientation of the primary donor macrocycle planes, and (B,D) a perpendicular orientation of the primary donor macrocycle planes. The (B)Chl molecules of the primary donor, (B)Chl₁, are shown in green, (B)Chl₂ in blue, and (B)Chl₃/(B)Pheo in red. The two (pseudo-)symmetric branches of cofactors are denoted as ‘A’ and ‘B,’ respectively.

FIGURE 2

The chemical structures of (A) chlorophyll a (Chl a) (B) chlorophyll b (Chl b), and (C) bacteriochlorophyll a (BChl a). The nitrogen atoms of the four pyrrole rings in each macrocycle are labeled as I, II, III, and IV, respectively.

FIGURE 3

Comparison of the mid-point potential of a variety of (B)Chls in vitro and primary donors in vivo. Isolated in vitro values are depicted in green and hetero and homodimeric primary donors are in blue and dark yellow, respectively.

SCHEME 1

Simple archetypes of charge separation models. (A) Excitation of primary donor, P_λ, leading to charge separation between P_λ and Chl₃. (B) Excitation of Chl₂, leading to charge separation between Chl₂ and Chl₃, followed by the hole on Chl₂ being filled by P_λ. (C) Excitation of highly coupled P_λ, Chl₂ (and potentially Chl₃). Please note that Chl₃ is a Pheo in Type II RCs.

FIGURE 4

(A) The core subunits (PsaA, green; PsaB, blue; and PsaC, yellow) and cofactors of PS I as observed by X-ray crystallography (PDB ID: 1jb0), (B) the cofactors that participate in the primary electron transfer pathway of PS I and (C) the binding pocket of the primary donor, P₇₀₀. (D) The core subunits (D1, red; D2, blue) and cofactors of PS II as observed by X-ray crystallography (PDB ID: 3wu2), (E) the cofactors that participate in the primary electron transfer pathway of PS II and (F) the binding pocket of the primary donor, P₆₈₀. Commonly used labels are in parentheses. Part (C,F) emphasize the prominent protein-matrix effects of the primary donor of PS I and PS II, respectively, where the residues that are hydrogen bonded to the primary donors are shown in red, and nearby non-polar or π-stacked residues are colored in gray.

FIGURE 5

Analysis of inter-cofactor distances and relative orientation of primary donors from the heterodimeric RCs: (A) Photosystem I, (B) Photosystem II, and the bacterial RC from (C) Rba. sphaeroides and (D) Rps. viridis.

FIGURE 6

Space filling models of (A) P₇₀₀ from PS I, (B) P₆₈₀ from PS II, (C) P₈₆₅ from the bRC of Rba. Sphaeroides and (D) P₉₆₀ from the bRC of Rps. Viridis.

FIGURE 7

(A) The core subunits (M, blue; and L, red) and cofactors of the bRC from Rba. sphaeroides as observed by X-ray crystallography (PDB ID: 1aij), (B) the cofactors that participate in the primary electron transfer pathway of the bRC from Rba. sphaeroides and (C) the binding pocket of the primary donor, P₈₆₅. (D) The core subunits (M, blue; and L, red) and cofactors of the bRC from Rps. viridis as observed by X-ray crystallography (PDB ID: 2jbl), (E) the cofactors that participate in the primary electron transfer pathway of the bRC from Rps. viridis and (F) the binding pocket of the primary donor, P₉₆₀. Commonly used labels are in parentheses. Part (C,F) emphasize the prominent protein-matrix effects of the primary donor of the bRC from Rba. sphaeroides and Rps. viridis, respectively, where the residues that are hydrogen bonded to the primary donors are shown in red, and nearby non-polar or π-stacked residues are colored in gray.

FIGURE 8

(A) The core subunits (PshA, Blue and Red) and cofactors of the HbRC from H. modesticaldum as observed by X-ray crystallography (PDB ID: 5v8k), (B) the cofactors that participate in the primary electron transfer pathway of the HbRC and (C) the binding pocket of the primary donor, P₈₀₀. (D) The core subunits (PscA₁, blue; PscA₂, red; and PscB, green) and cofactors GsbRC from C. tepidum as observed by cryo-electron microscopy (PDB ID: 6m32), (E) the cofactors that participate in the primary electron transfer pathway of the GsbRC and (F) the binding pocket of the primary donor, P₈₄₀. The residues in part (C,F) that are providing hydrogen bonds are shown in red, and nearby non-polar or π-stacked residues are colored in gray.

FIGURE 9

Analysis of inter-cofactor distances and relative orientation of primary donors from the homodimeric RCs: (A) P₈₀₀ from the HbRC, and (B) P₈₄₀ from the GsbRC.

FIGURE 10

Space filling models of (A) P₈₀₀ from the HbRC and (B) P₈₄₀ from the GsbRC.

FIGURE 11

Electron spin density distribution on the Chl_1A macrocycles of the homodimeric oxidized primary donor (A) P₈₀₀^⋅+ of the HbRC from Heliobacterium modesticaldum (PDB ID: 5v8k) (Gisriel et al., 2017) and (B) P₈₄₀^⋅+ of the GsbRC from Chlorobaculum tepidum (PDB ID: 6m32) (Chen et al., 2020) in the singly occupied molecular orbital (SOMO) as determined through DFT calculations.