Conformational Analysis of Quinone Anion Radicals in Photosystem II and Photosynthetic Bacteria

Abstract

Using density functional theory (DFT) techniques, we have investigated possible conformers of the radical anions of plastoquinone (psQ), ubiquinone (ubQ), and menaquinone (mnQ), which are formed in the reaction centers of photosynthetic bacteria, blue-green bacteria, and green plants. Replacing the hydrocarbon tail connected to the quinone ring by an ethyl group, we have computed the rotational potential energy surfaces for psQand ubQ -. Our results show that in the absence of environmental effects both systems have global minima for near-perpendicular orientations of the γ-carbon relative to the quinone ring. For psQ -, however, a low-lying local minimum is also observed for an in-plane arrangement with Cγ pointing away from the O4 oxygen. These differences in head-to-tail rotational energy surfaces may explain the experimentally observed differences in β-proton hyperfine couplings of psQvs ubQand mnQ -, and their corresponding model compounds. By replacing the C6 methyl group in ubQ and mnQ by hydrogen, or the C6 hydrogen in psQ by methyl, we show that the crucial factor determining the rotational arrangements of the quinones in biological systems (planar psQ in green plants; perpendicular ubQ and mnQ in bacteria) is the presence or absence of this methyl group. The computed barrier height to rotation in ubQ -, ca. 6 kcal/mol, and the β-proton hyperfine coupling constants for the planar vs perpendicular arrengements are in excellent accord with experimental data. Finally, we show that the methoxy group at the C2 position in ubiquinone displays a conformational preference as a result of the electron addition process, which may effect the hydrogen bonding pattern and hence promote the electron-transfer processes.

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex

“…Zhang et al 29 and Himo et al 58 calculated this potential energy in a vacuum using a quantum mechanical model for plastoquinone and semiplastoquinone radical anion (PQet − , where the first prenyl tail unit is replaced by a radical anion ethyl group), respectively. When comparing We determined the partition free energies for PQ9one, PQ1one/ol between water and octanol or cyclohexane (Table 1).…”

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective 2H and 15N Labeling, HYSCORE Spectroscopy, and DFT Modeling

“…In each series, as ingle parameter among r OH , a, b,o rf was set to ar ange of specific values while the three other parameters were kept constant.T he isoprenoid chain of the SQ was truncated after the fourth carbon atom and oriented perpendicular to the quinone plane to minimize steric interactions with O4 and the methyl group. [60,61] The range of explored a, b,a nd f values was limited by steric constraints inducedb yr eplacing the PCP molecule in the corresponding NarGHI crystal structure (PDB entry:1 Y4Z) by am enaquinone, assuming that negligible rearrangements of neighboring residues occur.T he a and b angles were investigated in the 08-308 range whereas the twist angle f was constrained between 08 and 458.T he hydrogen bond length r OH was varied between 1.60 and 1.90 .T his range includes the value r OH = 1.62 AE 0.02 ,w hich we evaluated from the measurement of the 2 Hn uclear quadrupole coupling constant of the hydrogen-bonded deuteron to MSK D . [23] Eventually,a symmetric hydrogen-bonded MSK model wasa lso tested as a reference, in which the SQ forms four hydrogen bonds with four 2-propanol molecules, as expected for af ree menaquinone in alcoholics olution.…”

Theoretical investigation of Q A −· -ligand interactions in bacterial reaction centers ofRhodobacter sphaeroides

“…Such calculations might moreover be helpful to gain further insight into structural details of the Qa binding site or into mechanisms leading to specific magnetic interactions. So lar, there are several theoretical studies on ubiquinone models which also relate to Qa in bRCs of Rhodobacter sphaeroides [45][46][47][48][49][50][51][52][53]. Most of them [45, The influence of several surrounding amino acids, a bivalent Zn 2+ metal center ~ and geometry relaxation of the ubisemiquinone on the magnetic properties of the Q;" binding site are discussed.…”