Lung Wa Chung,† W. M. C. Sameera,‡ Romain Ramozzi,‡ Alister J. Page, Miho Hatanaka,‡ Galina P. Petrova, Travis V. Harris,‡,⊥ Xin Li, Zhuofeng Ke, Fengyi Liu, Hai-Bei Li, Lina Ding, and Keiji Morokuma*,‡ †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710119, China School of Ocean, Shandong University, Weihai 264209, China School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China

The ONIOM Method and Its Applications

https://www.cell.com/biophysj/pdf/S0006-3495(15)00070-3.pdf

Controlling Electron Transfer between the Two Cofactor Chains of Photosystem I by the Redox State of One of Their Components

Mutations in algal and cyanobacterial Photosystem I that independently affect the yield of initial charge separation in the two electron transfer cofactor branches.

Uncovering the parameters underlying the electron transfer (ET) in photosynthetic reaction centres is of importance for understanding the molecular mechanisms underpinning their functionality. The reductive nature of most cofactors involved in photosynthetic ET makes the direct estimation of their properties difficult. Photosystem I (PSI) operates in a highly reducing regime, making the assessment of cofactor properties even more difficult. Kinetic modelling coupled to a non-adiabatic description of ET is a useful approach in overcoming this hindrance. Here we review the theory and modelling approaches that have been used in assessing parameters associated with ET reactions in PSI, with particular attention to ET reactions involving the phylloquinones and the iron-sulphur clusters. In most modelling studies, the goal is to estimate the driving force of ET, which is usually associated with the cofactor midpoint potentials. The driving force is sensitive to many factors, which define the ET rate, i.e. the reorganisation energy, the coupling with nuclear modes and the electronic matrix elements, which are explored and discussed here. The importance of an inclusive modelling of both forward and reverse ET processes is discussed and highlighted. It is shown that although estimates are indeed sensitive to the exact parameter sets employed in the modelling, a general consensus is still attained, pointing to a scenario where Δ G A 1 A → F X 0 / Δ G A 1 B → F X 0 is weakly endergonic/exergonic, respectively. It is emphasised that to further refine those estimates, it will require a joint effort between computational modelling and more wide-ranging experimental studies.

Modelling electron transfer in photosystem I: limits and perspectives.

The oxidation kinetics of phyllo(semi)quinone (PhQ), which acts as an electron transfer (ET) intermediate in the Photosystem I reaction centre, are described by a minimum of two exponential phases, characterised by lifetimes in the 10–30 ns and 150–300 ns ranges. The fastest phase is considered to be dominated by the oxidation of the PhQ molecule coordinated by the PsaB reaction centre subunit (PhQB), and the slowest phase is dominated by the oxidation of the PsaA coordinated PhQ (PhQA). Testing different energetic schemes within a unified theory-based kinetic modelling approach provides reliable limit-values for some of the physical–chemical parameters controlling these ET reactions: (i) the value of ΔG0 associated with PhQA oxidation is smaller than ∼+30 meV; (ii) the value of the total reorganisation energy (λt) likely exceeds 0.7 eV; (iii) different mean nuclear modes are coupled to PhQB and PhQA oxidation, the former being larger, and both being ≥100 cm−1.

Comparative kinetic and energetic modelling of phyllosemiquinone oxidation in Photosystem I

The phylloquinone acceptor PhQ(A) in photosystem I binds to the protein through a single H-bond to the backbone nitrogen of PsaA-L722. Here, we investigate the effect of this H-bond on the electron transfer (ET) kinetics by substituting threonine for PsaA-L722. Room temperature spin-polarized transient EPR measurements show that in the PsaA-L722T mutant, the rate of PhQ(A)(-) to F(X) ET increases and the hyperfine coupling to the 2-methyl group of PhQ(A) is much larger than in the wild type. Molecular dynamics simulations and ONIOM type electronic structure calculations indicate that it is possible for the OH group of the Thr side chain to form an H-bond to the carbonyl oxygen atom, O(4) of the phylloquinone, and that this results in an increase in the 2-methyl hyperfine couplings as observed in the transient EPR data. The Arrhenius plot of the PhQ(A)(-) to F(X) ET in the PsaA-L722T mutant suggests that the increased rate is probably the result of a slight change in the electronic coupling between PhQ(A)(-) and F(X). The strong deviation from Arrhenius behavior observed at ∼200 K can be reproduced using a semiclassical model, which takes the zero-point energy of the mode coupled to the ET into account. However, since the change in slope of the Arrhenius plot occurs at the protein glass transition temperature, it is argued that it could be the result of a change in the protein relaxation dynamics at this temperature rather than quantum mechanical effects.

Introduction of a hydrogen bond between phylloquinone PhQA and a threonine side-chain OH group in photosystem i

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Introduction of a hydrogen bond between phylloquinone PhQA and a threonine side-chain OH group in photosystem i