Force field development on pigments of photosystem 2 reaction centre

Abstract

We developed new parameters for molecular dynamics (MD) simulations, namely partial atomic charges, equilibrium bond-lengths, angles, dihedrals, atom types, and force constants of chlorophyll a (Chl) and plastoquinone (PQ), and both reduced and neutral form of primary acceptor (PHO) molecule. These parameters are essential for MD simulations that can interpret various structure functional relationships during primary processes of charge separation and stabilization in photosystem 2 reaction centres.Additional key words: chlorophyll; photosystem 2; plastoquinone.--Photosystem 2 (PS2) is a pigment-protein complex located in thylakoid membrane of cyanobacteria, algae, and higher plants. It performs series of light driven reactions, which result in a separation of charge and subsequently in a reduction of an electron-transport chain and water oxidation. Primary site of the energy conversion is located in so-called reaction centre (RC).Recently, changes in excitonic interactions of PS2 RC pigments upon light-induced oxidation of primary donor (P680) or reduction of primary acceptor PHO were analyzed using absorption and circular dichroism (CD) spectra (Vácha et al. 2002). In contrast to the oxidation of primary donor, the light-induced change in the CD spectrum upon primary acceptor reduction was temperature-dependent. This suggests a hypothesis that at a room temperature the reduced PHO induces conformational changes of the RC protein environment, which affects the excitonic interaction of the RC chlorophylls (Chls).Molecular modelling method such as MD (Allen and Tildesley 1987) coupled with quantum chemistry is a powerful tool for understanding and interpreting the upper mentioned optical spectra experiments (Vácha et al. 2005). Having chemically well defined three-dimensional (3D) molecular structure (Ferreira et al. 2004) and socalled force field (FF) parameters (MacKerell 2004), conformational study of the PS2 RC can be performed consequently by using MD technique.Various calculations with different methods have been performed in order to obtain reliable collection of FF parameters for the cofactors of bacterial and higher plant RCs (Brooks et al. 1983, Kuczera et al. 1990, Foloppe et al. 1995, Ceccarelli et al. 2003, Tsai and Simpson 2003, Autenrieth et al. 2004. Currently, the most extensive bio-molecular FFs are the CHARMM22 (Chemistry at HARvard Molecular Mechanics, version 22) (MacKerell et al. 1998) and CHARMM27. These include proteins, nucleic acids, lipids and, although limited, saccharides (MacKerell 2004). For the MD simulations on PS2 RC the present CHARMM22 and CHARM27 FF parameters are not fully applicable. Therefore, in this work we have focused on developing new CHARMM FF parameters, namely partial atomic charges, equilibrium bond-lengths, angles, dihedrals, atom types, and force constants of the PS2 RC pigments (Chl), plastoquinone (PQ), and both reduced and neutral forms of PHO molecule.

Dimerization Behavior of Methyl Chlorophyllideaas the Model of Chlorophyllain the Presence of Water Molecules—Theoretical Study

“…Finally, in literature, one observes an increasing interest for devising an accurate description of the interaction between chlorophylls (and related molecules) and with solvent molecules both with MM/MD, − as well as coarse-grain methods . We hope that the presented SAPT and DFT results can serve as a benchmark for the development of force fields suitable for the description of the photosynthetic pigments, as it is believed that only advanced parametrization techniques might yield input to computational methods, which would correctly predict the properties of chlorophylls and bacteriochlorophylls …”

Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching

“…These methods also predominantly utilize QM calculations to produce target data, for example, in the creation of FFs compatible with the popular AMBER FF for bacteriochlorophyll- a (bcl) (as well as other cofactors: methyl bacteriopheophytin- a and a ubiquinone derivative) . Further work transformed these parameters to create a chlorophyll- a (chl- a ) FF, compatible with another commonly used FF, CHARMM. Both these bcl and chl- a FFs have been utilized in several spectral density studies. ,, However, other works have criticized the development of these parameters for lacking detailed validation against experimental structure data and so developed more validated parameters for the AMBER FF of the chromophores (and other cofactors) of the photosystem II complex .…”

“…These methods also predominantly utilize QM calculations to produce target data, for example, in the creation of FFs compatible with the popular AMBER FF for bacteriochlorophyll-a (bcl) (as well as other cofactors: methyl bacteriopheophytin-a and a ubiquinone derivative). 31 Further work transformed these parameters to create a chlorophyll-a (chl-a) FF, 32 compatible with another commonly used FF, CHARMM. Both these bcl and chl-a FFs have been utilized in several spectral density studies.…”

Force field development for cofactors in the photosystem II

“…Previous efforts have been made to develop FF parameters for various cofactors in the photosynthetic systems. [24–29] Recently, a couple of research groups have put together FF parameters for all the cofactors in PSII and simulated the whole complex. [16, 17, 30] For example, Vasil'ev et al [16] parameterized the FF for BCR, and took the parameters for other cofactors either from the existing atom types in AMBER94 FF[18] or from those of the bacterial cofactors[25] without further validation.…”

“…[16, 17, 30] For example, Vasil'ev et al [16] parameterized the FF for BCR, and took the parameters for other cofactors either from the existing atom types in AMBER94 FF[18] or from those of the bacterial cofactors[25] without further validation. Palencar et al [27, 28] developed FF parameters compatible with CHARMM for three PSII cofactors (CLA, PL9, and PHO) based on the bacterial FF. [25] However, during the development of these FF parameters, no detailed validations against experimental structural data were performed.…”