An <i>ab initio</i> force field for the cofactors of bacterial photosynthesis

Ceccarelli, Matteo; Procacci, Piero; Marchi, Massimo

doi:10.1002/jcc.10198

Cited by 87 publications

(114 citation statements)

References 44 publications

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“…Our results suggest that the additional hydrogen bonds introduced by mutation provide a more rigid suspension of the special pair cofactors within the protein, which improves the coupling to the global low-frequency modes. However, there are also localized low-frequency vibrations, as inferred from resonance Raman spectroscopy (48) and density functional normal mode calculations of the BChl cofactors (49) that may contribute to J().…”

Section: Discussionmentioning

confidence: 99%

Structural, dynamic, and energetic aspects of long-range electron transfer in photosynthetic reaction centers

Kriegl

Nienhaus

2003

Proc. Natl. Acad. Sci. U.S.A.

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Intramolecular electron transfer within proteins plays an essential role in biological energy transduction. Electron donor and acceptor cofactors are bound in the protein matrix at specific locations, and protein-cofactor interactions as well as protein conformational changes can markedly influence the electron transfer rates. To assess these effects, we have investigated charge recombination from the primary quinone acceptor to the special pair bacteriochlorophyll dimer in wild-type reaction centers of Rhodobacter sphaeroides and four mutants with widely modified free energy gaps. After light-induced charge separation, the recombination kinetics were measured in the light-and dark-adapted forms of the protein from 10 to 300 K. The data were analyzed by using the spin-boson model, which allowed us to self-consistently determine the electronic coupling energy, the distribution of energy gaps, the spectral density of phonons, and the reorganization energy. The analysis revealed slow changes of the energy gap after charge separation. Interesting correlations of the control parameters governing electron transfer were found and related to structural and dynamic properties of the protein.T he bioenergetic pathways of living systems involve a multitude of electron transfer (ET) reactions. Within large protein-cofactor complexes, electrons tunnel between donor and acceptor sites over substantial distances (5-30 Å). In the weak coupling regime, the ET rate coefficient is obtained from perturbation theory as (1-4)where ប and V denote Planck's constant divided by 2 and the electronic coupling matrix element, respectively. The thermally averaged Franck-Condon factor, FC, represents the probability of forming a resonant complex between donor and acceptor. This quantity can be calculated in various ways, based on classical, semiclassical, or quantum-mechanical theories (4). In the celebrated classical Marcus theory (1),with Boltzmann's constant, k B , and absolute temperature, T. The free energy difference between the reactant and product states, , the nuclear reorganization energy, , and the electronic coupling, V, are the three system parameters that govern the ET rate. From these quantities, only the driving force, , is directly accessible to measurement, e.g., by delayed fluorescence (5), redox titration (6), or voltammetry (7). The other two parameters can be determined only indirectly from kinetic data and are difficult to disentangle in practice. The intrinsic flexibility of proteins adds an interesting dynamic aspect to the ET reaction. Proteins fluctuate thermally among many different conformations and respond to charge rearrangements with structural relaxations on time scales ranging from (below) picoseconds to (at least) seconds. These motions can strongly affect the ET parameters and hence the ET rates (8-10). For studying biological ET, the photosynthetic reaction center (RC) of the purple bacterium Rhodobacter sphaeroides is a superb model system. This membrane-spanning, 120-kDa, protein-pigment complex consists...

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Section: Discussionmentioning

confidence: 99%

Structural, dynamic, and energetic aspects of long-range electron transfer in photosynthetic reaction centers

Kriegl

Nienhaus

2003

Proc. Natl. Acad. Sci. U.S.A.

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“…The deviation from planarity measured as the angle of two oppositely lying CPM atoms and the central iron can be as large as 11 degrees in the case of Methylobacterium extorquens 32 (PDB accession code 1QN2). DFT calculations on porphyrin systems 17,20 and X-ray structures from S. cerevisiae (PDB accession codes 1YTC and 2YCC) 33 show that the reduced heme group is more planar compared to the oxidized form. This result is in full accord with the results of our calculations, in which the optimized structures of the two redox states differ from each other by three degrees even though we started both geometry optimizations from the same starting structure taken from X-ray structure of Rb.…”

Section: Geometriesmentioning

confidence: 99%

“…17 The Mulliken charges obtained by HF are very localized, and the major charge difference between the redox states are found in the central core. The periphery exhibits no significant differences between the reduced and the oxidized forms, and the different overall charge is distributed uniformly over the whole heme prosthetic group.…”

Section: Charge Distribution Of Heme In Reduced and Oxidized Formsmentioning

confidence: 99%

“…15,16 Our geometry optimizations employ density functional theory (DFT) calculations at the B3LYP level, which have been already successfully applied for parametrization of bacteriochlorophyll, a magnesium-porphyrin system. 17 DFT methods are widely applied to metalloproteins 18 and therefore also for modeling iron-porphyrin systems, and have been found to predict accurately nuclear magnetic resonance shifts 19 as well as binding energies for the iron-sulfur bond. 20 The original charge calculations for both CHARMM and AMBER force fields were done at the HF/6-31G* level for small chemical compounds.…”

Section: Introductionmentioning

confidence: 99%

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Classical force field parameters for the heme prosthetic group of cytochrome c

et al. 2004

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Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt c. The parameters are based on both protein X-ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6-31G* level. The simulations with the new parameter set reproduce the geometries of the X-ray structures and the interaction energies between water and heme prosthetic group obtained from B3LYP/6-31G* calculations. The parameter set developed here will provide new insights into docking processes of heme containing redox proteins.

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“…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.…”

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confidence: 99%

Force field development on pigments of photosystem 2 reaction centre

Palenčár¹,

Vacha²,

Kutý³

2005

Photosynt.

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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.

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An ab initio force field for the cofactors of bacterial photosynthesis

Cited by 87 publications

References 44 publications

Structural, dynamic, and energetic aspects of long-range electron transfer in photosynthetic reaction centers

Structural, dynamic, and energetic aspects of long-range electron transfer in photosynthetic reaction centers

Classical force field parameters for the heme prosthetic group of cytochrome c

Force field development on pigments of photosystem 2 reaction centre

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