Force field development for cofactors in the photosystem II

Zhang, Lu; Silva, Daniel Adriano C; Yan, YiJing; Huang, Xuhui

doi:10.1002/jcc.23016

Cited by 66 publications

(61 citation statements)

References 73 publications

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“…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).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

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

et al. 2015

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Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and β-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain. Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin.

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Section: ■ Results and Discussionmentioning

confidence: 99%

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

et al. 2015

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Section: Methodsmentioning

confidence: 99%

“…For the five cofactors (CLA, PHO, BCR, HEM and PL9), force field parameters were previously developed by us56. General Amber force field5758 was adopted for the lipids and bicarbonate, but with a re-fitting of the partial charges following a similar scheme used for the cofactors56. The force field parameters for POPC were taken from the previous work by Kasson et al 59 As suggested by a previous study44, we assigned the atomic charges of the OEC complex as follows: Mn1–Mn4, +3; O1–O5, −2; and Ca, +2.…”

Section: Methodsmentioning

confidence: 99%

Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

et al. 2014

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One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis.

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“…We followed the same procedure as we previously published [74] to derive both bonded and non-bonded force field parameters of choline. Specifically, we have obtained the stretching, bending and torsion parameters by fitting against the Quantum Mechanics (QM) calculations performed using the Density Functional Theory with B3LYP/6-31G* in the Gaussian software [75].…”

Section: Methodsmentioning

confidence: 99%

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

Silva

Xie

et al. 2014

PLoS Comput Biol

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Protein-ligand recognition plays key roles in many biological processes. One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism, which often results from a combination of induced fit and conformational selection. In this study, we have developed a three-pronged approach of Markov State Models, Molecular Dynamics simulations, and flux analysis to determine the contribution of each model. Using this approach, we have quantified the recognition mechanism of the choline binding protein (ChoX) to be ∼90% conformational selection dominant under experimental conditions. This is achieved by recovering all the necessary parameters for the flux analysis in combination with available experimental data. Our results also suggest that ChoX has several metastable conformational states, of which an apo-closed state is dominant, consistent with previous experimental findings. Our methodology holds great potential to be widely applied to understand recognition mechanisms underlining many fundamental biological processes.

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Force field development for cofactors in the photosystem II

Cited by 66 publications

References 73 publications

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

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

Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

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