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Bridging the Gap: Linking Molecular Simulations and Systemic Descriptions of Cellular Compartments

https://doi.org/10.1371/journal.pone.0014070
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Rechenberg, Ingo, Evolutionsstrategie — Optimierung technischer Systeme nach Prinzipien der biologischen Evolution. 170 S. mit 36 Abb. Frommann-Holzboog-Verlag. Stuttgart 1973. Broschiert
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Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective
inferredcites →https://doi.org/10.1007/0-306-47954-0openalex-snapshot
Anoxygenic Photosynthetic Bacteria
inferredcites →https://doi.org/10.1007/978-1-59745-525-1_5openalex-snapshot
Rule-Based Modeling of Biochemical Systems with BioNetGen
inferredcites →https://doi.org/10.1007/978-94-009-2269-3_14openalex-snapshot
Reaction centers from three herbicide-resistant mutants of Rhodobacter sphaeroides 2.4.1: sequence analysis and preliminary characterization
inferredcites →https://doi.org/10.1007/bf00016182openalex-snapshot
Anoxygenic photosynthetic bacteria
inferredcites →https://doi.org/10.1007/bf00047682openalex-snapshot
Reaction centers from three herbicide-resistant mutants of Rhodobacter sphaeroides 2.4.1: sequence analysis and preliminary characterization
inferredcites →https://doi.org/10.1016/0014-5793(94)01031-5openalex-snapshot
Calibration and time resolution of lumenal pH‐transients in chromatophores of Rhodobacter capsulatus following a single turnover flash of light: Proton release by the cytochrome bc1‐complex is strongly electrogenic
inferredcites →https://doi.org/10.1016/j.bbabio.2006.04.023openalex-snapshot
Proton in the well and through the desolvation barrier
inferredcites →https://doi.org/10.1016/j.bpj.2009.09.007openalex-snapshot
Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s
inferredcites →https://doi.org/10.1016/j.cell.2007.10.053openalex-snapshot
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
inferredcites →https://doi.org/10.1016/j.jbiotec.2006.12.018openalex-snapshot
Molecular stochastic simulations of chromatophore vesicles from Rhodobacter sphaeroides
inferredcites →https://doi.org/10.1016/j.sbi.2007.03.014openalex-snapshot
Bridging from molecular simulation to biochemical networks
inferredcites →https://doi.org/10.1016/s0006-3495(02)75470-2openalex-snapshot
Chromatophore Vesicles of Rhodobacter capsulatus Contain on Average One FOF1-ATP Synthase Each
inferredcites →https://doi.org/10.1021/bi00046a032openalex-snapshot
Role of PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 1. PufX is required for efficient light-driven electron transfer and photophosphorylation under anaerobic conditions.
inferredcites →https://doi.org/10.1021/bi00046a033openalex-snapshot
Role of the PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 2. PufX is required for efficient ubiquinone/ubiquinol exchange between the reaction center QB site and the cytochrome bc1 complex.
inferredcites →https://doi.org/10.1021/bi900045xopenalex-snapshot
Atomic Force Microscopy Studies of Native Photosynthetic Membranes
inferredcites →https://doi.org/10.1021/bi991563uopenalex-snapshot
Unbinding of Oxidized Cytochrome c from Photosynthetic Reaction Center of Rhodobacter sphaeroides Is the Bottleneck of Fast Turnover
inferredcites →https://doi.org/10.1021/j100363a004openalex-snapshot
Excited states, electron-transfer reactions, and intermediates in bacterial photosynthetic reaction centers
inferredcites →https://doi.org/10.1021/j100540a008openalex-snapshot
Exact stochastic simulation of coupled chemical reactions
inferredcites →https://doi.org/10.1023/b:pres.0000030444.52579.10openalex-snapshot
The Q-cycle – A Personal Perspective
inferredcites →https://doi.org/10.1038/279561a0openalex-snapshot
Photosynthetic bacteria
inferredcites →https://doi.org/10.1038/msb4100191openalex-snapshot
Modeling the electron transport chain of purple non‐sulfur bacteria
inferredcites →https://doi.org/10.1038/nature02289openalex-snapshot
Global organization of metabolic fluxes in the bacterium Escherichia coli
inferredcites →https://doi.org/10.1038/nri1374openalex-snapshot
Mathematical and computational models of immune-receptor signalling
inferredcites →https://doi.org/10.1046/j.1432-1033.2003.03845.xopenalex-snapshot
Kinetics of the quinone binding reaction at the QB site of reaction centers from the purple bacteria Rhodobacter sphaeroides reconstituted in liposomes
inferredcites →https://doi.org/10.1073/pnas.0706861104openalex-snapshot
Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle
inferredcites →https://doi.org/10.1074/jbc.m007444200openalex-snapshot
Confirmation of the Involvement of Protein Domain Movement during the Catalytic Cycle of the Cytochrome bc1Complex by the Formation of an Intersubunit Disulfide Bond between Cytochrome b and the Iron-Sulfur Protein
inferredcites →https://doi.org/10.1111/j.1432-1033.1991.tb15808.xopenalex-snapshot
ATP synthesis in chromatophores driven by artificially induced ion gradients
inferredcites →https://doi.org/10.1126/science.1069492openalex-snapshot
Systems Biology: A Brief Overview
inferredcites →https://doi.org/10.1142/s0218339094000131openalex-snapshot
ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE
inferredcites →https://doi.org/10.1529/biophysj.103.036962openalex-snapshot
The Proton-Driven Rotor of ATP Synthase: Ohmic Conductance (10 fS), and Absence of Voltage Gating
inferredcites →https://doi.org/10.1529/biophysj.105.067561openalex-snapshot
Reconstruction of a Kinetic Model of the Chromatophore Vesicles from Rhodobacter sphaeroides
inferredcites →https://doi.org/10.1529/biophysj.105.078501openalex-snapshot
A Spatial Model of the Chromatophore Vesicles of Rhodobacter sphaeroides and the Position of the Cytochrome bc1 Complex
inferredcites →https://doi.org/10.1529/biophysj.108.132852openalex-snapshot
Intrinsic Curvature Properties of Photosynthetic Proteins in Chromatophores

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.3365009openalex-extracted
inferred← citeshttps://doi.org/10.1007/978-3-319-62027-5_9openalex-snapshot
Modelling Giant Lipid Vesicles Designed for Light Energy Transduction
inferred← citeshttps://doi.org/10.1007/s00249-014-0963-zopenalex-snapshot
The binding of quinone to the photosynthetic reaction centers: kinetics and thermodynamics of reactions occurring at the QB-site in zwitterionic and anionic liposomes
inferred← citeshttps://doi.org/10.1016/j.cell.2019.10.021openalex-snapshot
Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism
inferred← citeshttps://doi.org/10.1016/j.sbi.2012.12.001openalex-snapshot
Modeling metabolic processes between molecular and systems biology
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b12335openalex-snapshot
Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural Models
inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b06180openalex-snapshot
Correction to “Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural Models”
inferred← citeshttps://doi.org/10.1073/pnas.1617593114openalex-snapshot
Highly oriented photosynthetic reaction centers generate a proton gradient in synthetic protocells
inferred← citeshttps://doi.org/10.1109/mci.2012.2215122openalex-snapshot
Data Mining Over Biological Datasets: An Integrated Approach Based on Computational Intelligence
inferred← citeshttps://doi.org/10.7554/elife.09541openalex-snapshot
Overall energy conversion efficiency of a photosynthetic vesicle
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