Systems biophysics: Global and target analysis of light harvesting and photochemical quenching in vivo

Stokkum, Ivo H. M. van

doi:10.1201/9781351242899-20

Cited by 3 publications

References 32 publications

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Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

Stokkum

Weißenborn

Weigand

et al. 2023

Photochem Photobiol Sci

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The dynamics of molecular systems can be studied with time-resolved spectroscopy combined with model-based analysis. A Python framework for global and target analysis of time-resolved spectra is introduced with the help of three case studies. The first study, concerning broadband absorption of intersystem crossing in 4-thiothymidine, demonstrates the framework's ability to resolve vibrational wavepackets with a time resolution of ≈10 fs using damped oscillations and their associated spectra and phases. Thereby, a parametric description of the “coherent artifact” is crucial. The second study addresses multichromophoric systems composed of two perylene bisimide chromophores. Here, pyglotaran's guidance spectra and lego-like model composition enable the integration of spectral and kinetic properties of the parent chromophores, revealing a loss process, the undesired production of a radical pair, that reduces the light harvesting efficiency. In the third, time-resolved emission case study of whole photosynthetic cells, a megacomplex containing ≈500 chromophores of five different types is described by a combination of the kinetic models for its elements. As direct fitting of the data by theoretical simulation is unfeasible, our global and target analysis methodology provides a useful ‘middle ground’ where the theoretical description and the fit of the experimental data can meet. The pyglotaran framework enables the lego-like creation of kinetic models through its modular design and seamless integration with the rich Python ecosystem, particularly Jupyter notebooks. With extensive documentation and a robust validation framework, pyglotaran ensures accessibility and reliability for researchers, serving as an invaluable tool for understanding complex molecular systems. Graphical abstract

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Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

Stokkum

Weißenborn

Weigand

et al. 2023

Photochem Photobiol Sci

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The rise and fall of the photoinhibition-related energy dissipation q_I

Nawrocki

Liu

Raber

et al. 2021

Preprint

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Photosynthesis converts sunlight into chemical energy, sustaining the vast majority of the biosphere. Photosystem II (PSII), the oxygen-forming enzyme that initiates photosynthesis, is however particularly prone to light-induced damage in a process known as photoinhibition, which limits the productivity of both aquatic and land photosynthesis. Photoinhibition is associated with an energy dissipation process of unknown origin, termed qI. Here, we present a detailed biophysical and biochemical in vivo study of qI in model green alga Chlamydomonas reinhardtii. Time-resolved fluorescence measurements demonstrate the origin of qI, and indicate the PSII reaction centre as the site of the quencher. Oxygen-dependence of quenching site formation, but not photoinhibition itself, is shown, suggesting that two types of PSII damage - donor and acceptor-side impairment - can be separated. We then demonstrate that the quenching loss takes place in the absence of PSII repair, and is mediated by the degradation of photoinhibited PSII cores by the FtsH protease. Finally, we integrate data ranging from picoseconds to hours in the context of structure-function excitation energy-transferring membrane patches, revealing the extent of PSII heterogeneity from the onset of photoinhibition until the breakdown of damaged PSII.

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Molecular origins of induction and loss of photoinhibition-related energy dissipation q _I

et al. 2021

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Systems biophysics: Global and target analysis of light harvesting and photochemical quenching in vivo

Cited by 3 publications

References 32 publications

Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

The rise and fall of the photoinhibition-related energy dissipation q_I

Molecular origins of induction and loss of photoinhibition-related energy dissipation q _I

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Systems biophysics: Global and target analysis of light harvesting and photochemical quenching in vivo

Cited by 3 publications

References 32 publications

Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

The rise and fall of the photoinhibition-related energy dissipation qI

Molecular origins of induction and loss of photoinhibition-related energy dissipation q I

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The rise and fall of the photoinhibition-related energy dissipation q_I

Molecular origins of induction and loss of photoinhibition-related energy dissipation q _I