Cross-species computational analysis of the PMF and its key characteristics

跨越类囊体膜的光合质子动力(PMF)在生物体能量代谢的调节中起着关键作用。产生、调节和依赖PMF的反应之间相互依赖的过程和可能的相互作用的数量是惊人的，它们对细胞的生物能量学的综合影响导致了非线性的复杂性。因此，有必要建立一个严格的框架，以便系统地解决其复杂性，以开发关于如何在光合作用物种中实现和调节PMF的概念。光合作用电子传输链的计算机制模型提供了一个量化框架，使比较研究成为可能。描述光合作用的模型很多，但其中许多只关注其与pH有关的成分(ΔpH)，这主要是因为它与一种重要的光保护机制--非光化学猝灭有关。依赖能量的猝灭以热的形式释放多余的光能，以保护光系统II免受损害。然而，由于光合作用的电子传递对离子浓度(如H+、K+、Mg~(2+)和Cl~(2+)−)非常敏感，因此膜电位(PPM)在产生PMF和光保护中的重要性不应被忽视。类囊体膜上的离子转运蛋白，如KEA3，允许H+的外流和阳离子的逆流入膜，影响PMF的质子基组分或电位驱动组分的贡献。通过对PMF两个组成部分的动态微调，光合作用生物能够动态适应环境变化，平衡其能量生产，以满足其能量需求。在这个项目中，我们的目标是构建一个统一的理论框架，描述由GoPMF合作伙伴研究的从蓝藻到绿色微藻再到高等植物等众多类别的光合作用生物的PMF动力学。在先前构建的光合作用电子传递链数学模型的基础上，我们将充分探索模型的模块化设计，以创建PMF调节的蓝图。在这个框架内，我们将能够系统地研究PMF分配对光合作用动力学的影响，并进行跨物种比较，以产生关于PMF调控的新假说。结合收集到的实验工作，我们的模型将指导蓝藻光驱动产氢的实验。我们的目标是建立一个平台，进一步探索GoPMF的目标1、2、4和5。

Photosynthetic proton motive force (PMF) across the thylakoid membrane plays a pivotal role in the regulation of organisms’ energy metabolism. The number of interdependent processes and possible cross-talks between reactions that generate, modulate and depend on PMF are astonishing and their combined effect on the cell’s bioenergetics leads to a nonlinear complexity. Hence, a rigorous framework that allows for a systematic disentangling of its complexity is necessary to develop concepts on how the PMF is achieved and regulated across photosynthetic species. Computational, mechanistic models of the photosynthetic electron transport chain offer a quantitative framework that enables comparative studies. Numerous models of photosynthesis describe PMF, but many of them focus solely on its pH-dependent component (ΔpH), mainly due to its link to the important photoprotective mechanism named non-photochemical quenching. Energy-dependent quenching releases excess light energy as heat, to protect photosystem II against damage. Yet, the importance of the membrane potential (ΔΨ) in the generation of PMF, and photoprotection, should not be ignored, as the photosynthetic electron transport is highly sensitive to the concentration of ions (e.g., H+, K+, Mg2+ and Cl−). Ion transport proteins in the thylakoid membrane, such as KEA3, allow for an out-flux of H+ with a counter-in-flux of cations into the membrane, affecting the contribution of proton-based or potential-driven components of PMF. By dynamic fine-tuning of the two PMF components, photosynthetic organisms can dynamically adapt to environmental changes and balance their energy production to meet their energy demand. In this project, we aim to construct a unifying theoretical framework describing the dynamics of PMF for numerous classes of photosynthetic organisms studied by the GoPMF partners, ranging from cyanobacteria to green microalgae to higher plants. Building on the previously constructed mathematical models of the photosynthetic electron transport chain, we will fully explore the modular design of our models to create a blueprint for PMF regulation. Within this framework, we will be able to systematically investigate the effect of PMF partitioning on the photosynthetic dynamics and perform cross-species comparisons to generate novel hypotheses regarding PMF regulation. Combined with the collected experimental work, our model will guide the experiment in the light-driven production of hydrogen in cyanobacteria. Our ambition is to construct a platform where Aims 1,2,4, and 5 of the GoPMF can be further explored.