Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.,Cell

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Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.
Cell ( IF 45.5 ) Pub Date : 2019-11-14 , DOI: 10.1016/j.cell.2019.10.021
Abhishek Singharoy ₁ , Christopher Maffeo ₂ , Karelia H Delgado-Magnero ₃ , David J K Swainsbury ₄ , Melih Sener ₅ , Ulrich Kleinekathöfer ₆ , John W Vant ₁ , Jonathan Nguyen ₁ , Andrew Hitchcock ₄ , Barry Isralewitz ₅ , Ivan Teo ₅ , Danielle E Chandler ₅ , John E Stone ₅ , James C Phillips ₅ , Taras V Pogorelov ₇ , M Ilaria Mallus ₆ , Christophe Chipot ₈ , Zaida Luthey-Schulten ₉ , D Peter Tieleman ₃ , C Neil Hunter ₄ , Emad Tajkhorshid ₁₀ , Aleksei Aksimentiev ₁₁ , Klaus Schulten ₂

Affiliation

School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA.
Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.
Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany.
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Laboratoire International Associé CNRS-UIUC, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France.
Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Departments of Biochemistry, Chemistry, Bioengineering, and Pharmacology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.

中文翻译：

原子到表型：细胞能量代谢的分子设计原理。

我们报告了整个细胞器（一种来自紫色细菌的光合色素囊泡）的 1 亿原子级模型，该模型揭示了能量转换步骤的级联，最终从阳光中产生 ATP。该囊泡的分子动力学模拟阐明了完整的膜复合物如何影响局部曲率以调节色素的光激发。色素细胞内小分子的布朗动力学探讨了不同 pH 和盐度条件下定向电荷传输的机制。动力学模型从原子细节再现表型特性，证明细菌的低光适应是优化色素细胞结构完整性和强大能量转换之间平衡的自发结果。与更普遍的线粒体生物能量机制相似，从中可以推断出对细胞衰老机制的分子尺度见解。我们的综合方法和光谱实验共同为整个活细胞的第一原理建模铺平了道路。

更新日期：2019-11-14

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