Atoms to phenotypes: Molecular design principles of cellular energy metabolism. 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. Cell, 2019.

Recent publications

Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01
Dora Pinto; Craig Fenwick; Christophe Caillat; Chiara Silacci; Serafima Guseva; Francois Dehez; Christophe Chipot; Sonia Barbieri; Andrea Minola; David Jarrossay; Georgia D. Tomaras; Xiaoying Shen; Agostino Riva; Maciej Tarkowski; Olivier Schwartz; Timothee Bruel; Jeremy Dufloo; Michael S. Seaman; David C. Montefiori; Antonio Lanzavecchia; Davide Corti; Giuseppe Pantaleo; Winfried Weissenhorn;
Microbe (2019) 26 (5): 623-637.e8
Enzyme-mimetic self-catalyzed polymerization of polypeptide helices
Ziyuan Song; Hailin Fu; Ryan Baumgartner; Lingyang Zhu; Kuo-Chih Shih; Yingchun Xia; Xuetao Zheng; Lichen Yin; Christophe Chipot; Yao Lin; Jianjun Cheng;
Nature Communications (2019) 121 (11): 3676-
Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism
Abhishek Singharoy; Christopher Maffeo; Karelia H. Delgado-Magnero; David J.K. Swainsbury; Melih Sener; Ulrich Kleinekathofer; John W. Vant; Jonathan Nguyen; Andrew Hitchcock; Barry Isralewitz; Ivan Teo; Danielle E. Chandler; John E. Stone; James C. Phillips; Taras V. Pogorelov; M. Ilaria Mallus; Christophe Chipot; Zaida Luthey-Schulten; D. Peter Tieleman; C. Neil Hunter; Emad Tajkhorshid; Aleksei Aksimentiev; Klaus Schulten;
Cell (2019) 179 (5): 1098-1111.e23


- Renewal of the Laboratoire International Associé CNRS-University of Illinois at Urbana-Champaign on November 2016
- An update of ParseFEP is available in the latest version of VMD.
- 新的分子动力学讲义 (Dissemination).


Laboratoire International Associé
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