@article{d0bce6b2001f4714a80b6c2dbb234821,
title = "Potential energy function for a photo-switchable lipid molecule",
abstract = "Photo-switchable lipids are synthetic lipid molecules used in photo-pharmacology to alter membrane lateral pressure and thus control opening and closing of mechanosensitive ion channels. The molecular picture of how photo-switchable lipids interact with membranes or ion channels is poorly understood. To facilitate all-atom simulations that could provide a molecular picture of membranes with photo-switchable lipids, we derived force field parameters for atomistic computations of the azobenzene-based fatty acid FAAzo-4. We implemented a Phyton-based algorithm to make the optimization of atomic partial charges more efficient. Overall, the parameters we derived give good description of the equilibrium structure, torsional properties, and non-bonded interactions for the photo-switchable lipid in its trans and cis intermediate states, and crystal lattice parameters for trans-FAAzo-4. These parameters can be extended to all-atom descriptions of various photo-switchable lipids that have an azobenzene moiety.",
keywords = "cis-azobenzene, force-field, photo-switchable lipids, potential energy function, trans-azobenzene",
author = "Oskar Klaja and Frank, {James A.} and Dirk Trauner and Bondar, {Ana Nicoleta}",
note = "Funding Information: Deutsche Forschungsgemeinschaft, Grant/Award Number: SPP1926; Excellence Initiative of the German Research Foundation, via the Freie Universit{\"a}t Berlin. Funding information Funding Information: Research was funded in part by the German Research Foundation (DFG) Priority Research Program SPP1926 (to A-NB and DT) and by the Freie Universit{\"a}t Berlin within the Excellence Initiative of the German Research Foundation (to A-NB). Computations were performed using the Soroban supercomputer cluster of the ZEDAT Freie Universit{\"a}t Berlin, and on the computer cluster of the Department of Physics of the Freie Universit{\"a}t Berlin. We thank Jens Dreger and the ZEDAT team for excellent technical support. We acknowledge the usage of parametrization scripts from the webpage of Prof. MacKerell at the University of Maryland. Open access funding enabled and organized by Projekt DEAL. Funding Information: Research was funded in part by the German Research Foundation (DFG) Priority Research Program SPP1926 (to A‐NB and DT) and by the Freie Universit{\"a}t Berlin within the Excellence Initiative of the German Research Foundation (to A‐NB). Computations were performed using the Soroban supercomputer cluster of the ZEDAT Freie Universit{\"a}t Berlin, and on the computer cluster of the Department of Physics of the Freie Universit{\"a}t Berlin. We thank Jens Dreger and the ZEDAT team for excellent technical support. We acknowledge the usage of parametrization scripts from the webpage of Prof. MacKerell at the University of Maryland. Open access funding enabled and organized by Projekt DEAL. Publisher Copyright: {\textcopyright} 2020 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.",
year = "2020",
month = oct,
day = "15",
doi = "10.1002/jcc.26387",
language = "English (US)",
volume = "41",
pages = "2336--2351",
journal = "Journal of Computational Chemistry",
issn = "0192-8651",
publisher = "John Wiley and Sons Inc.",
number = "27",
}