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000943339 1001_ $$0P:(DE-HGF)0$$aBertalan, Éva$$b0
000943339 245__ $$aC-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins
000943339 260__ $$aWashington, DC$$bAmerican Chemical Society$$c2021
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000943339 520__ $$aDynamic hydrogen-bond networks provide proteins with structural plasticity required to translate signals such as ligand binding into a cellular response or to transport ions and larger solutes across membranes and, thus, are of central interest to understand protein reaction mechanisms. Here, we present C-Graphs, an efficient tool with graphical user interface that analyzes data sets of static protein structures or of independent numerical simulations to identify conserved, vs unique, hydrogen bonds and hydrogen-bond networks. For static structures, which may belong to the same protein or to proteins with different sequences, C-Graphs uses a clustering algorithm to identify sites of the hydrogen-bond network where waters are conserved among the structures. Using C-Graphs, we identify an internal protein–water hydrogen-bond network common to static structures of visual rhodopsins and adenosine A2A G protein-coupled receptors (GPCRs). Molecular dynamics simulations of a visual rhodopsin indicate that the conserved hydrogen-bond network from static structure can recruit dynamic hydrogen bonds and extend throughout most of the receptor. We release with this work the code for C-Graphs and its graphical user interface.
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000943339 7001_ $$0P:(DE-HGF)0$$aLesca, Elena$$b1
000943339 7001_ $$0P:(DE-HGF)0$$aSchertler, Gebhard F. X.$$b2
000943339 7001_ $$0P:(DE-Juel1)187548$$aBondar, Ana-Nicoleta$$b3$$eCorresponding author
000943339 773__ $$0PERI:(DE-600)1491237-5$$a10.1021/acs.jcim.1c00827$$gVol. 61, no. 11, p. 5692 - 5707$$n11$$p5692 - 5707$$tJournal of chemical information and modeling$$v61$$x0095-2338$$y2021
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