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| Hauptseite > Publikationsdatenbank > C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins > print |
| Hauptseite > Publikationsdatenbank > C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins > print |
| 001 | 943339 | ||
| 005 | 20240625095119.0 | ||
| 024 | 7 | _ | |a 10.1021/acs.jcim.1c00827 |2 doi |
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| 245 | _ | _ | |a C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins |
| 260 | _ | _ | |a Washington, DC |c 2021 |b American Chemical Society |
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| 520 | _ | _ | |a Dynamic 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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| 700 | 1 | _ | |a Schertler, Gebhard F. X. |0 P:(DE-HGF)0 |b 2 |
| 700 | 1 | _ | |a Bondar, Ana-Nicoleta |0 P:(DE-Juel1)187548 |b 3 |e Corresponding author |
| 773 | _ | _ | |a 10.1021/acs.jcim.1c00827 |g Vol. 61, no. 11, p. 5692 - 5707 |0 PERI:(DE-600)1491237-5 |n 11 |p 5692 - 5707 |t Journal of chemical information and modeling |v 61 |y 2021 |x 0095-2338 |
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