%0 Journal Article
%A Bertalan, Éva
%A Lesca, Elena
%A Schertler, Gebhard F. X.
%A Bondar, Ana-Nicoleta
%T C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins
%J Journal of chemical information and modeling
%V 61
%N 11
%@ 0095-2338
%C Washington, DC
%I American Chemical Society
%M FZJ-2023-00945
%P 5692 - 5707
%D 2021
%X 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.
%F PUB:(DE-HGF)16
%9 Journal Article
%$ 34670076
%U <Go to ISI:>//WOS:000757001900035
%R 10.1021/acs.jcim.1c00827
%U https://juser.fz-juelich.de/record/943339