TY  - JOUR
AU  - Bertalan, Éva
AU  - Lesca, Elena
AU  - Schertler, Gebhard F. X.
AU  - Bondar, Ana-Nicoleta
TI  - C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins
JO  - Journal of chemical information and modeling
VL  - 61
IS  - 11
SN  - 0095-2338
CY  - Washington, DC
PB  - American Chemical Society
M1  - FZJ-2023-00945
SP  - 5692 - 5707
PY  - 2021
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - 34670076
UR  - <Go to ISI:>//WOS:000757001900035
DO  - DOI:10.1021/acs.jcim.1c00827
UR  - https://juser.fz-juelich.de/record/943339
ER  -