Biophysical Society Conference | Tahoe 2023

Proton Reactions: From Basic Science to Biomedical Applications

Wednesday Speaker Abstracts

MASSIVELY PARALLEL QM/M SIMULATIONS OF PROTON TRANSFER PROCESSES IN DIFFERENT ENVIRONMENT Paulo Carloni Forschungszentrum Jülich, Germany No Abstract PROTONS TAKEN HOSTAGE: DYNAMIC H-BOND NETWORKS OF THE PH SENSING GPR68 Bhav Kapur 1,2 ; Filippo Baldessari 3 ; Michalis Lazaratos 4 ; Herbert Nar 1 ; Gisela Schnapp 1 ; Alejandro Giorgetti 3,5 ; Ana-Nicoleta Bondar 5,6 ; 1 Boehringer Ingelheim Pharma GmbH Co. & KG, Biberach an der Riss, Germany 2 Christian-Albrechts-University of Kiel, Kiel, Germany 3 University of Verona, Department of Biotechnology, Verona, Italy 4 Freie Universität Berlin, Department of Physics, Berlin, Germany 5 Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations, Jülich, Germany 6 University of Bucharest, Faculty of Physics, Bucharest, Romania Proton-sensing G-Protein Coupled Receptors (GPCRs) play a vital role in cellular homeostasis by detecting changes in the extracellular pH. These receptors have been linked to various diseases involving pH-dependent physiological processes, which makes them an attractive target for drug development. Establishing a reliable mechanism of function is difficult due to the unavailability of experimental structures for these receptors in the public domain. Conflicting mechanisms for pH-sensing have been suggested for the extracellular histidine cluster and internal carboxylate triad. Our study involved investigation of the proton-sensing GPR68 using homology and AI-based models. We then extensively evaluated these models by comparing them to the known structural characteristics of class A GPCRs and conducting microsecond timescale atomistic simulations. To understand the structural features that could be involved in conformational changes of GPR68 caused due to protonation, we carried out independent atomistic simulations of the best GPR68 structural model with various protonation states and applied graph-based analysis to the H-bond networks to evaluate the changes induced by protonation. Our findings indicate that GPR68 exhibits a robust extensive hydrogen-bond network that inter-connects the extracellular histidine cluster to the internal carboxylic cluster and may even connect the intracellular G-protein binding site in a protonation dependent manner. We discovered that a cluster of residues previously suggested to form a positive allosteric modulator binding site were closely linked to the extracellular proton-binding residues, as well as the buried carboxylates of the receptor. The analysis suggests that GPR68 utilizes dynamic hydrogen-bond networks that are dependent on protonation to link the extracellular and internal proton-binding sites, and to elicit conformational changes at the intracellular G-protein binding site.

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