Thesis lecture of Ismael Rodríguez Espigares: “GPCRmd – A web platform for collection, visualization and analysis of molecular dynamics data for G protein-coupled receptors”

Next Wednesday, 4th April 2018 at 10h, Ismael Rodríguez Espigares, member of the GPCR drug discovery group of GRIB will defense his thesis "GPCRmd - A web platform for collection, visualization and analysis of molecular dynamics data for G protein-coupled receptors" at the Charles Darwin room, placed at the inner square of the PRBB building (Dr. Aiguader, 88).

Next Wednesday, 4th April 2018 at 10h, Ismael Rodríguez Espigares, member of the GPCR drug discovery group of GRIB will defense his thesis “GPCRmd – A web platform for collection, visualization and analysis of molecular dynamics data for G protein-coupled receptors” at the Charles Darwin room, placed at the inner square of the PRBB building (Dr. Aiguader, 88).You are all invited to this event.

Abstract:

In this thesis, we present GPCRmd, an online repository with a submission system and visualization platform specifically designed for storing and providing easy access to molecular dynamics (MD) data of G protein-coupled receptors (GPCRs).

This database stores MD trajectories and necessary metadata (e.g. force-field, simulation software, integration time-step) for posterior analysis, ensuring data reproducibility and integrity. Importantly, we demonstrate the usefulness of the analysis tools implemented in GPCRmd in three case studies related to GPCR signaling bias, membrane-induced GPCR modulation and cross-receptor analysis of allosteric sodium binding.

The developed tools enabled us to detect important structural rearrangements in the initial phase of β-arrestin signaling of the δ-opioid receptor. In addition, we captured relevant molecular mechanisms responsible for cholesterol-induced modulation of the 5-HT2A receptor. Finally, we provide a comprehensive view of structural determinants that drive sodium binding across 31 different GPCRs.