GPCRmd - A web platform for collection, visualization and analysis of molecular dynamics data for G protein-coupled receptors : Bridging the gap between dynamics and receptor functionality
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 receptor (GPCR). This database stores MD trajectories and necessary metadata (e...
| Autor: | |
|---|---|
| Formato: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2018 |
| País: | España |
| Recursos: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/664667 |
| Acesso em linha: | http://hdl.handle.net/10803/664667 |
| Access Level: | acceso abierto |
| Palavra-chave: | Molecular dynamics G protein-coupled receptors Repository Membrane-induced effects Biased signaling Dinàmica molecular Receptors acoblats a proteïnes G Repositori Efectes induïts per membrana Biaix de senyalització 577 |
| Resumo: | 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 receptor (GPCR). 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 implemented analysis tools in two case studies related to GPCR signaling bias and membrane-induced GPCR modulation. These tools enabled us to detect important structural rearrangement in the initial phase of β-arrestin signaling in the δ-opioid receptor. In addition, we captured relevant molecular mechanisms which are responsible for cholesterol-induced modulation of the 5-HT2A receptor. |
|---|