eprintid: 10185650
rev_number: 8
eprint_status: archive
userid: 699
dir: disk0/10/18/56/50
datestamp: 2024-01-18 11:51:28
lastmod: 2024-12-28 07:10:07
status_changed: 2024-01-18 11:51:28
type: article
metadata_visibility: show
sword_depositor: 699
creators_name: Calderón, Jacqueline C
creators_name: Plut, Eva
creators_name: Keller, Max
creators_name: Cabrele, Chiara
creators_name: Reiser, Oliver
creators_name: Gervasio, Francesco L
creators_name: Clark, Timothy
title: Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors
ispublished: pub
divisions: UCL
divisions: B04
divisions: C06
divisions: F56
note: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
abstract: A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.
date: 2024-01-08
date_type: published
publisher: American Chemical Society
official_url: https://doi.org/10.1021/acs.jcim.3c01574
oa_status: green
full_text_type: other
language: eng
primo: open
primo_central: open_green
verified: verified_manual
elements_id: 2137904
doi: 10.1021/acs.jcim.3c01574
medium: Print-Electronic
lyricists_name: Gervasio, Francesco Luigi
lyricists_id: FLGER36
actors_name: Gervasio, Francesco Luigi
actors_id: FLGER36
actors_role: owner
full_text_status: public
publication: Journal of Chemical Information and Modeling
volume: 64
number: 1
pagerange: 205-218
event_location: United States
issn: 1549-9596
citation:        Calderón, Jacqueline C;    Plut, Eva;    Keller, Max;    Cabrele, Chiara;    Reiser, Oliver;    Gervasio, Francesco L;    Clark, Timothy;      (2024)    Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors.                   Journal of Chemical Information and Modeling , 64  (1)   pp. 205-218.    10.1021/acs.jcim.3c01574 <https://doi.org/10.1021/acs.jcim.3c01574>.       Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/10185650/1/accepted.pdf