Calderon, Jacqueline C. and Plut, Eva and Keller, Max and Cabrele, Chiara and Reiser, Oliver and Gervasio, Francesco L. and Clark, Timothy (2023) 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. ISSN 1549-9596, 1549-960X
Full text not available from this repository. (Request a copy)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 V-2 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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | NEUROPEPTIDE-Y; UCSF CHIMERA; N-TERMINUS; BINDING; NEUROTENSIN; DISCOVERY; AFFINITY; ARGININE; VISUALIZATION; PHARMACOLOGY; |
| Subjects: | 500 Science > 540 Chemistry & allied sciences |
| Divisions: | Chemistry and Pharmacy > Institut für Organische Chemie > Lehrstuhl Prof. Dr. Oliver Reiser |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 13 Mar 2024 09:22 |
| Last Modified: | 13 Mar 2024 09:22 |
| URI: | https://pred.uni-regensburg.de/id/eprint/59845 |
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