Combined in silico and experimental approach to identify the peptide mimetic of the nanobody that stabilize functional conformational state of the beta2 adrenergic receptor (β2AR)
Апстракт
Stabilization of specific G-protein coupled receptor (GPCR) conformation is achieved by ligand binding to orthosteric or allosteric sites on a GPCRs. A crucial unresolved issue in GPCRs activation/signaling is the role of receptor structural conformations in G protein/effector protein selection. One of the possible approaches to get comprehensive depiction of GPCRs activation dynamics are molecular simulations and recently described nanobody-derived intrabodies. Monomeric single-domain antibody (nanobody) from the Camelid family was found to allosterically bind to and stabilizes distinct conformational states of the β2AR. By applying informational spectrum method (ISM), a virtual spectroscopy method for investigation of the protein-protein interactions, we have designed peptide mimetic of the nanobody related to the β2AR (nanobody derived peptide, NDP). Further, interaction between NDP and the ligand-bound β2AR active conformation have been studied by protein-peptide docking, molecular... dynamics simulations and metadynamics calculations of free energy binding. Finally, the affinity of selected NDPs towards agonist-activated β2AR was also studied by microscale thermophoresis (MST) and by bioluminescence resonance energy transfer (BRET) based β-arrestin 2 recruitment assay. MST data predicted micromolar range interaction of selected NDPs with the β2AR, while the preliminary β-arrestin 2 recruitment results suggest prospective further modification and optimization of NDPs toward effective modulators of the β2AR.
Кључне речи:
bioinformatics / informational spectrum method / molecular dynamics simulations / nanobody derived peptides / protein-protein interactionsИзвор:
Biologia Serbica : Belgrade BioInformatics Conference : BelBi2018 : program and the book of abstracts; June 18-22, 2018, 40, 1, 58-Издавач:
- Department of Biology and Ecology : Faculty of Sciences University of Novi Sad
Финансирање / пројекти:
- Примена EIIP/ISM биоинформатичке платформе у откривању нових терапеутских таргета и потенцијалних терапеутских молекула (RS-MESTD-Basic Research (BR or ON)-173001)
Напомена:
- Special Edition of Book of Abstracts
Институција/група
VinčaTY - CONF AU - Senćanski, Milan AU - Vrecl, Milka AU - Veljković, Nevena V. AU - Glišić, Sanja PY - 2018 UR - https://vinar.vin.bg.ac.rs/handle/123456789/11013 AB - Stabilization of specific G-protein coupled receptor (GPCR) conformation is achieved by ligand binding to orthosteric or allosteric sites on a GPCRs. A crucial unresolved issue in GPCRs activation/signaling is the role of receptor structural conformations in G protein/effector protein selection. One of the possible approaches to get comprehensive depiction of GPCRs activation dynamics are molecular simulations and recently described nanobody-derived intrabodies. Monomeric single-domain antibody (nanobody) from the Camelid family was found to allosterically bind to and stabilizes distinct conformational states of the β2AR. By applying informational spectrum method (ISM), a virtual spectroscopy method for investigation of the protein-protein interactions, we have designed peptide mimetic of the nanobody related to the β2AR (nanobody derived peptide, NDP). Further, interaction between NDP and the ligand-bound β2AR active conformation have been studied by protein-peptide docking, molecular dynamics simulations and metadynamics calculations of free energy binding. Finally, the affinity of selected NDPs towards agonist-activated β2AR was also studied by microscale thermophoresis (MST) and by bioluminescence resonance energy transfer (BRET) based β-arrestin 2 recruitment assay. MST data predicted micromolar range interaction of selected NDPs with the β2AR, while the preliminary β-arrestin 2 recruitment results suggest prospective further modification and optimization of NDPs toward effective modulators of the β2AR. PB - Department of Biology and Ecology : Faculty of Sciences University of Novi Sad C3 - Biologia Serbica : Belgrade BioInformatics Conference : BelBi2018 : program and the book of abstracts; June 18-22 T1 - Combined in silico and experimental approach to identify the peptide mimetic of the nanobody that stabilize functional conformational state of the beta2 adrenergic receptor (β2AR) VL - 40 IS - 1 SP - 58 UR - https://hdl.handle.net/21.15107/rcub_vinar_11013 ER -
@conference{ author = "Senćanski, Milan and Vrecl, Milka and Veljković, Nevena V. and Glišić, Sanja", year = "2018", abstract = "Stabilization of specific G-protein coupled receptor (GPCR) conformation is achieved by ligand binding to orthosteric or allosteric sites on a GPCRs. A crucial unresolved issue in GPCRs activation/signaling is the role of receptor structural conformations in G protein/effector protein selection. One of the possible approaches to get comprehensive depiction of GPCRs activation dynamics are molecular simulations and recently described nanobody-derived intrabodies. Monomeric single-domain antibody (nanobody) from the Camelid family was found to allosterically bind to and stabilizes distinct conformational states of the β2AR. By applying informational spectrum method (ISM), a virtual spectroscopy method for investigation of the protein-protein interactions, we have designed peptide mimetic of the nanobody related to the β2AR (nanobody derived peptide, NDP). Further, interaction between NDP and the ligand-bound β2AR active conformation have been studied by protein-peptide docking, molecular dynamics simulations and metadynamics calculations of free energy binding. Finally, the affinity of selected NDPs towards agonist-activated β2AR was also studied by microscale thermophoresis (MST) and by bioluminescence resonance energy transfer (BRET) based β-arrestin 2 recruitment assay. MST data predicted micromolar range interaction of selected NDPs with the β2AR, while the preliminary β-arrestin 2 recruitment results suggest prospective further modification and optimization of NDPs toward effective modulators of the β2AR.", publisher = "Department of Biology and Ecology : Faculty of Sciences University of Novi Sad", journal = "Biologia Serbica : Belgrade BioInformatics Conference : BelBi2018 : program and the book of abstracts; June 18-22", title = "Combined in silico and experimental approach to identify the peptide mimetic of the nanobody that stabilize functional conformational state of the beta2 adrenergic receptor (β2AR)", volume = "40", number = "1", pages = "58", url = "https://hdl.handle.net/21.15107/rcub_vinar_11013" }
Senćanski, M., Vrecl, M., Veljković, N. V.,& Glišić, S.. (2018). Combined in silico and experimental approach to identify the peptide mimetic of the nanobody that stabilize functional conformational state of the beta2 adrenergic receptor (β2AR). in Biologia Serbica : Belgrade BioInformatics Conference : BelBi2018 : program and the book of abstracts; June 18-22 Department of Biology and Ecology : Faculty of Sciences University of Novi Sad., 40(1), 58. https://hdl.handle.net/21.15107/rcub_vinar_11013
Senćanski M, Vrecl M, Veljković NV, Glišić S. Combined in silico and experimental approach to identify the peptide mimetic of the nanobody that stabilize functional conformational state of the beta2 adrenergic receptor (β2AR). in Biologia Serbica : Belgrade BioInformatics Conference : BelBi2018 : program and the book of abstracts; June 18-22. 2018;40(1):58. https://hdl.handle.net/21.15107/rcub_vinar_11013 .
Senćanski, Milan, Vrecl, Milka, Veljković, Nevena V., Glišić, Sanja, "Combined in silico and experimental approach to identify the peptide mimetic of the nanobody that stabilize functional conformational state of the beta2 adrenergic receptor (β2AR)" in Biologia Serbica : Belgrade BioInformatics Conference : BelBi2018 : program and the book of abstracts; June 18-22, 40, no. 1 (2018):58, https://hdl.handle.net/21.15107/rcub_vinar_11013 .