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Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR)
dc.creator | Senćanski, Milan | |
dc.creator | Glišić, Sanja | |
dc.creator | Kubale, Valentina | |
dc.creator | Cotman, Marko | |
dc.creator | Mavri, Janez | |
dc.creator | Vrecl, Milka | |
dc.date.accessioned | 2024-04-15T19:53:12Z | |
dc.date.available | 2024-04-15T19:53:12Z | |
dc.date.issued | 2024 | |
dc.identifier.issn | 2218-273X | |
dc.identifier.uri | https://www.mdpi.com/2218-273X/14/4/423 | |
dc.identifier.uri | https://imagine.imgge.bg.ac.rs/handle/123456789/2342 | |
dc.description.abstract | This study assessed the suitability of the complementarity-determining region 2 (CDR2) of the nanobody (Nb) as a template for the derivation of nanobody-derived peptides (NDPs) targeting active-state β2-adrenergic receptor (β2AR) conformation. Sequences of conformationally selective Nbs favoring the agonist-occupied β2AR were initially analyzed by the informational spectrum method (ISM). The derived NDPs in complex with β2AR were subjected to protein–peptide docking, molecular dynamics (MD) simulations, and metadynamics-based free-energy binding calculations. Computational analyses identified a 25-amino-acid-long CDR2-NDP of Nb71, designated P4, which exhibited the following binding free-energy for the formation of the β2AR:P4 complex (ΔG = −6.8 ± 0.8 kcal/mol or a Ki = 16.5 μM at 310 K) and mapped the β2AR:P4 amino acid interaction network. In vitro characterization showed that P4 (i) can cross the plasma membrane, (ii) reduces the maximum isoproterenol-induced cAMP level by approximately 40% and the isoproterenol potency by up to 20-fold at micromolar concentration, (iii) has a very low affinity to interact with unstimulated β2AR in the cAMP assay, and (iv) cannot reduce the efficacy and potency of the isoproterenol-mediated β2AR/β-arrestin-2 interaction in the BRET2-based recruitment assay. In summary, the CDR2-NDP, P4, binds preferentially to agonist-activated β2AR and disrupts Gαs-mediated signaling. | |
dc.language | en | |
dc.publisher | MDPI | |
dc.relation | Slovenian-Serbian bilateral project (BI-RS/20-21-045) | |
dc.relation | info:eu-repo/grantAgreement/MESTD/inst-2020/200017/RS// | |
dc.relation | nfo:eu-repo/grantAgreement/MESTD/inst-2020/200042/RS// | |
dc.rights | openAccess | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.source | Biomolecules | |
dc.source | Biomolecules | |
dc.subject | bioinformatics | |
dc.subject | cell-based in vitro assays | |
dc.subject | complementary-determining region 2 | |
dc.subject | molecular modeling | |
dc.subject | nanobody-derived peptides | |
dc.subject | β2-adrenergic receptor | |
dc.title | Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR) | |
dc.type | article | en |
dc.rights.license | BY | |
dc.citation.issue | 4 | |
dc.citation.spage | 423 | |
dc.citation.volume | 14 | |
dc.identifier.doi | 10.3390/biom14040423 | |
dc.identifier.fulltext | https://imagine.imgge.bg.ac.rs/bitstream/id/758909/biomolecules-14-00423-v2.pdf | |
dc.type.version | publishedVersion |