Extracellular loop 2 of G protein–coupled olfactory receptors is critical for odorant recognition

Yu, Yiqun; Ma, Zhenjie; Pacalon, Jody; Xu, Ling; Li, Weihao; Belloir, Christine; Topin, Jérémie; Briand, Loı̈c; Golebiowski, Jérôme; Cong, Xiaojing

doi:10.1016/j.jbc.2022.102331

Cited by 11 publications

(7 citation statements)

References 63 publications

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“…As mentioned above, the ECL2 folding is the most evident difference between the two models. The ECL2 is the largest and most structurally diverse extracellular loop of GPCRs, and those of ORs are among the longest ECL2 in class A GPCRs . Loop modeling is highly challenging when sequence length reaches the size of the OR ECL2. − A template selection based on sequence identity is rather difficult considering the high sequence and shape variability.…”

Section: Resultsmentioning

confidence: 99%

“…Odorant molecules are typically small organic compounds of less than 300 Da with high-to-moderate hydrophobicity, and their binding to ORs is driven by shape complementarity and mostly hydrophobic interactions. , ORs share very low sequence identity with nonsensory class A GPCRs. The small size of OR modulators and the low resolution of the structure modeling pose a major challenge to the investigation of the molecular recognition mechanisms of this important class of receptors.…”

Section: Discussionmentioning

confidence: 99%

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Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli

Haag

Marcinek

et al. 2023

J. Chem. Inf. Model.

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With approximately 400 encoding genes in humans, odorant receptors (ORs) are the largest subfamily of class A G protein-coupled receptors (GPCRs). Despite its high relevance and representation, the odorant-GPCRome is structurally poorly characterized: no experimental structures are available, and the low sequence identity of ORs to experimentally solved GPCRs is a significant challenge for their modeling. Moreover, the receptive range of most ORs is unknown. The odorant receptor OR5K1 was recently and comprehensively characterized in terms of cognate agonists. Here, we report two additional agonists and functional data of the most potent compound on two mutants, L104 3.32 and L255 6.51 . Experimental data was used to guide the investigation of the binding modes of OR5K1 ligands into the orthosteric binding site using structural information from AI-driven modeling, as recently released in the AlphaFold Protein Structure Database, and from homology modeling. Induced-fit docking simulations were used to sample the binding site conformational space for ensemble docking. Mutagenesis data guided side chain residue sampling and model selection. We obtained models that could better rationalize the different activity of active (agonist) versus inactive molecules with respect to starting models and also capture differences in activity related to minor structural differences. Therefore, we provide a model refinement protocol that can be applied to model the orthosteric binding site of ORs as well as that of GPCRs with low sequence identity to available templates.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli

Haag

Marcinek

et al. 2023

J. Chem. Inf. Model.

View full text Add to dashboard Cite

show abstract

“…The ECL2 is the largest and most structurally diverse extracellular loop of GPCRs, 70 and those of ORs are among the longest ECL2 in class A GPCRs. 71 Loop modeling is highly challenging when sequence length reaches the size of the OR ECL2. 72–74 A template selection based on sequence identity is rather difficult considering the high sequence and shape variability.…”

Section: Resultsmentioning

confidence: 99%

“…Odorant molecules are typically small organic compounds of less than 300 Da with high-to-moderate hydrophobicity and their binding to ORs is driven by shape complementarity and mostly hydrophobic interactions. 71, 95 ORs are class A GPCRs for which we do not have experimental structures and that share very low sequence identity with non-sensory GPCRs. The small size of OR modulators and the low resolution of the structure modeling pose a major challenge to the investigation of the molecular recognition mechanisms of this important class of receptors.…”

Section: Discussionmentioning

confidence: 99%

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli

Haag

Marcinek

et al. 2022

Preprint

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With approximately 400 encoding genes in humans, odorant receptors (ORs) are the largest subfamily of class A G protein-coupled receptors (GPCRs). Despite its high relevance and representation, the odorant-GPCRome is structurally poorly characterized: no experimental structures are available and the low sequence identity of ORs to experimentally solved GPCRs is a major challenge for their modeling. Moreover, the receptive range of most ORs is unknown. The odorant receptor OR5K1 was recently and comprehensively characterized in terms of cognate agonists. Here we investigate the binding modes of identified ligands into the OR5K1 orthosteric binding site using structural information both from AI-driven modeling, as recently released in the AlphaFold Protein Structure Database, and from template-based modeling. Induced-fit docking simulations were used to sample the binding site conformational space for ensemble docking. Side chain residue sampling and model selection were guided by mutagenesis data. We obtained models that could better rationalize the different activity of active (agonist) versus inactive molecules with respect to starting models, and also capture differences in activity related to small structural differences. We, therefore, provide a model refinement protocol that can be applied to model the orthosteric binding site of ORs as well as that of GPCRs with low sequence identity to available templates.

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“…Despite their potential as drug targets, the study of ORs has been hindered by the lack of structural data: the first experimental structure was published in March 2023, consisting of human OR51E2 in its active state, bound to an agonist (propionate) and a mini-G protein. In light of this limitation, the modeling community has approached the OR family with different techniques, from homology modeling − to de novo structure prediction. , Such computational models have provided useful insights into the mechanism of OR-ligand recognition at the atomistic level as well as pinpointed crucial residues for OR function, in combination with experimental mutagenesis data.…”

mentioning

confidence: 99%

Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor

Pirona,

Ballabio,

Alfonso-Prieto

et al. 2024

J. Chem. Inf. Model.

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Conformational changes as well as molecular determinants related to the activation and inactivation of olfactory receptors are still poorly understood due to the intrinsic difficulties in the structural determination of this GPCR family. Here, we perform, for the first time, the in silico inactivation of human olfactory receptor OR51E2, highlighting the possible role of calcium in this receptor state transition. Using molecular dynamics simulations, we show that a divalent ion in the ion binding site, coordinated by two acidic residues at positions 2.50 and 3.39 conserved across most ORs, stabilizes the receptor in its inactive state. In contrast, protonation of the same two acidic residues is not sufficient to drive inactivation within the microsecond timescale of our simulations. Our findings suggest a novel molecular mechanism for OR inactivation, potentially guiding experimental validation and offering insights into the possible broader role of divalent ions in GPCR signaling.

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Extracellular loop 2 of G protein–coupled olfactory receptors is critical for odorant recognition

Cited by 11 publications

References 63 publications

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor

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