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Pacalon J, Audic G, Magnat J, Philip M, Golebiowski J, Moreau CJ, Topin J. Elucidation of the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors. Nat Commun 2023; 14:8182. [PMID: 38081900 PMCID: PMC10713630 DOI: 10.1038/s41467-023-44058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
In numerous insects, the olfactory receptor family forms a unique class of heteromeric cation channels. Recent progress in resolving the odorant receptor structures offers unprecedented opportunities for deciphering their molecular mechanisms of ligand recognition. Unexpectedly, these structures in apo or ligand-bound states did not reveal the pathway taken by the ligands between the extracellular space and the deep internal cavities. By combining molecular modeling with electrophysiological recordings, we identified amino acids involved in the dynamic entry pathway and the binding of VUAA1 to Drosophila melanogaster's odorant receptor co-receptor (Orco). Our results provide evidence for the exact location of the agonist binding site and a detailed and original mechanism of ligand translocation controlled by a network of conserved residues. These findings would explain the particularly high selectivity of Orcos for their ligands.
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Affiliation(s)
- Jody Pacalon
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France
| | | | | | - Manon Philip
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Jérôme Golebiowski
- Department of Brain & Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, Republic of Korea
| | | | - Jérémie Topin
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France.
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2
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Ectopic Odorant Receptor Responding to Flavor Compounds: Versatile Roles in Health and Disease. Pharmaceutics 2021; 13:pharmaceutics13081314. [PMID: 34452275 PMCID: PMC8402194 DOI: 10.3390/pharmaceutics13081314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
Prompted by the ground-breaking discovery of the rodent odorant receptor (OR) gene family within the olfactory epithelium nearly 30 years ago, followed by that of OR genes in cells of the mammalian germ line, and potentiated by the identification of ORs throughout the body, our appreciation for ORs as general chemoreceptors responding to odorant compounds in the regulation of physiological or pathophysiological processes continues to expand. Ectopic ORs are now activated by a diversity of flavor compounds and are involved in diverse physiological phenomena varying from adipogenesis to myogenesis to hepatic lipid accumulation to serotonin secretion. In this review, we outline the key biological functions of the ectopic ORs responding to flavor compounds and the underlying molecular mechanisms. We also discuss research opportunities for utilizing ectopic ORs as therapeutic strategies in the treatment of human disease as well as challenges to be overcome in the future. The recognition of the potent function, signaling pathway, and pharmacology of ectopic ORs in diverse tissues and cell types, coupled with the fact that they belong to G protein-coupled receptors, a highly druggable protein family, unequivocally highlight the potential of ectopic ORs responding to flavor compounds, especially food-derived odorant compounds, as a promising therapeutic strategy for various diseases.
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Alfonso-Prieto M. Bitter Taste and Olfactory Receptors: Beyond Chemical Sensing in the Tongue and the Nose. J Membr Biol 2021; 254:343-352. [PMID: 34173018 PMCID: PMC8231087 DOI: 10.1007/s00232-021-00182-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022]
Abstract
Abstract The Up-and-Coming-Scientist section of the current issue of the Journal of Membrane Biology features the invited essay by Dr. Mercedes Alfonso-Prieto, Assistant Professor at the Forschungszentrum Jülich (FZJ), Germany, and the Heinrich-Heine University Düsseldorf, Vogt Institute for Brain Research.
Dr. Alfonso-Prieto completed her doctoral degree in chemistry at the Barcelona Science Park, Spain, in 2009, pursued post-doctoral research in computational molecular sciences at Temple University, USA, and then, as a Marie Curie post-doctoral fellow at the University of Barcelona, worked on computations of enzyme reactions and modeling of photoswitchable ligands targeting neuronal receptors. In 2016, she joined the Institute for Advanced Science and the Institute for Computational Biomedicine at the FZJ, where she pursues research on modeling and simulation of chemical senses.
The invited essay by Dr. Alfonso-Prieto discusses state-of-the-art modeling of molecular receptors involved in chemical sensing – the senses of taste and smell. These receptors, and computational methods to study them, are the focus of Dr. Alfonso-Prieto’s research. Recently, Dr. Alfonso-Prieto and colleagues have presented a new methodology to predict ligand binding poses for GPCRs, and extensive computations that deciphered the ligand selectivity determinants of bitter taste receptors. These developments inform our current understanding of how taste occurs at the molecular level. Graphic Abstract ![]()
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, Germany. .,Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Kowalewski J, Ray A. Predicting Human Olfactory Perception from Activities of Odorant Receptors. iScience 2020; 23:101361. [PMID: 32731170 PMCID: PMC7393469 DOI: 10.1016/j.isci.2020.101361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/31/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
Odor perception in humans is initiated by activation of odorant receptors (ORs) in the nose. However, the ORs linked to specific olfactory percepts are unknown, unlike in vision or taste where receptors are linked to perception of different colors and tastes. The large family of ORs (~400) and multiple receptors activated by an odorant present serious challenges. Here, we first use machine learning to screen ~0.5 million compounds for new ligands and identify enriched structural motifs for ligands of 34 human ORs. We next demonstrate that the activity of ORs successfully predicts many of the 146 different perceptual qualities of chemicals. Although chemical features have been used to model odor percepts, we show that biologically relevant OR activity is often superior. Interestingly, each odor percept could be predicted with very few ORs, implying they contribute more to each olfactory percept. A similar model is observed in Drosophila where comprehensive OR-neuron data are available. Machine learning predicted activity of 34 human ORs for ~0.5 million chemicals Activities of human ORs could predict odor character using machine learning Few OR activities were needed to optimize predictions of each odor percept Behavior predictions in Drosophila also need few olfactory receptor activities
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Affiliation(s)
- Joel Kowalewski
- Interdepartmental Neuroscience Program, University of California, Riverside, CA 92521, USA
| | - Anandasankar Ray
- Interdepartmental Neuroscience Program, University of California, Riverside, CA 92521, USA; Department of Molecular, Cell and Systems Biology, University of California, 3401 Watkins Drive, Riverside, CA 92521, USA.
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5
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Hu XS, Ikegami K, Vihani A, Zhu KW, Zapata M, de March CA, Do M, Vaidya N, Kucera G, Bock C, Jiang Y, Yohda M, Matsunami H. Concentration-Dependent Recruitment of Mammalian Odorant Receptors. eNeuro 2020; 7:ENEURO.0103-19.2019. [PMID: 32015097 PMCID: PMC7189481 DOI: 10.1523/eneuro.0103-19.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
A fundamental challenge in studying principles of organization used by the olfactory system to encode odor concentration information has been identifying comprehensive sets of activated odorant receptors (ORs) across a broad concentration range inside freely behaving animals. In mammals, this has recently become feasible with high-throughput sequencing-based methods that identify populations of activated ORs in vivo In this study, we characterized the mouse OR repertoires activated by the two odorants, acetophenone (ACT) and 2,5-dihydro-2,4,5-trimethylthiazoline (TMT), from 0.01% to 100% (v/v) as starting concentrations using phosphorylated ribosomal protein S6 capture followed by RNA-Seq. We found Olfr923 to be one of the most sensitive ORs that is enriched by ACT. Using a mouse line that genetically labels Olfr923-positive axons, we provided evidence that ACT activates the Olfr923 glomeruli in the olfactory bulb. Through molecular dynamics stimulations, we identified amino acid residues in the Olfr923 binding cavity that facilitate ACT binding. This study sheds light on the active process by which unique OR repertoires may collectively facilitate the discrimination of odorant concentrations.
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Affiliation(s)
- Xiaoyang Serene Hu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Kentaro Ikegami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Aashutosh Vihani
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710
| | - Kevin W Zhu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Marcelo Zapata
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Matthew Do
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Natasha Vaidya
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- North Carolina School of Science and Mathematics, Durham, NC 27705
| | - Gary Kucera
- DCI Rodent Cancer Models Shared Resource, Duke University Medical Center, Durham, NC 27710
| | - Cheryl Bock
- DCI Rodent Cancer Models Shared Resource, Duke University Medical Center, Durham, NC 27710
| | - Yue Jiang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Masafumi Yohda
- Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710
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6
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Jabeen A, Ranganathan S. Applications of machine learning in GPCR bioactive ligand discovery. Curr Opin Struct Biol 2019; 55:66-76. [PMID: 31005679 DOI: 10.1016/j.sbi.2019.03.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/17/2022]
Abstract
GPCRs constitute the largest druggable family having targets for 475 Food and Drug Administration (FDA) approved drugs. As GPCRs are of great interest to pharmaceutical industry, enormous efforts are being expended to find relevant and potent GPCR ligands as lead compounds. There are tens of millions of compounds present in different chemical databases. In order to scan this immense chemical space, computational methods, especially machine learning (ML) methods, are essential components of GPCR drug discovery pipelines. ML approaches have applications in both ligand-based and structure-based virtual screening. We present here a cheminformatics overview of ML applications to different stages of GPCR drug discovery. Focusing on olfactory receptors, which are the largest family of GPCRs, a case study for predicting agonists for an ectopic olfactory receptor, OR1G1, compares four classical ML methods.
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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Bushdid C, de March CA, Topin J, Do M, Matsunami H, Golebiowski J. Mammalian class I odorant receptors exhibit a conserved vestibular-binding pocket. Cell Mol Life Sci 2019; 76:995-1004. [PMID: 30599066 PMCID: PMC7313674 DOI: 10.1007/s00018-018-2996-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022]
Abstract
Odorant receptors represent the largest family of mammalian G protein-coupled receptors. Phylogenetically, they are split into two classes (I and II). By analyzing the entire subclass I odorant receptors sequences, we identified two class I-specific and highly conserved motifs. These are predicted to face each other at the extra-cellular portion of the transmembrane domain, forming a vestibular site at the entrance to the orthosteric-binding cavity. Molecular dynamics simulation combined with site-directed mutagenesis and in vitro functional assays confirm the functional role of this vestibular site in ligand-driven activation. Mutations at this part of the receptor differentially affect the receptor response to four agonists. Since this vestibular site is involved in ligand recognition, it could serve ligand design that targets specifically this sub-genome of mammalian odorant receptors.
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Affiliation(s)
- Caroline Bushdid
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jérémie Topin
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France
| | - Matthew Do
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC, 27710, USA.
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France.
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Republic of Korea.
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8
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Behrens M, Briand L, de March CA, Matsunami H, Yamashita A, Meyerhof W, Weyand S. Structure-Function Relationships of Olfactory and Taste Receptors. Chem Senses 2019; 43:81-87. [PMID: 29342245 DOI: 10.1093/chemse/bjx083] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The field of chemical senses has made major progress in understanding the cellular mechanisms of olfaction and taste in the past 2 decades. However, the molecular understanding of odor and taste recognition is still lagging far behind and will require solving multiple structures of the relevant full-length receptors in complex with native ligands to achieve this goal. However, the development of multiple complimentary strategies for the structure determination of G protein-coupled receptors (GPCRs) makes this goal realistic. The common conundrum of how multi-specific receptors that recognize a large number of different ligands results in a sensory perception in the brain will only be fully understood by a combination of high-resolution receptor structures and functional studies. This review discusses the first steps on this pathway, including biochemical and physiological assays, forward genetics approaches, molecular modeling, and the first steps towards the structural biology of olfactory and taste receptors.
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Affiliation(s)
- Maik Behrens
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Univ. de Bourgogne- Franche-Comté, France
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, USA
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Japan
| | - Wolfgang Meyerhof
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, UK
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9
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Zhang L, Yuan Y, Ren T, Guo Y, Li C, Pu X. Shining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor. Sci Rep 2018; 8:7824. [PMID: 29777138 PMCID: PMC5959861 DOI: 10.1038/s41598-018-26105-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Olfactory receptor (OR)-based bioelectronic nose is a new type of bio-affinity sensor applied for detecting numerous odorant molecules. In order to elucidate the effect of the adsorption of nanomaterial carriers on the receptor structure and its selectivity to odors, we used a systematic computation-scheme to study two OR models immobilized onto carbon nanotube. Our result indicates that there is a multistep OR-adsorption process driven by hydrophobic interaction. Many allosteric communication pathways exist between the absorbed residues and the pocket ones, leading to a significant shrinkage of the pocket. Consequently, the size-selectivity of the receptor to the odors is changed to some extent. But, the odor size and its hydrophobicity, rather than specific functional groups of the odor, still play a determinant role in binding OR, at least for the 132 odors under study. Regardless of the limitation for the odor size in initial recognition, the different-size odors could induce significant changes in the pocket conformation so that it could better match the pocket space, indicating the importance of the ligand-fit binding. Due to the CNT-induced shrinkage of the pocket, the CNT immobilization could increase the binding affinity through enhancing van der Waals interaction, in particular for the large odors.
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Affiliation(s)
- Liyun Zhang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu, 610041, P.R. China
| | - Tian Ren
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, 610064, P.R. China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China.
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de March CA, Topin J, Bruguera E, Novikov G, Ikegami K, Matsunami H, Golebiowski J. Odorant Receptor 7D4 Activation Dynamics. Angew Chem Int Ed Engl 2018; 57:4554-4558. [PMID: 29462498 PMCID: PMC6268213 DOI: 10.1002/anie.201713065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 12/17/2022]
Abstract
Deciphering how an odorant activates an odorant receptor (OR) and how changes in specific OR residues affect its responsiveness are central to understanding our sense of smell. A joint approach combining site-directed mutagenesis and functional assays with computational modeling has been used to explore the signaling mechanics of OR7D4. In this OR, a genetic polymorphism affects our perception of androstenone. Molecular simulations totaling 0.12 ms predicted that, similarly to observations for other G-protein-coupled receptors with known experimental structures, an activation pathway connects the ligand and the G-protein binding site. The 3D model activation mechanism correlates with in vitro data and notably predicts that the OR7D4 WM variant is not activated. Upon activation, an OR-specific sequence motif is the convergence point of the mechanism. Our study suggests that robust homology modeling can serve as a powerful tool to capture OR dynamics related to smell perception.
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Affiliation(s)
- Claire A. de March
- Institute of Chemistry - Nice, UMR 7272 CNRS – Université Côte d’Azur, 06108 Nice cedex, France, Dept. of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jérémie Topin
- Institute of Chemistry - Nice, UMR 7272 CNRS – Université Côte d’Azur, 06108 Nice cedex, France
| | - Elise Bruguera
- Dept. of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Gleb Novikov
- Institute of Chemistry - Nice, UMR 7272 CNRS – Université Côte d’Azur, 06108 Nice cedex, France
| | - Kentaro Ikegami
- Dept. of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA, Dept. of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiroaki Matsunami
- Dept. of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR 7272 CNRS – Université Côte d’Azur, 06108 Nice cedex, France, Dept. of Brain & Cognitive Sciences, DGIST, 333, Techno JungAng Daero, HyeongPoong Myeon, Daegu, 711-873, Rep. of Korea
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de March CA, Topin J, Bruguera E, Novikov G, Ikegami K, Matsunami H, Golebiowski J. Odorant Receptor 7D4 Activation Dynamics. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Claire A. de March
- Institute of Chemistry—Nice UMR 7272 CNRS, Université Côte d'Azur 06108 Nice cedex France
- Department of Molecular Genetics and Microbiology Duke University Medical Center Durham NC 27710 USA
| | - Jérémie Topin
- Institute of Chemistry—Nice UMR 7272 CNRS, Université Côte d'Azur 06108 Nice cedex France
| | - Elise Bruguera
- Department of Molecular Genetics and Microbiology Duke University Medical Center Durham NC 27710 USA
| | - Gleb Novikov
- Institute of Chemistry—Nice UMR 7272 CNRS, Université Côte d'Azur 06108 Nice cedex France
| | - Kentaro Ikegami
- Department of Molecular Genetics and Microbiology Duke University Medical Center Durham NC 27710 USA
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology Duke University Medical Center Durham NC 27710 USA
- Department of Neurobiology, Duke Institute for Brain Sciences Duke University Medical Center Durham NC 27710 USA
| | - Jérôme Golebiowski
- Institute of Chemistry—Nice UMR 7272 CNRS, Université Côte d'Azur 06108 Nice cedex France
- Department of Brain and Cognitive Sciences DGIST 333, Techno JungAng Daero, HyeongPoong Myeon Daegu 711-873 Republic of Korea
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Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by ( R)-muscone and diverse other musk-smelling compounds. Proc Natl Acad Sci U S A 2018; 115:E3950-E3958. [PMID: 29632183 DOI: 10.1073/pnas.1713026115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding olfaction at the molecular level is challenging due to the lack of crystallographic models of odorant receptors (ORs). To better understand the molecular mechanism of OR activation, we focused on chiral (R)-muscone and other musk-smelling odorants due to their great importance and widespread use in perfumery and traditional medicine, as well as environmental concerns associated with bioaccumulation of musks with estrogenic/antiestrogenic properties. We experimentally and computationally examined the activation of human receptors OR5AN1 and OR1A1, recently identified as specifically responding to musk compounds. OR5AN1 responds at nanomolar concentrations to musk ketone and robustly to macrocyclic sulfoxides and fluorine-substituted macrocyclic ketones; OR1A1 responds only to nitromusks. Structural models of OR5AN1 and OR1A1 based on quantum mechanics/molecular mechanics (QM/MM) hybrid methods were validated through direct comparisons with activation profiles from site-directed mutagenesis experiments and analysis of binding energies for 35 musk-related odorants. The experimentally found chiral selectivity of OR5AN1 to (R)- over (S)-muscone was also computationally confirmed for muscone and fluorinated (R)-muscone analogs. Structural models show that OR5AN1, highly responsive to nitromusks over macrocyclic musks, stabilizes odorants by hydrogen bonding to Tyr260 of transmembrane α-helix 6 and hydrophobic interactions with surrounding aromatic residues Phe105, Phe194, and Phe207. The binding of OR1A1 to nitromusks is stabilized by hydrogen bonding to Tyr258 along with hydrophobic interactions with surrounding aromatic residues Tyr251 and Phe206. Hydrophobic/nonpolar and hydrogen bonding interactions contribute, respectively, 77% and 13% to the odorant binding affinities, as shown by an atom-based quantitative structure-activity relationship model.
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Wolf S, Jovancevic N, Gelis L, Pietsch S, Hatt H, Gerwert K. Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR). Sci Rep 2017; 7:16007. [PMID: 29167480 PMCID: PMC5700038 DOI: 10.1038/s41598-017-16001-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 11/03/2017] [Indexed: 01/14/2023] Open
Abstract
We analysed the ligand-based activation mechanism of the prostate-specific G-protein coupled receptor (PSGR), which is an olfactory receptor that mediates cellular growth in prostate cancer cells. Furthermore, it is an olfactory receptor with a known chemically near identic antagonist/agonist pair, α- and β-ionone. Using a combined theoretical and experimental approach, we propose that this receptor is activated by a ligand-induced rearrangement of a protein-internal hydrogen bond network. Surprisingly, this rearrangement is not induced by interaction of the ligand with the network, but by dynamic van der Waals contacts of the ligand with the involved amino acid side chains, altering their conformations and intraprotein connectivity. Ligand recognition in this GPCR is therefore highly stereo selective, but seemingly lacks any ligand recognition via polar contacts. A putative olfactory receptor-based drug design scheme will have to take this unique mode of protein/ligand action into account.
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Affiliation(s)
- Steffen Wolf
- Department of Biophysics, ND 04 North, Ruhr-University Bochum, 44780, Bochum, Germany.
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China.
| | - Nikolina Jovancevic
- Department of Cellphysiology, ND 4, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Lian Gelis
- Department of Cellphysiology, ND 4, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Sebastian Pietsch
- Department of Biophysics, ND 04 North, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Hanns Hatt
- Department of Cellphysiology, ND 4, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, ND 04 North, Ruhr-University Bochum, 44780, Bochum, Germany
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China
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Wolf S, Gelis L, Dörrich S, Hatt H, Kraft P. Evidence for a shape-based recognition of odorants in vivo in the human nose from an analysis of the molecular mechanism of lily-of-the-valley odorants detection in the Lilial and Bourgeonal family using the C/Si/Ge/Sn switch strategy. PLoS One 2017; 12:e0182147. [PMID: 28763484 PMCID: PMC5538716 DOI: 10.1371/journal.pone.0182147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/13/2017] [Indexed: 01/20/2023] Open
Abstract
We performed an analysis of possible mechanisms of ligand recognition in the human nose. The analysis is based on in vivo odor threshold determination and in vitro Ca2+ imaging assays with a C/Si/Ge/Sn switch strategy applied to the compounds Lilial and Bourgeonal, to differentiate between different molecular mechanisms of odorant detection. Our results suggest that odorant detection under threshold conditions is mainly based on the molecular shape, i.e. the van der Waals surface, and electrostatics of the odorants. Furthermore, we show that a single olfactory receptor type is responsible for odor detection of Bourgeonal at the threshold level in humans in vivo. Carrying out a QM analysis of vibrational energies contained in the odorants, there is no evidence for a vibration-based recognition.
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Affiliation(s)
- Steffen Wolf
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Lian Gelis
- Department of Cellphysiology, Ruhr-University Bochum, Bochum, Germany
| | - Steffen Dörrich
- Institute of Inorganic Chemistry, University of Würzburg, Würzburg, Germany
| | - Hanns Hatt
- Department of Cellphysiology, Ruhr-University Bochum, Bochum, Germany
| | - Philip Kraft
- Fragrance Research, Givaudan Schweiz AG, Dübendorf, Switzerland
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Harini K, Sowdhamini R. Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening. PLoS One 2015. [PMID: 26221959 PMCID: PMC4519343 DOI: 10.1371/journal.pone.0131077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Olfactory receptors (ORs) belong to the class A G-Protein Coupled Receptor superfamily of proteins. Unlike G-Protein Coupled Receptors, ORs exhibit a combinatorial response to odors/ligands. ORs display an affinity towards a range of odor molecules rather than binding to a specific set of ligands and conversely a single odorant molecule may bind to a number of olfactory receptors with varying affinities. The diversity in odor recognition is linked to the highly variable transmembrane domains of these receptors. The purpose of this study is to decode the odor-olfactory receptor interactions using in silico docking studies. In this study, a ligand (odor molecules) dataset of 125 molecules was used to carry out in silico docking using the GLIDE docking tool (SCHRODINGER Inc Pvt LTD). Previous studies, with smaller datasets of ligands, have shown that orthologous olfactory receptors respond to similarly-tuned ligands, but are dramatically different in their efficacy and potency. Ligand docking results were applied on homologous pairs (with varying sequence identity) of ORs from human and mouse genomes and ligand binding residues and the ligand profile differed among such related olfactory receptor sequences. This study revealed that homologous sequences with high sequence identity need not bind to the same/ similar ligand with a given affinity. A ligand profile has been obtained for each of the 20 receptors in this analysis which will be useful for expression and mutation studies on these receptors.
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Affiliation(s)
- K. Harini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, India
- * E-mail:
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16
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de March CA, Yu Y, Ni MJ, Adipietro KA, Matsunami H, Ma M, Golebiowski J. Conserved Residues Control Activation of Mammalian G Protein-Coupled Odorant Receptors. J Am Chem Soc 2015; 137:8611-8616. [PMID: 26090619 PMCID: PMC4497840 DOI: 10.1021/jacs.5b04659] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Odorant receptor (OR) genes and proteins represent more than 2% of our genome and 4% of our proteome and constitute the largest subgroup of G protein-coupled receptors (GPCRs). The mechanism underlying OR activation remains poorly understood, as they do not share some of the highly conserved motifs critical for activation of non-olfactory GPCRs. By combining site-directed mutagenesis, heterologous expression, and molecular dynamics simulations that capture the conformational change of constitutively active mutants, we tentatively identified crucial residues for the function of these receptors using the mouse MOR256-3 (Olfr124) as a model. The toggle switch for sensing agonists involves a highly conserved tyrosine residue in helix VI. The ionic lock is located between the "DRY" motif in helix III and a positively charged "R/K" residue in helix VI. This study provides an unprecedented model that captures the main mechanisms of odorant receptor activation.
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Affiliation(s)
- Claire A. de March
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
| | - Yiqun Yu
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mengjue J. Ni
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kaylin A. Adipietro
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Minghong Ma
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
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17
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de March CA, Ryu S, Sicard G, Moon C, Golebiowski J. Structure-odour relationships reviewed in the postgenomic era. FLAVOUR FRAG J 2015. [DOI: 10.1002/ffj.3249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Claire A. de March
- Institut de Chimie de Nice; Université Nice Sophia Antipolis; UMR CNRS 7272, parc Valrose 06108 Nice cedex 02 France
| | - SangEun Ryu
- Laboratory of Chemical Senses, Department of Brain and Cognitive Science; DGIST (Daegu Gyeongbuk Institute of Science & Technology); 50-1 Sang-Ri, Hyeonpung-Myeon, Dalseong-Gun Daegu 711-873 Korea
| | - Gilles Sicard
- Neurobiology of Cellular Interactions and Neurophysiopathology; Aix-Marseille Université; UMR CNRS 7259 13331 Marseille cedex 03 France
| | - Cheil Moon
- Laboratory of Chemical Senses, Department of Brain and Cognitive Science; DGIST (Daegu Gyeongbuk Institute of Science & Technology); 50-1 Sang-Ri, Hyeonpung-Myeon, Dalseong-Gun Daegu 711-873 Korea
| | - Jérôme Golebiowski
- Institut de Chimie de Nice; Université Nice Sophia Antipolis; UMR CNRS 7272, parc Valrose 06108 Nice cedex 02 France
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18
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Don CG, Riniker S. Scents and sense:In silicoperspectives on olfactory receptors. J Comput Chem 2014; 35:2279-87. [DOI: 10.1002/jcc.23757] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/23/2014] [Accepted: 09/27/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Charleen G. Don
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
| | - Sereina Riniker
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
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19
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A computational microscope focused on the sense of smell. Biochimie 2014; 107 Pt A:3-10. [PMID: 24952349 DOI: 10.1016/j.biochi.2014.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/07/2014] [Indexed: 11/24/2022]
Abstract
In this article, we review studies of the protagonists of the perception of smell focusing on Odorant-Binding Proteins and Olfactory Receptors. We notably put forward studies performed by means of molecular modeling, generally combined with experimental data. Those works clearly emphasize that computational approaches are now a force to reckon with. In the future, they will certainly be more and more used, notably in the framework of a computational microscope meant to observe how the laws of physics govern the biomolecular systems originating our sense of smell.
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