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Wang X, Stephen Chan HC, Yuan S. Modeling of Olfactory Receptors. Methods Mol Biol 2023; 2627:183-193. [PMID: 36959448 DOI: 10.1007/978-1-0716-2974-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Olfactory receptors (ORs) form the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date. Homology modeling has become a popular strategy to propose plausible OR models, in order to study the structure-function relationships of the receptors and to aid the discovery and development of ligands capable of modulating receptor activity. In this chapter, we provide a general guideline for OR structure construction, including the collection of candidate templates, structure-based sequence alignment, 3D structure construction, ligand docking, and molecular dynamic simulation.
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Affiliation(s)
- Xueying Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - H C Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China.
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2
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Hot Spot Mutagenesis Improves the Functional Expression of Unique Mammalian Odorant Receptors. Int J Mol Sci 2021; 23:ijms23010277. [PMID: 35008703 PMCID: PMC8745346 DOI: 10.3390/ijms23010277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
Vertebrate animals detect odors through olfactory receptors (ORs), members of the G protein-coupled receptor (GPCR) family. Due to the difficulty in the heterologous expression of ORs, studies of their odor molecule recognition mechanisms have progressed poorly. Functional expression of most ORs in heterologous cells requires the co-expression of their chaperone proteins, receptor transporting proteins (RTPs). Yet, some ORs were found to be functionally expressed without the support of RTP (RTP-independent ORs). In this study, we investigated whether amino acid residues highly conserved among RTP-independent ORs improve the functional expression of ORs in heterologous cells. We found that a single amino acid substitution at one of two sites (NBW3.39 and 3.43) in their conserved residues (E and L, respectively) significantly improved the functional expression of ORs in heterologous cells. E3.39 and L3.43 also enhanced the membrane expression of RTP-dependent ORs in the absence of RTP. These changes did not alter the odorant responsiveness of the tested ORs. Our results showed that specific sites within transmembrane domains regulate the membrane expression of some ORs.
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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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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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Wang P, Zhang R, Yu S, Lee C, Wang H. Simulative structure and binding sites of lyral with olfactory receptor 10J5 using computational prediction methods. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2020; 83:1-8. [PMID: 32019422 DOI: 10.1080/15287394.2019.1706269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Olfactory receptor (OR) genes are extensively distributed throughout the human organism. Although these receptors are predominantly located in the olfactory epithelium, binding between odorant chemicals and corresponding ORs initiates downstream events in other tissues. In particular, exposure to allergen fragrances results in the induction of contact dermatitis. At present, current methodologies are limited in their ability to predict the consequences of fragrancy chemicals on humans. The aim of this study was designed to simulate the bindingstructure between lyral and OR10J5, a known allergen which produces contact dermatitis, and its corresponding OR OR10J5 in an effort to predict dermal outcomes using computational methods. Results demonstrated that binding between lyral and OR10J5 involved amino acid residues Phe104, Val105, Cyx178, Ile180, and Tyr258, respectively, which were located on binding sites of the receptor transmembrane 3(TM3), TM3, extracellular loop 2(EL2), EL2, TM6. Evidence indicates that computer simulating binding interactions occurred between an odorant chemical and its receptors which initiated downstream alterations accounting possibly for the observed in vivo contact dermatitis.
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Affiliation(s)
- Pu Wang
- School of Health Sciences, University of Newcastle, Newcastle, Australia
| | - Rui Zhang
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumchi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shunbang Yu
- School of Health Sciences, University of Newcastle, Newcastle, Australia
| | - Charles Lee
- School of Health Sciences, University of Newcastle Singapore Campus, Singapore
| | - He Wang
- School of Health Sciences, University of Newcastle, Newcastle, Australia
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Alfonso-Prieto M, Navarini L, Carloni P. Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations. Front Mol Biosci 2019; 6:29. [PMID: 31131282 PMCID: PMC6510167 DOI: 10.3389/fmolb.2019.00029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022] Open
Abstract
Human G-protein coupled receptors (GPCRs) convey a wide variety of extracellular signals inside the cell and they are one of the main targets for pharmaceutical intervention. Rational drug design requires structural information on these receptors; however, the number of experimental structures is scarce. This gap can be filled by computational models, based on homology modeling and docking techniques. Nonetheless, the low sequence identity across GPCRs and the chemical diversity of their ligands may limit the quality of these models and hence refinement using molecular dynamics simulations is recommended. This is the case for olfactory and bitter taste receptors, which constitute the first and third largest GPCR groups and show sequence identities with the available GPCR templates below 20%. We have developed a molecular dynamics approach, based on the combination of molecular mechanics and coarse grained (MM/CG), tailored to study ligand binding in GPCRs. This approach has been applied so far to bitter taste receptor complexes, showing significant predictive power. The protein/ligand interactions observed in the simulations were consistent with extensive mutagenesis and functional data. Moreover, the simulations predicted several binding residues not previously tested, which were subsequently verified by carrying out additional experiments. Comparison of the simulations of two bitter taste receptors with different ligand selectivity also provided some insights into the binding determinants of bitter taste receptors. Although the MM/CG approach has been applied so far to a limited number of GPCR/ligand complexes, the excellent agreement of the computational models with the mutagenesis and functional data supports the applicability of this method to other GPCRs for which experimental structures are missing. This is particularly important for the challenging case of GPCRs with low sequence identity with available templates, for which molecular docking shows limited predictive power.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.,Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Paolo Carloni
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.,Institute for Neuroscience and Medicine INM-11, Forschungszentrum Jülich, Jülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Vietnam
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Geithe C, Protze J, Kreuchwig F, Krause G, Krautwurst D. Structural determinants of a conserved enantiomer-selective carvone binding pocket in the human odorant receptor OR1A1. Cell Mol Life Sci 2017; 74:4209-4229. [PMID: 28656349 PMCID: PMC11107518 DOI: 10.1007/s00018-017-2576-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/29/2017] [Accepted: 06/16/2017] [Indexed: 12/17/2022]
Abstract
Chirality is a common phenomenon within odorants. Most pairs of enantiomers show only moderate differences in odor quality. One example for enantiomers that are easily discriminated by their odor quality is the carvones: humans significantly distinguish between the spearmint-like (R)-(-)-carvone and caraway-like (S)-(+)-carvone enantiomers. Moreover, for the (R)-(-)-carvone, an anosmia is observed in about 8% of the population, suggesting enantioselective odorant receptors (ORs). With only about 15% de-orphaned human ORs, the lack of OR crystal structures, and few comprehensive studies combining in silico and experimental approaches to elucidate structure-function relations of ORs, knowledge on cognate odorant/OR interactions is still sparse. An adjusted homology modeling approach considering OR-specific proline-caused conformations, odorant docking studies, single-nucleotide polymorphism (SNP) analysis, site-directed mutagenesis, and subsequent functional studies with recombinant ORs in a cell-based, real-time luminescence assay revealed 11 amino acid positions to constitute an enantioselective binding pocket necessary for a carvone function in human OR1A1 and murine Olfr43, respectively. Here, we identified enantioselective molecular determinants in both ORs that discriminate between minty and caraway odor. Comparison with orthologs from 36 mammalian species demonstrated a hominid-specific carvone binding pocket with about 100% conservation. Moreover, we identified loss-of-function SNPs associated with the carvone binding pocket of OR1A1. Given carvone enantiomer-specific receptor activation patterns including OR1A1, our data suggest OR1A1 as a candidate receptor for constituting a carvone enantioselective phenotype, which may help to explain mechanisms underlying a (R)-(-)-carvone-specific anosmia in humans.
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Affiliation(s)
- Christiane Geithe
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Franziska Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Dietmar Krautwurst
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany.
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Fierro F, Suku E, Alfonso-Prieto M, Giorgetti A, Cichon S, Carloni P. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis. Front Mol Biosci 2017; 4:63. [PMID: 28932739 PMCID: PMC5592726 DOI: 10.3389/fmolb.2017.00063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany
| | - Eda Suku
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Biotechnology, University of VeronaVerona, Italy
| | - Sven Cichon
- Institute of Neuroscience and Medicine INM-1, Forschungszentrum JülichJülich, Germany.,Institute for Human Genetics, Department of Genomics, Life&Brain Center, University of BonnBonn, Germany.,Division of Medical Genetics, Department of Biomedicine, University of BaselBasel, Switzerland
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule AachenAachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National UniversityHanoi, Vietnam
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Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw132. [PMID: 27694208 PMCID: PMC5045865 DOI: 10.1093/database/baw132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/28/2016] [Indexed: 01/15/2023]
Abstract
We present here an exploration of the evolution of three well-established, web-based resources dedicated to the dissemination of information related to olfactory receptors (ORs) and their functional ligands, odorants. These resources are: the Olfactory Receptor Database (ORDB), the Human Olfactory Data Explorer (HORDE) and ODORactor. ORDB is a repository of genomic and proteomic information related to ORs and other chemosensory receptors, such as taste and pheromone receptors. Three companion databases closely integrated with ORDB are OdorDB, ORModelDB and OdorMapDB; these resources are part of the SenseLab suite of databases (http://senselab.med.yale.edu). HORDE (http://genome.weizmann.ac.il/horde/) is a semi-automatically populated database of the OR repertoires of human and several mammals. ODORactor (http://mdl.shsmu.edu.cn/ODORactor/) provides information related to OR-odorant interactions from the perspective of the odorant. All three resources are connected to each other via web-links. Database URL: http://senselab.med.yale.edu; http://genome.weizmann.ac.il/horde/; http://mdl.shsmu.edu.cn/ODORactor/
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Affiliation(s)
| | - Rixin Wang
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Elspeth Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Xinyi Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Chiquito Crasto
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
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Responsiveness of G protein-coupled odorant receptors is partially attributed to the activation mechanism. Proc Natl Acad Sci U S A 2015; 112:14966-71. [PMID: 26627247 DOI: 10.1073/pnas.1517510112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammals detect and discriminate numerous odors via a large family of G protein-coupled odorant receptors (ORs). However, little is known about the molecular and structural basis underlying OR response properties. Using site-directed mutagenesis and computational modeling, we studied ORs sharing high sequence homology but with different response properties. When tested in heterologous cells by diverse odorants, MOR256-3 responded broadly to many odorants, whereas MOR256-8 responded weakly to a few odorants. Out of 36 mutant MOR256-3 ORs, the majority altered the responses to different odorants in a similar manner and the overall response of an OR was positively correlated with its basal activity, an indication of ligand-independent receptor activation. Strikingly, a single mutation in MOR256-8 was sufficient to confer both high basal activity and broad responsiveness to this receptor. These results suggest that broad responsiveness of an OR is at least partially attributed to its activation likelihood.
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11
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de March CA, Kim SK, Antonczak S, Goddard WA, Golebiowski J. G protein-coupled odorant receptors: From sequence to structure. Protein Sci 2015; 24:1543-8. [PMID: 26044705 PMCID: PMC4570547 DOI: 10.1002/pro.2717] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/25/2015] [Indexed: 12/14/2022]
Abstract
Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition.
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Affiliation(s)
- Claire A de March
- Institute of Chemistry—Nice, UMR 7272 CNRS—University Nice—Sophia AntipolisNice Cedex 2, 06108, France
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (MC139-74), California Institute of TechnologyPasadena, California, 91125
| | - Serge Antonczak
- Institute of Chemistry—Nice, UMR 7272 CNRS—University Nice—Sophia AntipolisNice Cedex 2, 06108, France
| | - William A Goddard
- Materials and Process Simulation Center (MC139-74), California Institute of TechnologyPasadena, California, 91125
| | - Jérôme Golebiowski
- Institute of Chemistry—Nice, UMR 7272 CNRS—University Nice—Sophia AntipolisNice Cedex 2, 06108, France
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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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Topin J, de March CA, Charlier L, Ronin C, Antonczak S, Golebiowski J. Discrimination between olfactory receptor agonists and non-agonists. Chemistry 2014; 20:10227-30. [PMID: 25043138 DOI: 10.1002/chem.201402486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Indexed: 01/27/2023]
Abstract
A joint approach combining free-energy calculations and calcium-imaging assays on the broadly tuned human 1G1 olfactory receptor is reported. The free energy of binding of ten odorants was computed by means of molecular-dynamics simulations. This state function allows separating the experimentally determined eight agonists from the two non-agonists. This study constitutes a proof-of-principle for the computational deorphanization of olfactory receptors.
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Affiliation(s)
- Jérémie Topin
- Université de Nice - Sophia Antipolis, Institut de Chimie de Nice UMR 7272, Parc Valrose 28, Avenue Valrose 06108, Nice, Cedex 2 (France)
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