1
|
Haag F, Ahmed L, Reiss K, Block E, Batista VS, Krautwurst D. Copper-mediated thiol potentiation and mutagenesis-guided modeling suggest a highly conserved copper-binding motif in human OR2M3. Cell Mol Life Sci 2020; 77:2157-2179. [PMID: 31435697 PMCID: PMC7256108 DOI: 10.1007/s00018-019-03279-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Sulfur-containing compounds within a physiological relevant, natural odor space, such as the key food odorants, typically constitute the group of volatiles with the lowest odor thresholds. The observation that certain metals, such as copper, potentiate the smell of sulfur-containing, metal-coordinating odorants led to the hypothesis that their cognate receptors are metalloproteins. However, experimental evidence is sparse-so far, only one human odorant receptor, OR2T11, and a few mouse receptors, have been reported to be activated by sulfur-containing odorants in a copper-dependent way, while the activation of other receptors by sulfur-containing odorants did not depend on the presence of metals. Here we identified an evolutionary conserved putative copper interaction motif CC/CSSH, comprising two copper-binding sites in TMH5 and TMH6, together with the binding pocket for 3-mercapto-2-methylpentan-1-ol in the narrowly tuned human receptor OR2M3. To characterize the copper-binding motif, we combined homology modeling, docking studies, site-directed mutagenesis, and functional expression of recombinant ORs in a cell-based, real-time luminescence assay. Ligand activation of OR2M3 was potentiated in the presence of copper. This effect of copper was mimicked by ionic and colloidal silver. In two broadly tuned receptors, OR1A1 and OR2W1, which did not reveal a putative copper interaction motif, activation by their most potent, sulfur-containing key food odorants did not depend on the presence of copper. Our results suggest a highly conserved putative copper-binding motif to be necessary for a copper-modulated and thiol-specific function of members from three subfamilies of family 2 ORs.
Collapse
Affiliation(s)
- Franziska Haag
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany
| | - Lucky Ahmed
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Eric Block
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Sharma A, Kumar R, Aier I, Semwal R, Tyagi P, Varadwaj P. Sense of Smell: Structural, Functional, Mechanistic Advancements and Challenges in Human Olfactory Research. Curr Neuropharmacol 2019; 17:891-911. [PMID: 30520376 PMCID: PMC7052838 DOI: 10.2174/1570159x17666181206095626] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/08/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
Olfaction, the sense of smell detects and discriminate odors as well as social cues which influence our innate responses. The olfactory system in human beings is found to be weak as compared to other animals; however, it seems to be very precise. It can detect and discriminate millions of chemical moieties (odorants) even in minuscule quantities. The process initiates with the binding of odorants to specialized olfactory receptors, encoded by a large family of Olfactory Receptor (OR) genes belonging to the G-protein-coupled receptor superfamily. Stimulation of ORs converts the chemical information encoded in the odorants, into respective neuronal action-potentials which causes depolarization of olfactory sensory neurons. The olfactory bulb relays this signal to different parts of the brain for processing. Odors are encrypted using a combinatorial approach to detect a variety of chemicals and encode their unique identity. The discovery of functional OR genes and proteins provided an important information to decipher the genomic, structural and functional basis of olfaction. ORs constitute 17 gene families, out of which 4 families were reported to contain more than hundred members each. The olfactory machinery is not limited to GPCRs; a number of non- GPCRs is also employed to detect chemosensory stimuli. The article provides detailed information about such olfaction machinery, structures, transduction mechanism, theories of odor perception, and challenges in the olfaction research. It covers the structural, functional and computational studies carried out in the olfaction research in the recent past.
Collapse
Affiliation(s)
| | | | | | | | | | - Pritish Varadwaj
- Address correspondence to this author at the Department of Applied Science, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India; E-mail:
| |
Collapse
|
4
|
Maßberg D, Hatt H. Human Olfactory Receptors: Novel Cellular Functions Outside of the Nose. Physiol Rev 2018; 98:1739-1763. [PMID: 29897292 DOI: 10.1152/physrev.00013.2017] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Olfactory receptors (ORs) are not exclusively expressed in the olfactory sensory neurons; they are also observed outside of the olfactory system in all other human tissues tested to date, including the testis, lung, intestine, skin, heart, and blood. Within these tissues, certain ORs have been determined to be exclusively expressed in only one tissue, whereas other ORs are more widely distributed in many different tissues throughout the human body. For most of the ectopically expressed ORs, limited data are available for their functional roles. They have been shown to be involved in the modulation of cell-cell recognition, migration, proliferation, the apoptotic cycle, exocytosis, and pathfinding processes. Additionally, there is a growing body of evidence that they have the potential to serve as diagnostic and therapeutic tools, as ORs are highly expressed in different cancer tissues. Interestingly, in addition to the canonical signaling pathways activated by ORs in olfactory sensory neurons, alternative pathways have been demonstrated in nonolfactory tissues. In this review, the existing data concerning the expression, as well as the physiological and pathophysiological functions, of ORs outside of the nose are highlighted to provide insights into future lines of research.
Collapse
Affiliation(s)
- Désirée Maßberg
- Ruhr-University Bochum, Department of Cell Physiology , Bochum , Germany
| | - Hanns Hatt
- Ruhr-University Bochum, Department of Cell Physiology , Bochum , Germany
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Mukherjee S, Karolak A, Debant M, Buscaglia P, Renaudineau Y, Mignen O, Guida WC, Brooks WH. Molecular Dynamics Simulations of Membrane-Bound STIM1 to Investigate Conformational Changes during STIM1 Activation upon Calcium Release. J Chem Inf Model 2017; 57:335-344. [PMID: 28151650 DOI: 10.1021/acs.jcim.6b00475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Calcium is involved in important intracellular processes, such as intracellular signaling from cell membrane receptors to the nucleus. Typically, calcium levels are kept at less than 100 nM in the nucleus and cytosol, but some calcium is stored in the endoplasmic reticulum (ER) lumen for rapid release to activate intracellular calcium-dependent functions. Stromal interacting molecule 1 (STIM1) plays a critical role in early sensing of changes in the ER's calcium level, especially when there is a sudden release of stored calcium from the ER. Inactive STIM1, which has a bound calcium ion, is activated upon ion release. Following activation of STIM1, there is STIM1-assisted initiation of extracellular calcium entry through channels in the cell membrane. This extracellular calcium entering the cell then amplifies intracellular calcium-dependent actions. At the end of the process, ER levels of stored calcium are reestablished. The main focus of this work was to study the conformational changes accompanying homo- or heterodimerization of STIM1. For this purpose, the ER luminal portion of STIM1 (residues 58-236), which includes the sterile alpha motif (SAM) domain plus the calcium-binding EF-hand domains 1 and 2 attached to the STIM1 transmembrane region (TM), was modeled and embedded in a virtual membrane. Next, molecular dynamics simulations were performed to study the conformational changes that take place during STIM1 activation and subsequent protein-protein interactions. Indeed, the simulations revealed exposure of residues in the EF-hand domains, which may be important for dimerization steps. Altogether, understanding conformational changes in STIM1 can help in drug discovery when targeting this key protein in intracellular calcium functions.
Collapse
Affiliation(s)
- Sreya Mukherjee
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Aleksandra Karolak
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Marjolaine Debant
- INSERM ESPRI, ERI29/EA2216 Laboratory of Immunotherapy and B Cell Pathologies, Laboratory of Immunology and Immunotherapy, CHRU Morvan, European University of Brittany , F29609 Brest, France.,Network "Ion channels and cancer-Cancéropole Grand Ouest (IC-CGO)" , F29609 Brest, France.,INSERM U1078, Brest University Medical School , F29609 Brest, France
| | - Paul Buscaglia
- Network "Ion channels and cancer-Cancéropole Grand Ouest (IC-CGO)" , F29609 Brest, France.,INSERM U1078, Brest University Medical School , F29609 Brest, France
| | - Yves Renaudineau
- INSERM ESPRI, ERI29/EA2216 Laboratory of Immunotherapy and B Cell Pathologies, Laboratory of Immunology and Immunotherapy, CHRU Morvan, European University of Brittany , F29609 Brest, France.,Network "Ion channels and cancer-Cancéropole Grand Ouest (IC-CGO)" , F29609 Brest, France
| | - Olivier Mignen
- Network "Ion channels and cancer-Cancéropole Grand Ouest (IC-CGO)" , F29609 Brest, France.,INSERM U1078, Brest University Medical School , F29609 Brest, France
| | - Wayne C Guida
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Wesley H Brooks
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| |
Collapse
|
8
|
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/
Collapse
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
| |
Collapse
|
9
|
Sliozberg YR, Chantawansri TL. Mechanism resulting in chemical imbalance due to cellular damage associated with mechanoporation: A molecular dynamics study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
10
|
|
11
|
Spyrakis F, Benedetti P, Decherchi S, Rocchia W, Cavalli A, Alcaro S, Ortuso F, Baroni M, Cruciani G. A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. J Chem Inf Model 2015; 55:2256-74. [DOI: 10.1021/acs.jcim.5b00169] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Francesca Spyrakis
- Department of Life
Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Paolo Benedetti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Sergio Decherchi
- CONCEPT Lab, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
- BiKi Technologies s.r.l., via XX Settembre 33, 16121 Genova, Italy
| | - Walter Rocchia
- CONCEPT Lab, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
| | - Andrea Cavalli
- CompuNet, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
- Department of Pharmacy
and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Stefano Alcaro
- Department of Health Science, University Magna Graecia of Catanzaro, Campus “S Venuta”, Viale Europa 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Department of Health Science, University Magna Graecia of Catanzaro, Campus “S Venuta”, Viale Europa 88100, Catanzaro, Italy
| | - Massimo Baroni
- Molecular Discovery Limited, 215
Marsh Road, Pinner Middlesex, London HA5-5NE, United Kingdom
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| |
Collapse
|
12
|
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.
Collapse
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:
| |
Collapse
|
13
|
Kim SK, Goddard WA. Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1. J Comput Aided Mol Des 2014; 28:1175-90. [PMID: 25224127 DOI: 10.1007/s10822-014-9793-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/02/2014] [Indexed: 11/24/2022]
Abstract
Olfactory receptors (ORs) are responsible for mediating the sense of smell; they allow humans to recognize an enormous number of odors but the connection between binding and perception is not known. We predict the ensemble of low energy structures for the human OR1G1 (hOR1G1) and also for six other diverse ORs, using the G protein-coupled receptor Ensemble of Structures in Membrane BiLayer Environment complete sampling method that samples 13 trillion different rotations and tilts using four different templates to predict the 24 structures likely to be important in binding and activation. Our predicted most stable structures of hOR1G1 have a salt-bridge between the conserved D3.49 and K6.30 in the D(E)RY region, that we expect to be associated with an inactive form. The hOR1G1 structure also has specific interaction in transmembrane domains (TMD) 3-6 (E3.39 and H6.40), which is likely an important conformational feature for all hORs because of the ~94 to 98 % conservation among all hOR sequences. Of the five ligands studied (nonanal, 9-decen-1-ol, 1-nonanol, camphor, and n-butanal), we find that the 4 expected to bind lead to similar binding energies with nonanol the strongest.
Collapse
Affiliation(s)
- Soo-Kyung Kim
- Materials and Process Simulation Center (MC139-74), California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA,
| | | |
Collapse
|
14
|
|
15
|
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.
Collapse
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)
| | | | | | | | | | | |
Collapse
|
16
|
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.
Collapse
|
17
|
Lai PC, Guida B, Shi J, Crasto CJ. Preferential binding of an odor within olfactory receptors: a precursor to receptor activation. Chem Senses 2014; 39:107-23. [PMID: 24398973 PMCID: PMC3894857 DOI: 10.1093/chemse/bjt060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using computational methods, which allow mechanistic insights at a molecular level, we explored the olfactory receptor (OR)-odor interactions for 2 mouse ORs, S79 and S86. Both ORs have been previously experimentally, functionally characterized. The odors used were mostly carboxylic acids, which differed in chain length, substituents on the primary carbon atom-chain and degree of unsaturation. These odors elicited varied activation responses from both ORs. Our studies revealed that both receptors have 2 distinct binding sites. Preferential binding in 1 of the 2 sites is correlated with OR activation. The activating odorants: nonanedioic acid, heptanoic acid, and octanoic acid for OR S79 and nonanoic acid for OR S86 preferentially bind in the region bound by transmembranes (TMs [helical domains]) III, IV, V, and VI. The non excitatory odorants heptanol for S79 and heptanoic acid for S86 showed a greater likelihood of binding in the region bound by TMs I, II, III, and VII. Nanosecond-scale molecular dynamics simulations of the physiologically relevant conditions of docked OR-odorant complexes enabled us to quantitatively assess the roles of individual OR amino acids in odor binding. Amino acid-odorant contact maps and distance determinations over the course of the simulations lend support to our conclusions.
Collapse
Affiliation(s)
- Peter C Lai
- Department of Genetics, Division of Research, University of Alabama at Birmingham, 720 20th Street S., Birmingham, AL 35294, USA.
| | | | | | | |
Collapse
|
18
|
Marenco LN, Bahl G, Hyland L, Shi J, Wang R, Lai PC, Miller PL, Shepherd GM, Crasto CJ. Databases in SenseLab for the genomics, proteomics, and function of olfactory receptors. Methods Mol Biol 2013; 1003:3-22. [PMID: 23585030 DOI: 10.1007/978-1-62703-377-0_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We present here, the salient aspects of three databases: Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of ORs; OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory rectors; and OdorModelDB disseminates information related to computational models of olfactory receptors (ORs). The data stored among these databases is integrated. Presented in this chapter are descriptions of these resources, which are part of the SenseLab suite of databases, a discussion of the computational infrastructure that enhances the efficacy of information storage, retrieval, dissemination, and automated data population from external sources.
Collapse
Affiliation(s)
- Luis N Marenco
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Peeping into human renal calcium oxalate stone matrix: characterization of novel proteins involved in the intricate mechanism of urolithiasis. PLoS One 2013; 8:e69916. [PMID: 23894559 PMCID: PMC3722206 DOI: 10.1371/journal.pone.0069916] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The increasing number of patients suffering from urolithiasis represents one of the major challenges which nephrologists face worldwide today. For enhancing therapeutic outcomes of this disease, the pathogenic basis for the formation of renal stones is the need of hour. Proteins are found as major component in human renal stone matrix and are considered to have a potential role in crystal-membrane interaction, crystal growth and stone formation but their role in urolithiasis still remains obscure. METHODS Proteins were isolated from the matrix of human CaOx containing kidney stones. Proteins having MW>3 kDa were subjected to anion exchange chromatography followed by molecular-sieve chromatography. The effect of these purified proteins was tested against CaOx nucleation and growth and on oxalate injured Madin-Darby Canine Kidney (MDCK) renal epithelial cells for their activity. Proteins were identified by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF MS) followed by database search with MASCOT server. In silico molecular interaction studies with CaOx crystals were also investigated. RESULTS Five proteins were identified from the matrix of calcium oxalate kidney stones by MALDI-TOF MS followed by database search with MASCOT server with the competence to control the stone formation process. Out of which two proteins were promoters, two were inhibitors and one protein had a dual activity of both inhibition and promotion towards CaOx nucleation and growth. Further molecular modelling calculations revealed the mode of interaction of these proteins with CaOx at the molecular level. CONCLUSIONS We identified and characterized Ethanolamine-phosphate cytidylyltransferase, Ras GTPase-activating-like protein, UDP-glucose:glycoprotein glucosyltransferase 2, RIMS-binding protein 3A, Macrophage-capping protein as novel proteins from the matrix of human calcium oxalate stone which play a critical role in kidney stone formation. Thus, these proteins having potential to modulate calcium oxalate crystallization will throw light on understanding and controlling urolithiasis in humans.
Collapse
|