CoChat
Sign Up
PreprintCited by 2Receptor Mechanisms and SignalingComputational Drug Discovery MethodsProtein Structure and Dynamics

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

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

Open access
Nicoli, Alessandro, Haag, Franziska, Marcinek, Patrick, He, Ruiming, Kreißl, Johanna, Stein, Jörg, Marchetto, Alessandro, Dunkel, Andreas, Hofmann, Thomas, Krautwurst, Dietmar, Di Pizio, Antonella·2022·bioRxiv (Cold Spring Harbor Laboratory)
DOI 10.1101/2022.06.01.494157

Preprint — published as 10.1021/acs.jcim.2c00752 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

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

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2022.06.01.494157

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 6 references

Research works printed but not linked: 131

  1. 10.1083/jcb.145.5.927 · DOI
  2. 10.1038/nrm908 · DOI
  3. 10.1124/mol.63.6.1256 · DOI · Paper page
  4. 2008, GPCRTree: online hierarchical classification of GPCR function, BMC Res Notes, 1, 67, 10.1186/1756-0500-1-67 · DOI
  5. 10.1093/molbev/msr061 · DOI
  6. 10.1016/j.tibs.2018.11.011 · DOI
  7. 2020, Impact of GPCR Structures on Drug Discovery, Cell, 181, 81, 10.1016/j.cell.2020.03.003 · DOI
  8. 2017, G Protein-Coupled Receptors Contain Two Conserved Packing Clusters, Biophys J, 112, 2315, 10.1016/j.bpj.2017.04.051 · DOI
  9. 10.1186/1479-7364-4-2-107 · DOI
  10. 10.1186/1471-2164-13-414 · DOI
  11. 10.1016/0092-8674(91)90418-X · DOI · Paper page
  12. 10.1016/j.tibs.2021.08.006 · DOI
  13. 10.1073/pnas.0307882100 · DOI
  14. 10.1007/s003350010196 · DOI
  15. 10.1038/nn800 · DOI
  16. 10.1073/pnas.0501922102 · DOI
  17. 2021, Conserved C-terminal motifs in odorant receptors instruct their cell surface expression and cAMP signaling, FASEB J, 35, e21274
  18. 10.1002/pro.2717 · DOI
  19. 10.1021/jacs.5b04659 · DOI
  20. 10.1110/ps.03296404 · DOI
  21. 2019, Mammalian class I odorant receptors exhibit a conserved vestibular-binding pocket, Cell Mol Life Sci, 76, 995, 10.1007/s00018-018-2996-4 · DOI
  22. 10.1002/anie.201103980 · DOI
  23. 2022, Large-Scale G Protein-Coupled Olfactory Receptor–Ligand Pairing, ACS Central Science, 8, 379, 10.1021/acscentsci.1c01495 · DOI
  24. 2008, Expressing exogenous functional odorant receptors in cultured olfactory sensory neurons, Neural development, 3, 22, 10.1186/1749-8104-3-22 · DOI
  25. 10.1093/chemse/bjw117 · DOI
  26. 10.1523/JNEUROSCI.21-16-06018.2001 · DOI
  27. 10.1016/S0092-8674(00)80581-4 · DOI
  28. 10.1523/JNEUROSCI.1282-11.2011 · DOI
  29. 10.1126/scisignal.2000016 · DOI
  30. 10.1371/journal.pgen.1002821 · DOI
  31. 2015, Human olfactory receptor responses to odorants, Scientific data, 2, 150002, 10.1038/sdata.2015.2 · DOI
  32. 2017, OR2M3: A Highly Specific and Narrowly Tuned Human Odorant Receptor for the Sensitive Detection of Onion Key Food Odorant 3-Mercapto-2-methylpentan-1-ol, Chemical senses, 42, 195, 10.1093/chemse/bjw118 · DOI
  33. 2022, The key food odorant receptive range of broadly tuned receptor OR2W1, Food Chem, 375, 131680, 10.1016/j.foodchem.2021.131680 · DOI
  34. 10.1007/s00018-012-1116-0 · DOI
  35. Jabeen, A. ; de March, C. A. ; Matsunami, H. ; Ranganathan, S. , Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors. Int J Mol Sci 2021, 22. · DOI
  36. Di Pizio, A. ; Behr, J. ; Krautwurst, D. , Toward the Digitalization of Olfaction. In Reference Module in Neuroscience and Biobehavioral Psychology, 2021. · DOI
  37. 10.1124/pharmrev.120.000246 · DOI
  38. 10.1021/acs.jafc.8b04471 · DOI
  39. 2018, Agonists of G-Protein-Coupled Odorant Receptors Are Predicted from Chemical Features, J Phys Chem Lett, 9, 2235, 10.1021/acs.jpclett.8b00633 · DOI
  40. 2019, Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds, Commun Biol, 2, 141, 10.1038/s42003-019-0384-8 · DOI
  41. Haag, F. ; Ahmed, L. ; Reiss, K. ; Block, E. ; Batista, V. S. ; Krautwurst, D. , Copper-mediated thiol potentiation and mutagenesis-guided modeling suggest a highly conserved copper-binding motif in human OR2M3. Cell Mol Life Sci 2019. · DOI
  42. Cong, X. ; Ren, W. ; Pacalon, J. ; Xu, R. ; Xu, L. ; Li, X. ; de March, C. A. ; Matsunami, H. ; Yu, H. ; Yu, Y. ; Golebiowski, J. , Large-Scale G Protein-Coupled Olfactory Receptor–Ligand Pairing. ACS Central Science 2022. · DOI
  43. 2020, Homology modeling in the time of collective and artificial intelligence, Comput Struct Biotechnol J, 18, 3494, 10.1016/j.csbj.2020.11.007 · DOI
  44. 10.1126/science.abj8754 · DOI · Paper page
  45. 10.1093/NAR/GKAB1061 · DOI · Paper page
  46. 10.1126/sciadv.aax0396 · DOI · Paper page
  47. 2021, An evolutionary conserved olfactory receptor for foodborne and semiochemical alkylpyrazines, FASEB J, 35, e21638
  48. 2020, The Sensing Liver: Localization and Ligands for Hepatic Murine Olfactory and Taste Receptors, Front Physiol, 11, 574082, 10.3389/fphys.2020.574082 · DOI
  49. 2017, Retort beef aroma that gives preferable properties to canned beef products and its aroma components, Anim Sci J, 88, 2050, 10.1111/asj.12876 · DOI
  50. 2019, Characterization of the Volatile Compounds and Taste Attributes of Sesame Pastes Processed at Different Temperatures, J Oleo Sci, 68, 551, 10.5650/jos.ess19014 · DOI
  51. 10.1007/s10719-016-9694-y · DOI · Paper page
  52. 10.1111/nph.12800 · DOI
  53. 10.1038/s41598-018-20953-6 · DOI
  54. 10.1371/journal.pone.0061753 · DOI
  55. 2015, The scent of wolves: pyrazine analogs induce avoidance and vigilance behaviors in prey, Front Neurosci, 9, 363
  56. 2017, Structure-Activity Relationships of Alkylpyrazine Analogs and Fear-Associated Behaviors in Mice, J Chem Ecol, 43, 263, 10.1007/s10886-017-0822-3 · DOI
  57. 1971, Semiochemical--structure and function, Biol Reprod, 4, 309, 10.1093/biolreprod/4.3.309 · DOI
  58. 2014, Computational Studies of Smell and Taste Receptors, Israel Journal of Chemistry, 54, 1205, 10.1002/ijch.201400027 · DOI
  59. 10.1529/biophysj.106.082313 · DOI
  60. 10.1002/anie.201713065 · DOI
  61. 10.1016/j.sbi.2022.102372 · DOI · Paper page
  62. 2019, Universal Activation Index for Class A GPCRs, J Chem Inf Model, 59, 3938, 10.1021/acs.jcim.9b00604 · DOI
  63. Heo, L. ; Feig, M. , Multi-State Modeling of G-protein Coupled Receptors at Experimental Accuracy. 2022. · DOI · Paper page
  64. He, X. H. ; You, C. Z. ; Jiang, H. L. ; Jiang, Y. ; Xu, H. E. ; Cheng, X. , AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors. Acta Pharmacol Sin 2022. · DOI
  65. 2022, Classification Model for the Second Extracellular Loop of Class A GPCRs, J Chem Inf Model, 62, 511, 10.1021/acs.jcim.1c01056 · DOI
  66. 2022, Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition, J Biol Chem, 298, 102331, 10.1016/j.jbc.2022.102331 · DOI · Paper page
  67. 2017, Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family, Mol Cell Endocrinol, 449, 3, 10.1016/j.mce.2016.11.023 · DOI
  68. 10.1007/s10822-019-00196-x · DOI
  69. 2018, GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors, J Chem Inf Model, 58, 1234, 10.1021/acs.jcim.8b00148 · DOI
  70. 10.1007/s00018-019-03194-2 · DOI
  71. Zhang, Y. ; Vass, M. ; Shi, D. ; Abualrous, E. ; Chambers, J. ; Chopra, N. ; Higgs, C. ; Kasavajhala, K. ; Li, H. ; Nandekar, P. ; Sato, H. ; Miller, E. ; Repasky, M. ; Jerome, S. , Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery. ChemRxiv 2022. · DOI · Paper page
  72. Lee, C. ; Su, B. H. ; Tseng, Y. J. , Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors. Brief Bioinform 2022, 23. · DOI
  73. 10.1126/science.abn9422 · DOI
  74. 10.1038/d41586-022-00997-5 · DOI
  75. 10.1007/s00018-017-2576-z · DOI
  76. 2021, G protein-coupled receptors: structure-and function-based drug discovery, Signal Transduct Target Ther, 6, 7, 10.1038/s41392-020-00435-w · DOI
  77. Di Pizio, A. ; Nicoli, A. , In Silico Molecular Study of Tryptophan Bitterness. Molecules 2020, 25. · DOI
  78. 2015, Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening, PLoS One, 10, e0131077, 10.1371/journal.pone.0131077 · DOI
  79. 2018, Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations, Biochem Biophys Res Commun, 498, 366, 10.1016/j.bbrc.2018.01.160 · DOI
  80. 2020, In Silico Investigation of Bitter Hop-Derived Compounds and Their Cognate Bitter Taste Receptors, J Agric Food Chem, 68, 10414, 10.1021/acs.jafc.9b07863 · DOI
  81. 10.1110/ps.03296404 · DOI
  82. 10.1074/jbc.M609355200 · DOI
  83. 10.1073/pnas.1713026115 · DOI
  84. 10.1021/bi1017396 · DOI
  85. 2015, Exchanging ligand-binding specificity between a pair of mouse olfactory receptor paralogs reveals odorant recognition principles, Sci Rep, 5, 14948, 10.1038/srep14948 · DOI
  86. 10.1021/jacs.5b04659 · DOI
  87. 10.1523/JNEUROSCI.4723-04.2005 · DOI
  88. 2019, Beyond the Flavour: The Potential Druggability of Chemosensory G Protein-Coupled Receptors, Int J Mol Sci, 20, 1402, 10.3390/ijms20061402 · DOI
  89. 2018, Molecular Features Underlying Selectivity in Chicken Bitter Taste Receptors, Front Mol Biosci, 5, 6, 10.3389/fmolb.2018.00006 · DOI
  90. Terwilliger, T. C. ; Liebschner, D. ; Croll, T. I. ; Williams, C. J. ; McCoy, A. J. ; Poon, B. K. ; Afonine, P. V. ; Oeffner, R. D. ; Richardson, J. S. ; Read, R. J. ; Adams, P. D. , AlphaFold predictions: great hypotheses but no match for experiment. 2022. · DOI · Paper page
  91. 1996, Detection of Odor-Active Ethenylalkylpyrazines in Roasted Coffee, Journal of Agricultural and Food Chemistry, 44, 3268, 10.1021/jf9600824 · DOI
  92. 10.1021/jf405529b · DOI
  93. 2020, Enantioselective synthesis of tri-deuterated (-)-geosmin to be used as internal standard in quantitation assays, J Labelled Comp Radiopharm, 63, 476, 10.1002/jlcr.3874 · DOI
  94. 10.14440/jbm.2017.206 · DOI
  95. 2017, A bi-functional IL-6-HaloTag((R)) as a tool to measure the cell-surface expression of recombinant odorant receptors and to facilitate their activity quantification, J Biol Methods, 4, e82, 10.14440/jbm.2017.207 · DOI
  96. 10.1099/0022-1317-36-1-59 · DOI · Paper page
  97. 10.1016/j.cell.2004.11.021 · DOI
  98. 10.1074/jbc.M411508200 · DOI
  99. 10.1126/science.2499043 · DOI
  100. 10.1523/JNEUROSCI.5563-12.2013 · DOI
  101. 10.1016/j.copbio.2009.02.013 · DOI
  102. 1978, Simultaneous analysis of families of sigmoidal curves: application to bioassay, radioligand assay, and physiological dose-response curves, Am J Physiol, 235, e97
  103. 2017, A bi-functional IL-6-HaloTag® as a tool to measure the cell-surface expression of recombinant odorant receptors and to facilitate their activity quantification, J Biol Methods, 4, e82, 10.14440/jbm.2017.207 · DOI
  104. 10.1093/nar/gkw1071 · DOI · Paper page
  105. 10.1093/molbev/msy096 · DOI
  106. 10.1093/nar/22.22.4673 · DOI · Paper page
  107. 10.1093/oxfordjournals.molbev.a040454 · DOI
  108. 10.2307/2408678 · DOI
  109. Zuckerkandl, E. ; Pauling, L. , Evolutionary divergence and convergence in proteins. 1965; p 97–166. · DOI · Paper page
  110. 2021, GPCRdb in 2021: integrating GPCR sequence, structure and function, Nucleic Acids Res, 49, D335, 10.1093/nar/gkaa1080 · DOI · Paper page
  111. Eswar, N. ; Webb, B. ; Marti-Renom, M. A. ; Madhusudhan, M. S. ; Eramian, D. ; Shen, M. Y. ; Pieper, U. ; Sali, A. , Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics 2006, Chapter 5, Unit-5 6. · DOI
  112. 10.1016/0263-7855(96)00018-5 · DOI · Paper page
  113. 10.1093/nar/gkaa440 · DOI
  114. I, R. T, 2020, GPCRmd uncovers the dynamics of the 3D-GPCRome, Nat Methods, 17, 777, 10.1038/s41592-020-0884-y · DOI
  115. 10.1021/acs.jctc.6b00049 · DOI
  116. 2013, Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools, Comput Struct Biotechnol J, 5, e201302014, 10.5936/csbj.201302014 · DOI
  117. 10.1093/bioinformatics/btk023 · DOI
  118. 10.1021/ct9000685 · DOI
  119. 10.1002/jcc.23354 · DOI
  120. 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V · DOI
  121. 10.1063/1.470117 · DOI
  122. 10.1093/bioinformatics/btr168 · DOI
  123. 10.1524/auto.2011.0951 · DOI
  124. 10.1109/mcse.2007.55 · DOI · Paper page
  125. 10.1021/jm0306430 · DOI · Paper page
  126. 10.1021/jm051256o · DOI
  127. 10.1021/jm050540c · DOI
  128. 10.1038/s41592-019-0506-8 · DOI
  129. 10.1016/j.cpc.2013.09.018 · DOI
  130. 10.1016/j.cpc.2009.05.011 · DOI
  131. 2020, UCSF ChimeraX: Structure visualization for researchers, educators, and developers, Protein Science, 30, 70

Metadata

Authors
Nicoli, A., Haag, F., Marcinek, P., He, R., Kreißl, J., Stein, J., Marchetto, A., Dunkel, A., Hofmann, T., Krautwurst, D., & Di Pizio, A.
Affiliations
  • Leibniz-Institute for Food Systems Biology at the Technical University of Munich (DE)
  • Forschungszentrum Jülich (DE)
  • Technical University of Munich (DE)
Corresponding author
Krautwurst, Dietmar
ORCID
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2022-06-01
DOI
10.1101/2022.06.01.494157
OpenAlex
W4281657507
Cited by
2
References
6
Citations by year
2024: 1 · 2023: 1
Type
posted content
Language
en
Open access
Locations
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • RWTH Publications (RWTH Aachen) (publishedVersion, other-oa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
olfactory receptors, G protein-coupled receptors, orthosteric binding site, ligand binding, agonists, induced fit docking, ensemble docking, homology modeling, AlphaFold, low sequence identity, receptor mutagenesis, model refinement, olfaction

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. https://app.cochat.ai/papers/10.1101/2022.06.01.494157
The paper
Nicoli, A., Haag, F., Marcinek, P., He, R., Kreißl, J., Stein, J., Marchetto, A., Dunkel, A., Hofmann, T., Krautwurst, D., & Di Pizio, A. (2022). Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. bioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/2022.06.01.494157