1
|
Kim WK, Lee Y, Jang SJ, Hyeon C. Kinetic Model for the Desensitization of G Protein-Coupled Receptor. J Phys Chem Lett 2024; 15:6137-6145. [PMID: 38832827 DOI: 10.1021/acs.jpclett.4c00967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Desensitization of G-protein-coupled receptors (GPCR) is a general regulatory mechanism adopted by biological organisms against overstimulation of G protein signaling. Although the details of the mechanism are extensively studied, it is not easy to gain an overarching understanding of the process constituted by a multitude of molecular events with vastly differing time scales. To offer a semiquantitative yet predictive understanding of the mechanism, we formulate a kinetic model for the G protein signaling and desensitization by considering essential biochemical steps from ligand binding to receptor internalization. The internalization, followed by receptor depletion from the plasma membrane, attenuates the downstream signal. Together with the kinetic model and its full numerics of the expression derived for the dose-response relation, an approximated form of the expression clarifies the role played by the individual biochemical processes and allows us to identify four distinct regimes for the downregulation that emerge from the balance between phosphorylation, dephosphorylation, and the cellular level of β-arrestin.
Collapse
Affiliation(s)
- Won Kyu Kim
- Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea
| | - Seogjoo J Jang
- Korea Institute for Advanced Study, Seoul 02455, Korea
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- PhD programs in Chemistry and Physics Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | | |
Collapse
|
2
|
Kim WK, Choi K, Hyeon C, Jang SJ. General Chemical Reaction Network Theory for Olfactory Sensing Based on G-Protein-Coupled Receptors: Elucidation of Odorant Mixture Effects and Agonist-Synergist Threshold. J Phys Chem Lett 2023; 14:8412-8420. [PMID: 37712530 DOI: 10.1021/acs.jpclett.3c02310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
This work presents a general chemical reaction network theory for olfactory sensing processes that employ G-protein-coupled receptors as olfactory receptors (ORs). The theory can be applied to general mixtures of odorants and an arbitrary number of ORs. Reactions of ORs with G-proteins, in both the presence and absence of odorants, are explicitly considered. A unique feature of the theory is the definition of an odor activity vector consisting of strengths of odorant-induced signals from ORs relative to those due to background G-protein activity in the absence of odorants. It is demonstrated that each component of the odor activity defined this way reduces to a Michaelis-Menten form capable of accounting for cooperation or competition effects between different odorants. The main features of the theory are illustrated for a two-odorant mixture. Known and potential mixture effects, such as suppression, shadowing, inhibition, and synergy, are quantitatively described. Effects of relative values of rate constants, basal activity, and G-protein concentration are also demonstrated.
Collapse
Affiliation(s)
- Won Kyu Kim
- Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 02455, Korea
| | - Kiri Choi
- Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 02455, Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 02455, Korea
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- PhD Programs in Chemistry and Physics, Graduate Center, City University of New York, New York, New York 10016, United States
| |
Collapse
|
3
|
Qian WW, Wei JN, Sanchez-Lengeling B, Lee BK, Luo Y, Vlot M, Dechering K, Peng J, Gerkin RC, Wiltschko AB. Metabolic activity organizes olfactory representations. eLife 2023; 12:e82502. [PMID: 37129358 PMCID: PMC10154027 DOI: 10.7554/elife.82502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
Hearing and vision sensory systems are tuned to the natural statistics of acoustic and electromagnetic energy on earth and are evolved to be sensitive in ethologically relevant ranges. But what are the natural statistics of odors, and how do olfactory systems exploit them? Dissecting an accurate machine learning model (Lee et al., 2022) for human odor perception, we find a computable representation for odor at the molecular level that can predict the odor-evoked receptor, neural, and behavioral responses of nearly all terrestrial organisms studied in olfactory neuroscience. Using this olfactory representation (principal odor map [POM]), we find that odorous compounds with similar POM representations are more likely to co-occur within a substance and be metabolically closely related; metabolic reaction sequences (Caspi et al., 2014) also follow smooth paths in POM despite large jumps in molecular structure. Just as the brain's visual representations have evolved around the natural statistics of light and shapes, the natural statistics of metabolism appear to shape the brain's representation of the olfactory world.
Collapse
Affiliation(s)
- Wesley W Qian
- OsmoCambridgeUnited States
- Google Research, Brain TeamCambridgeUnited States
| | | | | | - Brian K Lee
- Google Research, Brain TeamCambridgeUnited States
| | - Yunan Luo
- Department of Computer Science, University of IllinoisUrbanaUnited States
| | | | | | - Jian Peng
- Department of Computer Science, University of IllinoisUrbanaUnited States
| | - Richard C Gerkin
- OsmoCambridgeUnited States
- Google Research, Brain TeamCambridgeUnited States
| | | |
Collapse
|
4
|
Choi K, Kim WK, Hyeon C. Polymer Physics-Based Classification of Neurons. Neuroinformatics 2023; 21:177-193. [PMID: 36190621 DOI: 10.1007/s12021-022-09605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2022] [Indexed: 11/26/2022]
Abstract
Recognizing that diverse morphologies of neurons are reminiscent of structures of branched polymers, we put forward a principled and systematic way of classifying neurons that employs the ideas of polymer physics. In particular, we use 3D coordinates of individual neurons, which are accessible in recent neuron reconstruction datasets from electron microscope images. We numerically calculate the form factor, F(q), a Fourier transform of the distance distribution of particles comprising an object of interest, which is routinely measured in scattering experiments to quantitatively characterize the structure of materials. For a polymer-like object consisting of n monomers spanning over a length scale of r, F(q) scales with the wavenumber [Formula: see text] as [Formula: see text] at an intermediate range of q, where [Formula: see text] is the fractal dimension or the inverse scaling exponent ([Formula: see text]) characterizing the geometrical feature ([Formula: see text]) of the object. F(q) can be used to describe a neuron morphology in terms of its size ([Formula: see text]) and the extent of branching quantified by [Formula: see text]. By defining the distance between F(q)s as a measure of similarity between two neuronal morphologies, we tackle the neuron classification problem. In comparison with other existing classification methods for neuronal morphologies, our F(q)-based classification rests solely on 3D coordinates of neurons with no prior knowledge of morphological features. When applied to publicly available neuron datasets from three different organisms, our method not only complements other methods but also offers a physical picture of how the dendritic and axonal branches of an individual neuron fill the space of dense neural networks inside the brain.
Collapse
Affiliation(s)
- Kiri Choi
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 02455, Korea
| | - Won Kyu Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 02455, Korea
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 02455, Korea.
| |
Collapse
|
5
|
Li H, Li W, Miao C, Wang G, Zhao M, Yuan G, Guo X. Identification of the differences in olfactory system between male and female oriental tobacco budworm Helicoverpa assulta. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 107:e21829. [PMID: 34191347 DOI: 10.1002/arch.21829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
The olfactory system of insects facilitates their search for host and mates, hence it plays an essential role for insect survival and reproduction. Insects recognize odor substances through olfactory neurons and olfactory genes. Previous studies showed that there are significant sex-specific differences in how insects identify odorant substances, especially sex pheromones. However, whether the sex-specific recognition of odorant substances is caused by differences in the expression of olfaction-related genes between males and females remains unclear. To clarify this problem, the whole transcriptome sequence of the adult Helicoverpa assulta, an important agricultural pest of tobacco and other Solanaceae plants, was obtained using Pacbio sequencing. RNA-seq analysis showed that there were 27 odorant binding proteins (OBPs), 24 chemosensory proteins, 4 pheromone-binding proteins (PBPs), 68 odorant receptors and 2 sensory neuron membrane proteins (SNMPs) genes, that were expressed in the antennae of male and female H. assulta. Females had significantly higher expression of General odorant-binding protein 1-like, OBP, OBP3, PBP3 and SNMP1 than males, while males had significantly higher expression of GOBP1, OBP7, OBP13, PBP2 and SNMP2. These results improve our understanding of mate search and host differentiation in H. assulta.
Collapse
Affiliation(s)
- Haichao Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences/Institute of Palnt Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weizheng Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Changjian Miao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Gaoping Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Man Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Guohui Yuan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xianru Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
6
|
Raka RN, Wu H, Xiao J, Hossen I, Cao Y, Huang M, Jin J. Human ectopic olfactory receptors and their food originated ligands: a review. Crit Rev Food Sci Nutr 2021; 62:5424-5443. [PMID: 33605814 DOI: 10.1080/10408398.2021.1885007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ectopic olfactory receptors (EORs) are expressed in non-nasal tissues of human body. They belong to the G-protein coupled receptor (GPCR) superfamily. EORs may not be capable of differentiating odorants as nasal olfactory receptors (ORs), but still can be triggered by odorants and are involved in different biological processes such as anti-inflammation, energy metabolism, apoptosis etc. Consumption of strong flavored foods like celery, oranges, onions, and spices, is a good aid to attenuate inflammation and boost our immune system. During the digestion of these foods in human digestive system and the metabolization by gut microbiota, the odorants closely interacting with EORs, may play important roles in various bio-functions like serotonin release, appetite regulation etc., and ultimately impact health and diseases. Thus, EORs could be a potential target linking the ligands from food and their bioactivities. There have been related studies in different research fields of medicine and physiology, but still no systematic food oriented review. Our review portrays that EORs could be a potential target for functional food development. In this review, we summarized the EORs found in human tissues, their impacts on health and disease, ligands interacting with EORs exerting specific biological effects, and the mechanisms involved.
Collapse
Affiliation(s)
- Rifat Nowshin Raka
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China.,Beijing Laboratory for Food Quality and Safety, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing, China
| | - Hua Wu
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Key Lab of Plant Resource Research and Development, Beijing, China
| | - Junsong Xiao
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China.,Beijing Laboratory for Food Quality and Safety, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing, China
| | - Imam Hossen
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China.,Beijing Laboratory for Food Quality and Safety, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing, China
| | - Yanping Cao
- Beijing Technology and Business University, Beijing, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing, China
| | - Mingquan Huang
- Beijing Technology and Business University, Beijing, China.,Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
| | - Jianming Jin
- Beijing Technology and Business University, Beijing, China.,Beijing Key Lab of Plant Resource Research and Development, Beijing, China
| |
Collapse
|
7
|
Muelbert M, Bloomfield FH, Pundir S, Harding JE, Pook C. Olfactory Cues in Infant Feeds: Volatile Profiles of Different Milks Fed to Preterm Infants. Front Nutr 2021; 7:603090. [PMID: 33521036 PMCID: PMC7843498 DOI: 10.3389/fnut.2020.603090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/11/2020] [Indexed: 01/05/2023] Open
Abstract
Background: Smell is determined by odor-active volatile compounds that bind to specific olfactory receptors, allowing us to discriminate different smells. Olfactory stimulation may assist with digestion and metabolism of feeds in the neonate by activation of the cephalic phase response of digestion. Infants' physiological responses to the smell of different milks suggest they can distinguish between breastmilk and infant formula. We aimed to describe the profile of volatile compounds in preterm breastmilk and investigate how this differed from that of other preterm infant feeding options including pasteurized donor breastmilk, breastmilk with bovine milk-based fortifier, human milk-based products and various infant formulas. Methods: Forty-seven milk samples (13 different infant formulas and 34 human milk-based samples) were analyzed. Volatile compounds were extracted using Solid Phase Micro Extraction. Identification and relative quantification were carried out by Gas Chromatography with Mass Spectrometry. Principal Component Analysis (PCA) and one-way Analysis of Variance (ANOVA) with Tukey's HSD (parametric data) or Conover's post-hoc test (non-parametric data) were used as appropriate to explore differences in volatile profiles among milk types. Results: In total, 122 compounds were identified. Breastmilk containing bovine milk-based fortifier presented the highest number of compounds (109) and liquid formula the lowest (70). The profile of volatile compounds varied with 51 compounds significantly different (adjusted p < 0.001) among milk types. PCA explained 47% of variability. Compared to preterm breastmilk, the profile of volatile compounds in breastmilk with added bovine milk-based fortifier was marked by presence of fatty acids and their esters, ketones and aldehydes; infant formulas were characterized by alkyls, aldehydes and furans, and human milk-based products presented high concentrations of aromatic hydrocarbons, terpenoids and specific fatty acids. Conclusions: Sensory-active products of fatty acid oxidation are the major contributors to olfactory cues in infant feeds. Analysis of volatile compounds might be useful for monitoring quality of milk and detection of oxidation products and environmental contaminants. Further research is needed to determine whether these different volatile compounds have biological or physiological effects in nutrition of preterm infants.
Collapse
Affiliation(s)
- Mariana Muelbert
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Shikha Pundir
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Jane E Harding
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Chris Pook
- Liggins Institute, University of Auckland, Auckland, New Zealand
| |
Collapse
|
8
|
Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| |
Collapse
|