scholarly journals Competitive binding predicts nonlinear responses of olfactory receptors to complex mixtures

2019 ◽  
Vol 116 (19) ◽  
pp. 9598-9603 ◽  
Author(s):  
Vijay Singh ◽  
Nicolle R. Murphy ◽  
Vijay Balasubramanian ◽  
Joel D. Mainland

In color vision, the quantitative rules for mixing lights to make a target color are well understood. By contrast, the rules for mixing odorants to make a target odor remain elusive. A solution to this problem in vision relied on characterizing receptor responses to different wavelengths of light and subsequently relating these responses to perception. In olfaction, experimentally measuring receptor responses to a representative set of complex mixtures is intractable due to the vast number of possibilities. To meet this challenge, we develop a biophysical model that predicts mammalian receptor responses to complex mixtures using responses to single odorants. The dominant nonlinearity in our model is competitive binding (CB): Only one odorant molecule can attach to a receptor binding site at a time. This simple framework predicts receptor responses to mixtures of up to 12 monomolecular odorants to within 15% of experimental observations and provides a powerful method for leveraging limited experimental data. Simple extensions of our model describe phenomena such as synergy, overshadowing, and inhibition. We demonstrate that the presence of such interactions can be identified via systematic deviations from the competitive-binding model.

2018 ◽  
Author(s):  
Vijay Singh ◽  
Nicolle R. Murphy ◽  
Vijay Balasubramanian ◽  
Joel D. Mainland

In color vision, the quantitative rules for mixing lights to make a target color are well understood. By contrast, the rules for mixing odorants to make a target odor remain elusive. A solution to this problem in vision relied on characterizing receptor responses to different wavelengths of light and subsequently relating these responses to perception. In olfaction, experimentally measuring receptor responses to a representative set of complex mixtures is intractable due to the vast number of possibilities. To meet this challenge, we develop a biophysical model that predicts mammalian receptor responses to complex mixtures using responses to single odorants. The dominant nonlinearity in our model is competitive binding (CB): only one odorant molecule can attach to a receptor binding site at a time. This simple framework predicts receptor responses to mixtures of up to twelve monomolecular odorants to within 15% of experimental observations and provides a powerful method for leveraging limited experimental data. Simple extensions of our model describe phenomena such as synergy, overshadowing, and inhibition. We demonstrate that the presence of such interactions can be identified via systematic deviations from the competitive binding model.


2016 ◽  
Vol 18 (32) ◽  
pp. 22531-22539 ◽  
Author(s):  
Y. Akdogan ◽  
M. Emrullahoglu ◽  
D. Tatlidil ◽  
M. Ucuncu ◽  
G. Cakan-Akdogan

EPR spectroscopy is a very promising technique to understand the details of drug binding and competitive drug binding to proteins.


2021 ◽  
Vol 12 ◽  
Author(s):  
Qian Wang ◽  
Xiaojian Wen ◽  
Yi Lu ◽  
Junbao Wen

The tree-of-heaven root weevil (Eucryptorrhynchus scrobiculatus) and the tree-of-heaven trunk weevil (Eucryptorrhynchus brandti) are closely related species that monophagously feed on the same host plant, the Ailanthus altissima (Mill) Swingle, at different locations. However, the mechanisms of how they select different parts of the host tree are unclear. As chemosensory systems play important roles in host location and oviposition, we screened candidate chemosensory protein genes from the transcriptomes of the two weevils at different developmental stages. In this study, we identified 12 candidate chemosensory proteins (CSPs) of E. scrobiculatus and E. brandti, three EscrCSPs, and one EbraCSPs, respectively, were newly identified. The qRT-PCR results showed that EscrCSP7/8a/9 and EbraCSP7/8/9 were significantly expressed in adult antennae, while EscrCSP8a and EbraCSP8 shared low sequence identity, suggesting that they may respond to different odorant molecule binding. Additionally, EbraCSP6 and EscrCSP6 were mainly expressed in antennae and proboscises and likely participate in the process of chemoreception. The binding simulation of nine volatile compounds of the host plant to EscrCSP8a and EbraCSP8 indicated that (1R)-(+)-alpha-pinene, (–)-beta-caryophyllene, and beta-elemen have higher binding affinities with EscrCSP8a and lower affinities with EbraCSP8. In addition, there were seven, two, and one EbraCSPs mainly expressed in pupae, larvae, and eggs, respectively, indicating possible developmental-related roles in E. brandti. We screened out several olfactory-related possible CSP genes in E. brandti and E. scrobiculatus and simulated the binding model of CSPs with different compounds, providing a basis for explaining the niche differentiation of the two weevils.


2019 ◽  
Author(s):  
Emiliano Marachlian ◽  
Ramon Huerta ◽  
Fernando F. Locatelli

A conserved principle of the olfactory system, in most, if not all animals, is that each olfactory receptor interacts with different odorant molecules and each odorant molecule interacts with different olfactory receptors. This broad receptive field of the receptors constitutes the basis of a combinatorial code that allows animals to discriminate many more odorants than the actual number of receptor types that they express. A drawback is that high odorant concentrations recruit lower affinity receptors, which can give rise to the perception of qualitatively different odors. Here we addressed the contribution that early signal-processing in the honey bee antennal lobe does to keep odor representation stable across concentrations. We describe the contribution that GABA-A and GABA-B receptors-dependent-inhibition plays in terms of the amplitude and temporal profiles of the signals that convey odor information from the antennal lobes to the mushroom bodies. GABA reduces the amplitude of odor elicited signals and the number of glomeruli that are recruited in a concentration-dependent way. Blocking GABA-A and GABA-B receptors decreases the correlation among glomerular activity patterns elicited by different concentrations of the same odor. Based on the results we built a realistic computational model of the antennal lobe that could be further used to evaluate the signal processing properties of the AL network under conditions that cannot be achieved in physiology experiments. Interestingly, even though based on rather simplistic topology and interactions among cells solely mediated by GABA-A and GABA-B interactions, the AL model reproduced the key features of the AL stable response in relation to different concentrations.


2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Jack Xiaoyu Chen ◽  
Harrison Steel ◽  
Yin-Hu Wu ◽  
Yun Wang ◽  
Jiabao Xu ◽  
...  

ABSTRACT A simple aspirin-inducible system has been developed and characterized in Escherichia coli by employing the Psal promoter and SalR regulation system originally from Acinetobacter baylyi ADP1. Mutagenesis at the DNA binding domain (DBD) and chemical recognition domain (CRD) of the SalR protein in A. baylyi ADP1 suggests that the effector-free form, SalRr, can compete with the effector-bound form, SalRa, binding the Psal promoter and repressing gene transcription. The induction of the Psal promoter was compared in two different gene circuit designs: a simple regulation system (SRS) and positive autoregulation (PAR). Both regulatory circuits were induced in a dose-dependent manner in the presence of 0.05 to 10 µM aspirin. Overexpression of SalR in the SRS circuit reduced both baseline leakiness and the strength of the Psal promoter. The PAR circuit forms a positive feedback loop that fine-tunes the level of SalR. A mathematical simulation based on the SalRr/SalRa competitive binding model not only fit the observed experimental results in SRS and PAR circuits but also predicted the performance of a new gene circuit design for which weak expression of SalR in the SRS circuit should significantly improve induction strength. The experimental result is in good agreement with this prediction, validating the SalRr/SalRa competitive binding model. The aspirin-inducible systems were also functional in probiotic strain E. coli Nissle 1917 and SimCells produced from E. coli MC1000 ΔminD. These well-characterized and modularized aspirin-inducible gene circuits would be useful biobricks for synthetic biology. IMPORTANCE An aspirin-inducible SalR/Psal regulation system, originally from Acinetobacter baylyi ADP1, has been designed for E. coli strains. SalR is a typical LysR-type transcriptional regulator (LTTR) family protein and activates the Psal promoter in the presence of aspirin or salicylate in the range of 0.05 to 10 µM. The experimental results and mathematical simulations support the competitive binding model of the SalR/Psal regulation system in which SalRr competes with SalRa to bind the Psal promoter and affect gene transcription. The competitive binding model successfully predicted that weak SalR expression would significantly improve the inducible strength of the SalR/Psal regulation system, which is confirmed by the experimental results. This provides an important mechanism model to fine-tune transcriptional regulation of the LTTR family, which is the largest family of transcriptional regulators in the prokaryotic kingdom. In addition, the SalR/Psal regulation system was also functional in probiotic strain E. coli Nissle 1917 and minicell-derived SimCells, which would be a useful biobrick for environmental and medical applications.


2019 ◽  
Vol 176 (24) ◽  
pp. 4731-4744
Author(s):  
Victoria Georgi ◽  
Alexey Dubrovskiy ◽  
Stephan Steigele ◽  
Amaury E. Fernández‐Montalván

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