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  • Open Access

Theoretical upper bound of multiplexing in biological sensory receptors

Asawari Pagare*, Sa Hoon Min*, and Zhiyue Lu†

  • Department of Chemistry, University of North Carolina-Chapel Hill, North Carolina 27599, USA

  • *These authors contributed equally to this work.
  • †zhiyuelu@unc.edu

Phys. Rev. Research 5, 023032 – Published 17 April, 2023

DOI: https://doi.org/10.1103/PhysRevResearch.5.023032

Abstract

Biological sensory receptors provide excellent examples of microscopic scale information transduction amidst stochastic noise. We argue that stochasticity is not always a hindrance to sensing. Instead, it could allow a single stochastic sensor to perform multiplexing: simultaneously transducing multiple types of environmental information to the downstream sensory network. Through a Langevin dynamics simulation of a ligand-receptor sensor in a bath of ligands, we demonstrate that a binary-state receptor can simultaneously encode multiple independent environmental variables, such as ligand concentration and the speed of media flow. We develop a general theory of stochastic sensory multiplexing and suggest two theoretical upper bounds. Furthermore, we conjecture that randomly generated sensors typically saturate the tighter upper bound. The theoretical framework developed in this study, which involves a rank-deficient maximum likelihood analysis (rd-MLE), provides a systematic approach to comprehensively assess a sensor's sensory ability without any initial assumptions. This theoretical framework can inspire the design of more efficient artificial sensors.

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References (36)

  1. Y. E. Antebi, J. M. Linton, H. Klumpe, B. Bintu, M. Gong, C. Su, R. McCardell, and M. B. Elowitz, Combinatorial signal perception in the BMP pathway, Cell 170, 1184 (2017).
  2. Y. E. Antebi, N. Nandagopal, and M. B. Elowitz, An operational view of intercellular signaling pathways, Curr. Opin. Syst. Biol. 1, 16 (2017).
  3. I. Lestas, G. Vinnicombe, and J. Paulsson, Fundamental limits on the suppression of molecular fluctuations, Nature (London) 467, 174 (2010).
  4. M. Hinczewski and D. Thirumalai, Cellular Signaling Networks Function as Generalized Wiener-Kolmogorov Filters to Suppress Noise, Phys. Rev. X 4, 041017 (2014).
  5. H. C. Berg and E. M. Purcell, Physics of chemoreception, Biophys. J. 20, 193 (1977).
  6. W. Bialek and S. Setayeshgar, Physical limits to biochemical signaling, Proc. Natl. Acad. Sci. USA 102, 10040 (2005).
  7. K. Kaizu, W. De Ronde, J. Paijmans, K. Takahashi, F. Tostevin, and P. R. Ten Wolde, The Berg-Purcell limit revisited, Biophys. J. 106, 976 (2014).
  8. T. Mora and I. Nemenman, Physical Limit to Concentration Sensing in a Changing Environment, Phys. Rev. Lett. 123, 198101 (2019).
  9. M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, and T. Mora, Receptor crosstalk improves concentration sensing of multiple ligands, Phys. Rev. E 99, 022423 (2019).
  10. B. Hu, W. Chen, W.-J. Rappel, and H. Levine, Physical Limits on Cellular Sensing of Spatial Gradients, Phys. Rev. Lett. 105, 048104 (2010).
  11. P. François and A. Zilman, Physical approaches to receptor sensing and ligand discrimination, Curr. Opin. Syst. Biol. 18, 111 (2019).
  12. V. Singh and I. Nemenman, Accurate sensing of multiple ligands with a single receptor, arXiv:1506.00288.
  13. V. Singh and I. Nemenman, Universal Properties of Concentration Sensing in Large Ligand-Receptor Networks, Phys. Rev. Lett. 124, 028101 (2020).
  14. V. Singh and I. Nemenman, Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor, PLoS Comput. Biol. 13, e1005490 (2017).
  15. C. C. Govern and P. R. ten Wolde, Fundamental Limits on Sensing Chemical Concentrations with Linear Biochemical Networks, Phys. Rev. Lett. 109, 218103 (2012).
  16. M. Ahuja, M. R. Bhatnagar et al., Capacity of ligand receptor channel with markovian symbol detection, in Proceedings of the 2020 IEEE International Conference on Advanced Networks and Telecommunications Systems (ANTS) (IEEE, Piscataway, NJ, 2020), pp. 1–6.
  17. H. Nguyen, P. Dayan, and G. Goodhill, How receptor diffusion influences gradient sensing, J. R. Soc. Interface 12, 20141097 (2015).
  18. E. Marder, Variability, compensation, and modulation in neurons and circuits, Proc. Natl. Acad. Sci. USA 108, 15542 (2011).
  19. T. S. Hatakeyama and K. Kaneko, Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration, Proc. Natl. Acad. Sci. USA 109, 8109 (2012).
  20. G. Kurosawa and Y. Iwasa, Temperature compensation in circadian clock models, J. Theor. Biol. 233, 453 (2005).
  21. M. Thomas and A. T. Joy, Elements of Information Theory (Wiley-Interscience, Hoboken, NJ, 2006).
  22. G. Minas, D. J. Woodcock, L. Ashall, C. V. Harper, M. R. White, and D. A. Rand, Multiplexing information flow through dynamic signalling systems, PLoS Comput. Biol. 16, e1008076 (2020).
  23. R. G. Endres and N. S. Wingreen, Maximum Likelihood and the Single Receptor, Phys. Rev. Lett. 103, 158101 (2009).
  24. T. M. Cover and J. A. Thomas, Elements of Information Theory (John Wiley & Sons, Hoboken, NJ, 2012).
  25. K. Khamaru and R. Mazumder, Computation of the maximum likelihood estimator in low-rank factor analysis, Math. Program. 176, 279 (2019).
  26. D. Robertson and J. Symons, Maximum likelihood factor analysis with rank-deficient sample covariance matrices, J. Multivariate Anal. 98, 813 (2007).
  27. J. D. Weeks, D. Chandler, and H. C. Andersen, Perturbation theory of the thermodynamic properties of simple liquids, J. Chem. Phys. 55, 5422 (1971).
  28. J. J. Hopfield, Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity, Proc. Natl. Acad. Sci. USA 71, 4135 (1974).
  29. H. Qian, Reducing intrinsic biochemical noise in cells and its thermodynamic limit, J. Mol. Biol. 362, 387 (2006).
  30. A. Murugan, D. A. Huse, and S. Leibler, Speed, dissipation, and error in kinetic proofreading, Proc. Natl. Acad. Sci. USA 109, 12034 (2012).
  31. J. M. Horowitz and H. Sandberg, Second-law-like inequalities with information and their interpretations, New J. Phys. 16, 125007 (2014).
  32. Notice that this argument is general and the time-lag between s(i) and s(i+1) does not need to be equal to lag between s(j) and s(j+1), for 1≤i,j≤nt−1. The effective time lags and effective time points nt are limited by the self-correlation of the trajectory s(t) and by the property of the downstream kernel.
  33. P. F. Arndt, Yang-Lee Theory for a Nonequilibrium Phase Transition, Phys. Rev. Lett. 84, 814 (2000).
  34. Derivatives in the θ-space are evaluated as finite differentials with increments δθ=(4.8459%μ*,5%T*,5%vx*). The two-point trajectory probabilities used in the analysis are obtained by chopping a long simulation 1010 steps (each step increases time by dt=0.01). Each two-point trajectory is sampled from two time points with the time difference of 100 steps, which is equivalent to time lag 100dt=1.
  35. Notice that although the dynamics of the six-state composite system is Markovian, its projection to the sensor's state space is no longer Markovian and have a history dependence.
  36. https://github.com/ljpotential/StochasticSensoryReceptor.jl.

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