Team:ETH Zurich/Modeling/Photoinduction

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Contents

Photoinduction

Introduction

Photoreceptors are light-sensitive proteins, which are able to perform specific actions in the cell (e.g. act as kinases) upon light induction. Photoreceptors typically make use of photopigments (like flavin and bilin), which are structurally changed (Photoisomerization) or reduced (Photoreduction) as reaction to excitation by photons. Some photoreceptors can be activated and deactivated by light; others follow an exponential decay to a ground state after excitation. In either case for an estimation of a receptor’s activity level it is necessary to compute the number of induction events, i.e. light has to be treated as particles.

For E.colipse we needed to know the activation of various receptors (Lov-Tap, BLUF-EAL, Ccas1, Cph8, UVR-8) to predict the behaviour of our system. For each of the receptors we tested several light conditions and computed the effects of visible and UV-light. In particular we analysed whether we can identify the amount of UV radiation with the given receptors.


Methods

Quantification of light

For our project we needed to quantify the irradiance of different light sources, like sun light, room light, various bulbs, LEDs and a UV transiluminator. We discretized the irradiance spectra of these sources [J m-2 s-1 nm-1] and converted the power (at a wavelength) to the photons flux Nλ [mol m-2 s-1 nm-1]. We were aware, that light can be polarized, directed and non-coherent, but these characteristics were not relevant for our approximation.

Photoconversion cross section

To compute the fraction of the photon flux, which in fact triggers an event, we used the photoconversion cross section σ. This is a measure of the probability of such an event and derived from Beer-Lambert law.

ETH photoinduction crosssection.png

where ε is the molar extinction coefficient and Φ is the quantum yield, i.e. the fractions of “hits” causing an event. Since for most of the receptors we only had absorption spectra and extinction coefficients at absorption peak wavelengths we assumed, that the extinction coefficient at each wavelength is proportional to absorption. Furthermore we assumed the quantum yield would be independent of wavelength.

Reaction rate constants

The first order reaction rate constants can be computed as integral over all wavelengths of the product of the photoconversion cross section σ and photon flux Nλ.

ETH photoinduction rateconstant.png

Additionally our ODE model used dark decay rate constants to approximate the activation of receptors.

Validation

The results of our method are consistent with the results of [Mancinelli, 1994] and of the 2010 ETH Zuerich Team’s model. In both cases we reached high accordance. The small difference can be explained by our approximation of the extinction coefficient.

Results & Discussion

Our primary target was to compute rate constants as input for our ODE models. Nevertheless we already gained first insights from these rate constants.

Receptor activation

We took a frist glimpse on the expected receptor activation by approximating the steady state solution for the ODE system.

ETH photoinduction activation.png

From the results we had to assume that all receptors would be fully activated at low irradiation. "Low" refers to the fraction of original irradiance, e.g. actual sun light intensity or the irradiance caused by a certain light bulb (at a given distance: 2 m).

Expected steady state activation of receptors for intensities from 0 to 100 % of original source intensity. Read: 90 % of Ycgf is at steady state in active state at 10 % of sun's original irradiance.

Fraction of UV light

UV fraction is too low to distinguish the activity of a blue and a red/green light receptor under real light conditions




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