Basic Phytochrome B Calculations

Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to calculate the steady-state amounts of phytochrome subspecies relative to the total phytochrome molecule population. Starting from a simplified two-state system we expand and apply the technique to the extended phytochrome dimer model. Additionally, we provide a Python package that can automatically calculate the proportion of phytochrome B in a particular state given specific experimental conditions.</p

Signal amplification and transduction in phytochrome photosensors

[Introduction] Page 2 of 20 Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light sensing kinases that control diverse cell ular functions in plants, bacteria, and fungi. 1-9 Bacterial phytochro mes consist of a photosensory core and a C-te rminal regulatory domain. 10,11 Structures of photosensory cores are reported in the resting state 12-18 and conformational responses to light activat ion have been proposed in the vicinity of the chromophore. 19-23 However, the structure of the signalling state and the mechanism of downstream signal re lay through the photosensory core remain elusive. Here, we report crystal and solution structures of the resting and active states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans . The structures reveal an open and closed form of the dimeric protein for the signalling an d resting state, respectively. This nanometre scale rearrangement is controlled by refolding of an evolutionarily conserved “tongue” , which is in contact with the chromophore. The findings reveal an unus ual mechanism where atomic scale conformational ch anges around the chromopho re are first amplified into an Ångström scale distance change in the tongue, and further grow into a nanometre scale conformational sign al. The structural mechanism is a blueprint for understanding how the sensor proteins connect to the cellular signalling network.peerReviewe