Unearthing the transition rates between photoreceptor conformers

Area of Science:

• Biophysics
• Molecular Biology
• Systems Biology

Background:

• Accurate estimation of biological reaction rates is crucial for understanding biological networks and experimental manipulation.
• Experimental limitations often necessitate mathematical algorithms for estimating unmeasurable enzymatic rates.
• Light-regulated proteins, such as phytochromes, switch between active and inactive states influenced by various factors.

Purpose of the Study:

• To develop a methodology for calculating the photoconversion cross-sections of light-regulated proteins.
• To accurately determine these rates even in the presence of multiple non-light regulated reactions.
• To provide a tool for comparing photoreceptor performance across different systems.

Main Methods:

• A three-step approach: calculating thermal reversion rates, defining search spaces for photoconversion cross-sections, and estimating extinction coefficients.
• Validation using simulated test cases, including scenarios with noise, multiple thermal reactions, and dimerization.
• Application to an Arabidopsis phyB N-terminal fragment.

Main Results:

• The methodology accurately calculates photoconversion cross-sections.
• Simulated test cases confirmed the approach's robustness under realistic conditions.
• Photoconversion cross-sections for a common Arabidopsis phyB fragment were determined.

Conclusions:

• The developed method allows direct comparisons of photoconversion cross-sections and response speeds of photoreceptors.
• This offers new insights for photoreceptor and synthetic biologists.
• The general procedure could be applied to determine the photoconversion cross-sections and quantum yields of any photoreceptor.