title: Unearthing the transition rates between photoreceptor conformers.
abstract: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (PA) and inactive (PI) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions.
  
  
  
  Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and; iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools.
  
  
  
  The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained.
authors.affiliation: Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.|LifeGlimmer GmbH, Markelstrasse 38, Berlin, 12163, Germany.
authors.forename: Robert W
authors.identifier: 0000-0001-9657-7477
authors.initials: RW
authors.lastname: Smith
authors.affiliation: Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.|Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands.
authors.forename: Britta
authors.initials: B
authors.lastname: Helwig
authors.affiliation: Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands.
authors.forename: Adrie H
authors.initials: AH
authors.lastname: Westphal
authors.affiliation: Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.|Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands.
authors.forename: Eran
authors.initials: E
authors.lastname: Pel
authors.affiliation: Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19A, Freiburg, 79104, Germany.|Faculty of Biology & BioSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Hörner
authors.affiliation: Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19A, Freiburg, 79104, Germany.|Faculty of Biology & BioSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany.
authors.forename: Hannes M
authors.initials: HM
authors.lastname: Beyer
authors.affiliation: Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19A, Freiburg, 79104, Germany.|Institute of Synthetic Biology, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany.
authors.forename: Sophia L
authors.initials: SL
authors.lastname: Samodelov
authors.affiliation: Faculty of Biology & BioSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany.
authors.forename: Wilfried
authors.initials: W
authors.lastname: Weber
authors.affiliation: Institute of Synthetic Biology, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany.
authors.forename: Matias D
authors.initials: MD
authors.lastname: Zurbriggen
authors.affiliation: Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands.
authors.forename: Jan Willem
authors.initials: JW
authors.lastname: Borst
authors.affiliation: Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands. christian.fleck@wur.nl.
authors.forename: Christian
authors.initials: C
authors.lastname: Fleck
mesh_terms: D017360:Arabidopsis / Q000378:metabolism / Q000528:radiation effects; D019295:Computational Biology; D007700:Kinetics; D008027:Light; D008954:Models, Biological; D051939:Phytochrome B / Q000737:chemistry* / Q000378:metabolism*; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D011789:Quantum Theory; D013696:Temperature
chemical_list: D051939:Phytochrome B
keywords: Optimisation; Optogenetics; Photoconversion; Phytochromes