title: Mapping networks of light-dark transition in LOV photoreceptors.
abstract: BACKGROUND
  In optogenetics, designing modules of long or short signaling state lifetime is necessary for control over precise cellular events. A critical parameter for designing artificial or synthetic photoreceptors is the signaling state lifetime of photosensor modules. Design and engineering of biologically relevant artificial photoreceptors is based on signaling mechanisms characteristic of naturally occurring photoreceptors. Therefore identifying residues important for light-dark transition is a definite first step towards rational design of synthetic photoreceptors. A thorough grasp of detailed mechanisms of photo induced signaling process would be immensely helpful in understanding the behaviour of organisms.
  
  
  RESULTS
  Herein, we introduce the technique of differential networks. We identify key biological interactions, using light-oxygen-voltage domains of all organisms whose dark and light state crystal structures are simultaneously available. Even though structural differences between dark and light states are subtle (other than the covalent bond formation between flavin chromophore and active site Cysteine), our results successfully capture functionally relevant residues and are in complete agreement with experimental findings from literature. Additionally, using sequence-structure alignments, we predict functional significance of interactions found to be important from network perspective yet awaiting experimental validation. Our approach would not only help in minimizing extensive photo-cycle kinetics procedure but is also helpful in providing first-hand information on the fundamentals of photo-adaptation and rational design of synthetic photoreceptors in optogenetics.
  
  
  BACKGROUND
  devrani.dbs@presiuniv.ac.in or soumen@jcbose.ac.in
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bose Institute, Kolkata 700 009, India and.
authors.forename: Rajdeep
authors.initials: R
authors.lastname: Kaur Grewal
authors.affiliation: Department of Biological Sciences, Presidency University, Kolkata 700 073, India.
authors.forename: Devrani
authors.initials: D
authors.lastname: Mitra
authors.affiliation: Bose Institute, Kolkata 700 009, India and.
authors.forename: Soumen
authors.initials: S
authors.lastname: Roy
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry; D003624:Darkness; D005656:Fungal Proteins / Q000737:chemistry; D008027:Light; D010786:Photoreceptor Cells / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D017434:Protein Structure, Tertiary; D015398:Signal Transduction
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D005656:Fungal Proteins; D010940:Plant Proteins