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. Author manuscript; available in PMC: 2014 Apr 21.
Published in final edited form as: Chem Soc Rev. 2013 Jan 29;42(8):3441–3452. doi: 10.1039/c3cs35458j

Table 2.

The proposed modifications and mutations of the photosensory module of BphPs to achieve specific photochemical effect or biochemical function.

Phenotype Template Modification and Mutations Effect or Function Ref
Fluorescent proteins and chromoproteins
Short NIR PAS-GAF or PAS- GAF-PHY domains Truncation of PHY domain; Truncation of up to two amino acids before Cys12; 194A,H,K,L,S; 247A Stabilization of the chromophore in the Pr state with disabling of Pr→Pfr photoconvertion 32, 38, 41
194A,H,K,L,S; 250F; 277Q Increase in quantum yield 12, 41, 42
163H, 185L, 195D, 459A, 453A, 277A,Q Stabilization of the Pr state with limited/reduced photoconversion 32, 33, 38, 41
Long NIR PAS-GAF-PHY domains of bathy BphPs 261A Stabilization of the Pfr state with disabling Pfr→Pr photoconvertion 38
163A; 241A; 275A Stabilization of the Pfr state with reducing Pfr→Pr photoconvertion 38
PS and PA NIR (switching on) PAS-GAF-PHY domains 188L; 275A; 190A; 163H; 250F Decreasing rate of Pr→Pfr dark reversion (from minutes to hours) 33, 38
241A; 163A Increasing rate of Pr →Pfr dark reversion (faster than 3 min) 38
PA NIR (switching off) PAS-GAF domains 194A,T,Q; 260A,S Reversible bleaching of Pr state with no photoconversion to Pfr state 41
Monomeric PAS-GAF or PAS- GAF-PHY domains 131S; 295E; 298D,K; 301D,R; 305R Disruption of the dimer interface 11, 12
Biosensors
Redox sensor Optimized BphP- derived FPs Residues located in close proximity to the thioether linkage between BV and apoprotein Catalyzing thioether bond formation and influencing its reactivity 41, 58
Metal sensor PAS-GAF domains Truncation of PHY domain Increasing solvent access to chromophore 13, 32, 34, 59
Residues within 4.5Å from the chromophore Improving interactions between metal ion and chromophore
Split and insertion based sensors * Optimized BphP- derived FPs Split/insertion between 112–119 amino acid residues Unstructured linker between PAS and GAF domains 3234, 38, 60, 61
Varying the linkers between PAS domain and sensing moiety, and GAF and sensing moiety Optimization of PAS and GAF domains collocation for their better interactions
Optogenetic tools
Optogenetic tools with different effector modules PAS-GAF-PHY domains of BphP and a knowledge-based chosen effector module Varying the α-helix linker between photosensor and effector modules Ability of light signal propagation to effector 18, 62, 63
Point mutations in the α-helix linker and PAS domain Efficiency of light signal propagation to effector 64
188L; 275A; 190A; 163H; 250F; 241A; 163A Optimization of photopreception 32, 33, 38, 47
*

Structure of the PAS-GAF domains contains a 4-crossover knot that may complicate reconstitution of a split protein. Residues at the indicated positions provide the respective phenotype in concerted manner or independently. Residue numbering follows that for PaBphP. See Fig. 3 for the amino acid alignment of several BphPs.