Table 1.

Reported functional SRM studies of biomolecule interactions and biochemical activities in living cells with genetically encoded indicators.

Application	Name	Target	Class	FP	FP Config.	Split Site(s)	Microscopy	Localization Precision 1	FWHM 2	Kinetics	Reversibility	Cell Type(s)	Ref.
Rapamycin-induced FKBP and FRB interaction	refSOFI	Protein-protein interaction	BiFC	DMVF	cp; split	a.a. 181	SOFI	N/A	~100 nm	Slow 3	No	HeLa	[58]
Interaction of receptor tyrosine kinases HER2 & 3	refSOFI	Protein-protein interaction	BiFC	DMVF	cp; split	a.a. 181	SOFI	N/A	~100 nm	Slow 3	No	HeLa	[58]
Interaction of ER Ca2+ sensor STIM1 and Ca2+ channel protein ORAI1	refSOFI	Protein-protein interaction	BiFC	DMVF	cp; split	a.a. 181	SOFI	N/A	~100 nm	Slow 3	No	HeLa	[58]
Interactions of small GTPase Ras and its effector Raf	BiFC-PALM	Protein-protein interaction	BiFC	PA-mCherry1	split	a.a. 159	PALM	18 nm	N/A	Slow 3	No	U2OS	[59]
Interaction of MreB and EF-Tu	BiFC-PALM	Protein-protein interaction	BiFC	mEos3.2	split	a.a. 164	PALM	12 nm	N/A	Slow 3	No	E. coli	[60]
Homodimerization of microtubule plus-end hub protein EB1	BiFC-PALM	Protein-protein interaction	BiFC	PA-GFP	split	not specified	PALM	23 nm	N/A	Slow 3	No	HeLa; MCF7	[61]
Formation of bJun/bFos complexes	BiFC-PALM	Protein-protein interaction	BiFC	mIrisFP	split	a.a. 150; a.a. 165	PALM	18 nm	N/A	Slow 3	No	Vero cells	[62]
Interaction among αs, β1, and γ2 subunits of Gs ternary complex	TFFC-PALM	Protein-protein interaction	TFFC 4	mIrisFP	split	a.a. 150 & a.a. 165	PALM	18 nm	N/A	Slow 3	No	Vero cells	[62]
Interaction of Bcl-xL and Bak	BiFC-RESOLFT	Protein-protein interaction	BiFC	rsEGFP2	split	a.a. 158	RESOLFT	N/A	113 nm	Slow 3	No	Hela	[63]
Membrane-binding of proteins in EGF signaling pathway	PAINT-PALM	Proteinprotein interaction	PAINT	mEos3.2	default	N/A	PALM	35 nm	N/A	fast	Yes 5	HeLa; CHO	[67]
Binding of PCNA and Mcm4 proteins to genomic DNA	PAINT-PALM	Protein-DNA interaction	PAINT	mEos3.1	default	N/A	PALM	11 nm	N/A	fast	Yes 5	fission yeast	[68]
Dynamics of RNA Pol II clustering at β-actin gene locus	PAINT-PALM	Protein-RNA interaction	PAINT	Dendra2	default	N/A	PALM	31 nm	N/A	fast	Yes 5	MEF	[71]
Protein Kinase A (PKA) activity	FLINC-AKAR1	Biochemical activity	FLINC	TagRFP-T	default	N/A	SOFI	N/A	107–179 nm	fast	Yes	HeLa; α4CHO	[77]
Extracellular signal-regulated kinase (ERK) activity	FLINC-EKAR1	Biochemical activity	FLINC	TagRFP-T	default	N/A	SOFI	N/A	160 nm	fast	Yes	HEK293	[77]
Rapamycin-induced FKBP and FRB interaction	bimolecular FLINC	Protein-protein interaction	FLINC	TagRFP-T	default	N/A	SOFI	N/A	~107–160 nm	fast	Yes	HeLa	[77]
Interaction of FHA1 and PKA phosphosubstrate	bimolecular FLINC-AKAR1	Protein–protein interaction	FLINC	TagRFP-T	default	N/A	SOFI	N/A	~107–160 nm	fast	Yes	HeLa	[77]

¹ Localization Precision is a parameter to report optic resolution in single-molecule localization microscopy. ² Full width at half maximum (FWHM) is a parameter to report structural resolution in microscopy. Separation of structural features, i.e., intensity peak-to-peak distance, is also used to report structural resolution in a few cases in Table 1. ³ The onset of fluorescence in BiFC and TFFC systems are rate limited by maturation speed of the chromophore. ⁴ Three-fragment fluorescence complementation (TFFC) is a variant of BiFC for detecting interactions among three protein components. ⁵ Although photoconversion of the FPs from green to red emission is irreversible, new pre-converted probes are replenished from the surrounding environment thus enable de novo binding to target molecules. a.a.: amino acid; N/A: not applicable.