340
Synthetic Protein SwitcheS: MethodS and ProtocolS
Index
F
Firefly luciferase ��119–129, 132–137, 142,
221, 223, 224, 227, 231, 234
Firefly luminescent intermediate-based protein-protein
interaction assay (FlimPIA) ��119–129
Fluorescence activated cell sorting (FACS) �� 14, 16,
17, 297, 303, 325, 334–335
Fluorescence microscopy �� 115, 228, 259,
261, 263, 265–268
Fluorescence spectroscopy �� 79, 205
Fluorescent enzyme assays �� 10, 154
Fluorescent protein (FP) ��4, 14, 17, 30, 71,
82, 85, 89–99, 101–103, 109, 137, 180, 244, 333
Fluorescent protein sensors ��13
Förster resonance energy transfer (FRET) �� 9, 13,
16, 30, 38, 40, 71–86, 89–99, 101, 104, 109, 114, 133,
134, 167, 180
FREX (protein/fragment exchange)� See Protein/fragment
exchange (FREX)
G
Genetic assays �� 17, 18, 308
Genetic complementation ��18
Genetic screening ��16, 17
Genetic selection ��17, 18
Green fluorescent protein (GFP) �� 6, 10, 13, 17,
221, 227, 229, 230, 232, 333, 335
I
Ion channel engineering �� 273, 278
M
Mammalian cell culture
lentiviral transduction �� 134, 263, 264
protein expression ��17
transfection �� 114, 263, 264, 312
Membrane recruitment�� 259, 267
Mouse �� 97, 132, 134–136,
139, 140, 142–144
O
Optogenetics �� 258, 265, 269, 272
P
Peptide fibrils��59–66
Peptide switches ��59
Periplasmic-binding proteins (PBPs) ��9, 17
Phosphorylation ��257
Photoreceptor engineering
Cry2-CIB1 ��257–269
Lov2 �� 18, 243, 247, 248, 254, 272, 273
Photoreceptors��242–244, 247–249, 252,
254, 258, 288, 290, 298, 301
Photosensitive degron �� 242, 243, 245, 252
Phylogenetic analysis �� 73, 75–77, 82–84
Polymerase chain reaction (PCR)
multiplex inverse PCR �� 44, 45, 48, 54
overlap extension PCR ��10, 11, 35, 155,
156, 275, 278, 279
PATCHY ��289, 290, 293, 294, 296–302
Proteases
receptors �� 198, 199, 201–205, 210–212, 216
sensors ��169, 173, 176, 197–217
split-TEV sensors ��219
switches �� 198, 199, 203, 204, 209–214, 216, 217
transducers �� 198–201, 203, 206, 209–213, 216, 217
Protein analysis
SDS-PAGE ��112, 159, 171, 266, 314
semi-native SDS-PAGE �� 183, 190
western blotting ��133, 137, 139, 144, 150, 153–154,
159–160, 231, 259–261, 263, 265–267, 269
Protein circular permutation �� 31, 44, 52, 53, 73, 85, 107
Protein complementation assay �� 121, 141, 151, 220
Protein conjugation �� 185, 186, 188, 189
Protein degradation ��251
Protein-DNA conjugation ��179
Protein engineering
chemical conjugation �� 38, 91, 182, 185
computational �� 7, 18, 105
domain insertion ��6, 10
high-throughput screening and selection�� 10, 13,
18, 200, 208, 209
modular ��10
rational �� 13, 200
Protein evolution �� 76, 77, 322
Protein expression �� 17, 91, 122, 153,
156–157, 170–173, 181–182, 185, 201, 202, 231, 273,
311–315, 333
Protein/fragment exchange (FREX ) �� 28–30, 34, 35,
37, 39, 40
Protein kinases
AKT kinase ��258
ATM kinase sensor ��131–144
histidine kinase sensor �� 290, 298, 300
Protein linker engineering
glycine-serine ��11
polyproline ��108
Protein phosphorylation �� 198, 307
Protein purification
His/TALON-tag affinity �� 111, 181
Strep-tag affinity �� 111, 181
Protein receptors �� 322, 326
Protein refolding �� 150, 159
Protein sensors �� 7, 8, 310

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