Caspases,Paracaspases, and Metacaspases Methods and Protocols

LmjMCA ................................................. 1 90–193, 196–200
Luminophore ......................................................................4 2
Lymphocyte .............................................................. 1 77–179

M

Mass spectrometry ........................................ 6 2, 66, 255, 257
Metacaspase(s)
in Leishmania ...................................................... 189–201
in plants .............................................. 2 37–252, 255–260
in Saccharomyces cerevisiae .................................... 223–235
in Trypanosoma ................................................... 203–220
Metacaspase AtMC4 ........................................ 242, 249, 250
Metacaspase AtMC9 ........................................................191
Metacaspase disrupted yeast cells .....................................1 93
Metacaspase knockout plant .............................................2 58
Metacaspase McII-Pa ............................... 2 38, 239, 243, 248
Metacaspase substrates ..................................... 2 46, 255–260
Metacaspase TbMCA2 ....................................................204
Metacaspase YCA1 .................................................. 223–235
Michaelis-Menten’s constant ..............................................2 2
Michaelis-Menten equation ................................... 1 4, 15, 21
Michaels-Menten plot ........................................................5 5
Microseeding ............................................................ 2 08, 211
Mitochondria ............................ 1 19, 120, 123, 124, 130–133
Mitochondrial outer membrane permeabilization
(MOMP) .......................................... 7 2, 130–132
Monoubiquitination ................................................. 1 80, 184
Multi-channel pipette ................................... 4 5, 47, 242, 250

N

Near-infrared caspase substrate ........................ 1 24, 135–136
Necroptosis .........................................................................3 6
Neo-N-termini .................................................................2 55
NF-kB ...................................................................... 1 77–179
N-hydroxysuccinimide ester (NHS) ................... 2 3, 258–260
Ninhydrin test ........................................................ 5 2–54, 57
Nuclear morphology ................................. 1 21, 123, 133–134

O

Oocyte ................................................................ 7 2, 119–139
Ostresh procedure ......................................................... 4 2, 43

P

Paracaspase MALT1 .................................... 44, 57, 177–186
Paracaspase substrates ............................................... 177–188
Peptidic inhibitor .................................................... 1 8, 74, 76
Peptograph ....................................................... 6 2, 64, 66–69
pESC-His vector .............................................. 1 90–193, 198
pET system ........................... 7 , 28, 29, 75, 78, 102, 105–107
Phosphorylation ................................................... 4 , 120, 179
Photobleaching ......................................................... 1 14, 153
PIDDosome ................................................................. 1 9, 71

Piperidine deprotection .................................... 4 6, 52, 53, 57

p LysS plasmid ................................................................. 7 , 28

P-nitroanilide (p-NA) ........................................ 7 6, 145, 159

Polymerase chain reaction (PCR) .............................. 9 4, 102,

190, 208

Poly(ADP ribose) polymerase (PARP) ........................ 2 2, 23,

121, 123, 125, 133, 134, 142, 144, 151,

158, 159, 162

Positional proteomics ........................................................2 56

Positional scanning substrate combinatorial library

(PS-SCL) ........................................... 4 1–58, 145

Programmed cell death (PCD) ................. 1 01, 110, 203, 224

Promoter .................................. 7 , 80, 105, 129, 190, 243, 251

Proteasomal degradation .......................................... 1 78, 179

Protein extraction .......................................7 5, 194, 197, 225,

227–228, 260

Protein topography and migration analysis platform

(PROTOMAP) ..........................................6 1–70

Proteostasis ............................................................... 2 23–235

Protozoan parasites ...........................................................1 89

ProtParam algorithm .................................................. 3 1, 220

Pseudo-first order conditions ....................................... 2 2, 35

Pseudopeptidase ...............................................................2 04

Q

Q-VD-OPh .................................................... 7 6, 79, 81, 170

R

Rabbit reticulocyte system .......................... 8 1, 103, 106, 129

Recombinant protease ......................................2 2, 23, 35, 73,

75, 79, 95, 102

Relative fluorescence units (RFU) ............................... 1 6, 17,

21, 34, 47–49, 54–57, 80

Reverse-phase chromatography (RP-HPLC) ..................2 57

RNA interference ..................................... 113, 158, 159, 172

Rosetta cells ...................................................... 2 05, 219, 243

S

Samarium acetate ............................................. 2 08, 213, 214

Schechter-Berger nomenclature ................................... 1 5, 24

Sedimentation assay ................................................. 2 25, 228

Seeding ..............................................2 05, 207–208, 219, 220

SEQUEST software ..................................................... 6 4, 66

Shotgun liquid chromatography-electrospray tandem

mass spectrometry (LC-MS/MS) .....................6 2

Size exclusion chromatography ........................ 2 06, 210, 219

Skin ...................................................................... 9 0, 97, 134

SlyD protein .......................................................................3 0

[^35 S] Methionine ................................................... 7 4, 77, 81,

103, 105, 106, 122, 130, 138, 242, 249, 250

Specific activity ........................................................... 7 3, 215

Spectral counting .......................................................... 6 2, 67

CASPASES, PARACASPASES, AND METACASPASES: METHODS AND PROTOCOLS

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