Table III.

Probable and putative caspase substrate sites in proteins identified by LC/MS/MS

Probable Csp6 sites are identified as (I/D/E/L/T/V)(E/D/Q)XD based on combinatorial chemistry (43, 44). Because of the identification of unusual Csp6 substrate sites (see Table IV), we also added putative VXXD or XEXD sites. The accession numbers of the sequence used for the analyses are listed in the right-hand column. Bold indicates sites that were already defined as Caspase-6 substrate sites in other proteins.

Protein	VXXD or XEXD	(I/D/E/L/T/V)(D/E/Q)XD	GenBank no.
Cytoskeleton and cytoskeleton-associated
Drebrin 1 isoform a	86VGED89, 626PEID629	122EDID125, 453IETD456	AAH00283
β-Actin	212VALD215, 360QEYD363		AAH08633
Spinophilin	386SEAD389, 615GEDD618	197LDAD200, 375EEVD378, 408LEED411, 409EEDD412, 411DDED414, 412DEDD415, 415DEED418, 437EEED440, 463EDYD466, 470EDVD473, 497LEKD500, 548VEVD551, 626TDED629, 790EEMD793	NP_115984
α-Actinin-1	15PEED18, 440FESD443, 462NELD465, 888GESD891	17EDWD20, 55IEED58, 481DQWD484, 688LEGD691	AAP35871
α-Actinin-4	34QEDD37, 459FESD462, 481NELD484, 907GESD910	36DDWD39, 74IDED77, 210IEYD213, 500DQWD503, 801VEND804, 840TDTD843	NP_004915
Capping protein α	32VFND35, 111EEAD114		AAH00144
Ezrin	228YEKD231	389LEAD392	NP_003370
Cofilin I	14VFND17		NP_005498
Glial fibrillary acidic protein	174QEAD177	139VERD142, 222VELD225	AAH41765
α-Tubulin	66VFVD69, 303VKCD306, 324VPKD327, 435VGVD438	30IQPD33, 428LEKD331	AAD33871
Signaling
14-3-3ζ	276AELD279	307TQGD310	AAH51814
14-3-3ε	204AELD207		BAA32538
Inhibitor-2 of protein phosphatase 2A	207VIKD210, 40NEID43, 97GEED100, 232GEED235, 257GEED260, 269GEED272, 274GEDD 277	233EEDD236, 234EDDD237, 235DDDD238, 236DDDD239, 246EDID249, 250EEGD253, 259EDED262, 260DEDD263, 261EDDD264	AAQ79833
Chaperones
Hsp90α	172VRTD175, 230VSDD233, 262VGSD265, 224KERD227, 650AEAK653	698IDED701, 699DEDD702, 719LEGD722, 729EEVD732	NP_005339
Heat shock protein gp96 precursor	19VRAD22, 232VIAD235, 496VIED499, 596VKFD599, 784VGTD787, 223WESD226, 364KESD367, 581PEFD584, 798AEKD801	23DEVD26, 25VDVD28, 31VEED34, 259LELD262, 304EESD307, 350VEED353, 437VDSD440, 703EDED706, 704DEDD707, 749IDPD752, 774TEQD777, 780EEMD783	NP_003290
Valosin-containing protein	70VLSD74, 176VAPD179, 201VGYD204, 407VGAD410, 447VTMD450, 666VAKD669, 365REVD368	166VETD169, 304DELD307, 392DDVD395, 577DELD580, 606TEMD609, 722VEED725, 723EEDD726, 798EDND801	CAH70993
Protein synthesis and conjugation
Eukaryotic elongation factor 1γ	61FEGD64	102VDSD105, 261EEMD264	AAH13918
Metabolism
Inorganic pyrophosphatase	276VPTD279, 150GETD153	162DDPD165, 278TDVD281	AAP97214
Glyceraldehyde-3-phosphate dehydrogenase	163VIHD166, 282VSSD285, 78QERD81, 222PELD225		CAA25833
Proteases
Neurolysin (EC 3.4.24.16)	112VSSD115, 207NEDD210, 350FEYD353	123TEAD125, 234TDDD237, 520VETD523	CAC27329
Prolyl endopeptidase (prolyl oligopeptidase, EC 3.4.21.26)	9VYRD12, 112VFLD115, 288GEYD291, 333HEKD336, 623PEAD626	32EDPD35	BA A04661
Membrane and lipid binding
Rab GDP dissociation factor inhibitor α	151YEND154	3EEYD6, 413TEND416	BAA08078
Chain A, crystal structure of brain fatty acid-binding protein oleic acid	84VSLD87, 44QEGD47	68EEFD71, 86LDGD89	IFE3_A
Annexin V	141VVGD144, 277SEID280, 317GEDD320	137LEDD140, 172VEQD175	AAH01429