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Table 2

Relative Cleavage Efficiencies Determine Ratio of Substrate Fragments Generated In Vivo

Autoantigenkcat/Km (M−1.s−1) for cleavageProminent fragment type generated in:
Caspase-3Granzyme BLAK/K562 system
Topoisomerase-I 3.4 × 104 1.6 × 106 Granzyme B 
DNA-PKcs 7.5 × 106 2.5 × 106 Granzyme B/caspase-3 
Mi-2 2.0 × 105 8.5 × 104 Granzyme B/caspase-3 
U1-70kD 2.5 × 106 1.3 × 104 Caspase-3 
PARP 5.0 × 106 2.3 × 104 Caspase-3 
Autoantigenkcat/Km (M−1.s−1) for cleavageProminent fragment type generated in:
Caspase-3Granzyme BLAK/K562 system
Topoisomerase-I 3.4 × 104 1.6 × 106 Granzyme B 
DNA-PKcs 7.5 × 106 2.5 × 106 Granzyme B/caspase-3 
Mi-2 2.0 × 105 8.5 × 104 Granzyme B/caspase-3 
U1-70kD 2.5 × 106 1.3 × 104 Caspase-3 
PARP 5.0 × 106 2.3 × 104 Caspase-3 

Autoantigens that are cleaved by granzyme B with similar or greater efficiency than by caspase-3 give rise to prominent granzyme B fragments in the LAK/K562 system. In this system, granzyme B fragments are not observed when substrates are cleaved less efficiently by granzyme B than by caspase-3, unless caspases are inhibited (see Fig. 6). kcat/Km values for caspase-3 cleavage of DNA-PKcs, PARP, and U1-70kD are from reference 23, and values for granzyme B cleavage of DNA-PKcs and PARP are from reference 21. The remaining kcat/Km values were calculated as described in Materials and Methods.

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