Table II Comparison of Surface Accessibility to Percent Reactivity for PARP-1 Domain C reacted with NN in a 1:5 molar ratio protein/NN. Surface accessibility for shortened structure was calculated using GetArea for pdb 2JVN and for the full native structure based on the top five structures predicted by ITASSER (IT1-IT5). Percent reactivity was calculated using equation 1. The bold box highlights the best model structure correlating with percent reactivity. β€œNA” indicates a peptide that was not found in either its modified or unmodified form. Standard deviations ranged from 10–20% for all percent reactivities
ResidueSurface accessibility %% Reactivity
ShortenedIT1IT2IT3IT4IT5TrypticGluCArgC
GLY 1–7690100727995100100
LYS 41008778917688938595
LYS 781707971759142385
LYS 1085766364717731010
LYS 202116202930101909
LYS 246556483770401900
LYS 25655562575856000
LYS 33493533343456000
LYS 409376878577821718
LYS 769562454548620NA7
LYS 91546755636745000
LYS 95745036424144000
LYS 1026569666352378800
LYS 108706792847471516535
LYS 1172537424237134200
LYS 1188846504655624310098
LYS 1202541535052262000
LYS 122438483747653000
LYS 12310084838480543600