Table 1.
Protein structural determinants of lysine succinylation
| Parameter | Value non-Ksucc (n = 7044) | Value Ksucc (n = 1908) |
Value Ksucc (mt) (n = 1331) |
p-value Ksucc | p-value Ksucc (mt) |
|---|---|---|---|---|---|
| Surface accessibility (relative) | 0.516076 | 0.524961 | 0.521774 | 2.27E-02 | 2.00E-01 |
| Helix (q3) | 0.445350 | 0.521543 | 0.507872 | 2.25E-11 | 2.95E-06 |
| Sheet (q3) | 0.114046 | 0.106577 | 0.117029 | 2.62E-01 | 7.07E-01 |
| Coil (q3) | 0.440603 | 0.371880 | 0.375099 | 1.63E-11 | 3.88E-08 |
| 310 helix (q8) | 0.038865 | 0.035246 | 0.035238 | 1.56E-01 | 2.37E-01 |
| α-helix (q8) | 0.404213 | 0.485332 | 0.472161 | 1.90E-12 | 4.73E-07 |
| π-helix (q8) | 0.003918 | 0.003664 | 0.003419 | 7.18E-01 | 5.73E-01 |
| β-bridge (q8) | 0.006241 | 0.006129 | 0.006593 | 8.32E-01 | 5.94E-01 |
| Extended strand (q8) | 0.107690 | 0.099686 | 0.109870 | 2.21E-01 | 7.80E-01 |
| Bend (q8) | 0.067766 | 0.070762 | 0.072459 | 4.00E-01 | 2.61E-01 |
| H-bonded turn (q8) | 0.099616 | 0.094841 | 0.097013 | 2.99E-01 | 6.38E-01 |
| Coil (q8) | 0.271690 | 0.204339 | 0.203246 | 9.54E-18 | 3.86E-14 |
| ϕ angle | −78.512599 | −77.455463 | −77.554781 | 8.26E-02 | 1.87E-01 |
| ψ angle | 26.115213 | 17.358207 | 20.789474 | 6.22E-06 | 1.97E-02 |
| Disorder | 0.125166 | 0.059944 | 0.055479 | 1.18E-36 | 4.30E-33 |
NetSurfP-2.0 was used to predict a probability value (or angular value) for each lysine within all proteins with at least one Ksucc site identified in this study. The average values for all lysines that were not found to be succinylated (value non-Ksucc) were compared with the average values for all lysines that were found to be succinylated (value Ksucc) and to all lysines that were found to be succinylated in the mature forms of the proteins (i.e., without the MTS, which were predicted using TargetP-2.0 (value Ksucc (mt))). p-values are listed. A significance threshold of p < 0.05 was used, and statistically significant categories are in bold. Surface accessibility was statistically significant in the “Ksucc” category only.