Table 2.
Solvent accessible area alterations of amino acid residue and its active environment before and after modification (mounting of PTM) in breast and ovarian cancer-specific proteins.
| Gene (Protein name) | Sequence of peptide carrying PTM | Secondary structure localization | PDB structures | Average area accessible to the solvent, Å2 | Helices | Motives | |||
|---|---|---|---|---|---|---|---|---|---|
| Amino acid | Active environment | ||||||||
| Intact | PTM | Intact | PTM | ||||||
| Ovarian cancer | |||||||||
| A1AT (Alpha-1-antitrypsin) | ac(K)-QINDYVEK | Helix | 35 | 119,99 | 167,54 | 335,14 | 364,17 | 4 | 1 |
| TDTSHHDQDHPTFN-ac(K)-ITPNLAEFAFSLYR | Connection | 23 | 109,78 | 153,36 | 346,66 | 377,32 | |||
| ALBU (Albumin) | EQL-ac(K)-AVMDDFAAFVEK | Helix | 156 | 113,03 | 135,71 | 441,31 | 431,30 | 30 | 4 |
| ac(k)-VPQVSTPTLVEVSR | helix | 172 | 21,5 | 37,29 | 320,08 | 312,11 | 3 | ||
| NYAEa-ac(K)-DVFLGMFLYEYAR | Connection | 162 | 82,02 | 108,97 | 294,16 | 305,17 | 3 | ||
| RHPYF-p(Y)-APELLFFAK | Helix | 163 | 22,49 | 31,01 | 165,83 | 154,03 | 3 | ||
| VFDEF-ac(K)-PLVEEPQNLIK | Helix | 162 | 131,78 | 179,83 | 278,90 | 316,22 | 2 | ||
| APOA2 (Apolipoprotein A-II) | EPCVE-p(S)-LVSQYFQTVTDYGK | Helix | 56 | 69,47 | 101,31 | 498,39 | 501,38 | 4 | n/d* |
| CO3 (Complement C3) | YF-ac(k)-PGMPFDLMVFVTNPDGSPAYR | Helix | 51 | 13,86 | 16,87 | 134,78 | 110,5 | 1 | n/d |
| HV307 (Ig heavy chain V-III) | DDS-ac(K)-NTLYLQMNSLR | Connection | 2 | 126,05 | 177,7 | 316 | 349,85 | 0 | 0 |
| IGHA1 (Ig alpha-1 chain) | SGNTFRPEVHLLPPP-p(S)-EELALNELVTLTCLAR | Helix | 34 | 103,55 | 168,88 | 318,55 | 361,30 | 3 | 1 |
| Breast cancer | |||||||||
| ALBU (Albumin) | NYAEA-ac(K)-DVFLGMFLYEYA | Helix | 162 | 82,02 | 108,97 | 294,16 | 305,17 | 30 | 3 |
| EQL-ac(K)-AVMDDFAAFVEK | Helix | 156 | 113,03 | 135,71 | 441,31 | 431,30 | 4 | ||
| APOA1 (Apolipoprotein A-I) | QLNL ac(K)-LLDNWDSVTSTFSK | Helix | 6 | 136,75 | 184,78 | 317,5 | 348,78 | 8 | n/d |
| TRFE (Serotransferrin) | ac(K)-SASDLTWDNLK | Helix | 32 | 111,32 | 155,53 | 322,75 | 349,13 | 22 | 12 |
| MDA-ac(K)-MYLGYEYVTAIR | Connection | 72 | 64,48 | 104,60 | 260,24 | 279,48 | 22 | 12 | |
Bold values indicate the exact affected (modified) amino acid residue to attract readers' attention and for easier navigation.
n/d* – motives with interacting helices are not found; PDB structures – the number of PDB structures matching the target polypeptide chain; PTM SEQQ – amino acid sequence of polypeptide chain carrying the detected and identified PTM.