P53 known 3D structure conformations covered by PFVM
Many P53_HUMAN structures are available in PDB from X-ray crystallization measurements. Twelve of protein 3D structures of P53 (4AGP, 2YBG, 2XWR, 2X0U, 2J1X, 2J1Y, 2FEJ, 2BIN, 3D05, 3D06, 3ZME and 5LAP) are displayed in Figure 4. The PSCF strings as folding conformations are obtained directly according 3D structures of regions (101-200) in sequence of 12 given P53 structures, and are aligned and displayed on the top section of Table 6. Also, the PFVM as local folding variations is obtained according merely the sequence (101-200) of P53 and 5AAPFSC database, and is displayed on the bottom section.
The PFVM is able to cover all conformations of given 3D structures of P53 protein. In order to verify what types of local folding shapes occur in these given P53 structures, all PFSC letters in 2YBG are first highlighted by yellow as starting point in Table 6, and then the PFSC letters for other 3D structures are checked down each column against 2YBG. If the PFSC letters are not covered by 2YBG, the letters will be highlighted by yellow. Thus, all local folding variations existing in these given structures are shown by yellow. Furthermore, to find out whether the folding conformations of 12 given structures are enclosed by PFVM, the PFSC letters in each column in PFVM are marked by yellow if the PFSC letter in same column appears in given 12 structures. Therefore, it is easy to observe the local folding conformations of 12 given structures are indeed enclosed by PFVM. For examples, the PFVM in column 104 provides 8 types of folding shapes (B, V, U, E, Y, C, A and W) covering the folds of “B” and “V” in the given structures; the PFVM in column 105 provides 4 types of folding shapes (W, A, Y and P) covering the folds of “W” and “A” in the given structures; the PFVM in column 120 provides 11 types of folding shapes (Y, A, V, P, Z, E, J, $, B, D and R) covering the folds of “Y” and “Z” in the given structures; the PFVM in column 139 provides 7 types of folding shapes (W, P, A, S, B, V and J) covering the folds of “P” and “W” in the given structures; the PFVM in column 199 provides 6 types of folding shapes (A, J, Y, C, P and S) covering the folds of “A”, “Y” and “J” in the given structures and etc. In conclusion, the PFVM is able to cover the local folding shapes of 12 given 3D structures for P53 protein, and the PFVM reserves far more local folding variations for P53 protein in other environments.
The PFVM provides the information to predict the possible fording conformation for protein. Despite a massive number of folding conformations for P53 protein can be generated with the combination of various PFSC letters in PFVM, the PFSC string at the first row in PFVM, which is named as PFVM-01, represents one of the most possible conformations for P53 protein. The PFVM-01 can be compared with the conformations of 12 given 3D structures in Table 6. Overall, with observation in color, the secondary structure fragments of PFVM-01 conformation are well aligned with all 12 conformations of given 3D structures of P53 protein. Also, 99 among 100 PFSC letters in the PFVM-01 conformation appear in the 12 given 3D conformations of P53 protein. Therefore, the PFSC string in the first row of PFVM provides one of best conformations for P53 protein prediction.