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.