Table 6. The PFVM of P53_HUMAN embracing folding conformations of known 3D structures. Top section: the sequence (101-200) of P53_HUMAN protein with numeric ruler. Middle section: the PSCF strings for 12 known 3D structures of P53_HUMAN which are available in PDB: 2YBG, 4AGP, 2XWR, 2X0U, 2J1X, 2J1Y, 2FEJ, 2BIM, 3D05, 3D06, 3ZME and 5LAP. All PFSC letters for 2YBG is first marked by yellow color. Other PFSC letters in same column for these given 3D structures are marked by yellow color if they differ from 2YBG. Some pieces of missed fragments without atomic coordinate data in structure database in PDB are indicated by dots. Bottom section: the PFVM of P53_HUMAN protein. The PFSC letters in each column in PFVM are highlighted by yellow color if the corresponding local folding shapes for 5 successive amino acids in given 3D structures are yellow. The PFSC letters are marked by colors: red is for typical helix fold; blue for typical beta fold; pink and light blue for folds with partial helix or beta; black for irregular folds.
Astronomical Number of Conformations
The number of total conformations for a protein can be figured out according the aggregation of local folding variations in the PFVM. Generally known, total number of possible folding conformations for protein is large, but the so called astronomical number of conformations for any protein is blurred. However, with PFVM, the number of total conformations for a protein can be explicitly calculated based on the PFVM because total number of conformations for a protein is the product of numbers of PFSC letters at each column in PFVM. The total numbers of all possible conformations for ten proteins as samples are listed in Table 7. These samples represent a wider variety of proteins and the lengths of sequences with a range from 101 to 1,382 of amino acids. The results show that the total numbers of possible conformations for these proteins are large which have a scope from 1077 to 10784. Two proteins among these samples, PDCD1_MOUSE and PDCD1_HUMAN, belong to same gene code PDCD1 with equal length of sequence, but they are respectively for human and mouse species. Despite both proteins having the equal length of sequence of 288 amino acids, the alignment revealed 172 of amino acids identical (about 60%) between two protein sequences. According PFVM of both proteins, total numbers of conformations respectively are 3.028x10151 and 2.827x10147 because of the protein differentiation in sequence for different organisms. The results demonstrated that the total number of conformations of protein related to the length of sequence as well as the composition of amino acids in sequence. In summary, based on protein sequence, the PFVM does not only expose the comprehensive local folding variations and predicted the most possible conformations, but also provided the actual number of total conformations for a protein.