Figure 2. Acquirement of Protein Folding Variation Matrix (PFVM). The
sequence is listed at the top horizontally. Then PFSC letters with color
in column, which represent local folding shapes of 5 consecutive amino
acids along sequences, are directly extracted from 5AAPFSC database.
Starting from N-terminus, each step moves forward by one residue sharing
4 amino acids next each other. The PFSC letters for each 5 successive
amino acids are vertically aligned down under the center of 5 amino
acids. 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.
All possible folding conformations.
Astronomical number of folding conformations for a protein can be
constructed by the local folding variations in PFVM. To take one PFSC
letter from each column in the PFVM is able to form one PFSC string,
which is corresponding to one folding conformation. With fully using all
of local folding variations from each column, all possible folding
conformations will be constructed. Thus, the PFVM is one of the best
optimized approach to stores all folding information for entire protein.
The actual number of all possible folding conformations is able to be
figured out. Under PFSC scheme, an astronomical number of all possible
folding conformations for a protein is the product by multiplying the
numbers of PFSC letters of each columns in PFVM.
\(\text{Number\ of\ All\ Possible\ Conformations\ }=\ \prod_{i=1}^{n}{m(i)}=m\left(1\right)*m\left(2\right)*m\left(3\right)\ldots m(n)\)
Where n is the number of columns in PFVM matrix andm (i ) is the number of PFSC letters in column i .
RESULTS
PFVM Assembling Local Folding Variations.
Based on protein sequence, the local folding variations of 5 successive
amino acids can be directly obtained and exhibited in the PFVM. All PFSC
letters for any 5 amino acids are extracted from the 5AAPFSC database,
and vertically aligned down under the center of corresponding 5 amino
acids. The order of PFSC letters in each vertical column is ranked
according to the probability of occurrence from higher to lower and the
free energy from lower to higher. Thus, the local folding variations for
an entire protein can be meaningfully displayed in PFVM. Two of human
proteins, small ubiquitin-related modifier 1(SUMO1)and cellular tumor
antigen p53 (P53), are taken as examples, and their PFVM will be
acquired according the sequences respectively.