PFVM for P53 protein
The protein of Human Cellular tumor antigen p53(P53_HUMAN)is another sample to illustrate how the local folding variations in PFVM correlate with the order of amino acid along sequence. The p53 involves many mechanisms for anticancer functions and plays a role in apoptosis, genomic stability, and inhibition of angiogenesis. The human TP53 gene encodes 9 of protein isoforms11Surget S, Khoury MP, Bourdon JC, ”Uncovering the role of p53 splice variants in human malignancy: a clinical perspective”. OncoTargets and Therapy. 7: 57–68, (2013)., and the canonical sequence of isoform p53-alpha with 393 amino acids is available in UniProt database. According the sequence, the PFVM of P53_HUMAN protein is obtained and shown in Table 3. Although the protein of p53-alpha for human has 393 amino acids in sequence, the PFVM of p53-alpha was acquired within one minute using a personal computer. First, the PFVM directly displayed the fluctuation of local folding variations along the sequence. For examples, some sets of 5 successive amino acids have only one folding shape representing with one PFSC letter in PFVM, such as fragments in sequence of “DEAPR” (61-65), “EAPRM” (62-66), “APSWP” (88-92), “PSWPL” (89-93), “NKMFC” (131-135) and “KMFCQ” (132-136) etc. Some sets of 5 successive amino acids have more folding shapes representing with higher number of PFSC letters in PFVM, such as “PLSQE” (13-17) has 14 folding shapes; “SDGLA” (185-189) has 13; “SSGNL” (260-264) 15 and “SKKGQ” (371-375) 16 etc. Second, the pattern of folding variations of P53_HUMAN in PFVM showed many regions agree with the disorder determined by PDB which is displayed on the bottom of Table 3. For examples, regions of 20-25, 124-136, 230-241 and 332-347 have less variations and disorder. However, the PFVM may exposed the folding variations more detail. Third, all possible conformations for the p53-alpha protein can be constructed by various combinations with taking one PFSC letter from each column in PFVM. Actually, with PFVM, an astronomical number of folding conformations for the p53-alpha protein can be constructed and represented by 2.008x10270 of PFSC strings. It showed that the astronomical number of all possible conformations for p53-alpha protein were not vague anymore because the number can be explicitly calculated based on PFVM.