Analysis of the Peptides (Prp106-126, MSI-78A, and Oxaldie 1) with the Same Biological Activity by Discrete Fourier Transform: Toward a Selection Rule in Ligand-Receptor Interaction

Abstract

Here, we first report a novel method in which the "desired cross-spectrum" of the peptides Prp106-126, MSI-78A, and oxaldie 1 with the same biological activities is obtained by the multiplication of two cross-spectra derived from the RNA sequence and from the cognate amino acid sequence by discrete Fourier transform (DFT), respectively. Based on a well-known method reported previously, we investigated the cross-spectrum by the multiplication of two of three desired cross-spectra. As a result, we found that one prominent peak occurring in the three cross-spectra showed the same frequency when a binary scale was used as a parameter of nucleotide or amino acid in the analysis. Moreover, we examined the relationship between a binary scale and other physicochemical ones. Almost the same results could be reproduced when the absolute electronegativity scale (or the absolute hardness one) was used, but not in the case of the hydrophobic or electron-ion interacting potential scale reported previously. This indicates that either the absolute electronegativity scale (or the absolute hardness one) or a binary scale, or both is very useful in extracting the information desired for various proteins by the present method from the amino acid and the RNA sequence.

Prediction of Three-Independent Scales Endowed on Poliovirus Proteinase 2A Sequence

“…Based on these, both the same physicochemical scale and almost the same resonant frequency (f) value would be conserved in the same succession of a signal transduction process in a Poliovirus-infected cell. Furthermore, the 2A could play a trigger role to cause cancer, prion disease, bone disease, or speech and language disorder.Key words mitogen-activated protein kinase; Poliovirus 2A; apoptotic protein activating factor 1; fibroblast growth factor receptor; forkhead box P2; human DNA replicationWe have already developed a novel method by which a specific (simple and concerted) protein-protein (or DNA, RNA) interactions, [1][2][3][4][5][6] including active site of protein, 7) can be successfully elucidated from both amino acid (aa) and the corresponding RNA (or DNA) (na) sequence 2) with the sequence Fourier analysis (SFA). We defined it as the intermolecular frequency symmetry (IFS) rule.…”

“…2) In the rule, the average nuclear (N) scale, 1) the Garel's (G) relative hydropathy one, 2) the Lacey's relative hydropathy (H) one 3,4) or the Mulliken's absolute electronegativity (M) one, 5,6) is employed as the parameterization. Both the calculation process (see computational method and groups 9-12 described in ref.…”

“…We have already developed a novel method by which a specific (simple and concerted) protein-protein (or DNA, RNA) interactions, [1][2][3][4][5][6] including active site of protein, 7) can be successfully elucidated from both amino acid (aa) and the corresponding RNA (or DNA) (na) sequence 2) with the sequence Fourier analysis (SFA). We defined it as the intermolecular frequency symmetry (IFS) rule.…”

“…Both the calculation process (see computational method and groups 9-12 described in ref. 6) and the criteria to select the resonant peak between proteins (see a working procedure in ref. 5 and a definition condition described in ref.…”

“…Almost the same resonant f value would be conserved in the same succession of a signal transduction passway in a cell. 14,30) Furthermore, referred to the previous studies about the f value, [1][2][3][4][5][6] a pair of the f values can roughly be classified into three groups (i.e., fϭca. 0.20/0.30, ca.…”