Application of Sequence Fourier Analysis to a Specific Interaction in Arabidopsis thaliana

Abstract

The sequence Fourier analysis reported previously seems to be applicable to elucidating a simple and concerted interaction in Arabidopsis thaliana, similar to that in Homo sapiens.Key words sequence Fourier analysis; MAP kinase cascade; Homo sapiens; Arabidopsis thaliana; hydrophobic scaleWe have recently reported a novel sequence Fourier analysis (SFA) for effective elucidation of a simple and concerted interaction between mainly human proteins using both the mRNA and the cognate amino acid sequence.1-3) Based on the analytical results, two kinds of physicochemical scales, i.e., the Milliken's absolute electronegativity one (M scale) 2) and the Lacey's hydrophobic one (H scale), 1) seem to be independently conserved in a specific interaction, though their difference has to be determined. Based on this, we had a great interest in examining a similar specific interaction in MAP kinase cascade [4][5][6][7] of Homo sapiens and Arabidopsis thaliana. Because the cascade is evolutionary conserved from unicellular to eukaryote organisms.First, in H. sapiens cascade we examined a specific interaction between one of three kinds of ser/thr protein kinases, 8,9) that is, extracellular signal-regulated kinase 1 (ERK1; 379aa), 10) c-Jun N-terminal kinase 1 (JNK1; 427aa) or p38 MAPKs (a: 360aa, b: 372aa, g: 367aa, d: 365aa)], and oncogene ELK1 (428aa) as the binding partner. The former acts downstream of the MAP cascade when the cell is exposed to various external stimuli (or stress). The ELK1 is a transcription factor. In other step of the cascade, a third component such a scaffolding/adapter (i.e., MP1 or JIP1) protein has been involved in a signal transduction.Under the condition of the H scale 1) and the same criteria, 2) one (fϭ0.2021) of two characteristic peaks ( Fig. 1a; fϭ0.2021, 0.3081) derived from the desired cross-spectrum of ERK1 almost overlapped with a characteristic peak (Fig. 2: fϭ0.1963) from ELK1. By the way, we also examined the relationship between ERK2 (360aa) and ELK1. It is because ERK2 is ca. 90% identical sequence to ERK1. 11) Differing from ERK1, however, ERK2 expressed a characteristic peak ( Fig. 1b; fϭ0.3296), which is almost overlapped with one (fϭ0.3267) of two peaks ( Fig. 2; fϭ0.1763, 0.3267) from ELK1. Note the difference between the characteristic peak position (Fig. 1b; fϭ0.3296) derived from ERK2 and that ( Fig. 1a; fϭ0.2021) from ERK1. It is reason why the two major peaks (Fig. 1b; fϭ0.2021, 0.3081) expressed in the sense amino acid sequence of ERK2 do not exist in its antisense one (Fig. not shown).Furthermore, a characteristic peak was observed in between JNK1 (Fig. 1c; fϭ0.1963, 0.3052) and ELK1 (fϭ0.1963), and not between any one of p38 analogs (a, b, g, d) and ELK1 (data not shown). The homology degree (ca. 65%) of amino acid sequence between JNK1 and ERK1 is almost the same as that (ca. 68%) between JNK1 and ERK2.12) On the other hand, no specific interaction between any ser/thr protein kinase and the binding partner ELK1 could be observed with the M scale.In A. thaliana, based ...

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.…”

“…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.…”

“…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.…”

“…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.…”

A Fourth Scale Sensitive to the Magnetic Field; Intermolecular Frequency Symmetry in a Specific Interaction between Protein and Low-Molecular Compound

“…We had already reported a method that a specific protein-protein (or DNA, RNA) interaction can be successfully elucidated from both amino acid (aa) sequence and the corresponding RNA (na) one with a sequence Fourier analysis, [1][2][3][4][5] on which some of the Mulliken's absolute electronegativity (M) scale (row 1a in Table 1), 4,5) the Lacey's relative hydropathy (H) one (row 2 in Table 1) 1,3) or the Garel's (G) one (row 3 in Table1), 1) is assigned as a parameterization. Both the calculation process 5) and the criteria (including two kinds of symmetry operation) 1,4) had been already reported.…”