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.
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.
Numao
Naganori
N
BioFrontier Institute Inc., Sagamihara, Kanagawa, Japan. numao-n@sssc.co.jp
Fujii
Hisashi
H
Fukazawa
Yoshiyuki
Y
Yoshioka
Ken
K
Okada
Mayumi
M
Tanaka
Kazuyoshi
K
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry*; D015195:Drug Design; D005583:Fourier Analysis; D008024:Ligands; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011328:Prions / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry; D011955:Receptors, Drug / Q000737:chemistry / Q000187:drug effects; D013329:Structure-Activity Relationship
D000596:Amino Acids; D023181:Antimicrobial Cationic Peptides; D008024:Ligands; D009696:Nucleic Acids; D010446:Peptide Fragments; D010455:Peptides; D011328:Prions; D012333:RNA, Messenger; D011955:Receptors, Drug; C083607:oxaldie 1; C082632:prion protein (106-126); C093828:pexiganan