The Molecular Recognition Mechanism of Nucleic Acid Structure by Beta-Turn Motif of Protein

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To date there are four different recognition motifs of DNA base sequence by protein, helix-turn-helix, beta-sheet, Zn-finger and leucin zipper. By Suzuki M., a quite new mode is expected in sea urchin spermatogenic histones. H1 and H2B. The DNA-binding arms are composed of repeats of Ser-Pro-Lys (Arg)-Lys (Arg) residues. From amino acid sequence, this region may adopt the beta-turn structure, so this offers the novel recognition mechanism. X-ray structure analysis determines the molecular structure at atomic level of this complex formation.(1) Four oligopeptide fragments containing this tandem amino acid sequence were chemically synthe-sized, which correspond to the N-terminal region of H1 of P. angulosus. Several oligonucleotides which have adenine (-tymine) track at the central region in molecule were also chemically synthesized. Several crystallizations of complex by using these compounds have been done, but to date no suitable crystal for X-ray analysis has been obtained. A series of investigations about complex formation in solution are necessary.(2) The complex structure of antibiotic Chromomycin and DNA oligomer was determined based on NMR spectra and computer graphics system. This model offers the recognition mechanism of DNA base sequence by drug which is quite novel motif, a widely spread hydrophobic surface interaction.(3) A computer program of calculating and drawing the structural parameters for DNA-protein complex was developed and is suitable to characterize the complex interaction.