• Proceedings of the Korean Society of Applied Pharmacology
• /
• 1994.04a
• /
• pp.267-267
• /
• 1994

In order to obtain insight into the mechanism by which DNA containing a thymine photo-dimer is recognized by the excision repair enzyme, T$_4$ endonuclease V, we have taken NMR study of this protein and its complex with oligonucleotides. The conformations of five different DNA duplexes DNA I : d(GCGGATGGCG).d(CGCCTACCGC), DNA II d(GCGGTTGGCG) .d(CGCCAACCGC), DNA III : d(GCGGT ^ TGGCG) .d(CGCCAACCGC), DNA IV d(GCGGGCGGCG).d(CGCCCGCCGC) and DNA V d(GCGGCCGGCG) . d(CGCCGGCCGC) were studied by $^1$H NMR. The NMR spectra of these five DNA duplexes in the absence of the enzyme clearly show that the formation of a thymine dimer within the DNA induces only a minor distortion in the structure, and that the overall structure of B type DNA is retained. The photo-dimer formation is found to cause a large change in chemical shifts at the GC7 base pair, which is located at the 3'-side of the thymine dimer, accompanied by the major conformational change at the thymine dimer site. The binding of a mutant T$_4$ endonuclease V (E23Q), which is unable to digest DNA containing a thymine dimer, to the DNA duplex d(GCGGT ^ TGGCG)ㆍd(CGCCAACCGC) causes a large down-field shift in the imino proton resonance of GC7. Therefore, this position is thought to be either the crucial point of the interaction wi th T$_4$ endonuclease V, or the si to of a conformational change in the DNA caused by the binding of T$_4$ endonuclease V. Usually, it is very difficult to assign NMR peaks in DNA * protein complex because of severe peak overlaps. In order to overcome these peak overlaps, we used a method of deuterium incorporation.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.19 no.7
• /
• pp.95-104
• /
• 2018

The structures and energies of the anhydrate and hydrate (hydrate rate: h of 1) states of L-alanine (LA) and glycine (G) were calculated by quantum chemical calculations (QCCs) using B3LYP/6-31G(d,p) for four types of conformers (${\beta}$-extended: ${\Phi}/{\Psi}=t-/t+$, $PP_{II}$: g-/t+, $PP_{II}$-like: g-/g+, and ${\alpha}$-helix: g-/g-). In LA and G, which have an imino proton (NH), three conformation types of ${\beta}$-extended, $PP_{II}$-like, and ${\alpha}$-helix were obtained, and water molecules were inserted mainly between the intra-molecular hydrogen bond of $CO{\cdots}HN$ in $PP_{II}$-like and ${\alpha}$-helix, and attached to the CO group in ${\beta}$-extended. In LA and G, $PP_{II}$-like conformers were most stable in the anhydrate and hydrate states, and the result for LA was different from some experimental and theoretical results from other studies reporting that the main stable conformation of alanine oligopeptide was $PP_{II}$. The formation pattern and stability of the conformation of the oligopeptide was strongly dominated by the presence/absence of intra-molecular hydrogen bonding of $CO{\cdots}HN$, or the presence/absence of an $NH_2$ group in the starting amino acid.