Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex (W-TGCGCAC)(2).
Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex (W-TGCGCAC)(2).
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氨酰基封端的寡脱氧核糖核苷酸双链体 (W-TGCGCAC) 的溶液结构(2)。
DOI：
10.1021/bi991169w
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发表时间：
1999
期刊：
影响因子：
2.9
通讯作者：
Richert,C
中科院分区：
文献类型：
--
作者：
Ho,WC;Steinbeck,C;Richert,C
这里报告的是氨酰-DNA双链体（W-TGCGCAC）2的溶液结构。该双链体形成由核碱基和氨基酸侧链组成的连续π堆叠螺旋。根据NMR和UV分析，该双链体在合作转变中熔化，并且具有比对照双链体（TGCGCAC）2高1.3 - 1.8%的增色性。在不同浓度下UV熔点的van 't霍夫分析表明，在10 mM盐浓度下，两个色氨酸残基对复合物形成的ΔH°贡献4.8 kcal/mol，在150 mM盐浓度下小于1 kcal/mol。在10 mM盐浓度下，存在氨基酸残基时双链缔合的熵成本比对照高13卡/摩尔K，在0.15离子强度下比对照低3卡/摩尔K。通过限制扭转角分子动力学确定的双链体形式的W-TGCGCAC的构象显示出不受干扰的B型DNA双链体，具有悬挂的3 '末端。在5 '端的双羟基残基紧密地包裹在T2和腺嘌呤的近端部分上，而不参与氢键。虽然没有提供双链体的强的疏水净稳定性，但双链体上的色氨酸“帽”似乎确实减少了末端的磨损，表明有助于分子动力学的熵和疏水因子的微妙平衡。该结构还表明，至少在目前的序列背景下，在末端碱基对上的堆积比嵌入更有利，这可能是因为与破坏DNA碱基对之间的堆积相关的生物学成本不能通过与色氨酸的吲哚环的有利π堆积相互作用来支付。这些结果对于理解蛋白质-DNA复合物中的堆积相互作用，特别是涉及暴露的核碱基的酶-底物复合物中的堆积相互作用具有重要意义。
Reported here is the solution structure of the aminoacyl-DNA duplex (W-TGCGCAC)2. This duplex forms a continuously π-stacked helix consisting of both nucleobases and amino acid side chains. According to NMR and UV analyses, the duplex melts in a cooperative transition and with 1.3−1.8% greater hyperchromicity than the control duplex (TGCGCAC)2. A van't Hoff analysis of UV melting points at different concentrations shows that the two tryptophan residues contribute 4.8 kcal/mol to the ΔH° of complex formation at 10 mM salt concentration and less than 1 kcal/mol at 150 mM salt. The entropic cost for duplex association in the presence of the amino acid residues is 13 cal/molK greater than that for the control at 10 mM salt concentration, and 3 cal/molK lower than that of the control at 0.15 ionic strength. The conformation of W-TGCGCAC in duplex form, determined via restrained torsion angle molecular dynamics, shows an undisturbed B-form DNA duplex with dangling 3‘-termini. The tryptophanyl residue at the 5‘-terminus packs tightly against T2 and the proximal part of adenine, without engaging in hydrogen bonding. While not providing strong enthalpic net stabilization of the duplex, the tryptophan “cap” on the duplex does seem to reduce the fraying at the termini, indicating a subtle balance of entropic and enthalpic factors contributing to the molecular dynamics. The structure also shows that, at least in the present sequence context, stacking on the terminal base pair is more favorable than intercalation, probably because the enthalpic cost associated with breaking up the stacking between DNA base pairs cannot be paid for by favorable π-stacking interactions with the indole ring of tryptophan. These results are of importance for understanding stacking interactions in protein−DNA complexes, particularly those in enzyme−substrate complexes involving exposed nucleobases.