On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules.
On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules.
复制标题
关于氨基氮原子作为大分子氢键受体的潜在作用。
DOI：
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发表时间：
1998
影响因子：
5.6
通讯作者：
Z. Shakked
中科院分区：
文献类型：
--
作者：
B. Luisi;M. Orozco;J. Šponer;F. Luque;Z. Shakked
双链 DNA 的晶体学研究表明，相对的环外氨基可能形成紧密的 NH⋯:N 接触。为了研究这种相互作用的本质，我们检查了小分子、高分辨率晶体结构的数据库，以获取此类非常规相互作用的更准确的例子。我们发现鸟嘌呤和腺嘌呤碱基中的氨基接受来自常规供体（例如氨基或羟基）的氢键。更常见的是，嘌呤氨基与带正电的 C-H 基团紧密接触。对核酸结构数据库的搜索也产生了几个例子，其中嘌呤氨基与大分子中的氢键供体接触。从头计算表明，当氨基从所有原子与基底共面的常规几何形状转变为氢原子位于平面外且氮位于金字塔顶点的几何形状时，氢-氨基接触得到了显着改善，导致氨基极化。结合的结构和理论数据表明，氨基是柔性的，并且可以适应紧密接触，因为由此产生的极化允许正电原子比其传统范德华半径预期更接近氨基氮。氨基的灵活性可能允许特定的DNA构象，加强氢-氨基接触以优化有利的堆积相互作用，并且它可能在核苷的识别中发挥作用。我们推测，大分子中的氨基在特殊情况下可以接受氢键，并且这种能力可能在脱氨或氨基转移等催化过程中发挥机械作用。
Crystallographic studies of duplex DNA have indicated that opposing exocyclic amino groups may form close NH⋯:N contacts. To study the nature of such interactions, we have examined the database of small molecule, high-resolution crystal structures for more accurate examples of this type of unconventional interaction. We have found cases where the amino groups in guanine and adenine bases accept hydrogen bonds from conventional donors, such as amino or hydroxyl groups. More frequently, the purine amino group was found to contact closely electropositive C-H groups. Searches of the nucleic acid structural databases also yielded several examples where the purine amino group is contacted by hydrogen bond donors in macromolecules. Ab initio calculations indicate that the hydrogen-amino contact is improved energetically when the amino group moves from the conventional geometry, where all atoms are co-planar with the base, to one in which the hydrogen atoms lie out of the plane and the nitrogen is at the apex of a pyramid, resulting in polarization of the amino group. The combined structural and theoretical data suggest that the amino group is flexible, and can accommodate close contacts, because the resulting polarization permits electropositive atoms to approach the amino group nitrogen more closely than expected for their conventional van der Waals radii. The flexibility of the amino group may permit particular DNA conformations that enforce hydrogen-amino contacts to optimize favorable stacking interactions, and it may play a role in the recognition of nucleosides. We speculate that the amino group can accept hydrogen bonds under special circumstances in macromolecules, and that this ability might play a mechanistic role in catalytic processes such as deamination or amino transfer.
DOI：
10.1073/pnas.90.16.7523
发表时间：
1993-08-15
影响因子：
11.1
作者：
KIM, JJP;WANG, M;PASCHKE, R
通讯作者：
PASCHKE, R
影响因子：
13.8
作者：
M. Wahl;M. Sundaralingam
通讯作者：
M. Wahl;M. Sundaralingam
影响因子：
5.6
作者：
Juo, ZS;Chiu, TK;Dickerson, RE
通讯作者：
Dickerson, RE