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首页> 外文期刊>Biochemistry >Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water
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Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water

机译：用肽骨架和谷氨酰胺和水中天冬酰胺侧链的模型化合物定量核碱基原子的相互作用

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摘要

Alkylureas display hydrocarbon and amide groups, the primary functional groups of proteins. To obtain the thermodynamic information that is needed to analyze interactions of amides and proteins with nucleobases and nucleic acids, we quantify preferential interactions of alkylureas with nucleobases differing in the amount and composition of water-accessible surface area (ASA) by solubility assays. Using an established additive ASA-based analysis, we interpret these thermodynamic results to determine interactions of each alkylurea with five types of nucleobase unified atoms (carbonyl sp~(2)O, amino sp~(3)N, ring sp~(2)N, methyl sp~(3)C, and ring sp~(2)C). All alkylureas interact favorably with nucleobase sp~(2)C and sp~(3)C atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase sp~(2)O are most favorable for urea, less favorable for methylurea and ethylurea, and unfavorable for dialkylated ureas. Contributions to overall alkylurea–nucleobase interactions from interactions with each nucleobase atom type are proportional to the ASA of that atom type with proportionality constant (interaction strength) α, as observed previously for urea. Trends in α-values for interactions of alkylureas with nucleobase atom types parallel those for corresponding amide compound atom types, offset because nucleobase α-values are more favorable. Comparisons between ethylated and methylated ureas show interactions of amide compound sp~(3)C with nucleobase sp~(2)C, sp~(3)C, sp~(2)N, and sp~(3)N atoms are favorable while amide sp~(3)C–nucleobase sp~(2)O interactions are unfavorable. Strongly favorable interactions of urea with nucleobase sp~(2)O but weakly favorable interactions with nucleobase sp~(3)N indicate that amide sp~(2)N–nucleobase sp~(2)O and nucleobase sp~(3)N–amide sp~(2)O hydrogen bonding (NH···O═C) interactions are favorable while amide sp~(2)N–nucleobase sp~(3)N interactions are unfavorable. These
机译：烷基脲展示烃和酰胺基团，蛋白质的主要官能团。为了获得分析氨基碱基和核酸的酰胺和蛋白质相互作用所需的热力学信息，我们通过溶解性测定量化烷基脲对烷基脲的优先相互作用，其溶解性测定是可进样表面积（ASA）的量和组成。使用既定的添加剂基于ASA的分析，我们解释了这些热力学结果，以确定每种烷基脲的相互作用与五种类型的核杂物酶统一原子（羰基Sp〜（2）O，氨基Sp〜（3）n，环SP〜（2） n，甲基sp〜（3）c，环sp〜（2）c）。所有烷基脲都与核碱酶SP〜（2）C和SP〜（3）C原子相互作用。这些相互作用随着尿素的烷基化水平的增加而变得更加有利。与核碱酶SP〜（2）o的相互作用对尿素最有利，对甲基脲和乙基脲的较低，并且对司烷基化脲不利。对与每个核碱基原子型相互作用的对总体烷基脲脲酶的贡献与具有比例常数（相互​​作用强度）α的原子型的ASA成比例，如前所述用于尿素。 α-值与烷基酶原子的相互作用的趋势平行于相应的酰胺化合物原子类型，因为核碱基α-值更有利。乙基化脲与甲基化脲之间的比较显示氨基化合物Sp〜（3）C与核碱基Sp〜（2）c，sp〜（3）c，sp〜（2）n和sp〜（3）n原子的相互作用是有利的amide sp〜（3）c-核碱酶sp〜（2）o相互作用是不利的。尿素与核碱酶SP〜（2）o但与核碱基SP〜（3）n的弱良好相互作用表明酰胺SP〜（2）N-核碱基SP〜（2）o和核碱基sp〜（3）n - 酰胺SP〜（2）O氢键（NH···O = C）相互作用在酰胺SP〜（2）N-核碱基SP〜（3）N相互作用是不利的。这些

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  • 来源
    《Biochemistry》 |2018年第15期|共11页
  • 作者

    Xian Cheng; Irina A. Shkel; Cristen Molzahn; David Lambert; Rezwana Karim; M. Thomas Record;

  • 作者单位

    Program in Biophysics Department of Biochemistry and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin 53706 United States;

    Program in Biophysics Department of Biochemistry and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin 53706 United States;

    Program in Biophysics Department of Biochemistry and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin 53706 United States;

    Program in Biophysics Department of Biochemistry and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin 53706 United States;

    Program in Biophysics Department of Biochemistry and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin 53706 United States;

    Program in Biophysics Department of Biochemistry and Department of Chemistry University of Wisconsin—Madison Madison Wisconsin 53706 United States;

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  • 正文语种 eng
  • 中图分类 生物化学;
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