Comparisons of Ribonuclease HI Homologs and Mutants Uncover a Multistate Model for Substrate Recognition.
Comparisons of Ribonuclease HI Homologs and Mutants Uncover a Multistate Model for Substrate Recognition.
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核糖核酸酶HI同系物和突变体的比较揭示了底物识别的多态模型。
DOI：
10.1021/jacs.1c11897
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发表时间：
2022-03-30
影响因子：
15
通讯作者：
Palmer, Arthur G., III
中科院分区：
文献类型：
--
作者：
Martin, James A.;Palmer, Arthur G., III
核糖核酸酶HI（RNHI）在无数生物过程中非特异性地切割RNA：DNA杂合双链体中的RNA链。几个RNHI同源物含有一个延伸的结构域，称为手柄区，这是关键的底物结合。核磁共振（NMR）光谱和分子动力学（MD）模拟已经提出了一种动力学模型，其中柄区可以在位置88处含有精氨酸或赖氨酸的同系物中以开放（底物结合能力）或封闭（底物结合能力）状态存在（使用E. coliRNHI），而柄区在同源物中以残基88处的天冬酰胺占据开放和闭合构象体之间的中间状态[斯塔福德，K.一、例如，PLoS Comput. 2013，9，1-10]。表征柄区动力学的NMR参数与具有双态（开放/闭合）柄区的RNHI同系物的酶活性高度相关[Martin，J.A.，例如，Biochemistry 2020，59，3201-3205]。本文提出的工作表明，含有天冬酰胺88的同系物与含有精氨酸或赖氨酸88的同系物相比，显示出不同的结构特征。RNHI同源物和定点突变体与天冬酰胺88的比较支持手柄区动力学的动力学模型，包括8个构象之间的12个独特的转换。总的来说，这些研究结果提出了一个例子的结构-功能关系的酶和聚光灯的使用NMR光谱和MD模拟揭示的构象偏好的细节。
Ribonuclease HI (RNHI) non-specifically cleaves the RNA strand in RNA:DNA hybrid duplexes in a myriad of biological processes. Several RNHI homologs contain an extended domain, termed the handle region, that is critical to substrate binding. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have suggested a kinetic model in which the handle region can exist in open (substrate-binding competent) or closed (substrate-binding incompetent) states in homologs containing arginine or lysine at position 88 (using sequence numbering of E. coli RNHI), while the handle region populates states intermediate between the open and closed conformers in homologs with asparagine at residue 88 [Stafford, K. A., et al., PLoS Comput. Biol. 2013, 9, 1–10]. NMR parameters characterizing handle region dynamics are highly correlated with enzymatic activity for RNHI homologs with two-state (open/closed) handle regions [Martin, J. A., et al., Biochemistry 2020, 59, 3201–3205]. The work presented herein shows that homologs containing asparagine 88 display distinct structural features compared with their counterparts containing arginine or lysine 88. Comparisons of RNHI homologs and site-directed mutants with asparagine 88 support a kinetic model for handle region dynamics that includes 12 unique transitions between eight conformations. Overall, these findings present an example of the structure-function relationships of enzymes and spotlight the use of NMR spectroscopy and MD simulations in uncovering fine details of conformational preferences.
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影响因子：
5.6
作者：
Iwai, S;Wakasa, M;Nakamura, H
通讯作者：
Nakamura, H
DOI：
10.1111/j.1742-4658.2009.06909.x
发表时间：
2009-03
期刊：
The FEBS journal
影响因子：
--
作者：
Champoux JJ;Schultz SJ
通讯作者：
Schultz SJ
影响因子：
16
作者：
Nowotny, Marcin;Gaidamakov, Sergei A.;Yang, Wei
通讯作者：
Yang, Wei
影响因子：
4.8
作者：
Goedken, ER;Marqusee, S
通讯作者：
Marqusee, S
影响因子：
2.9
作者：
Ratcliff, Kathleen;Corn, Jacob;Marqusee, Susan
通讯作者：
Marqusee, Susan