通过分子动力学模拟方法研究c-Myb在<italic style="font-style: italic">mim-1</italic>启动子区域伪回文序列的结合特性揭示DNA特异性识别机制

翁金如; 杨朔; 沈金康; 刘宏森; 许煜梓; 郝东云; 王杉

doi:10.1631/jzus.B2200634

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通过分子动力学模拟方法研究c-Myb在mim-1启动子区域伪回文序列的结合特性揭示DNA特异性识别机制

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Research Articles | Updated：2023-09-25

通过分子动力学模拟方法研究c-Myb在mim-1启动子区域伪回文序列的结合特性揭示DNA特异性识别机制
Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter
浙江大学学报（英文版）（B辑：生物医学和生物技术） 2023年24卷第10期页码：883-895
Affiliations：

1.Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China
2.Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130021, China
3.Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (JAAS), Changchun 130033, China
Funds：

the National Key Research and Development Program of China(2022YFC2402900;2022YFC2402901);the Fundamental Research Funds for the Central Universities(226-2022-00213);the Joint Funds of the Zhejiang Provincial Natural Science Foundation of China(LHDMD23H300001);Acknowledgement: We thank Tsukuba Life Sciences Center, the Institute of Physical and Chemical Research (RIKEN), Japan for the assistance on the quantitative EMSA experiments accomplished by Prof. Dongyun HAO during his post-doctoral study. We also thank Dr. Shichen WANG from the Texas A&M AgriLife Research;for the assistance on bioinformatics experiments
DOI：10.1631/jzus.B2200634
中图分类号：
CSTR：

翁金如, 杨朔, 沈金康, 等. 通过分子动力学模拟方法研究c-Myb在mim-1启动子区域伪回文序列的结合特性揭示DNA特异性识别机制[J]. 浙江大学学报（英文版）（B辑：生物医学和生物技术）, 2023,24(10):883-895.

Jinru WENG, Shuo YANG, Jinkang SHEN, et al. Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter[J]. Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology), 2023,24(10):883-895.
翁金如, 杨朔, 沈金康, 等. 通过分子动力学模拟方法研究c-Myb在mim-1启动子区域伪回文序列的结合特性揭示DNA特异性识别机制[J]. 浙江大学学报（英文版）（B辑：生物医学和生物技术）, 2023,24(10):883-895. DOI： 10.1631/jzus.B2200634.

Jinru WENG, Shuo YANG, Jinkang SHEN, et al. Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter[J]. Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology), 2023,24(10):883-895. DOI： 10.1631/jzus.B2200634.

摘要

本研究旨在探索c-Myb转录因子在调控细胞早期分化和增殖过程中的DNA特异性识别机制。我们以鸡髓系基因,mim-1,为研究对象，研究其潜在双c-Myb结合位点的结合特异性。,mim-1,的c-Myb结合位点是一个伪回文序列AACGGTT，正反方向分别包含1个c-Myb结合保守序列AACNG。不同条件下的重复分子动力学模拟研究表明，c-Myb与,mim-1,正链的结合（复合物F）比与反链的结合（复合物R）更稳定。主成分分析（PCA）动力学轨迹分析表明，在330 K温度下，c-Myb识别螺旋R2和R3（R2R3）的开放运动导致复合物R中DNA与c-Myb解离，且此开放运动是由R2R3表面静电势降低引起。同时，DNA构象和氢键相互作用分析表明，复合物R中DNA的大沟宽度增加影响了R2R3与DNA间的氢键形成，直接导致DNA与R2R3的解离。拉伸分子动力学模拟研究进一步表明，静电势、DNA大沟宽度和氢键对DNA特异性识别起到重要作用。体外实验证实了计算模拟结果，即c-Myb只与,mim-1,正链结合。本研究表明，除一维保守序列AACNG外，三维结构特性对c-Myb的DNA特异性识别也起着重要作用。本研究结果有助于理解c-Myb在细胞早期分化和增殖中的调控机制，以及预测开发由c-Myb结合位点增多引起的肿瘤发生标志物。

Abstract

This study aims to gain insight into the DNA-specific recognition mechanism of c-Myb transcription factor during the regulation of cell early differentiation and proliferation. Therefore, we chose the chicken myeloid gene, mitochondrial import protein 1 (,mim-1,), as a target to study the binding specificity between potential dual-Myb-binding sites. The c-Myb-binding site in ,mim-1 ,is a pseudo-palindromic sequence AACGGTT, which contains two AACNG consensuses. Simulation studies in different biological scenarios revealed that c-Myb binding with ,mim-1 ,in the forward strand (complex F) is,more stable than that in,the,reverse strand (complex R). The principal component analysis (PCA) dynamics trajectory analyses suggested an opening motion of the recognition helices of R2 and R3 (R2R3), resulting in the dissociation of DNA from c-Myb in complex R at 330 K, triggered by the reduced electrostatic potential on the surface of R2R3. Furthermore, the DNA confirmation and hydrogen-bond interaction analyses indicated that the major groove width of DNA increased in complex R, which affected on the hydrogen-bond formation ability between R2R3 and DNA, and directly resulted in the dissociation of DNA from R2R3. The steered molecular dynamics (SMD) simulation studies also suggested that the electrostatic potential, major groove width, and hydrogen bonds made major contribution to the DNA‍-specific recognition. In vitro trials confirmed the simulation results that c-Myb specifically bound to ,mim-1 ,in the forward strand. This study indicates that the three-dimensional (3D) structure features play an important role in the DNA-specific recognition mechanism by c-Myb besides the AACNG consensuses, which is beneficial to understanding the cell early differentiation and proliferation regulated by c-Myb, as well as the prediction of novel c-Myb-binding motifs in tumorigenesis.

关键词

c-MybDNA特异性识别机制分子动力学模拟DNA大沟宽度静电势

Keywords

c-MybDNA-specific recognition mechanismMolecular dynamics simulationDNA major groove widthElectrostatic potential

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Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides#

通过分子动力学模拟方法研究c-Myb在mim-1启动子区域伪回文序列的结合特性揭示DNA特异性识别机制

Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter

DOI：10.1631/jzus.B2200634

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