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

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2023年第10期24卷 883-895页

作者： Jinru WENG Shuo YANG Jinkang SHEN Hongsen LIU Yuzi XU Dongyun HAO Shan WANG Stomatology Hospital School of StomatologyZhejiang University School of MedicineZhejiang Provincial Clinical Research Center for Oral DiseasesKey Laboratory of Oral Biomedical Research of Zhejiang ProvinceCancer Center of Zhejiang UniversityEngineering Research Center of Oral Biomaterials and Devices of Zhejiang ProvinceHangzhou 310000China Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education Jilin UniversityChangchun 130021China Institute of Agricultural Biotechnology Jilin Academy of Agricultural Sciences(JAAS)Changchun 130033China

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 ***,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 *** c-Myb-binding site in mim-1 is a pseudo-palindromic sequence AACGGTT,which contains two AACNG *** 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 ***,the dna confirmation and hydrogen-bond interaction analyses indicated that the major groove width of dna increased in complex R,which affected on the hydrogenbond formation ability between R2R3 and dna,and directly resulted in the dissociation of dna from *** 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 *** vitro trials confirmed the simulation results that c-Myb specifically bound to mim-1 in the forward *** 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-Myb dna-specific recognition mechanism Molecular dynamics simulation dna major groove width Electrostatic potential

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