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Journal of Zhejiang University SCIENCE B 2023 Vol.24 No.10 P.883-895

http://doi.org/10.1631/jzus.B2200634


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


Author(s):  Jinru WENG, Shuo YANG, Jinkang SHEN, Hongsen LIU, Yuzi XU, Dongyun HAO, Shan WANG

Affiliation(s):  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; more

Corresponding email(s):   shan_wang@zju.edu.cn, dyhao@cjaas.com

Key Words:  c-Myb, DNA-specific recognition mechanism, Molecular dynamics simulation, DNA major groove width, Electrostatic potential


Jinru WENG, Shuo YANG, Jinkang SHEN, Hongsen LIU, Yuzi XU, Dongyun HAO, Shan WANG. 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, 2023, 24(10): 883-895.

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author="Jinru WENG, Shuo YANG, Jinkang SHEN, Hongsen LIU, Yuzi XU, Dongyun HAO, Shan WANG",
journal="Journal of Zhejiang University Science B",
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number="10",
pages="883-895",
year="2023",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B2200634"
}

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%T Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter
%A Jinru WENG
%A Shuo YANG
%A Jinkang SHEN
%A Hongsen LIU
%A Yuzi XU
%A Dongyun HAO
%A Shan WANG
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%I Zhejiang University Press & Springer
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A1 - Jinru WENG
A1 - Shuo YANG
A1 - Jinkang SHEN
A1 - Hongsen LIU
A1 - Yuzi XU
A1 - Dongyun HAO
A1 - Shan WANG
J0 - Journal of Zhejiang University Science B
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B2200634


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.

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

翁金如1,杨朔2,沈金康1,刘宏森1,许煜梓1,郝东云3,王杉1
1浙江大学医学院附属口腔医院,浙江大学口腔医学院,浙江省口腔疾病临床医学研究中心,浙江省口腔生物医学研究重点实验室,浙江大学癌症研究院,口腔生物材料与器械浙江省工程研究中心,中国杭州市,310000
2吉林大学分子酶学与工程教育部重点实验室,中国长春市,130021
3吉林省农业科学院农业生物技术研究所,中国长春市,130033
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。

关键词:c-Myb;DNA特异性识别机制;分子动力学模拟;DNA大沟宽度;静电势

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Reference

[1]AbazaMSI, Al-AttiyahRJ, Al-SaffarAM, et al., 2004. Antisense oligodeoxynucleotide directed against c-myb has anticancer activity and potentiates the antiproliferative effect of conventional anticancer drugs acting by different mechanisms in human colorectal cancer cells. Tumor Biol, 24(5):241-257.

[2]AggarwalP, BhaveshNS, 2021. Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter. Nucleic Acids Res, 49(10):5943-5955.

[3]BerendsenHJC, van der SpoelD, van DrunenR, 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Comp Phys Comm, 91(1-3):43-56.

[4]BernsteinFC, KoetzleTF, WilliamsGJB, et al., 1978. The protein data bank: a computer-based archival file for macromolecular structures. Arch Biochem Biophys, 185(2):584-591.

[5]BhattaraiG, LeeYH, LeeMH, et al., 2013. Gene delivery of c-myb increases bone formation surrounding oral implants. J Dent Res, 92(9):840-845.

[6]BiedenkappH, BorgmeyerU, SippelAE, et al., 1988. Viral myb oncogene encodes a sequence-specific DNA-binding activity. Nature, 335(6193):835-837.

[7]CiciròY, SalaA, 2021. MYB oncoproteins: emerging players and potential therapeutic targets in human cancer. Oncogenesis, 10(2):19.

[8]CleshamK, Walf-VorderwülbeckeV, GasparoliL, et al., 2022. Identification of a c-MYB-directed therapeutic for acute myeloid leukemia. Leukemia, 36(6):1541-1549.

[9]DaiLQ, YuJ, 2020. Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA. Biochem Biophys Res Commun, 533(1):97-103.

[10]EssmannU, PereraL, BerkowitzML, et al., 1995. A smooth particle mesh Ewald method. J Chem Phys, 103(19):8577-8593.

[11]FuglerudBM, LemmaRB, WanichawanP, et al., 2017. A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. Nucleic Acids Res, 45(13):7681-7696.

[12]GautamS, FioravantiJ, ZhuW, et al., 2019. The transcription factor c-Myb regulates CD8+ T cell stemness and antitumor immunity. Nat Immunol, 20(3):337-349.

[13]GondaTJ, LeoP, RamsayRG, 2008. Estrogen and MYB in breast cancer: potential for new therapies. Expert Opin Biol Ther, 8(6):713-717.

[14]GrafT, 1992. Myb: a transcriptional activator linking proliferation and differentiation in hematopoietic cells. Curr Opin Genet Dev, 2(2):249-255.

[15]GreigKT, de GraafCA, MurphyJM, et al., 2010. Critical roles for c-Myb in lymphoid priming and early B-cell development. Blood, 115(14):2796-2805.

[16]HaoDY, Ohme-TakagiM, SaraiA, 1998. Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J Biol Chem, 273(41):26857-26861.

[17]HaoDY, YamasakiK, SaraiA, et al., 2002. Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs. Biochemistry, 41(13):4202-4208.

[18]HessB, BekkerH, BerendsenHJC, et al., 1997. LINCS: a linear constraint solver for molecular simulations. J Comput Chem, 18(12):1463-1472. https://doi.‍org/10.1002/(SICI)1096-987X(199709)18:‍12<1463::AID-JCC4>3.0.CO;2-H

[19]HeuserC, GattinoniL, 2022. c-Myb redefines the hierarchy of stem-like T cells. Nat Immunol, 23(10):1405-1407.

[20]HugoH, CuresA, SuraweeraN, et al., 2006. Mutations in the MYB intron I regulatory sequence increase transcription in colon cancers. Genes Chromosomes Cancer, 45(12):1143-1154.

[21]Kanei-IshiiC, YasukawaT, MorimotoRI, et al., 1994. c-Myb-induced trans-activation mediated by heat shock elements without sequence-specific DNA binding of c-Myb. J Biol Chem, 269(22):15768-15775.

[22]KatzenAL, KornbergTB, BishopJM, 1985. Isolation of the proto-oncogene c-myb from D. melanogaster. Cell, 41(2):449-456.

[23]KawasakiM, OdaM, 2021. DNA-binding function of c-Myb R2R3 around thermal denaturation temperature. Biophys Physicobiol, 18:78-84.

[24]KrissinelE, HenrickK, 2007. Inference of macromolecular assemblies from crystalline state. J Mol Biol, 372(3):‍774-797.

[25]LauriaA, IppolitoM, AlmericoAM, 2009. Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors. Comput Biol Chem, 33(5):386-390.

[26]LaveryR, MoakherM, MaddocksJH, et al., 2009. Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res, 37(17):5917-5929.

[27]LeeYH, KimHS, KimJS, et al., 2016. C-myb regulates autophagy for pulp vitality in glucose oxidative stress. J Dent Res, 95(4):430-438.

[28]Lindorff-LarsenK, PianaS, PalmoK, et al., 2010. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8):1950-1958.

[29]LuH, WangY, HuangY, et al., 2013. Expression and prognostic role of c-Myb as a novel cell cycle protein in esophageal squamous cell carcinoma. Clin Transl Oncol, 15(10):796-801.

[30]MadanA, RadhaPK, HosurRV, et al., 1995. Bacterial expression, characterization and DNA binding studies on Drosophila melanogaster c-Myb DNA-binding protein. Eur J Biochem, 232(1):150-158.

[31]MalaterreJ, MantamadiotisT, DworkinS, et al., 2008. c-Myb is required for neural progenitor cell proliferation and maintenance of the neural stem cell niche in adult brain. Stem Cells, 26(1):173-181.

[32]MansourMR, AbrahamBJ, AndersL, et al., 2014. Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science, 346(6215):1373-1377.

[33]MauriceD, HooperJ, LangG, et al., 2007. c-myb regulates lineage choice in developing thymocytes via its target gene Gata3. EMBO J, 26(15):3629-3640.

[34]MitaniY, LiJ, RaoPH, et al., 2010. Comprehensive analysis of the MYB-NFIB gene fusion in salivary adenoid cystic carcinoma: incidence, variability, and clinicopathologic significance. Clin Cancer Res, 16(19):4722-4731.

[35]MiyazakiT, PanY, JoshiK, et al., 2012. Telomestatin impairs glioma stem cell survival and growth through the disruption of telomeric G-quadruplex and inhibition of the proto-oncogene, c-Myb. Clin Cancer Res, 18(5):‍1268-1280.

[36]MorrisGM, HueyR, LindstromW, et al., 2009. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem, 30(16):2785-2791.

[37]NessSA, 1996. The Myb oncoprotein: regulating a regulator. Biochim Biophys Acta, 1288(3):F123-F139.

[38]NessSA, MarknellÅ, GrafT, 1989. The v-myb oncogene product binds to and activates the promyelocyte-specific mim-1 gene. Cell, 59(6):1115-1125.

[39]NiSJ, ZhuJY, ZhangJG, et al., 2015. Expression and clinical role of NF45 as a novel cell cycle protein in esophageal squamous cell carcinoma (ESCC). Tumor Biol, 36(2):747-756.

[40]NishinaY, NakagoshiH, ImamotoF, et al., 1989. Trans-activation by the c-myb proto-oncogene. Nucleic Acids Res, 17(1):107-117.

[41]O'BoyleNM, BanckM, JamesCA, et al., 2011. Open Babel: an open chemical toolbox. J Cheminform, 3:33.

[42]OgataK, HojoH, AimotoS, et al., 1992. Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci USA, 89(14):6428-6432.

[43]OgataK, MorikawaS, NakamuraH, et al., 1994. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell, 79(4):639-648.

[44]OgataK, MorikawaS, NakamuraH, et al., 1995. Comparison of the free and DNA-complexed forms of the DMA-binding domain from c-Myb. Nat Struct Biol, 2(4):‍‍309-320.

[45]OgataK, Kanei-IshiiC, SasakiM, et al., 1996. The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nat Struct Biol, 3(2):178-187.

[46]OhIH, ReddyEP, 1999. The myb gene family in cell growth, differentiation and apoptosis. Oncogene, 18(19):‍3017-3033.

[47]OrdingE, KvåvikW, BostadA, et al., 1994. Two functionally distinct half sites in the DNA-recognition sequence of the Myb oncoprotein. Eur J Biochem, 222(1):113-120.

[48]PadroniG, WithersJM, Taladriz-SenderA, et al., 2019. Sequence-selective minor groove recognition of a DNA duplex containing synthetic genetic components. J Am Chem Soc, 141(24):9555-9563.

[49]PanJH, Adair-KirkTL, PatelAC, et al., 2014. Myb permits multilineage airway epithelial cell differentiation. Stem Cells, 32(12):3245-3256.

[50]PanYP, NussinovR, 2007. Structural basis for p53 binding-induced DNA bending. J Biol Chem, 282(1):691-699.

[51]Pardo-SagantaA, LawBM, TataPR, et al., 2015. Injury induces direct lineage segregation of functionally distinct airway basal stem/progenitor cell subpopulations. Cell Stem Cell, 16(2):184-197.

[52]PattS, ThielG, MaasS, et al., 1993. Chromosomal changes and correspondingly altered proto-oncogene expression in human gliomas. Value of combined cytogenetic and molecular genetic analysis. Anticancer Res, 13(1):113-118.

[53]Paz-AresJ, GhosalD, WienandU, et al., 1987. The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. EMBO J, 6(12):3553-3558.

[54]RamsayRG, GondaTJ, 2008. MYB function in normal and cancer cells. Nat Rev Cancer, 8(7):523-534.

[55]RohsR, WestSM, SosinskyA, et al., 2009. The role of DNA shape in protein-DNA recognition. Nature, 461(7268):1248-1253.

[56]RossonD, ReddyEP, 1986. Nucleotide sequence of chicken c-myb complementary DNA and implications for myb oncogene activation. Nature, 319(6054):604-606.

[57]SarkarS, SinghPC, 2020. Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability. Biochim Biophys Acta Gen Subj, 1864(3):129498.

[58]TanFE, VladarEK, MaL, et al., 2013. Myb promotes centriole amplification and later steps of the multiciliogenesis program. Development, 140(20):4277-4286.

[59]TanikawaJ, YasukawaT, EnariM, et al., 1993. Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci USA, 90(20):9320-9324.

[60]TelemanO, JönssonB, EngströmS, 1987. A molecular dynamics simulation of a water model with intramolecular degrees of freedom. Mol Phys, 60(1):193-203.

[61]TorelliG, VenturelliD, ColóA, et al., 1987. Expression of c-myb protooncogene and other cell cycle-related genes in normal and neoplastic human colonic mucosa. Cancer Res, 47(20):5266-5269.

[62]WallrappC, Müller-PillaschF, Solinas-ToldoS, et al., 1997. Characterization of a high copy number amplification at 6q24 in pancreatic cancer identifies c-myb as a candidate oncogene. Cancer Res, 57(15):3135-3139.

[63]WangS, YangS, AnBY, et al., 2011. Molecular dynamics analysis reveals structural insights into mechanism of nicotine N-demethylation catalyzed by tobacco cytochrome P450 mono-oxygenase. PLoS ONE, 6(8):e23342.

[64]WolffL, 1996. Myb-induced transformation. Crit Rev Oncog, 7(3-4):245-260.

[65]XuLH, ZhaoF, YangWW, et al., 2019. MYB promotes the growth and metastasis of salivary adenoid cystic carcinoma. Int J Oncol, 54(5):1579-1590.

[66]YangLW, EyalE, BaharI, et al., 2009. Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics, 25(5):606-614.

[67]ZhaoL, GlazovEA, PattabiramanDR, et al., 2011. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb. Nucleic Acids Res, 39(11):‍4664-4679.

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