title: Effect of CpG methylation on DNA binding protein: molecular dynamics simulations of the homeodomain PITX2 bound to the methylated DNA.
abstract: A large number of studies have argued that aberrant CpG methylation is associated with some human cancers. One possible mechanism of the cancer caused by CpG methylation is the gene repression, which is a binding-inhibition of the sequence-specific transcription factors bound to specific DNA-binding sites. Exploring the effects of CpG methylation on the structure and the thermodynamic property of DNA-binding transcription factors will help to gain an insight into how CpG methylation affects the repression of gene transcription in cancer. We have performed molecular dynamics (MD) simulations and free energy calculations of the protein bound to the native or the methylated DNA, in which the solution structure of the K50-class homeodomain PITX2 bound to DNA was used as a template. The simulation results indicate that the methylated CpG located at the DNA major groove can enhance the protein-DNA interactions, and the residue side-chains near the methylated CpG pair appear to have an unusually high affinity with DNA. The structural analysis and calculated energy values demonstrate that the binding-induced structural changes were further encouraged as the CpG methylation upon the complexation. Moreover, the CpG methylation may reduce the unfavorable effect of the conformational entropy and increase the electrostatic contribution to the binding free energy of DNA-PITX2. The changes in specific binding sites and the excessive affinity between DNA and protein caused by the CpG methylation could affect the gene transcriptional activity.
authors.affiliation: School of Chemistry and Chemical Engineering, Qujing Normal University, Sanjiang Road, Qinig District, Qujing City 655011, Yunnan Province, PR China. yangsiyall@163.com
authors.forename: Si-Ya
authors.initials: SY
authors.lastname: Yang
authors.forename: Xiao-Li
authors.initials: XL
authors.lastname: Yang
authors.forename: Li-Feng
authors.initials: LF
authors.lastname: Yao
authors.forename: Hai-Bo
authors.initials: HB
authors.lastname: Wang
authors.forename: Chen-Ke
authors.initials: CK
authors.lastname: Sun
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018899:CpG Islands; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005786:Gene Expression Regulation; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000235:genetics; D011485:Protein Binding; D011487:Protein Conformation; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism*; D000097577:Homeobox Protein PITX2
chemical_list: D003596:Cytosine; D004247:DNA; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D014157:Transcription Factors; D000097577:Homeobox Protein PITX2