Affiliations 

  • 1 Department of Pathology, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
  • 2 Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
  • 3 Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
  • 4 Institute of Biochemistry, National Chung Hsing University, 250, Guoguang Rd., Taichung City 402, Taiwan
  • 5 Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Sci Rep, 2016 08 09;6:31210.
PMID: 27502833 DOI: 10.1038/srep31210

Abstract

DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.