Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis

Abstract

DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation, which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical stack and into the active site of protein provides DNA methyltransferases with an opportunity to access and modify the genetic information hidden in DNA. To investigate the conversion process of base flipping in the HhaI methyltransferase (M.HhaI), we performed different molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The results demonstrate that the nonspecific binding of DNA to M.HhaI is initially induced by electrostatic interactions. Differences in chemical environment between the major and minor grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop motion is a key factor during this process. Our study indicates that base flipping is likely to be an “induced-fit” process. This study provides a solid foundation for future studies on the discovery and development of mechanism-based DNA methyltransferases regulators.

The sequence preference of DNA methylation variation in mammalians

“…Both DNMTs and TETs make use of the base flipping mechanism in order to modify the target cytosine/methylcytiosine. Several steps involve in the base flipping mechanism: first, the target sites are recognized by the recognition domain of protein; the target cytosine or methylcytosine flips out via their interactions with the catalytic domain of the protein; and finally the target is modified in the active pocket[ 30 – 32 ]. Since the substrates of modification are cytosine for methylation and methylcytosine for demethylation, the chemical reactions of methylation (or demethylation) in the catalytic pocket are the same among N 5 CGN 3 (or N 5 mCGN 3 ), leaving the base flipping process a possible cause of the flanking base dependence.…”

Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1

“…Notably, the corresponding sequence of the dynamic region in M.Hha I, the prokaryotic DNA (cytosine-C5)-methyltransferase, contains the active-site loop following the catalytic nucleophile (residue C81). The loop adopts an open conformation in the absence of DNA and a closed conformation after DNA binding (Figure S3A), 15–21 which is similar to DNMT1. Moreover, the corresponding region in DNMT3A is an active site loop that is stabilized by DNMT3L, which stimulates the activity of DNMT3A 22,23 via interactions with the C-terminal part of the active site loop (residues G722, L723, and Y724) (Figure S3B).…”

Improvement of SNAr Reaction Rate by an Electron‐Withdrawing Group in the Crosslinking of DNA Cytosine‐5 Methyltransferase by a Covalent Oligodeoxyribonucleotide Inhibitor

“…From the results, ODN– Cl P CN :G can form the complex in the absence of SAM, although the formation rate is lower than that in the presence of SAM. DNMT recognizes DNA, finds the target site, and the resulting complex causes an induced fit to the loop, which locks the conformation for the methylation reaction in the presence of SAM . Our results may reveal that the induced fit of DNMT is more important for complex formation with our ODN.…”