Exploring the bistable equilibrium of methylated CpG DNA recognition by the MBD2 protein
6 affiliations
- 1Computer Chemistry Center, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg , Nägelsbachstrasse 25, 91052 Erlangen ,
- 2Institute for Drug Discovery and Institute for Medical Physics and Biophysics, Leipzig University Medical School , 04103 Leipzig ,
- 3Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine , Chapel Hill, NC 27599, United States
- 4Institute of Physics and Astronomy, University of Potsdam , Potsdam 14476 ,
- 5Fachbereich Physik, Freie Universität Berlin , 14195 Berlin ,
- 6Institute of Chemistry, Martin Luther-University Halle-Wittenberg , Weinbergweg 22, Halle (Saale) 06120 ,
Abstract
Methyl-CpG binding domain 2 (MBD2) is a critical epigenetic regulator that selectively binds methylated CpG dinucleotides, key marks controlling gene regulation and chromatin organization. Understanding the interactions and conformational dynamics underlying this high selectivity is essential to elucidate MBD2’s regulatory role. Here, using extensive classical MD simulations, we explored the formation of the MBD2–mCpG recognition complex. By initially positioning MBD2 one base pair downstream of its target, we observed its transition to the target site within microseconds. Notably, upon binding, MBD2 adopts two distinct stable conformations: a primary state closely resembling the X-ray crystal structure, and a secondary state of reduced affinity that nevertheless retains comparable selectivity for mCpG. Our results establish S189 as a key macro-switch; loss of its interaction with the methylcytosine backbone shifts the equilibrium toward the secondary state. This is corroborated by MD simulations of the S189A mutant, which preferentially adopts the secondary state-like conformation. Complementary NMR experiments confirm that S189A mutation does not alter mCpG selectivity, while fluorescence polarization measurements reveal a reduced binding affinity, consistent with our MD simulations results. Together, these findings indicate that MBD2 binding to methylated CpG involves a bistable equilibrium, providing new insights into how high affinity and adaptability are balanced in epigenetic recognition. In a broader context, our findings suggest that such alternative bound-state equilibria may represent an inherent feature of specific protein–DNA complexes.
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BibTeX
@article{volkenandt2026exploring,
title = {{Exploring the bistable equilibrium of methylated CpG DNA recognition by the MBD2 protein}},
author = {Senta Volkenandt and Julia Belyaeva and Torry Li and Matthias Elgeti and Ralf Metzler and Petra Imhof and David C Williams and Mahdi Bagherpoor Helabad},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag952},
url = {https://academic.oup.com/nar/article/doi/10.1093/nar/gkag952/8937190},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Exploring the bistable equilibrium of methylated CpG DNA recognition by the MBD2 protein
AU - Senta Volkenandt
AU - Julia Belyaeva
AU - Torry Li
AU - Matthias Elgeti
AU - Ralf Metzler
AU - Petra Imhof
AU - David C Williams
AU - Mahdi Bagherpoor Helabad
PY - 2026
DA - 2026/10/01
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag952
UR - https://academic.oup.com/nar/article/doi/10.1093/nar/gkag952/8937190
AB - Methyl-CpG binding domain 2 (MBD2) is a critical epigenetic regulator that selectively binds methylated CpG dinucleotides, key marks controlling gene regulation and chromatin organization. Understanding the interactions and conformational dynamics underlying this high selectivity is essential to elucidate MBD2’s regulatory role. Here, using extensive classical MD simulations, we explored the formation of the MBD2–mCpG recognition complex. By initially positioning MBD2 one base pair downstream of its target, we observed its transition to the target site within microseconds. Notably, upon binding, MBD2 adopts two distinct stable conformations: a primary state closely resembling the X-ray crystal structure, and a secondary state of reduced affinity that nevertheless retains comparable selectivity for mCpG. Our results establish S189 as a key macro-switch; loss of its interaction with the methylcytosine backbone shifts the equilibrium toward the secondary state. This is corroborated by MD simulations of the S189A mutant, which preferentially adopts the secondary state-like conformation. Complementary NMR experiments confirm that S189A mutation does not alter mCpG selectivity, while fluorescence polarization measurements reveal a reduced binding affinity, consistent with our MD simulations results. Together, these findings indicate that MBD2 binding to methylated CpG involves a bistable equilibrium, providing new insights into how high affinity and adaptability are balanced in epigenetic recognition. In a broader context, our findings suggest that such alternative bound-state equilibria may represent an inherent feature of specific protein–DNA complexes.
SN - 0305-1048
SN - 1362-4962
ER -