title: MeCP2 Binding Cooperativity Inhibits DNA Modification-Specific Recognition.
abstract: Methyl-CpG binding protein 2 (MeCP2) is a multifunctional protein that guides neuronal development through its binding to DNA, recognition of sites of methyl-CpG (mCpG) DNA modification, and interaction with other regulatory proteins. Our study explores the relationship between mCpG and hydroxymethyl-CpG (hmCpG) recognition mediated by its mCpG binding domain (MBD) and binding cooperativity mediated by its C-terminal polypeptide. Previous study of the isolated MBD of MeCP2 documented an unusual mechanism by which ion uptake is required for discrimination of mCpG and hmCpG from CpG. MeCP2 binding cooperativity suppresses discrimination of modified DNA and is highly sensitive to both the total ion concentration and the type of counterions. Higher than physiological total ion concentrations completely suppress MeCP2 binding cooperativity, indicating a dominant electrostatic component to the interaction. Substitution of SO4(2-) for Cl(-) at physiological total ion concentrations also suppresses MeCP2 binding cooperativity, This effect is of particular note as the intracellular Cl(-) concentration changes during neuronal development. A related effect is that the protein-stabilizing solutes, TMAO and glutamate, reduce MeCP2 (but not isolated MBD) binding affinity by 2 orders of magnitude without affecting the apparent binding cooperativity. These observations suggest that polypeptide flexibility facilitates DNA binding by MeCP2. Consistent with this view, nuclear magnetic resonance (NMR) analyses show that ions have discrete effects on the structure of MeCP2, both MBD and the C-terminal domains. Notably, anion substitution results in changes in the NMR chemical shifts of residues, including some whose mutation causes the autism spectrum disorder Rett syndrome. Binding cooperativity makes MeCP2 an effective competitor with histone H1 for accessible DNA sites. The relationship between MeCP2 binding specificity and cooperativity is discussed in the context of chromatin binding, neuronal function, and neuronal development.
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Sergei
authors.initials: S
authors.lastname: Khrapunov
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Yisong
authors.initials: Y
authors.lastname: Tao
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Huiyong
authors.initials: H
authors.lastname: Cheng
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Camille
authors.initials: C
authors.lastname: Padlan
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Richard
authors.initials: R
authors.lastname: Harris
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Aristea S
authors.initials: AS
authors.lastname: Galanopoulou
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: John M
authors.initials: JM
authors.lastname: Greally
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Girvin
authors.affiliation: Department of Biochemistry, ‡Departments of Neurology and Neuroscience, and §Department of Genetics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Brenowitz
mesh_terms: D004247:DNA / Q000235:genetics / Q000378:metabolism*; D044127:Epigenesis, Genetic; D006657:Histones / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D000070593:Methyl CpG Binding Domain / Q000235:genetics; D051783:Methyl-CpG-Binding Protein 2 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D055495:Neurogenesis; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015518:Rett Syndrome / Q000235:genetics / Q000378:metabolism
chemical_list: D006657:Histones; C497392:MECP2 protein, human; D051783:Methyl-CpG-Binding Protein 2; D011994:Recombinant Proteins; D004247:DNA