Molecular Dynamics Study of the Recognition of Dimethylated CpG Sites by MBD1 Protein
暂无分享,去创建一个
[1] M. Tang,et al. Cytosine methylation determines hot spots of DNA damage in the human P53 gene. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[2] P N Barlow,et al. The solution structure of the domain from MeCP2 that binds to methylated DNA. , 1999, Journal of molecular biology.
[3] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[4] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[5] K. Liedl,et al. C5-methylation of cytosine in B-DNA thermodynamically and kinetically stabilizes BI. , 2003, Journal of the American Chemical Society.
[6] J. Šponer,et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .
[7] M. Monk,et al. Regulation of X-Chromosome Inactivation in Development in Mice and Humans , 1998, Microbiology and Molecular Biology Reviews.
[8] K. Schulten,et al. Recognition of methylated DNA through methyl-CpG binding domain proteins , 2011, Nucleic acids research.
[9] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[10] E. Guàrdia,et al. Statistical Errors in Constrained Molecular Dynamics Calculations of the Mean Force Potential , 1992 .
[11] A. Bird,et al. Identification and Characterization of a Family of Mammalian Methyl-CpG Binding Proteins , 1998, Molecular and Cellular Biology.
[12] E. Ballestar,et al. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation , 1999, Nature Genetics.
[13] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[14] A. Bird,et al. Reading the DNA methylation signal. , 2004, Cold Spring Harbor symposia on quantitative biology.
[15] Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs , 1989, Cell.
[16] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[17] P. Kollman,et al. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .
[18] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[19] A. Bird,et al. Mbd1 Is Recruited to both Methylated and Nonmethylated CpGs via Distinct DNA Binding Domains , 2004, Molecular and Cellular Biology.
[20] Nicholas M. Luscombe,et al. Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level , 2001, Nucleic Acids Res..
[21] D. Trono,et al. In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions , 2011, Molecular cell.
[22] H. G. Petersen,et al. Error estimates on averages of correlated data , 1989 .
[23] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[24] M. Nakao,et al. Solution Structure of the Methyl-CpG Binding Domain of Human MBD1 in Complex with Methylated DNA , 2001, Cell.
[25] Albert Jeltsch,et al. Beyond Watson and Crick: DNA Methylation and Molecular Enzymology of DNA Methyltransferases , 2002, Chembiochem : a European journal of chemical biology.
[26] H. Margalit,et al. A role for CH...O interactions in protein-DNA recognition. , 1998, Journal of molecular biology.
[27] D. Sutor. 204. Evidence for the existence of C–H⋯O hydrogen bonds in crystals , 1963 .
[28] A. Bird,et al. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. , 1993, Nucleic acids research.
[29] R. Blumenthal,et al. A common mode of recognition for methylated CpG. , 2013, Trends in biochemical sciences.
[30] M. Nakao,et al. Methylation-Mediated Transcriptional Silencing in Euchromatin by Methyl-CpG Binding Protein MBD1 Isoforms , 1999, Molecular and Cellular Biology.
[31] Olga Kennard,et al. Crystallographic evidence for the existence of CH.cntdot..cntdot..cntdot.O, CH.cntdot..cntdot..cntdot.N and CH.cntdot..cntdot..cntdot.Cl hydrogen bonds , 1982 .
[32] A. Bird. DNA methylation patterns and epigenetic memory. , 2002, Genes & development.
[33] Krzysztof Szalewicz,et al. Potential energy surface and second virial coefficient of methane-water from ab initio calculations. , 2005, The Journal of chemical physics.
[34] M. Szyf,et al. Targeting DNA methylation in cancer , 2003, Ageing Research Reviews.
[35] David C. Williams,et al. Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence , 2011, Nucleic acids research.
[36] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997 .
[37] A. Bird,et al. DNA methylation specifies chromosomal localization of MeCP2 , 1996, Molecular and cellular biology.
[38] R. Zangi,et al. UHRF1 discriminates against binding to fully-methylated CpG-Sites by steric repulsion. , 2013, Biophysical chemistry.
[39] J. Glover,et al. Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues. , 2004, Journal of molecular biology.
[40] R. Zangi,et al. How to distinguish methyl-cytosine from cytosine with high fidelity. , 2012, Journal of molecular biology.
[41] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[42] Z. Derewenda,et al. The occurrence of C-H...O hydrogen bonds in proteins. , 1995, Journal of molecular biology.
[43] Peter A. Kollman,et al. Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins , 1995, J. Comput. Chem..
[44] M. Nakao,et al. Solution structure of the methyl‐CpG‐binding domain of the methylation‐dependent transcriptional repressor MBD1 , 1999, The EMBO journal.
[45] Wilfred F. van Gunsteren,et al. Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry , 1987, J. Comput. Aided Mol. Des..
[46] M. Ehrlich,et al. DNA methylation in cancer: too much, but also too little , 2002, Oncogene.
[47] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[48] H. Dyson,et al. Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso , 2012, Proceedings of the National Academy of Sciences.
[49] A. Bird,et al. MeCP2 binding to DNA depends upon hydration at methyl-CpG. , 2008, Molecular cell.