Computations Reveal a Rich Mechanistic Variation of Demethylation of N-Methylated DNA/RNA Nucleotides by FTO

The fat-mass and obesity-associated (FTO) protein employs an iron(IV) oxo species to demethylate N-methylated nucleic acids. Herein, we use atomistic-theoretical calculations to study the demethylation of the N-methylated DNA/RNA bases 6-methylated adenine (m6A), 3-methylated thymine (m3T), and 3-methylated uracil (m3U). The mechanisms involve in-enzyme hydroxylation of the methyl group, followed by hydrolysis of the oxidized intermediates in aqueous solution to demethylate the bases. The in-enzyme reactions have been studied using quantum mechanical/molecular mechanical (QM/MM) calculations, while the hydrolytic reactions occurring outside the enzyme have been explored with hybrid cluster-continuum (HCC) calculations. When the results obtained with these different methods are combined, the calculated barrier for the overall transformation is consistent with the experimental free energy barrier for the major route of m6A demethylation: in this pathway, adenine’s N1 site acts as an internal base catalyst i...

[1]  Sason Shaik,et al.  Quantum mechanical/molecular mechanical calculated reactivity networks reveal how cytochrome P450cam and Its T252A mutant select their oxidation pathways. , 2015, Journal of the American Chemical Society.

[2]  C. Rovira,et al.  Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. , 2015, Journal of the American Chemical Society.

[3]  Wenyou Zhu,et al.  Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions , 2015 .

[4]  Ruibo Wu,et al.  Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation , 2015 .

[5]  Chuan He,et al.  N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions , 2015, Nature.

[6]  Walter Thiel,et al.  Amine Oxidation Mediated by N-Methyltryptophan Oxidase: Computational Insights into the Mechanism, Role of Active-Site Residues, and Covalent Flavin Binding , 2015 .

[7]  Howard Y. Chang,et al.  Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. , 2015, Journal of the American Chemical Society.

[8]  I. Tuñón,et al.  Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase. , 2014, Journal of the American Chemical Society.

[9]  Sason Shaik,et al.  Theory uncovers an unusual mechanism of DNA repair of a lesioned adenine by AlkB enzymes. , 2014, Journal of the American Chemical Society.

[10]  Arieh Warshel,et al.  Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). , 2014, Angewandte Chemie.

[11]  F. Neese,et al.  Correlated Ab Initio and Density Functional Studies on H2 Activation by FeO(.). , 2014, Journal of chemical theory and computation.

[12]  C. Yi,et al.  Oxidative demethylation of DNA and RNA mediated by non-heme iron-dependent dioxygenases. , 2014, Chemistry, an Asian journal.

[13]  Chun-Xiao Song,et al.  Mechanism and function of oxidative reversal of DNA and RNA methylation. , 2014, Annual review of biochemistry.

[14]  Pietro Vidossich,et al.  An ionizable active-site tryptophan imparts catalase activity to a peroxidase core. , 2014, Journal of the American Chemical Society.

[15]  Samie R. Jaffrey,et al.  The dynamic epitranscriptome: N6-methyladenosine and gene expression control , 2014, Nature Reviews Molecular Cell Biology.

[16]  Gideon Rechavi,et al.  Gene expression regulation mediated through reversible m6A RNA methylation , 2014, Nature Reviews Genetics.

[17]  Judith B. Rommel,et al.  Reaction Mechanism of the Bicopper Enzyme Peptidylglycine α-Hydroxylating Monooxygenase* , 2014, The Journal of Biological Chemistry.

[18]  Alexey A. Sokol,et al.  ChemShell—a modular software package for QM/MM simulations , 2014 .

[19]  Ye Fu,et al.  Nucleic Acid Oxidation in DNA Damage Repair and Epigenetics , 2014, Chemical reviews.

[20]  Hao Wu,et al.  Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions , 2014, Cell.

[21]  Matthew G. Quesne,et al.  Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes. , 2014, Chemistry.

[22]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[23]  Martin Srnec,et al.  Elucidation of the Fe(iv)=O intermediate in the catalytic cycle of the halogenase SyrB2 , 2013, Nature.

[24]  Z. Cao,et al.  Chemical synthesis of lactic acid from cellulose catalysed by lead(II) ions in water , 2013, Nature Communications.

[25]  Richard L. Lord,et al.  Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. , 2013, The journal of physical chemistry. B.

[26]  Christine M. Bathelt,et al.  Quantum Mechanics/Molecular Mechanics Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9 , 2013, Journal of the American Chemical Society.

[27]  Chuan He,et al.  FTO-Mediated Formation of N6-Hydroxymethyladenosine and N6-Formyladenosine in Mammalian RNA , 2013, Nature Communications.

[28]  Michael A McDonough,et al.  Structural basis for inhibition of the fat mass and obesity associated protein (FTO). , 2013, Journal of medicinal chemistry.

[29]  M. W. van der Kamp,et al.  Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. , 2013, Biochemistry.

[30]  Howard Cedar,et al.  DNA methylation dynamics in health and disease , 2013, Nature Structural &Molecular Biology.

[31]  A. H. Smits,et al.  Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives , 2013, Cell.

[32]  Zexing Cao,et al.  How water molecules modulate the hydration of CO2 in water solution: Insight from the cluster‐continuum model calculations , 2013, J. Comput. Chem..

[33]  R. B. Sunoj,et al.  Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. , 2012, Physical chemistry chemical physics : PCCP.

[34]  M. Costas.  Selective C–H oxidation catalyzed by metalloporphyrins , 2011 .

[35]  C. Cramer,et al.  Use of solution-phase vibrational frequencies in continuum models for the free energy of solvation. , 2011, The journal of physical chemistry. B.

[36]  Z. Cao,et al.  Acid-catalyzed reactions of twisted amides in water solution: competition between hydration and hydrolysis. , 2011, Chemistry.

[37]  Yang Wang,et al.  Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA , 2011, Science.

[38]  Chuan He,et al.  Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine , 2011, Science.

[39]  Chengqi Yi,et al.  N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO , 2011, Nature chemical biology.

[40]  Markus Müller,et al.  The discovery of 5-formylcytosine in embryonic stem cell DNA. , 2011, Angewandte Chemie.

[41]  Hui Chen,et al.  The directive of the protein: how does cytochrome P450 select the mechanism of dopamine formation? , 2011, Journal of the American Chemical Society.

[42]  Z. Cao,et al.  Hydration of carbonyl groups: the labile H3O+ ion as an intermediate modulated by the surrounding water molecules. , 2011, Angewandte Chemie.

[43]  A. Borovik.  Role of metal-oxo complexes in the cleavage of C-H bonds. , 2011, Chemical Society reviews.

[44]  W. Thiel,et al.  Theoretical study on the mechanism of the oxygen activation process in cysteine dioxygenase enzymes. , 2011, Journal of the American Chemical Society.

[45]  Jan H. Jensen,et al.  PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. , 2011, Journal of chemical theory and computation.

[46]  Zexing Cao,et al.  Mechanism of acid-catalyzed hydrolysis of formamide from cluster-continuum model calculations: concerted versus stepwise pathway. , 2010, The journal of physical chemistry. A.

[47]  Roger D. Cox,et al.  Overexpression of Fto leads to increased food intake and results in obesity , 2010, Nature Genetics.

[48]  Cai-Guang Yang,et al.  Iron-Catalyzed Oxidation Intermediates Captured in a DNA Repair Dioxygenase , 2010, Nature.

[49]  K. Sen,et al.  Peroxo-iron mediated deformylation in sterol 14alpha-demethylase catalysis. , 2010, Journal of the American Chemical Society.

[50]  Qiang Wang,et al.  Crystal structure of the FTO protein reveals basis for its substrate specificity , 2010, Nature.

[51]  Julie A. Law,et al.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.

[52]  J. Essigmann,et al.  Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation. , 2009, Carcinogenesis.

[53]  H. Senn,et al.  Finite-temperature effects in enzymatic reactions - Insights from QM/MM free-energy simulations , 2009 .

[54]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[55]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[56]  Jens C. Brüning,et al.  Inactivation of the Fto gene protects from obesity , 2009, Nature.

[57]  C. Cramer,et al.  Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. , 2009, The journal of physical chemistry. B.

[58]  Haining Liu,et al.  A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB. , 2009, The journal of physical chemistry. B.

[59]  Walter Thiel,et al.  QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.

[60]  Chengqi Yi,et al.  Oxidative demethylation of 3‐methylthymine and 3‐methyluracil in single‐stranded DNA and RNA by mouse and human FTO , 2008, FEBS letters.

[61]  Chris P. Ponting,et al.  The Obesity-Associated FTO Gene Encodes a 2-Oxoglutarate-Dependent Nucleic Acid Demethylase , 2007, Science.

[62]  Lawrence Que,et al.  The road to non-heme oxoferryls and beyond. , 2007, Accounts of chemical research.

[63]  C. Walsh,et al.  Non-heme Fe(IV)-oxo intermediates. , 2007, Accounts of chemical research.

[64]  Beverley Balkau,et al.  Variation in FTO contributes to childhood obesity and severe adult obesity , 2007, Nature Genetics.

[65]  M. Jarvelin,et al.  A Common Variant in the FTO Gene Is Associated with Body Mass Index and Predisposes to Childhood and Adult Obesity , 2007, Science.

[66]  W. Nam,et al.  High-valent iron(IV)-oxo complexes of heme and non-heme ligands in oxygenation reactions. , 2007, Accounts of chemical research.

[67]  D. Truhlar,et al.  QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .

[68]  Walter Thiel,et al.  Enzymatic Hydroxylation in p-Hydroxybenzoate Hydroxylase:  A Case Study for QM/MM Molecular Dynamics. , 2005, Journal of chemical theory and computation.

[69]  J. Essigmann,et al.  Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Jan M. L. Martin,et al.  Development of density functionals for thermochemical kinetics. , 2004, The Journal of chemical physics.

[71]  S. C. Rogers,et al.  QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .

[72]  Erling Seeberg,et al.  AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli , 2002, Nature.

[73]  Robert P. Hausinger,et al.  Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage , 2002, Nature.

[74]  David A. Dixon,et al.  Absolute Hydration Free Energy of the Proton from First-Principles Electronic Structure Calculations , 2001 .

[75]  J. Riveros,et al.  The Cluster−Continuum Model for the Calculation of the Solvation Free Energy of Ionic Species , 2001 .

[76]  Walter Thiel,et al.  Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates , 2000 .

[77]  A. Rashin,et al.  Calculation of the aqueous solvation free energy of the proton , 1998 .

[78]  M. Tissandier,et al.  The Proton's Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster-Ion Solvation Data , 1998 .

[79]  W. Thiel,et al.  Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches , 1996 .

[80]  W Smith,et al.  DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. , 1996, Journal of molecular graphics.

[81]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[82]  Hans W. Horn,et al.  ELECTRONIC STRUCTURE CALCULATIONS ON WORKSTATION COMPUTERS: THE PROGRAM SYSTEM TURBOMOLE , 1989 .

[83]  C. Klots,et al.  Solubility of protons in water , 1981 .

[84]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.