Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB

• Published in: DNA repair Vol. 96; p. 102944
• Main Authors: Lenz, Stefan A.P., Li, Deyu, Wetmore, Stacey D.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2020
• Subjects: Adenine - analogs & derivatives; Adenine - metabolism; AlkB; AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase - chemistry; AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase - metabolism; Alkylation damage; Catalytic Domain; Computational Biology; Cytosine - analogs & derivatives; Cytosine - metabolism; Direct repair; DNA Adducts - chemistry; DNA Adducts - metabolism; DNA Repair; Enzymes; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Guanine - analogs & derivatives; Guanine - metabolism; Humans; Mixed Function Oxygenases - chemistry; Mixed Function Oxygenases - metabolism; Models, Molecular; Molecular dynamics; Molecular Dynamics Simulation; Protein Conformation; QM/MM methods; Substrate Specificity; Molecular dynamics; 1,N2-εG; Direct repair; SD; ONIOM; TDG; α-KG; MD; IC; QM; AlkB; AlkA; ssDNA; 3MeC; COM; MM; MBD4; Enzymes; Alkylation damage; QM/MM methods; CG; AAG; TET2; N2,3-εG; 3,N4-εC; MCPB; BER; 1MeA; SMUG1; RC; RESP; rmsd; 1,N6-εA; dsDNA; TS
• ISSN: 1568-7864; 1568-7856
• DOI: 10.1016/j.dnarep.2020.102944

•π–π interactions play key roles in positioning AlkB and ALKBH2 substrates for repair.•π–π interactions are disrupted when AlkB or ALKBH2 bind N2,3-εG.•Calculations predict small oxidation barriers for optimally placed substrates.•A large oxidation barrier is predicted for N2,3-εG repair.•The large barrier explains why N2,3-εG escapes AlkB-mediated repair. E. coli AlkB and human ALKBH2 belong to the AlkB family enzymes, which contain several α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases that repair alkylated DNA. Specifically, the AlkB enzymes catalyze decarboxylation of α-KG to generate a high-valent Fe(IV)-oxo species that oxidizes alkyl groups on DNA adducts. AlkB and ALKBH2 have been reported to differentially repair select etheno adducts, with preferences for 1,N6-ethenoadenine (1,N6-εA) and 3,N4-ethenocytosine (3,N4-εC) over 1,N2-ethenoguanine (1,N2-εG). However, N2,3-ethenoguanine (N2,3-εG), the most common etheno adduct, is not repaired by the AlkB enzymes. Unfortunately, a structural understanding of the differential activity of E. coli AlkB and human ALKBH2 is lacking due to challenges acquiring atomistic details for a range of substrates using experiments. This study uses both molecular dynamics (MD) simulations and ONIOM(QM:MM) calculations to determine how the active site changes upon binding each etheno adduct and characterizes the corresponding catalytic impacts. Our data reveal that the preferred etheno substrates (1,N6-εA and 3,N4-εC) form favorable interactions with catalytic residues that situate the lesion near the Fe(IV)-oxo species and permit efficient oxidation. In contrast, although the damage remains correctly aligned with respect to the Fe(IV)-oxo moiety, repair of 1,N2-εG is mitigated by increased solvation of the active site and a larger distance between Fe(IV)-oxo and the aberrant carbons. Binding of non-substrate N2,3-εG in the active site disrupts key DNA–enzyme interactions, and positions the aberrant carbon atoms even further from the Fe(IV)-oxo species, leading to prohibitively high barriers for oxidative catalysis. Overall, our calculations provide the first structural insight required to rationalize the experimentally-reported substrate specificities of AlkB and ALKBH2 and thereby highlight the roles of several active site residues in the repair of etheno adducts that directly correlates with available experimental data. These proposed catalytic strategies can likely be generalized to other α-KG/Fe(II)-dependent dioxygenases that play similar critical biological roles, including epigenetic and post-translational regulation.