A simple but effective modeling strategy for structural properties of non‐heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family

Abstract

To facilitate computational study of proteins in the AlkB family and related a-ketoglutarate/Fe(II)-dependent dioxygenases, we have tested a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple 12 point charge with Lennard-Jones parameters. Calculations for an AlkB active site model in the gas phase and $150 ns molecular dynamics (MD) simulations for two enzyme-dsDNA complexes (E. coli AlkB-dsDNA and ABH2-dsDNA) suggest that this simple modeling strategy provides a satisfactory description of structural properties of the Fe(II) site in AlkB enzymes, provided that care is exercised to control the binding mode of carboxylate (Asp) to the iron. MD simulations using the model for AlkB-dsDNA and ABH2-dsDNA systems find that although the structural features for the latter are overall in good agreement with the crystal structure, the dsDNA, and AlkB-dsDNA interface undergo substantial changes during the MD simulations from the crystal structure. Even for ABH2, new interactions form between a long loop region and dsDNA upon structural relaxation of the loop, supporting the role of this loop in DNA binding despite the lack of interactions between them in the crystal structure. Analysis of DNA backbone torsional distributions helps identify regions that adopt strained conformations. Collectively, the results highlight that crystal packing may have a significant impact on the structure of protein-DNA complexes; the simulations also provide additional insights regarding why AlkB and ABH2 prefer single-strand and double-strand DNA, respectively, as substrate.

Conformational flexibility influences structure–function relationships in nucleic acid N-methyl demethylases

“…Related computational strategies have been successfully implemented for investigating structure-function relationships of various other enzymes. [28][29][30][31][32][33] The results show conformational dynamics exercise distinct effects in AlkB and FTO and are important in determining substrate selectivity. Specific residues in AlkB/FTO play important roles in correlated motions/flexibility and are important in maintaining the productive geometry of reactant complexes.…”

Metal Ion Modeling Using Classical Mechanics

“…Pang et al parametrized the Fe 2+ ion with a 12-6 LJ potential for a nonheme site. 478 The parameters were derived on the basis of the QM PESs between Fe 2+ and the ligating ligands (two His residues, one Asp residue, one water, and one α-ketoglutarate ligand). They applied a weak harmonic restraint to favor the monodentate Asp binding mode over the bidentate mode frequently preferred by the 12-6 LJ nonbonded model.…”

Oxidative Demethylation of DNA and RNA Mediated by Non‐Heme Iron‐Dependent Dioxygenases

“…These findings provide the first insights into the protein folding of AlkB. [46] Andersson et al also applied EPR and UV/Vis spectroscopies to study ALKBH4 and confirmed that it is Fe II /a-KG-dependent. The characteristic absorption peak at 560 nm proved the existence of a bidentate a-KG bound to an Fe II ; a 9 nm shift occurred when excess amounts of single-stranded DNA (ssDNA) was added, thus indicating that a geometry change of the active site is induced by DNA binding.…”

“…[45] Cui et al used a simple + 2 point charge to replace the non-heme Fe II site in their computational study of the AlkB family proteins and also achieved a satisfactory description of the structural properties of the Fe II site in AlkB enzymes. [46] Andersson et al also applied EPR and UV/Vis spectroscopies to study ALKBH4 and confirmed that it is Fe II /a-KG-dependent. [47] In comparison with AlkB, the metal binding sites of other AlkB family dioxygenases are relatively less characterized.…”