Fig 1.
Input structures for the simulations.
In a) the whole protein-ATP complex is shown. In b-d) the initial binding site structures for the freely distributed Mg2+ case, the MgATP:Oα/Oβ and MgATP:Oβ/Oγ coordination are shown, respectively. Water molecules coordinating the Mg2+ ion and residues coordinating ATP are shown in licorice, while the Mg2+ ion is shown in VdW spheres.
Fig 2.
Distance distribution of the Mg2+ ion and free energy results.
Distance distribution when the Mg2+ ion a) is bound in a second sphere coordination to ATP, b) is bound in a first sphere coordination to ATP:Oα/Oβ and c) is bound in a first sphere coordination to ATP:Oβ/Oγ; ATP is bound to the protein in all cases. In a)–c) the black, red, green, blue and orange lines represent the minimal distance distributions of a Mg2+ ion towards ATP:O2’, ATP:O3’, ATP:Oα, ATP:Oβ and ATP:Oγ, respectively. The before mentioned data were extracted from conventional MD simulations. In d) the free energy calculations (Thermodynamic Integration) for the binding of Mg2+ towards ATP in second sphere coordination, when bound to ATP:Oα/Oβ or ATP:Oβ/Oγ are shown, respectively. It should be noted that in Fig b) the blue and the green lines are overlapping.
Table 1.
Hydrogen-bond and energetic analysis of ATP binding to the wild type and mutant ε subunit.
Fig 3.
Distance distribution of protein-ATP interactions.
Distance distribution of protein-ATP interactions of the Mg2+ bound to ATP:Oα/Oβ. Dotted lines represent distances found in the crystal structure of the wild type protein. The histogram in the top left represents nucleoside–protein interaction (black: ATP:N6 –D89:O, red: ATP:O2’–E:83:Oεx, green: ATP:O3’–E83:Oεx, blue: D89:N—ATP:N1, violet: R92:NHx—ATPO4’, cyan: R92:NHx—ATP:N3/7/9 and orange: R126:NHx—ATP:O5’). The three other diagrams represent protein—ATP:Oα/β/γ interactions (black: R92:Nε, red: R92:NHx, green: R99:Nε, blue: R99:NHx, brown: R122:Nε, cyan: R122:NHx, magenta: R126:Nε and orange: R126:NHx), respectively. The corresponding figures for the Mg2+ freely distributed state and Mg2+ coordinated to ATP:Oβ/Oγ are shown in S2 and S4 Figs in the Supporting Information, respectively. The corresponding data for the single runs is shown in S5 (Mg2+ not bound in first sphere), S6 (Mg2+ bound to ATP:Oα/Oβ) and S7 Figs (Mg2+ bound to ATP:Oβ/Oγ), respectively.
Fig 4.
Comparison of wild type and mutant ATP binding site.
ATP binding site of a representative snapshot of a) the wild type ε subunit [30] and b) the R103A/R115A double mutant derived by MD simulations. A structural comparison of the crystal structure and the R103A/R115A mutant is shown in the supporting information (S8 Fig). Figures containing molecular information have been produced using VMD [58].