Can we Execute Reliable MM-PBSA Free Energy Computations of Relative Energies of Different Guanine Quadruplex Folds ?

The self-assembly and stability of DNA G-quadruplexes (GQs) are substantially affected by the intrinsic stability of different GpG base steps embedded in their G-quartet stems. We have extended an earlier analysis of stability of the GQ GpG steps based on MD simulations and free energy computations of two-quartet GQ stems. MD simulations followed by MMPBSA free energy calculations were carried out on all known three-quartet intramolecular human telomeric GQ topologies. Along with the experimentally observed folds, we also studied antiparallel GQs with alternative synanti patterns of the G-quartets. We tested different ions, dihedral variants of the DNA force field, water models and simulation lengths. In total, ~35 μs of simulations have been carried out. The here studied systems are considerably more complete than the previously studied two-quartet stems. Among other effects, our computations could include the stem-loop coupling and ion ion interactions inside the stem. The calculations showed a broad agreement with the earlier predictions. However, the increase of the completeness of the system was associated with increased noise of the free energy data which could be related for example to the presence of long-living loop substates and rather complex dynamics of the two bound ions inside the G-stem. As the result, the MM-PBSA data were noisy and we could not improve their quantitative convergence even by expanding the simulations to 2.5 μs long trajectories. We also suggest that