Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

Abstract

A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by molecular-mechanics, Poisson Boltzmann, surface area) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolution experiments. This result is attributed to force field deficiencies, such as the potential misbalance between solute-cation and solvent-cation terms. The MD simulations are unable to maintain the stable coordination of the monovalent cations inside the diagonal loops as reported in a recent x-ray study. The optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture.

FIGURE 1

Depictions of lateral (left), diagonal (middle), and groove or propeller-like (right) G-DNA loop arrangements are shown. The strand directions are indicated by arrows, and anti and syn bases are indicated by solid and open boxes, respectively. All three loop types are common in G-DNA. Lateral (edge) and diagonal loops are attached to one of the terminal quartets. The lateral loops are positioned across the stem grooves, whereas diagonal loops extend across the channel entry. Finally, the loops may also connect quartets on the opposite side of the stem (bulged-out loops) leading to a propeller-type shape of the whole molecule (Parkinson et al., 2002). One base sequence can lead to several distinct quadruplex arrangements, depending on the environment.

FIGURE 2

Base positions and H-bonding in loop arrangements from C1 (outer left column) to C4 (outer right column) in several representations: bricks scheme (top) showing mutual positions of the bases with stacking and H-bonding interactions marked by solid and dashed arrows, respectively; H-bonding arrangements (middle), and stick representation of the loop geometry with bases highlighted (bottom).

FIGURE 3

Development of χ-angle of nucleotides T6 (A) and T7 (B) as a function of time (ps) during the LES run C1-L, second copy (see Supplementary Material for behavior of the remaining copies). Note the back and forth χ-switch of T6 ∼2.8–3.7 ns that is essential to allow further changes of the structure and the χ-adjustment of T7 at ∼4.7 ns leading to the final base rearrangement.

FIGURE 4

Stereoview of the C1 lateral loop geometry (top) and averaged C1-L-M geometry (bottom). PDB files are available in the Supplementary Material. The LES procedure completely changed the loop structure.

FIGURE 5

T5-T8 (top) and T17-T20 (bottom) loops localized by the second LES MD run K-M-L. Note that although the T17-T20 loop has essentially the same geometry as in the C1-L-M structure (Fig. 4), T5-T8 is different with one thymine looped into the solution.

FIGURE 6

Comparison of x-ray (N_diag), NMR (F_diag), and LES-MD (F_diag-L-M) diagonal loop geometries. (Top) The x-ray (solid) and NMR (shaded) structures. (Middle) T5-T8 loop, x-ray (solid) and F_diag-L-M (shaded). (Bottom) T17-T20 loop, x-ray (solid) and F_diag-L-M (shaded).

FIGURE 7

Selected developments of the MM-PBSA free energies along the trajectories over intervals 1–3 ns (except of the F_diag-M simulation). The dashed line shows the linear regression over the trajectory portion shown. Note that after 2.5 ns the free energy values are largely stabilized.