Inclusion of ionic interactions in force field calculations of charged biomolecules – DNA structural transitions

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Abstract
The potential of mean force (PMF) approach for treating polyion–diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA 81, 5116–5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER‐PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C‐G)6, and the B and heteronomous (H) conformations of dA12 · dT12, as a function of salt concentration. In the case of d(C‐G)6, the predicted B–ZI transition occurs at 2.4M and is essentially driven by the phosphate‐diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B‐DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl.In the range of 0.01–0.3M NaCl, the H form of dA12 · dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence.