Figure 4.

Dynamics of ion pairs of Lys side-chain NH₃⁺ groups and backbone phosphates. (A) Transitions between the contact ion pair (CIP) state and the solvent-separated ion pair (SIP) state observed in molecular dynamics (MD) simulations. (B) Probability distribution and free-energy landscape (i.e., potential of mean force [PMF]) as a function of the O···N distance obtained from MD trajectories.⁶⁵ (C) Histogram of the O···N distances for 3038 Lys NH₃⁺–DNA phosphate ion pairs found in high-resolution (<2.0 Å) crystal structures.⁶¹ PMF obtained from this histogram is also presented. These data represent experimental evidence of SIP as a metastable state in electrostatic interactions. (D) NMR data supporting the CIP–SIP transitions.⁶⁵ The ^h3J_NP coupling data show the presence of the CIP states. The S² and ³J_NζCγ data show good agreement with those obtained from MD trajectories, suggesting that these ion pairs are as dynamic as seen in the MD simulations.