Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P

Recent advances in the experimentally determined structures and dynamics of the domains within Lacl, provide a rare context for evaluating dynamics calculations. A 1500-ps trajectory was simulated for a variant of the Lacl DNA-binding domain, which consists of the first three helices in Lacl and the hinge helix of the homologous PurR. Order parameters derived from dynamics simulations are compared to those obtained for the Lacl DNA-binding domain with ¹⁵N relaxation NMR spectroscopy (Slijper et al., 1997. Biochemistry. 36:249=254). The MD simulations suggest that the unstructured loop between halices II and III does not exist in a discrete state under the conditions of no salt and neutral pH, but occupies a continuum of states between the DNA- bound and free structures. Simulations also indicate that the unstructured region between helix III and the hinge helix is very mobile, rendering motions of the hinge helix essentially independent of the rest of the protein. Finally, the α-helical hydrogen bonds in the hinge helix are broken after 1250 ps, perhaps as a prelude to helix unfolding.