COMPARISON OF SIMULATED AND EXPERIMENTALLY DETERMINED DYNAMICS FOR A VARIANT OF THE LACI DNA-BINDING DOMAIN, NLAC-P

Recent advances in the experimentally determined structures and dynami cs of the domains within Lad provide a rare context for evaluating dyn amics calculations. A 1500-ps trajectory was simulated for a variant o f the Lad DNA-binding domain, which consists of the first three helice s in Lad and the hinge helix of the homologous PurR. Order parameters derived from dynamics simulations are compared to those obtained for t he Lad DNA-binding domain with N-15 relaxation NMR spectroscopy (Slijp er et at., 1997. Biochemistry. 36:249-254). The MD simulations suggest that the unstructured loop between helices II and III does not exist in a discrete state under the conditions of no salt and neutral pH, bu t occupies a continuum of states between the DNA-bound and free struct ures. Simulations also indicate that the unstructured region between h elix ill and the hinge helix is very mobile, rendering motions of the hinge helix essentially independent of the rest of the protein. Finall y, the a-helical hydrogen bonds in the hinge helix are broken after 12 50 ps, perhaps as a prelude to helix unfolding.