Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

ABSTRACT: We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that

SUBMITTER: Calhoun JR 

PROVIDER: S-EPMC3814030 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature