Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.Calhoun, J.R., Liu, W., Spiegel, K., Dal Peraro, M., Klein, M.L., Valentine, K.G., Wand, A.J., Degrado, W.F.
(2008) Structure 16: 210-215
- PubMed: 18275812
- DOI: 10.1016/j.str.2007.11.011
- Structures With Same Primary Citation
- PubMed Abstract:
- Computational design and characterization of a monomeric helical dinuclear metalloprotein.
Calhoun, J.R., Kono, H., Lahr, S., Wang, W., DeGrado, W.F., Saven, J.G.
(2003) J Mol Biol 334: 1101
- Artificial diiron proteins: from structure to function.
Calhoun, J.R., Nastri, F., Magloi, O., Pavone, V., Lombardi, A., DeGrado, W.F.
(2005) Biopolymers 80: 264
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 ...
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 NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.
Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.