2HZ8

QM/MM structure refined from NMR-structure of a single chain diiron protein

Summary for 2HZ8

• Entry DOI: 10.2210/pdb2hz8/pdb
• Related: 1EC5 1JMB 1JMO 1MFT 1NVO 1u7j
• Descriptor: De novo designed diiron protein, ZINC ION (3 entities in total)
• Functional Keywords: four-helix bundle, de novo protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 13647.23

Authors

Calhoun, J.R.,Liu, W.,Spiegel, K.,Dal Peraro, M.,Klein, M.L.,Wand, A.J.,DeGrado, W.F. (deposition date: 2006-08-08, release date: 2007-07-17, Last modification date: 2024-05-29)

Primary citation

Calhoun, J.R.,Liu, W.,Spiegel, K.,Dal Peraro, M.,Klein, M.L.,Valentine, K.G.,Wand, A.J.,Degrado, W.F.
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.
Structure, 16:210-215, 2008

PubMed 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 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.

PubMed: 18275812
DOI: 10.1016/j.str.2007.11.011

Experimental method

SOLUTION NMR