2HZ8

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

2HZ8 の概要

• エントリーDOI: 10.2210/pdb2hz8/pdb
• 関連するPDBエントリー: 1EC5 1JMB 1JMO 1MFT 1NVO 1u7j
• 分子名称: De novo designed diiron protein, ZINC ION (3 entities in total)
• 機能のキーワード: four-helix bundle, de novo protein
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 13647.23

構造登録者

Calhoun, J.R.,Liu, W.,Spiegel, K.,Dal Peraro, M.,Klein, M.L.,Wand, A.J.,DeGrado, W.F. (登録日: 2006-08-08, 公開日: 2007-07-17, 最終更新日: 2024-05-29)

主引用文献

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

実験手法

SOLUTION NMR