2hz8
From Proteopedia
| Line 4: | Line 4: | ||
==Overview== | ==Overview== | ||
| - | + | 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. | |
==About this Structure== | ==About this Structure== | ||
| - | 2HZ8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ8 OCA]. | + | 2HZ8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+116'>AC1</scene> and <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A+117'>AC2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ8 OCA]. |
==Reference== | ==Reference== | ||
| - | + | Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement., Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Valentine KG, Wand AJ, Degrado WF, Structure. 2008 Feb;16(2):210-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18275812 18275812] | |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| Line 21: | Line 21: | ||
[[Category: Wand, A J.]] | [[Category: Wand, A J.]] | ||
[[Category: ZN]] | [[Category: ZN]] | ||
| + | [[Category: de novo protein]] | ||
[[Category: four-helix bundle]] | [[Category: four-helix bundle]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:42:32 2008'' |
Revision as of 07:42, 14 March 2008
|
QM/MM structure refined from NMR-structure of a single chain diiron protein
Overview
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.
About this Structure
2HZ8 is a Protein complex structure of sequences from Escherichia coli with as ligand. Known structural/functional Sites: and . Full crystallographic information is available from OCA.
Reference
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement., Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Valentine KG, Wand AJ, Degrado WF, Structure. 2008 Feb;16(2):210-5. PMID:18275812
Page seeded by OCA on Fri Mar 14 09:42:32 2008
