2hz8: Difference between revisions

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[[Image:2hz8.jpg|left|200px]]
{{Seed}}
[[Image:2hz8.png|left|200px]]


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{{STRUCTURE_2hz8|  PDB=2hz8  |  SCENE=  }}  
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'''QM/MM structure refined from NMR-structure of a single chain diiron protein'''
===QM/MM structure refined from NMR-structure of a single chain diiron protein===




==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 18275812 is the PubMed ID number.
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{{ABSTRACT_PUBMED_18275812}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ8 OCA].  
Full experimental 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://www.ncbi.nlm.nih.gov/pubmed/18275812 18275812]
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://www.ncbi.nlm.nih.gov/pubmed/18275812 18275812]
Computational design and characterization of a monomeric helical dinuclear metalloprotein., Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG, J Mol Biol. 2003 Dec 12;334(5):1101-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14643669 14643669]
Artificial diiron proteins: from structure to function., Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, DeGrado WF, Biopolymers. 2005;80(2-3):264-78. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15700297 15700297]
[[Category: Calhoun, J R.]]
[[Category: Calhoun, J R.]]
[[Category: DeGrado, W F.]]
[[Category: DeGrado, W F.]]
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[[Category: De novo protein]]
[[Category: De novo protein]]
[[Category: Four-helix bundle]]
[[Category: Four-helix bundle]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:53:33 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 18:49:26 2008''

Revision as of 15:49, 28 July 2008

File:2hz8.png

Template:STRUCTURE 2hz8

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

Template:ABSTRACT PUBMED 18275812

About this Structure

Full experimental 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

Computational design and characterization of a monomeric helical dinuclear metalloprotein., Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG, J Mol Biol. 2003 Dec 12;334(5):1101-15. PMID:14643669

Artificial diiron proteins: from structure to function., Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, DeGrado WF, Biopolymers. 2005;80(2-3):264-78. PMID:15700297

Page seeded by OCA on Mon Jul 28 18:49:26 2008

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