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1nvo

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{{STRUCTURE_1nvo| PDB=1nvo | SCENE= }}
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'''Solution structure of a four-helix bundle model, apo-DF1'''
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===Solution structure of a four-helix bundle model, apo-DF1===
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==Overview==
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De novo protein design provides an attractive approach to critically test the features that are required for metalloprotein structure and function. Previously we designed and crystallographically characterized an idealized dimeric model for the four-helix bundle class of diiron and dimanganese proteins [Dueferri 1 (DF1)]. Although the protein bound metal ions in the expected manner, access to its active site was blocked by large bulky hydrophobic residues. Subsequently, a substrate-access channel was introduced proximal to the metal-binding center, resulting in a protein with properties more closely resembling those of natural enzymes. Here we delineate the energetic and structural consequences associated with the introduction of these binding sites. To determine the extent to which the binding site was preorganized in the absence of metal ions, the apo structure of DF1 in solution was solved by NMR and compared with the crystal structure of the di-Zn(II) derivative. The overall fold of the apo protein was highly similar to that of the di-Zn(II) derivative, although there was a rotation of one of the helices. We also examined the thermodynamic consequences associated with building a small molecule-binding site within the protein. The protein exists in an equilibrium between folded dimers and unfolded monomers. DF1 is a highly stable protein (K(diss) = 0.001 fM), but the dissociation constant increases to 0.6 nM (deltadeltaG = 5.4 kcalmol monomer) as the active-site cavity is increased to accommodate small molecules.
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(as it appears on PubMed at http://www.pubmed.gov), where 12655072 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12655072}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NVO OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NVO OCA].
==Reference==
==Reference==
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[[Category: De novo protein design]]
[[Category: De novo protein design]]
[[Category: Diiron protein model]]
[[Category: Diiron protein model]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:10:12 2008''

Revision as of 21:10, 27 July 2008

Image:1nvo.png

Template:STRUCTURE 1nvo

Solution structure of a four-helix bundle model, apo-DF1

Template:ABSTRACT PUBMED 12655072

About this Structure

Full experimental information is available from OCA.

Reference

Preorganization of molecular binding sites in designed diiron proteins., Maglio O, Nastri F, Pavone V, Lombardi A, DeGrado WF, Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3772-7. Epub 2003 Mar 24. PMID:12655072

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