1nvo

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(New page: 200px<br /><applet load="1nvo" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nvo" /> '''Solution structure of a four-helix bundle mo...)
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'''Solution structure of a four-helix bundle model, apo-DF1'''<br />
'''Solution structure of a four-helix bundle model, apo-DF1'''<br />
==Overview==
==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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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.
==About this Structure==
==About this Structure==
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1NVO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with ACE and NH2 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NVO OCA].
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1NVO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=ACE:'>ACE</scene> and <scene name='pdbligand=NH2:'>NH2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NVO OCA].
==Reference==
==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12655072 12655072]
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12655072 12655072]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: DeGrado, W.F.]]
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[[Category: DeGrado, W F.]]
[[Category: Lombardi, A.]]
[[Category: Lombardi, A.]]
[[Category: Maglio, O.]]
[[Category: Maglio, O.]]
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[[Category: diiron protein model]]
[[Category: diiron protein model]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:53:13 2007''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:10:34 2008''

Revision as of 12:10, 21 February 2008


1nvo

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

Overview

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.

About this Structure

1NVO is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic 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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