Preorganization of molecular binding sites in designed diiron proteinsMaglio, O., Nastri, F., Pavone, V., Lombardi, A., DeGrado, W.F.
(2003) Proc Natl Acad Sci U S A 100: 3772-3777
- PubMed: 12655072
- DOI: 10.1073/pnas.0730771100
- Primary Citation of Related Structures:
- PubMed Abstract:
- Retrostructural Analysis of Metalloproteins. Application to the Design of a Minimal Model for Diiron Proteins
Lombardi, A., Summa, C.M., Geremia, S., Randaccio, L., Pavone, V., DeGrado, W.F.
(2000) Proc Natl Acad Sci U S A 97: 6298
- Tertiary Templates for the Design of Diiron Protein
Summa, C.M., Lombardi, A., Lewis, M., DeGrado, W.F.
(1999) Curr Opin Struct Biol 9: 500
- Toward the De Novo Design of a Catalytically Active Helix Bundle: a Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center
Di Costanzo, L., Wade, H., Geremia, S., Randaccio, L., Pavone, V., DeGrado, W.F., Lombardi, A.
(2001) J Am Chem Soc 123: 12749
- Sliding Helix and Change of Coordination Geometry in a Model di-Mn(II) Protein
DeGrado, W.F., Di Costanzo, L., Geremia, S., Lombardi, A., Pavone, V., Randaccio, L.
(2003) Angew Chem Int Ed Engl 42: 417
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)] ...
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.
Department of Chemistry, University of Napoli Federico II, Complesso Universitario Monte S. Angelo, I-80126 Napoli, Italy.