8 publications

8 publications

Alteration of the Oxygen-Dependent Reactivity of De Novo Due Ferri Proteins

DeGrado, W. F.

Nat. Chem., 2012, 10.1038/NCHEM.1454

De novo proteins provide a unique opportunity to investigate the structure–function relationships of metalloproteins in a minimal, well-defined and controlled scaffold. Here, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the Due Ferri family. Originally created to catalyse the O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyse the selective N-hydroxylation of arylamines by remodelling the substrate access cavity and introducing a critical third His ligand to the metal-binding cavity. Additional second- and third-shell modifications were required to stabilize the His ligand in the core of the protein. These structural changes resulted in at least a 106-fold increase in the relative rate between the arylamine N-hydroxylation and hydroquinone oxidation reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of the geometric and electronic factors that influence the catalytic tuning of di-iron active sites.


Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferro 1
Anchoring strategy: Dative
Optimization: Genetic
Reaction: N-Hydroxylation
Max TON: ---
ee: ---
PDB: 2LFD
Notes: ---

An Artificial Di-Iron Oxo-Orotein with Phenol Oxidase Activity

DeGrado, W. F.; Lombardi, A.

Nat. Chem. Biol., 2009, 10.1038/nchembio.257

Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.


Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferro 1
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Alcohol oxidation
Max TON: >50
ee: ---
PDB: 2KIK
Notes: kcat/KM ≈ 1380 M-1*min-1

Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferro 1
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Amine oxidation
Max TON: ---
ee: ---
PDB: 2KIK
Notes: kcat/KM ≈ 83 M-1*min-1

An Artificial Di-Iron Oxo-Orotein with Phenol Oxidase Activity

DeGrado, W. F.; Lombardi, A.

Nat. Chem. Biol., 2009, 10.1038/nchembio.257

Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.


Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferro 1
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Alcohol oxidation
Max TON: >50
ee: ---
PDB: 2KIK
Notes: kcat/KM ≈ 1380 M-1*min-1

Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferro 1
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Amine oxidation
Max TON: ---
ee: ---
PDB: 2KIK
Notes: kcat/KM ≈ 83 M-1*min-1

Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure

Review

DeGrado, W. F.; Lombardi, A.

Eur. J. Inorg. Chem., 2015, 10.1002/ejic.201500470


Notes: ---

Catalytic Efficiency of Designed Catalytic Proteins

Review

DeGrado, W. F.; Korendovych, I. V.

Curr. Opin. Struct. Biol., 2014, 10.1016/j.sbi.2014.06.006


Notes: ---

De Novo Design of Catalytic Proteins

DeGrado, W. F.

Proc. Natl. Acad. Sci. U. S. A., 2004, 10.1073/pnas.0404387101


Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferro 1
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Alcohol oxidation
Max TON: >100
ee: ---
PDB: ---
Notes: kcat/KM ≈ 1540 M-1*min-1

Design of a Switchable Eliminase

DeGrado, W. F.

Proc. Natl. Acad. Sci. U. S. A., 2011, 10.1073/pnas.1018191108


Metal: Ca
Ligand type: Amino acid
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Kemp elimination
Max TON: >40
ee: ---
PDB: 2KZ2
Notes: Ca acts as allosteric regulator, catalytically active site contains no metal

Diiron-Containing Metalloproteins: Developing Functional Models

Review

DeGrado, W. F.; Lombardi, A.

C. R. Chim., 2007, 10.1016/j.crci.2007.03.010


Notes: ---