PDBsum entry 3vb8

De novo protein

PDB id: 3vb8

Contents

Protein chains

153 a.a.

Ligands

SO4

Waters ×119

PDB id:

3vb8

Name:

De novo protein

Title:

Crystal structure of engineered protein, northeast structural genomics consortium target or43

Structure:

Engineered protein. Chain: a, b. Engineered: yes

Source:

Artificial gene. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.90Å R-factor: 0.244 R-free: 0.290

Authors:

J.Seetharaman,M.Su,E.Procko,D.Baker,C.Ciccosanti,S.Sahdev,R.Xiao, J.K.Everett,T.B.Acton,G.T.Montelione,J.F.Hunt,L.Tong,Northeast Structural Genomics Consortium (Nesg)

Key ref:

E.Procko et al. (2013). Computational design of a protein-based enzyme inhibitor. J Mol Biol, 425, 3563-3575. PubMed id: 23827138 DOI: 10.1016/j.jmb.2013.06.035

Date:

31-Dec-11 Release date: 06-Jun-12

Protein chains

No UniProt id for this chain

Struc: 153 a.a.

DOI no: 10.1016/j.jmb.2013.06.035

J Mol Biol 425:3563-3575 (2013)

PubMed id: 23827138

Computational design of a protein-based enzyme inhibitor.

E.Procko, R.Hedman, K.Hamilton, J.Seetharaman, S.J.Fleishman, M.Su, J.Aramini, G.Kornhaber, J.F.Hunt, L.Tong, G.T.Montelione, D.Baker.

ABSTRACT

While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.