Computational Design of a Protein-Based Enzyme Inhibitor
| Autor: | Keith Hamilton, Gaetano T. Montelione, Erik Procko, Min Su, James M. Aramini, David Baker, Liang Tong, Rickard Hedman, Jayaraman Seetharaman, John F. Hunt, G. Kornhaber, Sarel J. Fleishman |
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| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular Protein Conformation Protein Data Bank (RCSB PDB) Plasma protein binding Protein Engineering Article Protein–protein interaction chemistry.chemical_compound Protein structure Structural Biology Catalytic Domain Animals Protein Interaction Domains and Motifs Amino Acid Sequence Protein Interaction Maps Enzyme Inhibitors Saturated mutagenesis Molecular Biology biology Computational Biology Active site Protein engineering Molecular Docking Simulation Biochemistry chemistry Mutagenesis Site-Directed biology.protein Biophysics Muramidase Lysozyme Protein Binding |
| Zdroj: | Journal of Molecular Biology. 425:3563-3575 |
| ISSN: | 0022-2836 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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