Journal article
Computational Design of a Protein-Based Enzyme Inhibitor
Journal of Molecular Biology, Vol.425(18), pp.3563-3575
Sep/2013
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. Published by Elsevier Ltd.
Details
- Title
- Computational Design of a Protein-Based Enzyme Inhibitor
- Creators
- Erik Procko (null)Rickard Hedman (null)Keith Hamilton (null)Jayaraman Seetharaman (null)Sarel J. Fleishman (null)Min Su (null)James Aramini (null)Gregory Kornhaber (null)John F. Hunt (null)Liang Tong (null)Gaetano T. Montelione (null)David Baker (null)
- Resource Type
- Journal article
- Publication Details
- Journal of Molecular Biology, Vol.425(18), pp.3563-3575; Sep/2013
- Number of pages
- 13
- Language
- English
- DOI
- https://doi.org/10.1016/j.jmb.2013.06.035
- Grant note
- National Institute of General Medical Studies of the National Institutes of Health [P41 GM103533]; Defense Threat Reduction Agency [HDTRA1-10-0040]; Protein Structure Initiative of the National Institutes of Health [U54-GM094597]; Human Frontier Science ProgramThis work was supported by the National Institute of General Medical Studies of the National Institutes of Health under award number P41 GM103533, Defense Threat Reduction Agency grant HDTRA1-10-0040 and by a grant from the Protein Structure Initiative of the National Institutes of Health (U54-GM094597) to the Northeast Structural Genomics Consortium. S.J.F. was supported by the Human Frontier Science Program._ALMAME_DELIMITER_
- Record Identifier
- 993264160603596
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