Computer-aided Binding Mode Prediction and Affinity Maturation of LRR Protein Binder without Structural Determination
| Autor: | Choi, Yoonjoo, Jeong, Sukyo, Choi, Jung-Min, Ndong, Christian, Bailey-Kellogg, Chris, Griswold, Karl E., Kim, Hak-Sung |
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| Rok vydání: | 2019 |
| Předmět: | |
| Zdroj: | Datacite UnpayWall ORCID Microsoft Academic Graph bioRxiv |
| DOI: | 10.1101/2019.12.18.880534 |
| Popis: | Binding affinity maturation without structure determination remains a difficult challenge in the computer-aided protein engineering. Precise binding mode identification is a vital prerequisite for the affinity maturation. However, pure computational methods have been unreliable in practice so far and experimental structural biology techniques are generally too costly. Herein, we show that computational epitope localization followed by the full-atom energy minimization with intermediate experimental validation can yield precisely bound complex model structure, which ultimately enables effective affinity maturation and redesign of binding specificity. As a proof-of-concept, we targeted a leucine-rich repeat (LRR) protein binder which specifically binds to the human IgG1 (hIgG1). Based on the computationally predicted binding mode of the LRR protein binder to hIgG1, the binding affinity of the protein binder was significantly increased and its specificity was redesigned toward multiple IgGs from other species. Experimental determination of the complex structure showed that the predicted model closely matched the X-ray crystal structure. Through the benchmark of therapeutically relevant existing LRR protein complexes, we demonstrate that the present approach can be broadly applicable to other proteins which undergo small conformational changes upon binding.Significance StatementComputer-aided design of binding affinity and specificity of two interacting proteins without structural determination is a challenging problem in protein engineering. Despite recent advances in the computational biology techniques, however, in silico evaluation of binding energies has proven to be extremely difficult. We show that, in the cases of protein-protein interactions where only small structural changes upon binding occur, partial experimental validation of binding can greatly complement the computational energy. Using an LRR (leucine-rich repeat) protein binder as a model system, the binding orientation of two binding partners was precisely dentified by the hybrid approach. Based on the predicted model, we could successfully redesign the binding affinity and specificity of the protein binder by the full-atom energy calculation. |
| Databáze: | OpenAIRE |
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