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Binding mechanism of adenylate kinase-specific monobodies
Ibuki Nakamura1, Hiroshi Amesaka2, Satoshi Nagao3
1Division of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan.
Abstract:
Monobodies are synthetic antibody-mimetic proteins that regulate enzyme functions through protein-protein interactions. In this study, we investigated the binding mechanisms of monobodies to adenylate kinase (Adk). Calorimetric and X-ray crystallographic analyses revealed that CL-1, a monobody specific for the CLOSED form of Adk, binds to the CORE domain of Adk in an enthalpy-driven manner, forming several hydrogen bonds and a cation-π interaction at the protein interface, without perturbing the Adk backbone. In contrast, OP-4, an OPEN-form-specific monobody, exhibited entropy-driven binding. 1H-15N 2D nuclear magnetic resonance (NMR), 31P-NMR, and calorimetric studies revealed conformational perturbations to Adk by OP-4, while substrate access remained intact. The different thermodynamic and structural effects between the monobodies highlight the diverse binding mechanisms among monobodies.
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