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bioRxiv · 10.1101/2020.05.24.113209

Molecular interaction mechanism of 14-3-3ε protein with phosphorylated Myeloid leukemia factor 1 revealed by an enhanced conformational sampling

Higo, J.·Kawabata, T.·Kusaka, A.·Kasahara, K.·Kamiya, N.·Fukuda, I.·Mori, K.·Hata, Y.·Fukunishi, Y.·Nakamura, H.
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Abstract

Enhanced conformational sampling, a genetic-algorithm-guided multi-dimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semi-stable complex structures, and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3{varepsilon}, and a flexible peptide, phosphorylated Myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3{varepsilon}. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3{varepsilon} surface, and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spots are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding-constant changes resultant from alanine-mutation experiment for the residues. We performed a simulation of non-phosphorylated peptide and 14-3-3{varepsilon}, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3{varepsilon}.

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Higo, J., Kawabata, T., Kusaka, A., Kasahara, K., Kamiya, N., Fukuda, I., Mori, K., Hata, Y., Fukunishi, Y., Nakamura, H.. 2020-05-27. Molecular interaction mechanism of 14-3-3ε protein with phosphorylated Myeloid leukemia factor 1 revealed by an enhanced conformational sampling. https://doi.org/10.1101/2020.05.24.113209

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