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CSJ Journals

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2022, Vol.51, No.1

1-4

Integrated In Silico Studies on the Role of Nicotinamide Adenine Dinucleotide (NADH) Binding in Activating C-Terminal Binding Protein 2 (CtBP2)

Tsukasa Aoyagi ,1Ryunosuke Yoshino ,*2,3Yuki Mitsuta ,3,4Rikuri Morita ,3Ryuhei Harada ,3 and Yasuteru Shigeta *3
1Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
2Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
3Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
4Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
https://doi.org/10.1246/cl.210548

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Abstract

The C-terminal binding protein 2 (CtBP2) plays a role in apoptosis and embryogenesis. Genetic knockout studies have been demonstrated to cause severe developmental defects and embryonic lethality. CtBP2 has three key domains and dimerizes for a significant role by binding with nicotinamide adenine dinucleotide (NADH). However, the molecular mechanism of CtBP2 dimerization and the effect of NADH binding are unknown. In this study, we performed molecular dynamics (MD) and docking simulation to reveal the mechanism of C-terminal binding protein 2 (CtBP2) dimerization and the effect of NADH binding on the dimer formation. Our MD simulation results detected seven salt bridges that are important for CtBP2 dimerization. And docking simulation demonstrated that the holo-monomer gave a higher probability of correct docking pose than the apo-monomer. Moreover, in docking simulation using a PXDLS model peptide, that holo form gave more docking poses than that apo form. These results suggested that the holo form has a structure that facilitates the formation of dimers and the binding of PXDLS peptides.

figure

We performed molecular dynamics simulations to reveal the effect of NADH binding on the dimerization of CtBP2 and found that seven salt bridges are important for CtBP2 dimerization. Docking simulations for the holo and the apo forms indicate the former has a more favorable structure that facilitates both the formation of dimers and the binding of PXDLS peptides.

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