Original scientific paper

https://doi.org/10.5562/cca2916

Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study

Mario Gundić ; Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, HR-10000 Zagreb, Croatia
Antonija Tomić orcid.org/0000-0003-0109-3547 ; Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
Rebecca C. Wade orcid.org/0000-0001-5951-8670 ; Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
Mihaela Matovina orcid.org/0000-0001-7647-3339 ; Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
Zrinka Karačić ; Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
Saša Kazazić orcid.org/0000-0002-6185-2229 ; Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
Sanja Tomić orcid.org/0000-0002-0550-0878 ; Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia

Abstract

Kelch-like ECH associated protein 1 (Keap1) is a cellular sensor for oxidative stress and a negative regulator of the transcription factor Nrf2. Keap1 and Nrf2 control expression of nearly 500 genes with diverse cytoprotective functions and the Nrf2-Keap1 signaling pathway is a major regulator of cytoprotective responses to oxidative and electrophilic stress. It was found that the metallopeptidase dipeptidyl peptidase III (DPP III) contributes to Nrf2 activation by binding to Keap1, probably by binding to the Kelch domain, and thereby influences Nrf2 activity in cancer. We here first determined that the KD of the DPP III-Kelch domain complex is in the submicromolar range. In order to elucidate the molecular details of the DPP III – Kelch interaction we then built models of the complex between human DPP III and the Keap1 Kelch domain and performed coarse-grained and atomistic simulations of the complexes. In the most stable complexes, the ETGE motif in the DPP III flexible loop binds near the central pore of the six-blade β-propeller Kelch domain. According to the preliminary HD exchange experiments DPP III binds to the more unstructured end of Kelch domain. According to the results of MD simulations DPP III binding to the Kelch domain does not influence the overall DPP III structure or the long-range domain fluctuations. We can conclude that DPP III forms the stable complexes with the Keap1 Kelch domain by inserting the flexible loop into the entrance to the central pore of the six blade β-propeller Kelch domain at its more unstructured, N-terminus.

This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords

'protein-protein interaction'; dipeptidyl peptidase III; docking; molecular dynamics; Keap1; microscale thermophoresis (MST)

Hrčak ID:

166856

URI

https://hrcak.srce.hr/166856

Publication date:

21.6.2016.

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