Računalno istraživanje kompleksa dipeptidil peptidaze III (DPP III)–Kelch u svrhu predviđanja mutanta Kelch domene proteina Keap1 s povećanim afinitetom ZA DPP III

master's thesis

• Title (english): Computational investigation of the dipeptidyl peptidase III (DPP III)–Kelch complex to predict mutants of the Kelch domain of the Keap1 protein with increased affinity for DPP III
• Author: Karlo Zeman
• Mentor: Filip Šupljika (mentor)
• Mentor: Antonija Tomić (komentor)
• Committee member: Anita Horvatić (predsjednik povjerenstva)
• Committee member: Antonija Tomić (član povjerenstva)
• Committee member: Mihaela Matovina (član povjerenstva)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Chemistry and Biochemistry); (Laboratory for Physical Chemistry and Corrosion); Zagreb
• Defense date and country: 2024-12-18, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Signalni put Keap1–Nrf2 glavni je regulator staničnog odgovora na oksidativni stres. Transkripcijski faktor Nrf2, nakon prelaska u jezgru, aktivira citoprotektivne gene koji pomažu održavanju stanične redoks homeostaze. Dok aktivacija Nrf2 štiti zdrave stanice, pretjerana aktivacija u tumorskim stanicama dovodi do pojave kemorezistencije i radiorezistencije. Enzim dipeptidil peptidaza III (DPP III) kompetira Nrf2 za vezanje na Kelch domenu proteina Keap1, potičući Nrf2-ovisnu transkripciju. U okviru ovog diplomskog rada metodama računalne kemije istražena je mogućnost dizajna modificirane Kelch domene s većim afinitetom vezanja za DPP III od endogenog proteina Keap1 u svrhu sprječavanja prekomjerne aktivacije Nrf2 u tumorskim stanicama s pojačanom ekspresijom DPP III. Dugačkim simulacijama molekulske dinamike ispitana je struktura kompleksa, a metodom dekompozicije slobodne energije vezanja po aminokiselinama identificirane su aminokiseline iz Kelch domene koje destabiliziraju kompleks. Utjecaj mutacija tih aminokiselina na afinitet vezanja procijenjen je tzv. alanin scan metodom.

Abstract (english)

The Keap1–Nrf2 signaling pathway is the main regulator of the cellular response to oxidative stress. The transcription factor Nrf2, after translocating to the nucleus, activates cytoprotective genes that help maintain cellular redox homeostasis. While Nrf2 activation protects healthy cells, excessive activation in tumor cells lead to chemoresistance and radioresistance. The enzyme dipeptidyl peptidase III (DPP III) competes with Nrf2 for binding to the Kelch domain of Keap1, promoting Nrf2-dependent transcription. In this work, computational chemistry methods were used to explore the possibility of designing a modified Kelch domain with a higher binding affinity for DPP III than endogenous Keap1, in order to prevent excessive Nrf2 activation in tumor cells with increased DPP III expression. Extensive molecular dynamics simulations were performed to examine the structure of the complex, and per-residue binding free energy decomposition analysis was used to identify amino acids from the Kelch domain that destabilize the complex. The effect of mutations in these amino acids on binding affinity was assessed using the alanine scan method.

• Keywords: Kelch domena; dipeptidil peptidaza III; protein-protein interakcije; proteinski mutanti; simulacije molekulske dinamike
• Keywords (english): Kelch domain; dipeptidyl peptidase III; protein-protein interactions; protein mutants; molecular dynamic simulations
• Language: croatian
• URN:NBN: urn:nbn:hr:159:048271
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2025-01-13 13:50:25