Title Short catalytic peptides with intrinsic esterase activity
Title (english) Kratki linearni i ciklicki katalitički peptidi inspirirani esterazom
Author Patrizia Janković
Mentor Daniela Kalafatović (mentor)
Committee member Toni Todorovski (predsjednik povjerenstva)
Committee member Ruža Frkanec (član povjerenstva)
Granter University of Rijeka (Faculty of Biotechnology and Drug Development) Rijeka
Defense date and country 2024-07-01, Croatia
Scientific / art field, discipline and subdiscipline BIOTECHNICAL SCIENCES Biotechnology
Universal decimal classification (UDC ) 577 - Biochemistry. Molecular biology. Biophysics
Abstract In this dissertation, two key approaches for the design of catalytic peptides are explored: (i) the incorporation of amino acids from the catalytic triad and (ii) an approach
involving metal ions. To identify these main design approaches, a comprehensive dataset
based on the collection of published data about purely peptidic catalysts for ester hydrolysis was gathered and analyzed including both active and inactive sequences tested
towards the p-NPA and p-NPP substrates providing an insight into the currently developed
catalytic mechanisms. Additionally, this open-access dataset also includes the SMILESbased representation of peptides and it can be used for training of machine learning-based
models. Moreover, the standard p-NPA method was optimized. This extensively employed assay for determining catalytic activity, initially designed for enzymatic reactions,
is not directly applicable to peptides due to variations in reaction parameters, such as
the concentrations of catalysts and reaction times, when comparing peptides to enzymes.
Consequently, standardizing conditions, including temperature, pH, buffer choice, and
concentrations of both substrate and peptide, became essential to ensure accurate and
reliable results in peptide reactions. Furthermore, the synthesis of a set of histidine-rich
linear and cyclic peptides allowed us to understand the impact of amino acid arrangement,
cyclization, and inclusion of D-amino acids on their self-assembly, coordination of Zn2+
ions and ability to hydrolyze p-NPA. Investigating structural changes crucial to the functionality of short peptides contributes to the development of a new generation of catalytic
peptides and advances our understanding of the potential of self-assembly in improving
catalytic efficiency. Additionally, we investigated the feasibility of isolating the active
site of an enzyme to develop a minimalist catalyst, with a specific focus on recognizing
cysteine as a crucial component within the catalytic triad, essential for the effectiveness
of the peptide catalyst. The synthesis of a set of cysteine-rich peptides showing tunable
activity resulting from the sensitivity of the thiol groups to the redox environment could
open promising opportunities for tailored enzymatic catalysis. The overall goal of this
research is to gain a deeper insight into the relationship between the sequence and function of catalytic peptides, leading to the development of innovative peptide catalysts with
potential applications in various fields, including biocatalysis, pharmaceutical synthesis,
and other industrial processes.
Abstract (croatian) U ovoj disertaciji predstavljena su dva kljucna pristupa za dizajn katalitičkih peptida: (i) peptidne sekvence bazirane na aminokiselinama iz kataliticke trijade i (ii) pristup koji se temelji na interakciji peptida i metalnih iona. U svrhu identifikacije ovih glavnih pristupa, prikupljen je i analiziran sveobuhvatan skup podataka na temelju objavljenih katalitičkih peptida za hidrolizu estera, uključujući aktivne i neaktivne sekvence testirane na supstratima p-NPA i p-NPP, pružajuci uvid u trenutno razvijene katalitičke mehanizme. Ovaj skup podataka s otvorenim pristupom ukljucuje i računalnu reprezentaciju peptida u formatu SMILES koja se može koristiti za treniranje i razvoj modela zasnovanih na strojnom ucenju. Nadalje, optimizirana je standardna metoda p-NPA za određivanje katalitičke aktivnosti. Ovaj često korišteni esej, prvotno dizajniran za enzime, nije
izravno primjenjiv na peptide zbog varijacija u parametrima katalitiče reakcije, kao što su koncentracija katalizatora i trajanje reakcije u usporedbi peptida s enzimima. Stoga je bilo potrebno standardizirati uvjete, uključujući temperaturu, pH, izbor pufera i koncentracije supstrata i peptida, kako bi se osigurali tocni i pouzdani rezultati. Nadalje, sinteza skupa linearnih i ciklickih peptida bogatih histidinima omogućila nam je razumijevanje utjecaja rasporeda aminokiselina, ciklizacije i uključivanja D-aminokiselina na njihovu sposobnost samo-sastavljanja, koordinacije iona Zn2+ i sposobnost hidrolize pNPA. Istraživanje strukturnih promjena kljucnih za funkcionalnost kratkih peptida doprinosi razvoju nove generacije katalitičkih peptida i unaprjeđuje naše razumijevanje potencijala samo-sastavljanja u poboljšanju katalitičke učinkovitosti. Dodatno, ispitana je mogućnost izdvajanja aktivnog mjesta enzima radi razvoja minimalističkog katalitičkog peptida, s posebnim naglaskom na cistein kao ključnoj komponenti unutar katalitičke trijade, neophodnoj za učinkovitost takvih peptida. Sinteza seta cisteinom bogatih peptida koji pokazuju prilagodljivu aktivnost kao rezultat osjetljivosti tiolnih skupina na redoks okolinu, otvara nove mogućnosti za prilagodljivu peptidom posredovanu katalizu. Glavni cilj ovog istraživanja je razumjeti odnos izmedu sekvence i funkcije katalitičkih peptida, čime bi se omogućio razvoj inovativnih katalitičkih peptida primjenjivih u različitim područjima, uključujući biokatalizu, sintezu lijekova i industrijske procese.
Keywords
catalytic
peptides
p-NPA
self-assembly
Keywords (croatian)
katalitički
peptidi
p-NPA
samo-sastavljanje
Language english
URN:NBN urn:nbn:hr:193:335897
Promotion 2024
Study programme Title: Medicinal chemistry Study programme type: university Study level: postgraduate Academic / professional title: doktor/doktorica znanosti, interdisciplinarna područja znanosti, polje biotehnologija u biomedicini (doktor/doktorica znanosti, interdisciplinarna područja znanosti, polje biotehnologija u biomedicini)
Type of resource Text
File origin Born digital
Access conditions Open access
Terms of use
Created on 2024-07-10 09:18:27