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Molecular Dynamics Simulations of Carbonic Anhydrase's Thermostability for Carbon Capture Applications
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
2025 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Molekyldynamiska Simuleringar av Karbanhydras Termostabilitet för Koldioxidavskiljning (Swedish)
Abstract [sv]

Ett ökat utsläpp av CO2 har resulterat i den globala uppvärmningen, vilket utsätter hela mänskligheten för fara. Avskiljning och lagring av koldioxid (CCS) är en av de mest konventionella metoderna för koldioxidavskiljning. Möjligheten att tillsätta karbanhydras (CA) till dessa system har undersökts då de har en hög katalytisk aktivitet för koldioxidhydrering. Dock så måste dessa enzym klara av de höga temperaturer för att kunna tillämpas. Därmed eftersöktes mutanter med hög termostabilitet. Rekonstruktion av förfäderssekvenser (ASR) har använts för detta ändamål. I syfte att hitta en förundersökningsmetod för att identifiera mer termostabila mutanter före karakterisering av dem på laboratoriet, så har molekyldynamiska simuleringar (MD) undersökts. 

Ett fylogenetiskt träd med hjälp av ARS skapades från gensekvenser av CA från termofila mikroorganismer. Totalt simulerades 11 mutanter och en vildtyp-CA under 100 ns vid 363 K och 393 K. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), antal vätebindningar inom monomererna av enzymerna samt emellan monomererna av dimerena undersöktes. Inga fastställda resultat kunde bestämmas angående vilka mutanter som var mest termostabila. Förslag på de minst termostabila angavs (S_N3, S_N4, N2 och PmCA).

Abstract [en]

An increase in CO2 emission has led to global warming which puts the whole of humanity at risk. Carbon capture and storage (CCS) has become one of the most conventional methods for reversing global warming. Addition of carbonic anhydrase (CA) to these systems have been investigated due to their high catalytic activity of CO2 hydration. However these enzymes need to be able to withstand high temperatures in order to be applicable and therefore new thermostable mutants are searched for. Ancestral sequence reconstruction (ASR) was used for this purpose. In search of a pre screening method to identify more thermostable mutants before laboratory characterization, molecular dynamics (MD) has been investigated.

A phylogenetic tree by ARS was created from genome sequences of CA from thermophilic microorganisms. In total 11 mutants and one wild type CA were simulated for 100 ns at 363 K and 393 K. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds within the enzymatic monomer and in the interphase of the monomers in the dimers were investigated. No conclusive results regarding the most thermostable mutants could be drawn. Suggestions of the least thermostable mutants were given (S_N3, S_N4, N2 and PmCA).

Place, publisher, year, edition, pages
2025.
Series
TRITA-CBH-GRU ; 2025:191
Keywords [en]
Global warming, Carbon capture and storage, Carbonic anhydrase, Ancestral sequence reconstruction, Molecular dynamics
Keywords [sv]
Global uppvärmning, Avskiljning och lagring av koldioxid, Karbanhydras, Rekonstruktion av förfäderssekvenser, Molekyldynamiska simuleringar
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-364662OAI: oai:DiVA.org:kth-364662DiVA, id: diva2:1969920
Subject / course
Biotechnology
Educational program
Master of Science - Industrial and Environmental Biotechnology
Supervisors
Examiners
Available from: 2025-06-16 Created: 2025-06-16

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