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master's thesis
Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube
Split: University of Split, Faculty of Science, 2024. urn:nbn:hr:166:044828
Buljac, Lucia
University of Split
Faculty of Science

Institutional repository: Repository of Faculty of Science

Cite this document

Buljac, L. (2024). Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube (Master's thesis). Split: University of Split, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:166:044828

Buljac, Lucia. "Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube." Master's thesis, University of Split, Faculty of Science, 2024. https://urn.nsk.hr/urn:nbn:hr:166:044828

Buljac, Lucia. "Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube." Master's thesis, University of Split, Faculty of Science, 2024. https://urn.nsk.hr/urn:nbn:hr:166:044828

Buljac, L. (2024). 'Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube', Master's thesis, University of Split, Faculty of Science, accessed 20 December 2024, https://urn.nsk.hr/urn:nbn:hr:166:044828

Buljac L. Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube [Master's thesis]. Split: University of Split, Faculty of Science; 2024 [cited 2024 December 20] Available at: https://urn.nsk.hr/urn:nbn:hr:166:044828

L. Buljac, "Analysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube", Master's thesis, University of Split, Faculty of Science, Split, 2024. Available at: https://urn.nsk.hr/urn:nbn:hr:166:044828

Metadata
TitleAnalysis of molecular dynamics simulations of PQQ-GDH in interaction with carbon nanotube
Title (croatian)Analiza molekularne dinamike PQQ-GDH proteina u interakciji s ugljikovom nanocjevčicom
AuthorLucia Buljac
MentorŽeljka Sanader Maršić (mentor)
MentorAntonija Mravak (pomoć pri izradi, neposredni voditelj)
Committee memberŽeljka Sanader Maršić (predsjednik povjerenstva)
Committee memberAntonija Mravak (član povjerenstva)
Committee memberMartina Požar (član povjerenstva)
GranterUniversity of Split
Faculty of Science
Split
Defense date and country2024-10-01, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Physics
Abstract
Interest for enzymatic biofuel cells grows in the past years, due to their biological components which counteract noble-metal and alloy-based fuel cells. Soluble glucose dehydrogenase, or PQQ-GDH enzyme, showed exciting possibility for application in biosensing and bioenergetics, due to their high catalytic activity which is oxygen independent. Analysis of molecular dynamics simulations of the monomer of protein PQQ-GDH in complex with short and infinitely long carbon nanotube (CNT) has been carried out, using methods and tools of VMD program. To examine the stability and the strength of protein nanotube interactions, distances between certain residues and CNT wall were calculated. To examine protein stability and function preservation, root-mean-square deviation and radius of gyration of monomers with and without nanotube were computed. Finally, considering results from simulation analysis, a theoretical prototype of the enzymatic biosensor comprising PQQ-GDH enzyme in complex with a short CNT was constructed.
Abstract (croatian)
Interes za enzimatske biogorivne ćelije raste proteklih godina, zbog njihovih bioloških komponenti koje se suprotstavljaju gorivnim ćelijama na bazi plemenitih metala i legura. Topljiva glukoza dehidrogenaza, ili enzim PQQ-GDH, pokazao je obećavajuće pokušaje primjene u biosenzorima i bioenergetici, zbog svoje visoke katalitičke aktivnosti neovisne o kisiku. Koristeći metode i alate programa VMD, provedena je analiza simulacija molekularne dinamike monomera proteina PQQ-GDH u kompleksu s kratkom i beskonačno dugom ugljikovom nanocjevčicom (CNT). U svrhu ispitivanja stabilnosti i snage interakcija između monomera i nanocjevčice, izračunate su udaljenosti između određenih aminokiselinskih ostataka i stijenke CNT-a. U svrhu ispitivanja stabilnosti i očuvanja funkcije proteina, izračunate su standardne devijacije i radijusi giracije monomera sa i bez nanocjevčice. Na kraju, uzimajući u obzir rezultate analize simulacija, konstruiran je teorijski prototip enzimatskog biosenzora koji sadrži PQQ-GDH enzim u kompleksu s kratkom CNT.
Keywords
Keywords (croatian)
Languageenglish
URN:NBNurn:nbn:hr:166:044828
Study programmeTitle: Physics; specializations in: specialization in Education, specialization in Astrophysics and Elementary Particle Physics, specialization in Biophysics, specialization in Environmental Physics, specialization in Computational Physics
Course: specialization in Biophysics
Study programme type: university
Study level: graduate
Academic / professional title: sveučilišni/a magistar/magistra fizike (sveučilišni/a magistar/magistra fizike)
Type of resourceText
File originBorn digital
Access conditionsOpen access
Terms of useLicence In copyright icon
Created on2024-10-28 12:42:28