20.500.12556/DKUM-90305 Mehanizem stabilizacije humanega transportnega proteina transtiretina z rožmarinsko kislino Stabilisation mechanism of the human transthyretin transporter protein by rosmarinic acid Dedna transtiretinska amiloidoza je avtosomno dominantna bolezen. Nastane kot posledica mutacije v proteinu transtiretinu. Mutacije povzročajo strukturne spremembe proteina, ki jim sledi disociacija v monomere in kasneje agregacija monomerov ter tvorba amiloidnih vlakenc. Vlakenca se nalagajo v tkivih kot so živčevje, srce in ledvice. Nestabilno strukturo proteina, ki jo povzročajo mutacije, je možno stabilizirati z vezavo majhnih molekul na protein. Ena izmed takšnih molekul je rožmarinska kislina. V magistrskem delu smo z uporabo računalniških simulacij molekulske dinamike ugotavljali, kako mutacija V30M vpliva na stabilnost strukture proteina transtiretina. Na protein smo vezali tudi rožmarinsko kislino in opazovali, ali se z vezavo stabilnost proteina spremeni. Pri tem smo uporabili dva različna načina parametrizacije polja sil za rožmarinsko kislino. Za pripravo 6 simulacij molekulske dinamike smo uporabili program CHARMM-GUI, za samo izvedbo simulacij pa program NAMD. Rezultate smo vizualno pregledali in analizirali s programoma Chimera in Cytoscape. Analiza trajektorij molekulskih dinamik je obsegala izračun srednjega kvadrata odstopanja, analizo vodikovih vezi in analizo vseh nekovalentnih kontaktov. Rezultati, ki smo jih pri tem dobili, kažejo, da mutacija V30M povzroči manj stabilno strukturo transtiretina. Avtomatsko parametrizirana rožmarinska kislina na stabilnost kompleksa protein-ligand za nemutirani protein ni imela velikega vpliva, medtem ko je ročno parametrizirana rožmarinska kislina zmanjšala število kontaktov med nemutiranim proteinom in ligandom. V primeru vezave ročno parametrizirane rožmarinske kisline pa smo zaznali veliko število kontaktov med proteinom in ligandom. Ob vezavi rožmarinske kisline na nemutirani protein smo zaznali manjšo stabilnost proteina. Vezava rožmarinske kisline na mutirani protein pa izboljša stabilnost proteina. Hereditary transthyretin amyloidosis is an autosomal dominant disease. The disease is caused by a mutation in the transthyretin protein. Mutations cause structural changes in the protein, followed by dissociation into monomers and subsequent aggregation of the monomers to form amyloid fibrils. Fibrils are deposited in organs such as the nervous system, heart and kidneys. The unstable protein structure caused by mutations can be stabilised by binding small molecules to the protein. One such molecule is rosmarinic acid. In this thesis, we used computational molecular dynamics simulations to determine how the V30M mutation affects the stability of the structure of the transthyretin protein. We also bound rosmarinic acid to the protein and observed whether the binding changes the stability of the protein. Two different ways of the force field parameterisation for rosmarinic acid were used. We applied CHARMM-GUI to prepare the 6 molecular dynamics simulations and NAMD to run them. The results were visually examined and analysed using Chimera and Cytoscape. The analysis of the molecular dynamics trajectories included the calculation of the Root Mean Square Deviation, the analysis of hydrogen bonds and the analysis of all non-covalent contacts. The results obtained show that the V30M mutation results in a less stable transthyretin structure. The stability of the protein-ligand complex for the non-mutated protein was not significantly affected by the automatically parameterised rosmarinic acid, whereas the manually parameterised rosmarinic acid reduced the number of contacts between the non-mutated protein and the ligand. However, in the case of binding manually parameterised rosmarinic acid, a high number of contacts between the protein and the ligand was detected. Binding of rosmarinic acid to the mutated protein improves the stability of the protein. However, when rosmarinic acid was bound to the non-mutated protein, we detected lack of stability of the protein itself. transtiretin transtiretinska amiloidoza rožmarinska kislina simulacije molekulske dinamike polje sil stabilnost proteina transthyretin transthyretin amyloidosis rosmarinic acid molecular dynamics simulations force field protein stability true true false Slovenski jezik Angleški jezik Neznano 2024-08-28 20:42:47 2024-10-10 14:27:39 2025-01-29 12:03:51 0000-00-00 00:00:00 2020 0 Maribor 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 712.253(497.4Maribor) 24387075 0350-4972 MAG_Kocevar_Meta_2024.pdf MAG_Kocevar_Meta_2024.pdf 1 D4589AA5A568787C9AD12E3F9DB3CB20 9fe8f22630eba3a17f84382f9d9668da8657b6d4d1e945ff1d701882463d2867 f1446ad3-86fe-11ef-808f-00155d000105 https://dk.um.si/Dokument.php?lang=slv&id=186381 Fakulteta za kemijo in kemijsko tehnologijo 0 0 0