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Modeling of Conformational Transitions in Membrane Proteins with Coarse-Grained Methods
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
2015 (English)Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
Abstract [en]

Understanding the dynamics of proteins is crucial in order to understand life on a molecular level. In this Bachelor’s thesis large scale motions of the membrane protein SERCA has been investigated with coarse-grained methods. The goal was to find certain places in the structure where mutations could alter and affect the functionality of the protein, possibly leading to disease. The protein was modeled with an elastic network model and simulated with Langevin dynamics. Data from the simulations was used to calculate all the places were formation of stabilizing salt bridges were possible and these were then compared with mutations found in real cancerous cells. Promising results were obtained but need to be investigated further with more sophisticated methods before any conclusions can be drawn regarding their significance for the protein functionality. Likewise, the use of elastic network models together with Langevin dynamics showed to be a good alternative to sample large conformational changes in proteins.

Abstract [sv]

Kunskap om proteiners dynamik är av stor vikt för att kunna förstå mekanismerna bakomlivet på en molekylär nivå. I denna kandidatexamensuppsats har storskaliga rörelser i membranproteinet SERCA undersökts med hjälp grovkorniga metoder. Målet var att hitta särskilda platser i strukturen där mutationer kunde införas och påverka proteinetsfunktionalitet, något som möjligen skulle kunna leda till sjukdom. Proteinet modellerades som ett elastiskt nätverk och simulerades med Langevin-dynamik. Data från simuleringarna användes sedan för att beräkna samtliga platser där bildandet av stabiliserandesalt bryggor var möjlig, varpå dessa jämfördes med mutationer funna i riktiga cancerceller. Lovande resultat er hölls, men dessa måste dock undersökas vidare med mer sofistikerade metoder innan slutsatser kan dras gällande deras betydelse för proteinets funktionalitet. Där till visade sig användan det av elastiska nätverksmodeller tillsammans med Langevindynamik vara ett bra alternativ för att fånga stora strukturella förändringar i proteiner.

Place, publisher, year, edition, pages
2015. , 27 p.
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-168026OAI: oai:DiVA.org:kth-168026DiVA: diva2:813972
Supervisors
Available from: 2015-05-25 Created: 2015-05-25 Last updated: 2015-05-25Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
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