Computational Modeling Investigating the Interactions of Proteins with Fullerene-based Nanoparticles

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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en
dc.contributor.advisor Salonen, Emppu, Dr., Aalto University, Finland
dc.contributor.author Nedumpully Govindan, Praveen
dc.date.accessioned 2013-01-11T09:30:21Z
dc.date.available 2013-01-11T09:30:21Z
dc.date.issued 2013
dc.identifier.isbn 978-952-60-4980-9 (electronic)
dc.identifier.isbn 978-952-60-4979-3 (printed)
dc.identifier.issn 1799-4942 (electronic)
dc.identifier.issn 1799-4934 (printed)
dc.identifier.issn 1799-4934 (ISSN-L)
dc.identifier.uri https://aaltodoc.aalto.fi/handle/123456789/7309
dc.description.abstract In this work, the effects of fullerene-based nanoparticles (fullerene and two of its derivatives) on the structure and functioning of proteins were investigated. An approach combining two computational methods — molecular docking and molecular dynamics simulations — was used. The studies were based on, and complement experiments on the effects on nanoparticles on proteins. To make a better prospective, first, the properties of nanoparticle clusters in water were studied. The nature and stability of the clusters were found to depend on the surface properties of the nanoparticle. Nanoparticles with hydrophobic surfaces made strong and stable clusters, whereas hydrophilic nanoparticles made loose associations whose structure changed over time. In addition, the effects of nanoparticles on the secondary structure of small peptides were studied. For some peptides, a small increase in the alpha-helix content was observed in the presence of nanoparticles.  For protein-nanoparticle interactions, the inhibition of an enzyme protein, namely taq DNA polymerase, by fullerene derivatives was studied. Based on our studies, we predicted that the inhibition was caused by tertiary structural changes of the protein induced by the nanoparticles. Point mutation studies which could be used to examine our predictions were also proposed. In another study, the inhibition of tubulin self-assembly into microtubules by fullerene species was investigated. Simulation studies indicated that binding of nanoparticles to certain locations on tubulin was responsible for the inhibition. These binding sites are important for self-assembly as they are located in areas that make contact with the neighboring tubulins in microtubules. Finally, interactions of FUL and FUOH nanoparticles with ubiquitin was studied. Two more prominent binding sites, including one near the C-terminal tail was observed, and the biological implications of the binding are discussed.    en
dc.format.extent 114
dc.format.mimetype application/pdf
dc.language.iso en en
dc.publisher Aalto University en
dc.publisher Aalto-yliopisto fi
dc.relation.ispartofseries Aalto University publication series DOCTORAL DISSERTATIONS en
dc.relation.ispartofseries 12/2013
dc.subject.other Physics en
dc.title Computational Modeling Investigating the Interactions of Proteins with Fullerene-based Nanoparticles en
dc.type G4 Monografiaväitöskirja fi
dc.contributor.school Perustieteiden korkeakoulu fi
dc.contributor.school School of Science en
dc.contributor.department Teknillisen fysiikan laitos fi
dc.contributor.department Department of Applied Physics en
dc.subject.keyword proteins en
dc.subject.keyword nanoparticles en
dc.subject.keyword nanotoxicity en
dc.subject.keyword molecular dynamics en
dc.subject.keyword molecular docking en
dc.subject.keyword simulations en
dc.subject.keyword computational physics en
dc.identifier.urn URN:ISBN:978-952-60-4980-9
dc.type.dcmitype text en
dc.type.ontasot Doctoral dissertation (monograph) en
dc.type.ontasot Väitöskirja (monografia) fi
dc.contributor.supervisor Ala-Nissilä, Tapio, Prof., Aalto University, Finland
dc.opn Tieleman, Peter, Prof., University of Calgary, Canada
dc.contributor.lab SOFT en
dc.rev Faller, Roland, Prof., University of California Davis, USA
dc.rev Bunker, Alex, Dr., University of Helsinki, Finland
dc.date.defence 2013-01-15


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