Binding of Pollutants to Biomolecules: A Simulation Study

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dc.contributor.authorYildirim, Ahmet
dc.contributor.authorZhang, Jin
dc.contributor.authorManzetti, Sergio
dc.contributor.authorvan der Spoel, David
dc.date.accessioned2019-11-28T10:53:30Z
dc.date.available2019-11-28T10:53:30Z
dc.date.issued2016en_US
dc.departmentFen - Edebiyat Fakültesien_US
dc.description.abstractA number of cases around the world have been reported where animals were found dead or dying with symptoms resembling a thiamine (vitamin B) deficiency, and for some of these, a link to pollutants has been suggested. Here, we investigate whether biomolecules involved in thiamin binding and transport could be blocked by a range of different pollutants. We used in silico docking of five compound classes (25 compounds in total) to each of five targets (prion protein, ECF-type ABC transporter, thi-box riboswitch receptor, thiamin pyrophosphokinase, and YKoF protein) and subsequently performed molecular dynamics (MD) simulations to assess the stability of the complexes. The compound classes were thiamin analogues (control), pesticides, veterinary medicines, polychlorinated biphenyls, and dioxins, all of which are prevalent in the environment to some extent. A few anthropogenic compounds were found to bind the ECF-type ABC transporter, but none binds stably to prion protein. For the riboswitch, most compounds remained in their binding pockets during 50 ns of MD simulation, indicating that RNA provides a promiscuous binding site. In both YKoF and thiamin pyrophosphokinase (TPK), most compounds remain tightly bound. However, TPK biomolecules undergo pollutant-induced conformational changes. Although most compounds are found to bind to some of these targets, a larger data set is needed along with more quantitative methods like free energy perturbation calculations before firm conclusions can be drawn. This study is in part a test bed for large-scale quantitative computational screening of interactions between biological entities and pollutant molecules.en_US
dc.description.provenanceSubmitted by Ahmet Yıldırım (ahmedoyildirim@siirt.edu.tr) on 2019-11-28T10:53:30Z No. of bitstreams: 1 12.pdf: 3824805 bytes, checksum: 67dc75ee29ee699e5a6049a2ac9d6729 (MD5)en
dc.description.provenanceMade available in DSpace on 2019-11-28T10:53:30Z (GMT). No. of bitstreams: 1 12.pdf: 3824805 bytes, checksum: 67dc75ee29ee699e5a6049a2ac9d6729 (MD5) Previous issue date: 2016en
dc.identifier.pmid27603112
dc.identifier.scopus2-s2.0-84991698443
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://hdl.handle.net/20.500.12604/1883
dc.identifier.wosWOS:000385785600010
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorYildirim, Ahmet
dc.language.isootheren_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.snmzKG_20241224
dc.titleBinding of Pollutants to Biomolecules: A Simulation Studyen_US
dc.typeArticleen_US

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