Publicação
Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera
| Resumo: | Non-synonymous mutations lead to amino acid substitutions that can affect a protein’s structure and function, thereby influencing biological processes such as detoxification. ATP-binding cassette (ABC) transporters (an important superfamily of detoxification genes) play a critical role in the efflux of toxic compounds in honey bees (Apis mellifera), essential for their survival in environments exposed to natural and synthetic xenobiotics. In this study, non-synonymous mutations in 21 ABC transporter genes were identified. Then, computational tools were employed to investigate the structural and functional consequences of a non-synonymous mutation in the protein encoded by the ABC transporter gene LOC411997. Protein structures were generated from a FASTA file using AlphaFold3, converted from mmCIF to PDB format, and visualised in PyMOL, where mutations were introduced. Functional site predictions were performed using Proteins Plus, and molecular dynamics simulations were conducted in YASARA to assess stability and conformational changes. Our findings suggest that a mutation that replaces threonine with isoleucine alters the protein dynamics by modifying its energy landscape and stability. The total potential energy of the wild-type protein was calculated as -3,640,842 kcal/mol. In contrast, this value increased to -3,443,695 kcal/mol for the mutant protein. This difference suggests that the mutation may affect conformation, flexibility, and biological function of the protein encoded by the ABC transporter gene LOC411997. Understanding these conformational changes at the molecular level will contribute to strategies for improving honey bee’s resilience and conservation. |
|---|---|
| Autores principais: | Bashir, Sana |
| Outros Autores: | Li, Fernanda; Shiraishi, Carlos S.H.; Younes, Sarra Bin; Yadró Garcia, Carlos A.; Barbosa, Daniela; Abreu, Rui M.V.; Rufino, José; Pinto, M. Alice; Henriques, Dora |
| Assunto: | ATP-binding cassette (ABC) Apis mellifera |
| Ano: | 2025 |
| País: | Portugal |
| Tipo de documento: | documento de conferência |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Instituto Politécnico de Bragança |
| Idioma: | inglês |
| Origem: | Biblioteca Digital do IPB |
| _version_ | 1867173394425839616 |
|---|---|
| author | Bashir, Sana |
| author2 | Li, Fernanda Shiraishi, Carlos S.H. Younes, Sarra Bin Yadró Garcia, Carlos A. Barbosa, Daniela Abreu, Rui M.V. Rufino, José Pinto, M. Alice Henriques, Dora |
| author2_role | author author author author author author author author author |
| author_facet | Bashir, Sana Li, Fernanda Shiraishi, Carlos S.H. Younes, Sarra Bin Yadró Garcia, Carlos A. Barbosa, Daniela Abreu, Rui M.V. Rufino, José Pinto, M. Alice Henriques, Dora |
| author_role | author |
| contributor_name_str_mv | Biblioteca Digital do IPB |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Bashir, Sana\"},{\"Person.name\":\"Li, Fernanda\",\"Person.identifier.orcid\":\"0000-0003-0466-355X\"},{\"Person.name\":\"Shiraishi, Carlos S.H.\",\"Person.identifier.orcid\":\"0000-0002-4174-8985\"},{\"Person.name\":\"Younes, Sarra Bin\"},{\"Person.name\":\"Yadró Garcia, Carlos A.\",\"Person.identifier.orcid\":\"0000-0002-6916-3647\"},{\"Person.name\":\"Barbosa, Daniela\"},{\"Person.name\":\"Abreu, Rui M.V.\",\"Person.identifier.orcid\":\"0000-0002-7745-8015\"},{\"Person.name\":\"Rufino, José\",\"Person.identifier.orcid\":\"0000-0002-1344-8264\"},{\"Person.name\":\"Pinto, M. Alice\",\"Person.identifier.orcid\":\"0000-0001-9663-8399\"},{\"Person.name\":\"Henriques, Dora\",\"Person.identifier.orcid\":\"0000-0001-7530-682X\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Biblioteca Digital do IPB |
| datacite.creators.creator.creatorName.fl_str_mv | Bashir, Sana Li, Fernanda Shiraishi, Carlos S.H. Younes, Sarra Bin Yadró Garcia, Carlos A. Barbosa, Daniela Abreu, Rui M.V. Rufino, José Pinto, M. Alice Henriques, Dora |
| datacite.date.Accepted.fl_str_mv | 2025-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2026-02-13T14:59:30Z |
| datacite.date.embargoed.fl_str_mv | 2026-02-13T14:59:30Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | ATP-binding cassette (ABC) Apis mellifera |
| datacite.titles.title.fl_str_mv | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| dc.contributor.none.fl_str_mv | Biblioteca Digital do IPB |
| dc.creator.none.fl_str_mv | Bashir, Sana Li, Fernanda Shiraishi, Carlos S.H. Younes, Sarra Bin Yadró Garcia, Carlos A. Barbosa, Daniela Abreu, Rui M.V. Rufino, José Pinto, M. Alice Henriques, Dora |
| dc.date.Accepted.fl_str_mv | 2025-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2026-02-13T14:59:30Z |
| dc.date.embargoed.fl_str_mv | 2026-02-13T14:59:30Z |
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| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10198/35746 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.cclincense.fl_str_mv | http://creativecommons.org/licenses/by/4.0/ |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | ATP-binding cassette (ABC) Apis mellifera |
| dc.title.fl_str_mv | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_c94f |
| description | Non-synonymous mutations lead to amino acid substitutions that can affect a protein’s structure and function, thereby influencing biological processes such as detoxification. ATP-binding cassette (ABC) transporters (an important superfamily of detoxification genes) play a critical role in the efflux of toxic compounds in honey bees (Apis mellifera), essential for their survival in environments exposed to natural and synthetic xenobiotics. In this study, non-synonymous mutations in 21 ABC transporter genes were identified. Then, computational tools were employed to investigate the structural and functional consequences of a non-synonymous mutation in the protein encoded by the ABC transporter gene LOC411997. Protein structures were generated from a FASTA file using AlphaFold3, converted from mmCIF to PDB format, and visualised in PyMOL, where mutations were introduced. Functional site predictions were performed using Proteins Plus, and molecular dynamics simulations were conducted in YASARA to assess stability and conformational changes. Our findings suggest that a mutation that replaces threonine with isoleucine alters the protein dynamics by modifying its energy landscape and stability. The total potential energy of the wild-type protein was calculated as -3,640,842 kcal/mol. In contrast, this value increased to -3,443,695 kcal/mol for the mutant protein. This difference suggests that the mutation may affect conformation, flexibility, and biological function of the protein encoded by the ABC transporter gene LOC411997. Understanding these conformational changes at the molecular level will contribute to strategies for improving honey bee’s resilience and conservation. |
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| institution | Instituto Politécnico de Bragança |
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| language | eng |
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| person_str_mv | Bashir, Sana Li, Fernanda Li, Fernanda https://www.ciencia-id.pt/F115-6760-0EBB F115-6760-0EBB http://orcid.org/0000-0003-0466-355X 0000-0003-0466-355X Shiraishi, Carlos S.H. Shiraishi, Carlos S.H. https://www.ciencia-id.pt/6C11-86D5-73AE 6C11-86D5-73AE http://orcid.org/0000-0002-4174-8985 0000-0002-4174-8985 Younes, Sarra Bin Yadró Garcia, Carlos A. Yadró Garcia, Carlos A. https://www.ciencia-id.pt/F71F-B08E-EC39 F71F-B08E-EC39 http://orcid.org/0000-0002-6916-3647 0000-0002-6916-3647 Barbosa, Daniela Abreu, Rui M.V. Abreu, Rui M.V. https://www.ciencia-id.pt/0F19-0DE2-12A2 0F19-0DE2-12A2 http://orcid.org/0000-0002-7745-8015 0000-0002-7745-8015 Rufino, José Rufino, José https://www.ciencia-id.pt/C414-F47F-6323 C414-F47F-6323 http://orcid.org/0000-0002-1344-8264 0000-0002-1344-8264 Pinto, M. Alice Pinto, M. Alice https://www.ciencia-id.pt/F814-A1D0-8318 F814-A1D0-8318 http://orcid.org/0000-0001-9663-8399 0000-0001-9663-8399 Henriques, Dora Henriques, Dora https://www.ciencia-id.pt/291F-986F-07DA 291F-986F-07DA http://orcid.org/0000-0001-7530-682X 0000-0001-7530-682X |
| publishDate | 2025 |
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| spelling | engengNon-synonymous mutations lead to amino acid substitutions that can affect a protein’s structure and function, thereby influencing biological processes such as detoxification. ATP-binding cassette (ABC) transporters (an important superfamily of detoxification genes) play a critical role in the efflux of toxic compounds in honey bees (Apis mellifera), essential for their survival in environments exposed to natural and synthetic xenobiotics. In this study, non-synonymous mutations in 21 ABC transporter genes were identified. Then, computational tools were employed to investigate the structural and functional consequences of a non-synonymous mutation in the protein encoded by the ABC transporter gene LOC411997. Protein structures were generated from a FASTA file using AlphaFold3, converted from mmCIF to PDB format, and visualised in PyMOL, where mutations were introduced. Functional site predictions were performed using Proteins Plus, and molecular dynamics simulations were conducted in YASARA to assess stability and conformational changes. Our findings suggest that a mutation that replaces threonine with isoleucine alters the protein dynamics by modifying its energy landscape and stability. The total potential energy of the wild-type protein was calculated as -3,640,842 kcal/mol. In contrast, this value increased to -3,443,695 kcal/mol for the mutant protein. This difference suggests that the mutation may affect conformation, flexibility, and biological function of the protein encoded by the ABC transporter gene LOC411997. Understanding these conformational changes at the molecular level will contribute to strategies for improving honey bee’s resilience and conservation.application/pdfengComputational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis melliferaBashir, SanaPersonalLi, FernandaDSpacehttp://dspace.org/items/11ed7f07-945f-42e9-8950-eb6c59672e15DSpacehttp://dspace.org/items/11ed7f07-945f-42e9-8950-eb6c59672e15LiFernandaCiência IDhttps://www.ciencia-id.ptF115-6760-0EBBORCIDhttp://orcid.org0000-0003-0466-355XPersonalShiraishi, Carlos S.H.DSpacehttp://dspace.org/items/ad151be6-111b-4a00-b7c4-fe1573a796c3DSpacehttp://dspace.org/items/ad151be6-111b-4a00-b7c4-fe1573a796c3ShiraishiCarlos S.H.Ciência IDhttps://www.ciencia-id.pt6C11-86D5-73AEORCIDhttp://orcid.org0000-0002-4174-8985Younes, Sarra BinPersonalYadró Garcia, Carlos A.DSpacehttp://dspace.org/items/59212a6c-fc6a-45fd-b37a-51e90926c9e3DSpacehttp://dspace.org/items/59212a6c-fc6a-45fd-b37a-51e90926c9e3Yadró GarciaCarlos A.Ciência IDhttps://www.ciencia-id.ptF71F-B08E-EC39ORCIDhttp://orcid.org0000-0002-6916-3647Barbosa, DanielaPersonalAbreu, Rui M.V.DSpacehttp://dspace.org/items/cadb03a4-5e60-4745-b35f-fc3a97c071bcDSpacehttp://dspace.org/items/cadb03a4-5e60-4745-b35f-fc3a97c071bcAbreuRui M.V.Ciência IDhttps://www.ciencia-id.pt0F19-0DE2-12A2ORCIDhttp://orcid.org0000-0002-7745-8015Scopus Author IDhttps://www.scopus.com7003290613PersonalRufino, JoséDSpacehttp://dspace.org/items/1e24d2ce-a354-442a-bef8-eebadd94b385DSpacehttp://dspace.org/items/1e24d2ce-a354-442a-bef8-eebadd94b385RufinoJoséCiência IDhttps://www.ciencia-id.ptC414-F47F-6323ORCIDhttp://orcid.org0000-0002-1344-8264Scopus Author IDhttps://www.scopus.com55947199100Scopus Author IDhttps://www.scopus.com57188967176PersonalPinto, M. AliceDSpacehttp://dspace.org/items/0667fe04-7078-483d-9198-56d167b19bc5DSpacehttp://dspace.org/items/0667fe04-7078-483d-9198-56d167b19bc5PintoM. AliceCiência IDhttps://www.ciencia-id.ptF814-A1D0-8318ORCIDhttp://orcid.org0000-0001-9663-8399Scopus Author IDhttps://www.scopus.com8085507800PersonalHenriques, DoraDSpacehttp://dspace.org/items/d2abd09f-a90c-4cfb-9a60-7fc32f56184dDSpacehttp://dspace.org/items/d2abd09f-a90c-4cfb-9a60-7fc32f56184dHenriquesDoraCiência IDhttps://www.ciencia-id.pt291F-986F-07DAORCIDhttp://orcid.org0000-0001-7530-682XScopus Author IDhttps://www.scopus.com55761737300HostingInstitutionOrganizationalBiblioteca Digital do IPBe-mailmailto:dspace@ipb.ptdspace@ipb.pt2026-02-13T14:59:30Z20252025-01-01T00:00:00ZHandlehttp://hdl.handle.net/10198/35746http://purl.org/coar/access_right/c_abf2open accessATP-binding cassette (ABC)Apis mellifera476353 bytesother research producthttp://purl.org/coar/resource_type/c_c94fconference object2025http://creativecommons.org/licenses/by/4.0/http://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://bibliotecadigital.ipb.pt/bitstreams/f5e47293-b916-4138-81b2-36d8ea4195cd/downloadVI International Conference of the Portuguese Society of Genetics732025-06-05 |
| spellingShingle | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera Bashir, Sana ATP-binding cassette (ABC) Apis mellifera |
| status | SINGLETON |
| subject.fl_str_mv | ATP-binding cassette (ABC) Apis mellifera |
| title | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| title_full | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| title_fullStr | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| title_full_unstemmed | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| title_short | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| title_sort | Computational Insights into the Impact of NonSynonymous Mutations in the ABC Transporter Gene of Apis mellifera |
| topic | ATP-binding cassette (ABC) Apis mellifera |
| topic_facet | ATP-binding cassette (ABC) Apis mellifera |
| url | http://hdl.handle.net/10198/35746 |
| visible | 1 |