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Computational analysis to predict the impact of non-synonymous mutations in a protein: an example with the Odorant Receptor 49b

2025Documento de conferência Acesso aberto
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datacite.subject.fosCiências Naturais::Ciências da Terra e do Ambiente
datacite.subject.fosCiências Agrárias::Biotecnologia Agrária e Alimentar
datacite.subject.sdg04:Educação de Qualidade
datacite.subject.sdg13:Ação Climática
datacite.subject.sdg15:Proteger a Vida Terrestre
dc.contributor.authorBashir, Sana
dc.contributor.authorShiraishi, Carlos S.H.
dc.contributor.authorYadró Garcia, Carlos A.
dc.contributor.authorHenriques, Dora
dc.contributor.authorPinto, M. Alice
dc.contributor.authorAbreu, Rui M.V.
dc.date.accessioned2026-02-11T17:04:12Z
dc.date.available2026-02-11T17:04:12Z
dc.date.issued2025
dc.description.abstractNon-synonymous mutations lead to amino acid substitutions within proteins, potentially affecting protein structure and function. While some mutations have a minimal impact on protein structure and function, others can alter their stability, conformation, and biological activity. Therefore, predicting how mutations affect proteins is important when uncovering the genetic basis of honey bee response to selective pressures. In a recent whole-genome scan for signatures of selection in Apis mellifera syriaca, we found a non-synonymous mutation under selection in the Odorant Receptor 49b (Or49b) gene. According to the literature, this gene plays a role in honeybee foraging, communication, and environmental adaptation. In an attempt to understand the biological impact at the molecular level of the discovered mutation, we assembled a pipeline that integrates bioinformatics and protein modelling techniques to evaluate the structural and functional consequences of a mutation in a protein. Protein structures were generated from a FASTA file using AlphaFold3, converted from mmCIF to PDB format, and visualized 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 the mutation under selection in the OR49b gene, which replaces tyrosine with histidine, alters protein dynamics by modifying its energy landscape and stability. At the end of the molecular dynamics simulation, the total potential energy of the wild-type protein was calculated as -384,675 kcal/mol. In contrast, this value increased to -287,075 kcal/mol for the mutant protein. This difference suggests that the mutation may affect the OR49b conformation, flexibility, and eventually its biological function. Whether this change affects honey bee olfactory perception remains uncertain. However, given that the mutation is under selection, it is plausible that the alternative amino acid variants confer an adaptive advantage in different environments. From a practical perspective, understanding how mutations affect biological function can ultimately assist honey bee breeders in selecting colonies for breeding programs, enhancing resilience and adaptability.eng
dc.identifier.citationBashir, Sana; Shiraishi, Carlos S.H.; Yadró Garcia, Carlos A.; Henriques, Dora; Pinto, M. Alice; Abreu, Rui M.V. (2025). Computational analysis to predict the impact of non-synonymous mutations in a protein: an example with the Odorant Receptor 49b. Apimondia 2025. p. 295
dc.identifier.urihttp://hdl.handle.net/10198/35723
dc.language.isoeng
dc.peerreviewedyes
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectNon-synonymous mutations
dc.subjectApis mellifera
dc.titleComputational analysis to predict the impact of non-synonymous mutations in a protein: an example with the Odorant Receptor 49beng
dc.typeconference object
dspace.entity.typePublication
oaire.citation.conferenceDate2025
oaire.citation.conferencePlaceCopenhagen, Denmark
oaire.citation.startPage295
oaire.citation.titleApimondia 2025
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNameShiraishi
person.familyNameYadró Garcia
person.familyNameHenriques
person.familyNamePinto
person.familyNameAbreu
person.givenNameCarlos S.H.
person.givenNameCarlos A.
person.givenNameDora
person.givenNameM. Alice
person.givenNameRui M.V.
person.identifier.ciencia-id6C11-86D5-73AE
person.identifier.ciencia-idF71F-B08E-EC39
person.identifier.ciencia-id291F-986F-07DA
person.identifier.ciencia-idF814-A1D0-8318
person.identifier.ciencia-id0F19-0DE2-12A2
person.identifier.orcid0000-0002-4174-8985
person.identifier.orcid0000-0002-6916-3647
person.identifier.orcid0000-0001-7530-682X
person.identifier.orcid0000-0001-9663-8399
person.identifier.orcid0000-0002-7745-8015
person.identifier.scopus-author-id55761737300
person.identifier.scopus-author-id8085507800
person.identifier.scopus-author-id7003290613
relation.isAuthorOfPublicationad151be6-111b-4a00-b7c4-fe1573a796c3
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