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Phylogenetic divergence and in silico assessment of retinal binding by guppy (Poecilia reticulata) opsins in the context of Metazoan evolution
РИНЦ –
| DOI | https://doi.org/10.1016/j.insi.2026.100706 |
|---|---|
| Язык | Английский |
| Журнал | In Silico Research in Biomedicine ISSN: 3050-7871; Онлайн ISSN: – |
| Год | 2026 |
| Выходные данные | том: 2; статья: 100706; страниц (электронный ресурс): 11 |
| Авторы | |
| Даты |
Поступила в редакцию: 28.08.2026 После доработки: 22.10.2026 Принята к публикации: 23.10.2026 Опубликована онлайн: 26.10.2026 |
| Абстракт | This study investigates the structural and evolutionary features of guppy (Poecilia reticulata) opsins. We examined seven guppy opsin sequences representing major functional classes and constructed a maximum-likelihood phylogenetic tree for 23 opsins from diverse Metazoan taxa. The dataset was deliberately restricted to sequences with available docking-derived non-covalent retinal binding energies (ΔGdock). The deep branching between vertebrate and invertebrate opsins remains unresolved in this restricted dataset; the early-branching position of RH1 (98% support) likely reflects limited taxon sampling rather than true evolutionary history. The novelty of this work lies in in silico analysis of predicted docking scores across multiple guppy opsin classes and their apparent trend with functional specialisation. Homology modelling (Phyre2) and molecular docking (AutoDock Vina) revealed the most negative ΔGdock for the blue-sensitive opsin (−8.83 kcal/mol) and the least negative for rhodopsin (−7.05 kcal/mol). Comparative analysis with invertebrate opsins, including the experimentally characterised ctenophore opsin-2 [Schnitzler et al., 2012], suggests that pocket geometry may have evolved convergently or in parallel in short-wavelength opsins across different Metazoan lineages, whereas rhodopsin retains moderately negative values consistent with its role in dim-light vision. Importantly, ΔGdock reflects only the initial chromophore recognition step and does not always correlate with the spectral properties of the native pigment, which are determined by the covalent Schiff-base complex. While the phylogenetic relationships and opsin gene repertoire are largely consistent with established literature [Ward et al., 2008; Rennison et al., 2012; Sandkam et al., 2017], the binding energy analysis provides a quantitative framework for testable hypotheses regarding functional specialisation and convergent pocket geometry, which require experimental validation. Ключевые слова: opsins, guppy (Poecilia reticulata), retinal binding, molecular docking, phylogenetics |
| Сведения о финансировании, указанные в публикации | |
| URL | https://www.sciencedirect.com/science/article/pii/S3050787126005330 |
| Дополнительные сведения |
Запись создана: 08-11-2026 19:18
Последнее изменение: 08-11-2026 19:21
Библиографическая ссылка:
Kuznetsov A. V. Phylogenetic divergence and in silico assessment of retinal binding by guppy (Poecilia reticulata) opsins in the context of Metazoan evolution // In Silico Research in Biomedicine. 2026. Vol. 2. Art. no. 100706 (11 p.). https://doi.org/10.1016/j.insi.2026.100706
[РИНЦ –]
Kuznetsov A. V. Phylogenetic divergence and in silico assessment of retinal binding by guppy (Poecilia reticulata) opsins in the context of Metazoan evolution // In Silico Research in Biomedicine. 2026. Vol. 2. Art. no. 100706 (11 p.). https://doi.org/10.1016/j.insi.2026.100706
[РИНЦ –]
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