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Evaluation of the impact of functional diversification on Poaceae, Brassicaceae, Fabaceae, and Pinaceae alcohol dehydrogenase enzymes

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Abstract

The plant alcohol dehydrogenases (ADHs) have been intensively studied in the last years in terms of phylogeny and they have been widely used as a molecular marker. However, almost no information about their three-dimensional structure is available. Several studies point to functional diversification of the ADH, with evidence of its importance, in different organisms, in the ethanol, norepinephrine, dopamine, serotonin, and bile acid metabolism. Computational results demonstrated that in plants these enzymes are submitted to a functional diversification process, which is reinforced by experimental studies indicating distinct enzymatic functions as well as recruitment of specific genes in different tissues. The main objective of this article is to establish a correlation between the functional diversification occurring in the plant alcohol dehydrogenase family and the three-dimensional structures predicted for 17 ADH belonging to Poaceae, Brassicaceae, Fabaceae, and Pinaceae botanical families. Volume, molecular weight and surface areas are not markedly different among them. Important electrostatic and pI differences were observed with the residues responsible for some of them identified, corroborating the function diversification hypothesis. These data furnish important background information for future specific structure-function and evolutionary investigations.

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Acknowledgments

We would like to thank Dr. Ana Tereza R. Vasconcelos, Dr. Élgion L. S. Loreto, Dr. Laurent E. Dardenne, and Dr. Paulo M. Bisch for their helpful comments. This work was supported by the Institutos do Milênio and Programa de Apoio a Núcleos de Excelência, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul, and Pró-Reitoria de Pesquisa da Universidade Federal do Rio Grande do Sul.

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Authors and Affiliations

  1. Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970, Porto Alegre, RS, Brazil

    Claudia E. Thompson, Loreta B. de Freitas & Francisco M. Salzano

  2. Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, Faculdade de Informática, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga, 6681, Prédio 32 - Sala 608, 90619-900, Porto Alegre, RS, Brazil

    Cláudia L. Fernandes & Osmar Norberto de Souza

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  1. Claudia E. Thompson
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  2. Cláudia L. Fernandes
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  3. Osmar Norberto de Souza
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  4. Loreta B. de Freitas
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Correspondence to Claudia E. Thompson.

Electronic supplementary material

Table 1S

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Table 2S

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Table 3S

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Table 4S

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Table 5S

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Fig. 1S

Multiple alignment of the protein sequences modeled and the template used in the modeling (DOC 47 kb)

Fig. 2S

Percent identity of the ADH sequences. The horizontal axis presents the data values being plotted. The vertical axis shows the fraction of data points with as small or smaller a data value (DOC 67 kb)

Fig. 3S

3D_1D averaged scores, as determined by the VERIFY_3D program for the models of the Brassicaceae botanical family (DOC 30 kb)

Fig. 4S

3D_1D averaged scores, as determined by the VERIFY_3D program for the models of the Poaceae botanical family (DOC 94 kb)

Fig. 5S

3D_1D averaged scores, as determined by the VERIFY_3D program for the models of the Fabaceae and Pinaceae botanical families (DOC 169 kb)

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Thompson, C.E., Fernandes, C.L., Norberto de Souza, O. et al. Evaluation of the impact of functional diversification on Poaceae, Brassicaceae, Fabaceae, and Pinaceae alcohol dehydrogenase enzymes. J Mol Model 16, 919–928 (2010). https://doi.org/10.1007/s00894-009-0576-0

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  • DOI: https://doi.org/10.1007/s00894-009-0576-0

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