Journal of Molecular Modeling

, Volume 16, Issue 5, pp 919–928

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

Authors

    • Departamento de Genética, Instituto de BiociênciasUniversidade Federal do Rio Grande do Sul
  • Cláudia L. Fernandes
    • Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, Faculdade de InformáticaPontifícia Universidade Católica do Rio Grande do Sul
  • Osmar Norberto de Souza
    • Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, Faculdade de InformáticaPontifícia Universidade Católica do Rio Grande do Sul
  • Loreta B. de Freitas
    • Departamento de Genética, Instituto de BiociênciasUniversidade Federal do Rio Grande do Sul
  • Francisco M. Salzano
    • Departamento de Genética, Instituto de BiociênciasUniversidade Federal do Rio Grande do Sul
Original Paper

DOI: 10.1007/s00894-009-0576-0

Cite this article as:
Thompson, C.E., Fernandes, C.L., Norberto de Souza, O. et al. J Mol Model (2010) 16: 919. doi:10.1007/s00894-009-0576-0

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.

Keywords

ADHAlcohol dehydrogenaseFunctional diversificationMolecular evolutionMolecular modelingProtein structure

Supplementary material

894_2009_576_MOESM1_ESM.doc (114 kb)
Table 1S(DOC 158 kb)
894_2009_576_MOESM2_ESM.doc (109 kb)
Table 2S(DOC 114 kb)
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Table 3S(DOC 109 kb)
894_2009_576_MOESM4_ESM.doc (118 kb)
Table 4S(DOC 103 kb)
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Table 5S(DOC 118 kb)
894_2009_576_MOESM6_ESM.doc (68 kb)
Fig. 1SMultiple alignment of the protein sequences modeled and the template used in the modeling (DOC 47 kb)
894_2009_576_MOESM7_ESM.doc (30 kb)
Fig. 2SPercent 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)
894_2009_576_MOESM8_ESM.doc (94 kb)
Fig. 3S3D_1D averaged scores, as determined by the VERIFY_3D program for the models of the Brassicaceae botanical family (DOC 30 kb)
894_2009_576_MOESM9_ESM.doc (170 kb)
Fig. 4S3D_1D averaged scores, as determined by the VERIFY_3D program for the models of the Poaceae botanical family (DOC 94 kb)
894_2009_576_MOESM10_ESM.doc (158 kb)
Fig. 5S3D_1D averaged scores, as determined by the VERIFY_3D program for the models of the Fabaceae and Pinaceae botanical families (DOC 169 kb)

Copyright information

© Springer-Verlag 2009