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Example 1: Modeling lactate dehydrogenase from Trichomonas vaginalis based on a single template

A novel gene for lactate dehydrogenase was identified from the genomic sequence of Trichomonas vaginalis (TvLDH). The corresponding protein had a higher similarity to the malate dehydrogenase of the same species (TvMDH) than to any other LDH. We hypothesized that TvLDH arose from TvMDH by convergent evolution relatively recently [73]. Comparative models were constructed for TvLDH and TvMDH to study the sequences in the structural context and to suggest site-directed mutagenesis experiments for elucidating specificity changes in this apparent case of convergent evolution of enzymatic specificity. The native and mutated enzymes were expressed and their activities were compared [73]. The individual modeling steps of this study are described next.


Andras Fiser