Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmidReportar como inadecuado




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Theoretical Biology and Medical Modelling

, 6:22

First Online: 10 September 2009Received: 20 March 2009Accepted: 10 September 2009DOI: 10.1186-1742-4682-6-22

Cite this article as: Andrade, B.S., Taranto, A.G., Góes-Neto, A. et al. Theor Biol Med Model 2009 6: 22. doi:10.1186-1742-4682-6-22

Abstract

BackgroundThe filamentous fungus Moniliophthora perniciosa Stahel Aime and Phillips-Mora is a hemibiotrophic Basidiomycota that causes witches- broom disease of cocoa Theobroma cacao L

This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer. Fungal mitochondrial plasmids are usually invertrons encoding DNA and RNA polymerases. Plasmid insertions into host mitochondrial genomes are probably associated with modifications in host generation time, which can be involved in fungal aging. This association suggests activity of polymerases, and these can be used as new targets for drugs against mitochondrial activity of fungi, more specifically against witches- broom disease. Sequencing and modeling: DNA and RNA polymerases of M. perniciosa mitochondrial plasmid were completely sequenced and their models were carried out by Comparative Homology approach. The sequences of DNA and RNA polymerase showed 25% of identity to 1XHX and 1ARO pdb code using BLASTp, which were used as templates. The models were constructed using Swiss PDB-Viewer and refined with a set of Molecular Mechanics MM and Molecular Dynamics MD in water carried out with AMBER 8.0, both working under the ff99 force fields, respectively. Ramachandran plots were generated by Procheck 3.0 and exhibited models with 97% and 98% for DNA and RNA polymerases, respectively. MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.

ConclusionThis work contributes to the development of new alternatives for controlling the fungal agent of witches- broom disease.

Electronic supplementary materialThe online version of this article doi:10.1186-1742-4682-6-22 contains supplementary material, which is available to authorized users.

Bruno S Andrade, Alex G Taranto, Aristóteles Góes-Neto and Angelo A Duarte contributed equally to this work.

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Autor: Bruno S Andrade - Alex G Taranto - Aristóteles Góes-Neto - Angelo A Duarte

Fuente: https://link.springer.com/







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