Ferrer-Rodríguez I

Language: English
References: 23
Page: 53-60
PDF size: 198.26 Kb.

ABSTRACT

Introduction. Malaria drug resistance continues on the rise and constitutes a major health problem. Drug resistance in Plasmodia is a complex phenomenon often mediated by membrane proteins belonging to the ATP-Binding Cassette (ABC) superfamily of transporter, which are characterized by the presence of nucleotide binding sites (NBS) and membrane spanning domains (MSD).
Objective. The main objective of this paper is to analyze the performance of a variety of tools to predict the transmembrane topology of ABC proteins in P. yoelii.
Material and methods. ABC proteins were identified in PlasmoDB 5.4 using the Search term tool querying with ABC as keyword. Protein sequences were analyzed for prediction of NBS and MSD using seven different bioinformatics tools. Each program was rated based on the number of correct and incorrect predictions.
Results. Seven of the 23 proteins identified contain the typical architecture structure of ABC proteins with transmembrane regions. The number of transmembrane domains in the proteins ranged from four to 11. TMHMM 1.0 provided the best comparison to the reference annotation in PlasmoDB (TMHMM 2.0) with 51 correct predictions, followed by Phobius, TMPRED and HMMTOP. MEMSAT and SPLIT have the lowest number of correct predictions.
Conclusions. We performed topology predictions of membrane spanning regions in P. yoelii ABC proteins. These analyses should provide further information about the structure of the ABC proteins and could guide researchers to understand better the role that these proteins can play in biological processes in the parasite.

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