title: Computational approaches for classification and prediction of P-type ATPase substrate specificity in Arabidopsis.
abstract: As an extended gamut of integral membrane (extrinsic) proteins, and based on their transporting specificities, P-type ATPases include five subfamilies in Arabidopsis, inter alia, P4ATPases (phospholipid-transporting ATPase), P3AATPases (plasma membrane H(+) pumps), P2A and P2BATPases (Ca(2+) pumps) and P1B ATPases (heavy metal pumps). Although, many different computational methods have been developed to predict substrate specificity of unknown proteins, further investigation needs to improve the efficiency and performance of the predicators. In this study, various attribute weighting and supervised clustering algorithms were employed to identify the main amino acid composition attributes, which can influence the substrate specificity of ATPase pumps, classify protein pumps and predict the substrate specificity of uncharacterized ATPase pumps. The results of this study indicate that both non-reduced coefficients pertaining to absorption and Cys extinction within 280 nm, the frequencies of hydrogen, Ala, Val, carbon, hydrophilic residues, the counts of Val, Asn, Ser, Arg, Phe, Tyr, hydrophilic residues, Phe-Phe, Ala-Ile, Phe-Leu, Val-Ala and length are specified as the most important amino acid attributes through applying the whole attribute weighting models. Here, learning algorithms engineered in a predictive machine (Naive Bays) is proposed to foresee the Q9LVV1 and O22180 substrate specificities (P-type ATPase like proteins) with 100 % prediction confidence. For the first time, our analysis demonstrated promising application of bioinformatics algorithms in classifying ATPases pumps. Moreover, we suggest the predictive systems that can assist towards the prediction of the substrate specificity of any new ATPase pumps with the maximum possible prediction confidence.
authors.affiliation: Department of Agroecology, College of Agriculture and Natural Resources of Darab, Shiraz University, Shiraz, Iran.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Zinati
authors.affiliation: Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran.
authors.forename: Abbas
authors.initials: A
authors.lastname: Alemzadeh
authors.affiliation: Bonn-Aachen International Center for Information Technology B-IT, University of Bonn, Bonn, Germany.
authors.forename: Amir Hossein
authors.initials: AH
authors.lastname: KayvanJoo
keywords: Arabidopsis; Attribute weighting models; P-type ATPase; Supervised clustering algorithms