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Computational approaches for classification and prediction of P-type ATPase substrate specificity in Arabidopsis

Zinati, Zahra, Alemzadeh, Abbas, KayvanJoo, Amir Hossein
Physiology and molecular biology of plants 2016 v.22 no.1 pp. 163-174
Arabidopsis, Ca2-transporting ATPase, absorption, adenosinetriphosphatase, algorithms, amino acid composition, amino acids, bioinformatics, calcium, carbon, extinction, heavy metals, hydrogen, hydrophilicity, models, plasma membrane, prediction, proton pump, substrate specificity
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 (Ca²⁺ 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.