Abstract
PDZ domains have been identified as part of an array of signaling proteins that are often unrelated, except for the well-conserved structural PDZ domain they contain. These domains have been linked to many disease processes including common Avian influenza, as well as very rare conditions such as Fraser and Usher syndromes. Historically, based on the interactions and the nature of bonds they form, PDZ domains have most often been classified into one of three classes (class I, class II and others - class III), that is directly dependent on their binding partner. In this study, we report on three unique feature extraction approaches based on the bigram and trigram occurrence and existence rearrangements within the domain's primary amino acid sequences in assisting PDZ domain classification. Wavelet packet transform (WPT) and Shannon entropy denoted by wavelet entropy (WE) feature extraction methods were proposed. Using 115 unique human and mouse PDZ domains, the existence rearrangement approach yielded a high recognition rate (78.34%), which outperformed our occurrence rearrangements based method. The recognition rate was (81.41%) with validation technique. The method reported for PDZ domain classification from primary sequences proved to be an encouraging approach for obtaining consistent classification results. We anticipate that by increasing the database size, we can further improve feature extraction and correct classification.
Highlights
One of the most common and important protein domains that play an essential role in underlying cell signaling and organizing the post synaptic density region is represented by PDZ domain containing proteins [1,2,3]
Results were calculated and reported; the confidence interval states that 95% of the calculated recognition rate for each combination should be contained in this interval
FN is the number of false negative samples, which is the number of incorrectly classified class2 PDZ domains, where the testing samples were class2 PDZ domains
Summary
One of the most common and important protein domains that play an essential role in underlying cell signaling and organizing the post synaptic density region is represented by PDZ domain containing proteins [1,2,3]. PDZ domain proteins have been implicated in functions such as maintainers of cell polarity, regulating the post-synaptic density by mediating protein-protein interactions, and in directing protein trafficking amongst other functions [4,5,6]. Their function, or better yet malfunction, has been characterized in several disease states ranging from cystic fibrosis to cancer [7,8,9]. Most PDZ domains have a conserved 3D fold made of six β strands and two α helices. PDZ domains bind the PLOS ONE | DOI:10.1371/journal.pone.0122873. PDZ domains bind the PLOS ONE | DOI:10.1371/journal.pone.0122873 April 10, 2015
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