Abstract
Post-translational modifications (PTMs) play crucial roles in various cell functions and biological processes. Protein hydroxylation is one type of PTM that usually occurs at the sites of proline and lysine. Given an uncharacterized protein sequence, which site of its Pro (or Lys) can be hydroxylated and which site cannot? This is a challenging problem, not only for in-depth understanding of the hydroxylation mechanism, but also for drug development, because protein hydroxylation is closely relevant to major diseases, such as stomach and lung cancers. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods to address this problem. In view of this, a new predictor called “iHyd-PseAAC” (identify hydroxylation by pseudo amino acid composition) was proposed by incorporating the dipeptide position-specific propensity into the general form of pseudo amino acid composition. It was demonstrated by rigorous cross-validation tests on stringent benchmark datasets that the new predictor is quite promising and may become a useful high throughput tool in this area. A user-friendly web-server for iHyd-PseAAC is accessible at http://app.aporc.org/iHyd-PseAAC/. Furthermore, for the convenience of the majority of experimental scientists, a step-by-step guide on how to use the web-server is given. Users can easily obtain their desired results by following these steps without the need of understanding the complicated mathematical equations presented in this paper just for its integrity.
Highlights
Most proteins perform their functions after post-translational modifications (PTMs)
With a rapidly growing database in protein hydroxylation, the benchmark datasets used in the two methods definitely need to be updated; Second, some sequence order effects were missed, which would certainly affect their prediction quality; Third, none of them provided a publicly accessible web-server, and their practical usage value is substantially limited
The benchmark dataset was derived from dbPTM 3.0 [22] at http://dbptm.mbc.nctu.edu
Summary
Protein hydroxylation is one type of PTM that involves the conversion of a CH group into a COH group (Figure 1) and is closely relevant to the regulation of the transcription factor (hypoxia-inducible factor) [1] Both the proline and lysine residues in proteins can be hydroxylated, forming hydroxyproline (Figure 1a) or HyP and hydroxylysine (Figure 1b) or HyL, respectively. With a rapidly growing database in protein hydroxylation, the benchmark datasets used in the two methods definitely need to be updated; Second, some sequence order effects were missed, which would certainly affect their prediction quality; Third, none of them provided a publicly accessible web-server, and their practical usage value is substantially limited. Let us elaborate on how to deal with these five steps
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