Abstract
Protein hydroxylation is a posttranslational modification (PTM), in which a CH group in Pro (P) or Lys (K) residue has been converted into a COH group, or a hydroxyl group (−OH) is converted into an organic compound. Closely associated with cellular signaling activities, this type of PTM is also involved in some major diseases, such as stomach cancer and lung cancer. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of P or K, which ones can be hydroxylated, and which ones cannot? With the explosive growth of protein sequences in the post-genomic age, the problem has become even more urgent. To address such a problem, we have developed a predictor called iHyd-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition (PseAAC) and introducing the “Random Forest” algorithm to operate the calculation. Rigorous jackknife tests indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for iHyd-PseCp has been established at http://www.jci-bioinfo.cn/iHyd-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
Highlights
Protein post-translational modification (PTM or PTLM) is one of the most efficient biological mechanisms for expanding the genetic code and regulating cellular physiology
The success rates achieved by the new predictor iHyd-PseCp via the rigorous jackknife test on the 164 hydroxyproline proteins are given in Table 1, where for facilitating comparison, the corresponding rates obtained by the predictor iHyd-pseudo amino acid composition (PseAAC) [10] are listed
The jackknife success rates by the new predictor iHydPseCp on the 33 hydroxylysine proteins are given in Table 2, along with the corresponding rates obtained by the predictor iHyd-PseAAC [10]
Summary
Protein post-translational modification (PTM or PTLM) is one of the most efficient biological mechanisms for expanding the genetic code and regulating cellular physiology. Hydroxylation is one type of PTM that can take place in proteins to hydroxylate proline and lysine. Hydroxyproline (HyP) is the key factor in stabilizing collagens [1, 2], whose instability or abnormal activity may cause stomach cancer [3] and lung cancer [4, 5]. HyL sites in proteins is an indispensable step for decoding protein function. It is crucially important for in-depth understanding the physiological roles of hydroxylation. It can provide useful information for developing drugs to treat various diseases associated with hydroxylation
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