N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites

Authors

  • Tzong-Yi Lee,

    1. Department of Computer Science and Engineering, Yuan Ze University, Chung-Li 320, Taiwan
    Search for more papers by this author
    • Authors' Contributions: H.-D.H. conceived and supervised this project. T.-Y.L. was responsible for the design, computational analyses, implementation of the databases, web interface development and drafting of the manuscript, with revisions made by H.-D.H., J.B.-K.H., and W.-C.C. participated in the design, computational analyses, web interface development, and system maintenance. F.-M.L., W.-C.C., and P.-C.H. helped with web interface development, system maintenance, and data testing. All authors read and approved the final manuscript.

    • These authors contributed equally to this work.

  • Justin Bo-Kai Hsu,

    1. Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
    Search for more papers by this author
    • Authors' Contributions: H.-D.H. conceived and supervised this project. T.-Y.L. was responsible for the design, computational analyses, implementation of the databases, web interface development and drafting of the manuscript, with revisions made by H.-D.H., J.B.-K.H., and W.-C.C. participated in the design, computational analyses, web interface development, and system maintenance. F.-M.L., W.-C.C., and P.-C.H. helped with web interface development, system maintenance, and data testing. All authors read and approved the final manuscript.

    • These authors contributed equally to this work.

  • Feng-Mao Lin,

    1. Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
    Search for more papers by this author
    • Authors' Contributions: H.-D.H. conceived and supervised this project. T.-Y.L. was responsible for the design, computational analyses, implementation of the databases, web interface development and drafting of the manuscript, with revisions made by H.-D.H., J.B.-K.H., and W.-C.C. participated in the design, computational analyses, web interface development, and system maintenance. F.-M.L., W.-C.C., and P.-C.H. helped with web interface development, system maintenance, and data testing. All authors read and approved the final manuscript.

  • Wen-Chi Chang,

    Corresponding author
    1. Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
    • Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
    Search for more papers by this author
    • Authors' Contributions: H.-D.H. conceived and supervised this project. T.-Y.L. was responsible for the design, computational analyses, implementation of the databases, web interface development and drafting of the manuscript, with revisions made by H.-D.H., J.B.-K.H., and W.-C.C. participated in the design, computational analyses, web interface development, and system maintenance. F.-M.L., W.-C.C., and P.-C.H. helped with web interface development, system maintenance, and data testing. All authors read and approved the final manuscript.

  • Po-Chiang Hsu,

    1. Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsin-Chu 300, Taiwan
    Search for more papers by this author
    • Authors' Contributions: H.-D.H. conceived and supervised this project. T.-Y.L. was responsible for the design, computational analyses, implementation of the databases, web interface development and drafting of the manuscript, with revisions made by H.-D.H., J.B.-K.H., and W.-C.C. participated in the design, computational analyses, web interface development, and system maintenance. F.-M.L., W.-C.C., and P.-C.H. helped with web interface development, system maintenance, and data testing. All authors read and approved the final manuscript.

  • Hsien-Da Huang

    Corresponding author
    1. Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
    2. Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
    • Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
    Search for more papers by this author
    • Authors' Contributions: H.-D.H. conceived and supervised this project. T.-Y.L. was responsible for the design, computational analyses, implementation of the databases, web interface development and drafting of the manuscript, with revisions made by H.-D.H., J.B.-K.H., and W.-C.C. participated in the design, computational analyses, web interface development, and system maintenance. F.-M.L., W.-C.C., and P.-C.H. helped with web interface development, system maintenance, and data testing. All authors read and approved the final manuscript.


Abstract

Protein acetylation, which is catalyzed by acetyltransferases, is a type of post-translational modification and crucial to numerous essential biological processes, including transcriptional regulation, apoptosis, and cytokine signaling. As the experimental identification of protein acetylation sites is time consuming and laboratory intensive, several computational approaches have been developed for identifying the candidates of experimental validation. In this work, solvent accessibility and the physicochemical properties of proteins are utilized to identify acetylated alanine, glycine, lysine, methionine, serine, and threonine. A two-stage support vector machine was applied to learn the computational models with combinations of amino acid sequences, and the accessible surface area and physicochemical properties of proteins. The predictive accuracy thus achieved is 5% to 14% higher than that of models trained using only amino acid sequences. Additionally, the substrate specificity of the acetylated site was investigated in detail with reference to the subcellular colocalization of acetyltransferases and acetylated proteins. The proposed method, N-Ace, is evaluated using independent test sets in various acetylated residues and predictive accuracies of 90% were achieved, indicating that the performance of N-Ace is comparable with that of other acetylation prediction methods. N-Ace not only provides a user-friendly input/output interface but also is a creative method for predicting protein acetylation sites. This novel analytical resource is now freely available at http://N-Ace.mbc.NCTU.edu.tw/. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Ancillary