title: Computational prediction of the specificities of proteasome interaction with antigen protein.
abstract: In the processing and presentation of antigenic peptides bound by the major histocompatibility complex (MHC) class I molecule, the ubiquitin-proteasome system of the eukaryotic cells plays an important role in proteolysis and degradation. The ubiquitinated protein substrate is delivered into the 26S proteasome to be digested and degraded. The proteasome degrading substrate is actually protein-protein interactions. Some researches of predicting proteasome cleave site rarely gave the information of the proteasome interacting with its substrate, and so the accuracy and reliability of these proteasome cleavage predictive methods still need to be improved. This paper used support vector machine method (SVM) to predict the proteasomal cleavage sites, and the predictive accuracy of the model was 82.8%. We showed analytically that the cleavage specificities of the cleavage sites "|" and its adjacent positions, and gave the information about the proteasome interacting with its substrate from our research results. It demonstrates that the proteasome cleaving to target protein is selective, but not random.
authors.affiliation: College of Advanced Science and Technology, Dalian University of Technology, Dalian 116023, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.forename: Zhe
authors.initials: Z
authors.lastname: Song
authors.forename: Chunbo
authors.initials: C
authors.lastname: Jiao
authors.forename: Minghua
authors.initials: M
authors.lastname: Zhu
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Wang
mesh_terms: D000818:Animals; D017951:Antigen Presentation; D000941:Antigens / Q000378:metabolism*; D003198:Computer Simulation; D015395:Histocompatibility Antigens Class I / Q000276:immunology / Q000378:metabolism; D006801:Humans; D010455:Peptides; D011237:Predictive Value of Tests; D046988:Proteasome Endopeptidase Complex / Q000276:immunology / Q000378:metabolism*; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs / Q000276:immunology*; D011506:Proteins; D016415:Sequence Alignment; D013379:Substrate Specificity / Q000235:genetics / Q000276:immunology*
chemical_list: D000941:Antigens; D015395:Histocompatibility Antigens Class I; D010455:Peptides; D011506:Proteins; D046988:Proteasome Endopeptidase Complex