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. 2015 Jul 24;10(7):e0134114.
doi: 10.1371/journal.pone.0134114. eCollection 2015.

In Silico Analysis of Tumor Necrosis Factor α-Induced Protein 8-Like-1 (TIPE1) Protein

Pei Shen  1 , Hong Zhang  2 , Zhaoliang Su  3 , Shengjun Wang  3 , Huaxi Xu  3
Affiliations

In Silico Analysis of Tumor Necrosis Factor α-Induced Protein 8-Like-1 (TIPE1) Protein

Pei Shen et al. PLoS One. .

Abstract

Tumor necrosis factor α-induced protein 8 (TNFAIP8)-like protein 1 (TIPE1) was a member of TNFAIP8 family. Previous studies have shown that TIPE1 could induce apoptosis in hepatocellular carcinoma. In this study, we attempted to predict its potential structure. Bioinformatic analysis of TIPE1 was performed to predict its potential structure using the bioinfomatic web services or softwares. The results showed that the amino acid sequences of TIPE1 were well conserved in mammals. No signal peptide and no transmembrane domain existed in human TIPE1. The aliphatic index of TIPE1 was 100.75 and the theoretical pI was 9.57. TIPE1 was a kind of stable protein and its grand average of hydropathicity was -0.108. Various post-translational modifications were also speculated to exist in TIPE1. In addition, the results of Swiss-Model Server and Swiss-Pdb Viewer program revealed that the predicted three-dimensional structure of TIPE1 protein was stable and it may accord with the rule of stereochemistry. TIPE1 was predicted to interact with FBXW5, caspase8 and so on. In conclusion, TIPE1 may be a stable protein with no signal peptide and no transmembrane domain. The bioinformatic analysis of TIPE1 will provide the basis for the further study on the function of TIPE1.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Homology tree construction.
Homology tree is constructed by DNAMAN software and the homology of TIPE1 from various species is shown.
Fig 2
Fig 2. Prediction of signal peptide and transmembrane domain of TIPE1.
Signal peptide (A) and transmembrane domain (B) of TIPE1 are predicted by SignaIP Server and TMpred Server, respectively. X axis represents amino acid sequence from N- to C- terminal. Y axis represents scores computed by each server.
Fig 3
Fig 3. Prediction of hydrophilicity, accessibility, polarity, flexibility, mutability and bulkiness of TIPE1.
The hydrophilicity (A), accessibility (B), polarity (C), flexibility (D), mutability (E) and bulkiness (F) of TIPE1 are predicted using Protscale Server of expasy platform. X axis represents amino acid sequence from N- to C- terminal. Y axis represents scores computed by each algorithm.
Fig 4
Fig 4. Post-translational modifications of TIPE1.
(A) NetPhosK Server was performed to predict kinase specific phosphorylation sites in TIPE1. (B) NetPhos Server was performed to predict generic phosphorylation sites in TIPE1. X axis represents amino acid sequence from N- to C- terminal. Y axis represents values computed by the software. The values above the threshold mean the most potential of phosphorylation.
Fig 5
Fig 5. Homology modeling and evaluation of model stability.
(A) Homology modeling was performed by Swiss-Model Server and the predicted 3D structure of TIPE1 protein was shown. (B) Model quality was evaluated using the method of Ramachandran plot and the results represent the acceptable stability of 3D structure of TIPE1 protein.
Fig 6
Fig 6. Protein-protein interaction analysis for TIPE1.
STRING platform is used to predict protein interactions. FBXW5, caspase8, caspase10, POMP and et al. were predicted to be interacted with TIPE1.
See this image and copyright information in PMC

References

    1. Patel S, Wang FH, Whiteside TL, Kasid U. Identification of seven differentially displayed transcripts in human primary and matched metastatic head and neck squamous cell carcinoma cell lines: implications in metastasis and/or radiation response. Oral Oncol. 1997; 33: 197–203. - PubMed
    1. Sun H, Gong S, Carmody RJ, Hilliard A, Li L, Sun J, et al. TIPE2, a negative regulator of innate and adaptive immunity that maintains immune homeostasis. Cell. 2008; 133: 415–426. 10.1016/j.cell.2008.03.026 - DOI - PMC - PubMed
    1. Kumar D, Whiteside TL, Kasid U. Identification of a novel tumor necrosis factor-alpha-inducible gene, SCC-S2, containing the consensus sequence of a death effector domain of fas-associated death domain-like interleukin- 1beta-converting enzyme-inhibitory protein. J Biol Chem. 2000; 275: 2973–2978. - PubMed
    1. Freundt EC, Bidere N, Lenardo MJ. A different TIPE of immune homeostasis. Cell. 2008; 133: 401–402. 10.1016/j.cell.2008.04.017 - DOI - PMC - PubMed
    1. Zhang S, Zhang Y, Wei X, Zhen J, Wang Z, Li M, et al. Expression and regulation of a novel identified TNFAIP8 family is associated with diabetic nephropathy. Biochimica Et Biophysica Acta-Molecular Basis of Disease. 2010; 1802: 1078–1086. - PubMed

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