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

Shen P, Zhang H, Su Z, Wang S, Xu H - PLoS ONE (2015)

Bottom Line: The results showed that the amino acid sequences of TIPE1 were well conserved in mammals.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.In conclusion, TIPE1 may be a stable protein with no signal peptide and no transmembrane domain.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, Institute of Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China; Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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pone.0134114.g005: 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.

Mentions: Homology modeling was performed by Swiss-Model Server in expasy web and the predicted three-dimensional (3D) structure of TIPE1 protein was shown in Fig 5A. Then the model quality was evaluated using the method of Ramachandran plot (Fig 5B) and the results showed that TIPE1 had 0.6% residues in outlier region. The value obtained by the method of energy minimization was -20599.754 KJ/mol. Based on these data, the results of Ramachandran plot revealed that the modeled 3D structure of TIPE1 protein might have the acceptable stability and it conforms to the rule of stereochemistry.


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

Shen P, Zhang H, Su Z, Wang S, Xu H - PLoS ONE (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4514785&req=5

pone.0134114.g005: 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.
Mentions: Homology modeling was performed by Swiss-Model Server in expasy web and the predicted three-dimensional (3D) structure of TIPE1 protein was shown in Fig 5A. Then the model quality was evaluated using the method of Ramachandran plot (Fig 5B) and the results showed that TIPE1 had 0.6% residues in outlier region. The value obtained by the method of energy minimization was -20599.754 KJ/mol. Based on these data, the results of Ramachandran plot revealed that the modeled 3D structure of TIPE1 protein might have the acceptable stability and it conforms to the rule of stereochemistry.

Bottom Line: The results showed that the amino acid sequences of TIPE1 were well conserved in mammals.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.In conclusion, TIPE1 may be a stable protein with no signal peptide and no transmembrane domain.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, Institute of Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China; Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China.

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.

No MeSH data available.


Related in: MedlinePlus