Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling
Tumor necrosis factor alpha (TNF-) is known to be crucial in many biological activities of organisms. In this study, physicochemical properties and modeling of TNF- protein of fish was analyzed using in silico approach. TNF- proteins selected from fish species, including grass carp (Ctenopharyn...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Prince of Songkla University
2016-10-01
|
| Series: | Songklanakarin Journal of Science and Technology (SJST) |
| Subjects: | |
| Online Access: | http://rdo.psu.ac.th/sjstweb/journal/38-5/38-5-10.pdf |
| _version_ | 1818403046182354944 |
|---|---|
| author | Tran Ngoc Tuan Wang Gui-Tang Pham Minh Duc |
| author_facet | Tran Ngoc Tuan Wang Gui-Tang Pham Minh Duc |
| author_sort | Tran Ngoc Tuan |
| collection | DOAJ |
| description | Tumor necrosis factor alpha (TNF-) is known to be crucial in many biological activities of organisms. In this study,
physicochemical properties and modeling of TNF- protein of fish was analyzed using in silico approach. TNF- proteins
selected from fish species, including grass carp (Ctenopharyngodon idella), zebra fish (Danio rerio), Nile tilapia
(Oreochromis niloticus), goldfish (Carassius auratus), and rainbow trout (Oncorhynchus mykiss) were used in this study.
Physicochemical characteristics with molecular weight, theoretical isoelectric point, extinction coefficient, aliphatic index,
instability index, total number of negatively charged residues and positively charged residues, and grand average of hydropathicity
were computed. All proteins were classified as transmembrane proteins. The “transmembrane region” and “TNF”
domain were identified from protein sequences. The function prediction of proteins was also performed. Alpha helices and
random coils were dominating in the secondary structure of the proteins. Three-dimensional structures were predicted and
verified as good structures for the investigation of TNF- of fish by online server validation. |
| first_indexed | 2024-12-14T08:18:02Z |
| format | Article |
| id | doaj.art-147d3999c10949919e122234100300b7 |
| institution | Directory Open Access Journal |
| issn | 0125-3395 |
| language | English |
| last_indexed | 2024-12-14T08:18:02Z |
| publishDate | 2016-10-01 |
| publisher | Prince of Songkla University |
| record_format | Article |
| series | Songklanakarin Journal of Science and Technology (SJST) |
| spelling | doaj.art-147d3999c10949919e122234100300b72022-12-21T23:09:52ZengPrince of Songkla UniversitySongklanakarin Journal of Science and Technology (SJST)0125-33952016-10-0138554955710.14456/sjst-psu.2016.70Tumor necrosis factor alpha of teleosts: in silico characterization and homology modelingTran Ngoc Tuan0Wang Gui-Tang1Pham Minh Duc2Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, China.Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, China.College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Viet Nam.Tumor necrosis factor alpha (TNF-) is known to be crucial in many biological activities of organisms. In this study, physicochemical properties and modeling of TNF- protein of fish was analyzed using in silico approach. TNF- proteins selected from fish species, including grass carp (Ctenopharyngodon idella), zebra fish (Danio rerio), Nile tilapia (Oreochromis niloticus), goldfish (Carassius auratus), and rainbow trout (Oncorhynchus mykiss) were used in this study. Physicochemical characteristics with molecular weight, theoretical isoelectric point, extinction coefficient, aliphatic index, instability index, total number of negatively charged residues and positively charged residues, and grand average of hydropathicity were computed. All proteins were classified as transmembrane proteins. The “transmembrane region” and “TNF” domain were identified from protein sequences. The function prediction of proteins was also performed. Alpha helices and random coils were dominating in the secondary structure of the proteins. Three-dimensional structures were predicted and verified as good structures for the investigation of TNF- of fish by online server validation.http://rdo.psu.ac.th/sjstweb/journal/38-5/38-5-10.pdfin silicofishTNF- |
| spellingShingle | Tran Ngoc Tuan Wang Gui-Tang Pham Minh Duc Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling Songklanakarin Journal of Science and Technology (SJST) in silico fish TNF- |
| title | Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling |
| title_full | Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling |
| title_fullStr | Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling |
| title_full_unstemmed | Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling |
| title_short | Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling |
| title_sort | tumor necrosis factor alpha of teleosts in silico characterization and homology modeling |
| topic | in silico fish TNF- |
| url | http://rdo.psu.ac.th/sjstweb/journal/38-5/38-5-10.pdf |
| work_keys_str_mv | AT tranngoctuan tumornecrosisfactoralphaofteleostsinsilicocharacterizationandhomologymodeling AT wangguitang tumornecrosisfactoralphaofteleostsinsilicocharacterizationandhomologymodeling AT phamminhduc tumornecrosisfactoralphaofteleostsinsilicocharacterizationandhomologymodeling |