|
In silico analysis of freshwater fish major histocompatibility complex class II alpha |
|---|---|
| รหัสดีโอไอ | |
| Creator | Tran Ngoc Tuan |
| Title | In silico analysis of freshwater fish major histocompatibility complex class II alpha |
| Contributor | Pham Minh Duc |
| Publisher | Research and Technology Transfer Affairs Division.Khon Kaen University |
| Publication Year | 2559 |
| Journal Title | Asia-Pacific Journal of Science and Technology |
| Journal Vol. | 21 |
| Journal No. | 4 |
| Page no. | 1-8 |
| Keyword | Freshwater fish, MHC II?, physicochemical characterisation, protein structure. |
| URL Website | https://tci-thaijo.org/index.php/APST/index |
| Website title | https://tci-thaijo.org/index.php/APST/article/view/84838 |
| ISSN | 2539-6293 |
| Abstract | Major histocompatibility complex (MHC) plays important roles in the immune system of vertebrates. This current study aimed to clearly understand the properties and structures of the MHC class II alpha (MHC II?) proteins selected from freshwater fish species using in silico analysis. The MHC II? of Ctenopharyngodon idella, Oreochromis niloticus, Cyprinus carpio, Danio rerio, Oncorhynchus mykiss, and Ictalurus punctatus were used. The molecular weight of MHC II? of fish species was arranged from 17,054.5 to 26,358.9 Da. The three domains: "Class II histocompatibility antigen, alpha domain" (MHC_II_alpha), "Immunoglobulin C-Type" (IGc1) and "Transmembrane region" were found in the proteins. Physicochemical characterisation showed theoretical isoelectric point (pI: 4.31~5.3), total number of positive and negative residues (+R/-R: 19~32/13~20), extinction coefficient (EC: 18,910~29,910/19,410~30,410 M-1.cm-1, assuming that all pairs of cysteine residues form cysteines/all cysteines are reduced), instability index (II: 27.1~41.4), aliphatic index (AI: 73.3~93.3) and Grand average of hydropathicity (GRAVY: -0.240~0.156). Cysteine residues and disulphide bonds were determined from the proteins. In secondary structure prediction, excepting for the protein of common carp (extended strand was dominated), all proteins were composed of random coils as predominant, followed by extended strands, alpha helix and beta turn. Three dimensional structures of proteins were predicted performing SWISS-MODEL server. All models were evaluated being accepted and reliable based on structural evaluation and stereochemical analyses. This study provides knowledge of the physiochemical characterisations, structure features and functions of MHC II? from freshwater fishes that is useful for further researches on the field of immune-related study of aquatic animals in future. |
