3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla
| Autor: | N.K. Maiti, Padmaja Panda, Banikalyan Swain, Bikash R. Sahoo, Mrinal Samanta, Madhubanti Basu |
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| Rok vydání: | 2011 |
| Předmět: |
Carps
Molecular Sequence Data India Molecular Dynamics Simulation Catalysis Homology (biology) Inorganic Chemistry Molecular dynamics Immune system biology.animal Animals Humans Amino Acid Sequence Amino Acids Physical and Theoretical Chemistry Carp chemistry.chemical_classification biology Computers Organic Chemistry Vertebrate biology.organism_classification Catla Interleukin-10 Computer Science Applications Amino acid Fishery Interleukin 10 Computational Theory and Mathematics Biochemistry chemistry Structural Homology Protein Sequence Alignment Protein Binding |
| Zdroj: | Journal of Molecular Modeling. 18:1713-1722 |
| ISSN: | 0948-5023 1610-2940 |
| Popis: | Interleukin-10 (IL-10) is a pleiotropic immune-regulatory cytokine that is expressed in various species of fish and higher vertebrates, and is activated during infection. In spite of its important role, IL-10 has not been well characterized either functionally or structurally in fish. To analyze its properties and function, we constructed a 3D model of IL-10 in the Indian major carp, the catla (Catla catla), which is a highly preferred fish species and the most commercially important one in the Indian subcontinent. The catla IL-10 model was constructed by comparative modeling using human IL-10 (2ILK) as the template, and a 5 ns molecular dynamics (MD) simulation was carried out to characterize its structural and dynamical features, which was validated by the SAVES, WHAT IF and MolProbity servers. Analysis using the VAST server revealed a comparatively low level of homology between catla and human IL-10 amino acids at the N-terminal (22.7%) compared to the C-terminal (38.29%). Six conserved domains (A-F) were predicted in catla that threaded well with human IL-10, but their putative interaction sites varied significantly. The amino acid residues in helices A and F differed in length between catla and human IL-10, which may lead to the differences in the IL-10/IL-10R complexes of these two species. The existence of two highly conserved amino acid residues (Cys5 and Cys10) in fish IL-10 but not in higher vertebrate (including human) IL-10 was analyzed in this 3D model. CastP, cons-PPISP and InterProSurf server identified several binding pockets with various probe radii, but Cys5 and Cys10 did not form any significant bonds relating to structural stabilization or protein-protein interactions. |
| Databáze: | OpenAIRE |
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