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3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla

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Abstract

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.

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Acknowledgments

The work was financially supported by a grant from the National Agricultural Innovation Project, Indian Council of Agricultural Research (NAIP-ICAR; project code: C4-C30018). The authors gratefully acknowledge the aid of the Bioinformatics Resources and Applications Facility (BRAF) at the Center for Development of Advanced Computing (C-DAC), Pune, India, for the MD simulation studies. We thank the Director of the Central Institute of Freshwater Aquaculture (CIFA) for providing the necessary facilities to carry out this study.

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Authors and Affiliations

  1. Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Orissa, India, 751002

    Bikash R. Sahoo, Banikalyan Swain, Madhubanti Basu, Padmaja Panda, Nikhil K. Maiti & Mrinal Samanta

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  1. Bikash R. Sahoo
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  2. Banikalyan Swain
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  3. Madhubanti Basu
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  4. Padmaja Panda
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  5. Nikhil K. Maiti
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  6. Mrinal Samanta
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Correspondence to Mrinal Samanta.

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Fig. S1

Time profile of the secondary structure changes in the catla IL-10 model. The secondary structure during the trajectory (5 ns MD simulation) was generated by the VMD program. Secondary structure codes are as follows: T turn, E extended conformation, B isolated bridges, H alpha-helix, G 3–10 helix, I pi-helix, C coil. A key to the colors used is given in the figure. (JPEG 204 kb)

High-resolution image (EPS 1302 kb)

Supplementary video SV1

Time profile of structural changes during the trajectory in the catla IL-10 model. Additional cysteine residues (Cys5 and Cys10) that are present in fish (catla IL-10) are labeled. (M1V 11769 kb)

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Sahoo, B.R., Swain, B., Basu, M. et al. 3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla . J Mol Model 18, 1713–1722 (2012). https://doi.org/10.1007/s00894-011-1194-1

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  • DOI: https://doi.org/10.1007/s00894-011-1194-1

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