In silico Structural Prediction and Functional Analysis of Cold Tolerant Glycerol-3-Phosphate Dehydrogenase Protein of Rainbow Trout

Author: Ubaid Qayoom, Zahoor Mushtaq and Pabitra Barik

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Abstract

The present study aimed to investigate the glycerol-3-phosphate dehydrogenase (GPDH) protein of the rainbow trout (Oncorhynchus mykiss). Although the protein plays a crucial role in the cold tolerance pathway of fishes, especially rainbow trout, its structural and functional annotation remains to be studied. The present study was designed to enlist some of the physiochemical and functional properties of GPDH protein and generate information about its three-dimensional structure. The primary structure evaluation inferred that it is an acidic and hydrophobic protein with a molecular weight of 39.9 kDa. Functional analysis by InterPro classified the protein into NAD(P)-binding domain family having a biological role in the redox processes. The SOSUIGramN server indicated the cytoplasmic subcellular localization without any signal sequence. The three-dimensional model built using the Swiss-Model server was evaluated using QMEAN, ProQ, and ProSA programs. The predicted 3D structure will offer a good foundation for functional analysis of experimental origin crystal structures. The closest interacting protein was found to be belonging to the Glycerol-3-phosphate acyltransferase family having a score of >0.7 via the STRINGv 11.5 server. Overall, the present study of structural characterization of the trout glycerol-3-phosphate dehydrogenase will facilitate an improved understanding of its enzymatic actions as well as its role in the cold tolerance of rainbow trout.

Keywords

Oncorhynchus mykiss, GPDH, Homology modelling, Bioinformatics

Conclusion

In conclusion, genomic and proteomic sequencing projects have resulted in many protein sequences without any annotated functions or designated hypothetical/conserved proteins. The GPDH gene in rainbow trout plays a crucial role in cold stress physiology. In snow trouts of Himalayan rivers, Barat et al. (2012) characterized 1,012 bp of the GPDH gene from Schizothorax richardsonii and S. niger and showed a 19-fold increase in its expression in liver tissue at 5ºC compared to 15 ºC conditions suggesting a role in stress-linked responses in these endemic Himalayan fishes. However, the protein has not been physically characterized using NMR or X-ray crystallography. Consequently, it becomes imperative to utilise bioinformatic means to fathom these aspects of GPDH as well as other critical proteins in rainbow trout.

References

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How to cite this article

Ubaid Qayoom, Zahoor Mushtaq and Pabitra Barik (2022). In silico Structural Prediction and Functional Analysis of Cold Tolerant Glycerol-3-Phosphate Dehydrogenase Protein of Rainbow Trout. Biological Forum – An International Journal, 14(4): 811-818.