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Biocomputational Analysis and In Silico Characterization of an Angiogenic Protein (RNase5) in Zebrafish (Danio rerio)

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Abstract

Several types of RNase protein has been identified and characterized from different group of organism using advanced biocomputational techniques. Some of these RNase have crucial role for understanding and discovering the practical mechanism of cellular angiogenesis. To characterize the zebrafish (Danio rerio) RNase5 for its angiogenic properties multiple modern bioinformatics tools and server applied in present research. For accurate structural profiling of RNase5 protein through Ramachandran plot of PROCHECK and ProSA-web servers were applied. Subsequently, the CABS-flex server has been introduced to compute the Route Mean Square Fluctuation of all atoms for dynamic system simulation with a minimal residue fluctuation. Prediction of RNase5 protein’s sub-cellular localization, the TMHMM server also applied and confirmed its extracellular or secretory nature. Moreover, the sequence alignment with human angiogenin protein authenticates higher level of sequence similarity and reveals the conserved regions within protein of interest. Additionally, molecular docking with very low ACE value − 131.67 between the VEGF-binding domain of FLT-1 protein and zebrafish RNase5 able to generate the effective confirmation of cellular angiogenic activity. The molecular dynamic simulation by Normal Mode Analysis (NMA) also performed for functional mobility and structural stability of docking complex. Therefore, such In silico efforts definitely support the proper understanding of RNase5 enzyme mediated angiogenic activity. This effort certainly provides like a potential aid towards the future study of angiogenesis mechanism, as an important phenomenon of cancer metastasis in vertebrate model.

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Abbreviations

RNA:

Ribonucleic acid

VEGF:

Vascular endothelial growth factor

ALS:

Amyotropic lateral sclerosis

3D:

Three dimensional

UCSF:

University of California, San Francisco

PDB:

Protein data bank

RMSF:

Root mean square fluctuation

MD:

Molecular dynamics

T-COFFEE:

Tree-based consistency objective function for alignment evaluation

ACE:

Atomic contact energy

MSA:

Multiple sequence alignment

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Acknowledgements

This research work is supported by research project of Science for Equity Empowerment and Development (SEED), Department of Science and Technology (DST), Govt. of India (Grant No. SEED/WTP/059/2014/G).

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Author notes

  1. Prasanta Patra and Manojit Bhattacharya contributed equally the work.

Authors and Affiliations

  1. Department of Zoology, Vidyasagar University, Midnapore, West Bengal, 721102, India

    Prasanta Patra, Pratik Ghosh, Bidhan Chandra Patra & Manojit Bhattacharya

  2. Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, 721 102, India

    Bidhan Chandra Patra

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  1. Prasanta Patra
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  2. Pratik Ghosh
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Correspondence to Manojit Bhattacharya.

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Patra, P., Ghosh, P., Patra, B.C. et al. Biocomputational Analysis and In Silico Characterization of an Angiogenic Protein (RNase5) in Zebrafish (Danio rerio). Int J Pept Res Ther 26, 1687–1697 (2020). https://doi.org/10.1007/s10989-019-09978-1

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