Biocomputational Analysis and In Silico Characterization of an Angiogenic Protein (RNase5) in Zebrafish (Danio rerio)
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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.
KeywordsIn silico Angiogenesis RNase5 Zebrafish
Vascular endothelial growth factor
Amyotropic lateral sclerosis
University of California, San Francisco
Protein data bank
Root mean square fluctuation
Tree-based consistency objective function for alignment evaluation
Atomic contact energy
Multiple sequence alignment
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).
Compliance with Ethical Standards
Conflict of interest
The authors declare that they have no conflict of interest.
Research Involving Human and Animal Rights
This article does not contain any studies with human participants or animals performed by any of the authors.
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