Biocomputational Analysis and In Silico Characterization of an Angiogenic Protein (RNase5) in Zebrafish ( Danio rerio )
- PDF / 2,234,802 Bytes
- 11 Pages / 595.276 x 790.866 pts Page_size
- 62 Downloads / 180 Views
Biocomputational Analysis and In Silico Characterization of an Angiogenic Protein (RNase5) in Zebrafish (Danio rerio) Prasanta Patra1 · Pratik Ghosh1 · Bidhan Chandra Patra1,2 · Manojit Bhattacharya1 Accepted: 7 November 2019 © Springer Nature B.V. 2019
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. Keywords In silico · Angiogenesis · RNase5 · Zebrafish 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 Prasanta Patra and Manojit Bhattacharya contributed equally the work. * Manojit Bhattacharya [email protected] 1
Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102, India
Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal 721 102, India
2
T-COFFEE Tree-based consistency objective function for alignment evaluation ACE Atomic contact energy MSA Multiple sequence alignment
Introduction Ribonucleases (RNases) are the special kind of nuclease that primarily facilitates to RNA degradation. RNase also performed significant functions in RNA chain maturation. The zebrafish (Danio rerio) RNase sub type RNase5 is belongs to the R
Data Loading...
