Bioinformatics Tools Stuty on the Sequence and Structure Characteristics of Urinary Prokallikrein
Li Gun*, Yang Ru, Tian Han, Lu Jingqi
Copyright :© 2017 Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Urinary prokallikrein in human participates in the regulation of water and electrolyte balance. In this paper, several characteristics of urinary prokallikrein are studied via some bioinformatics tools. First, the chemical and physical properties such as the molecular weight, the isoelectric point and the hydrophobicity, etc, of urinary prokallikrein are predicted via ProtParam tool. The results show that the molecular formula is C1168H1764N310O363S14, the instability index is 37.98, the theoretical pI is 4.57, et al. the secondary structure of urinary prokallikrein is predicted via the SOPMA tool, the result shows that there are 57(23.95%) Alpha helix, 60(25.21%) Beta sheet, 31(13.03%) Turn and 90(37.82%) Coil. Finally, phosphorylation sites and the protein-protein interaction of urinary prokallikrein are respectively studied by the netphos tool and the STRING system.
1. Introduction
2. Materials And Methods
3. Results And Discussion
Hydrophobicity is determined by the amino acids sequences. The Hydrophobicity map of urinary prokallikrein sequences is calculated by the Hphoh. / Kyte & Doolittle scale in ExPASy's ProtScale program and the result is shown in Fig.1. In the Fig.1, while vertical value above 0 denotes the hydrophobic area. And it is easily can be seen that there are more hydrophilic residues than the hydrophobic residues in urinary prokallikrein.
The most common secondary structure is the α-helix, β-fold, turn and random coil. The secondary structure of urinary prokallikrein is predicted via SOPMA system, and the prediction result is shown in Fig.2. The result shows that there are 57(23.95%) alpha helix, 60(25.21%) beta sheet, 31(13.03%) turn and 90(37.82%) coil in the urinary prokallikrein sequence.
The main sites for protein phosphorylation are serine, threonine and tyrosine. These sites for phosphorylation in urinary prokallikrein are studied via the NetPhos system, and the result is shown in the Fig.3. There are 8 serine phosphorylation sites (potential value higher than 0.5), 5 threonine phosphorylation sites (potential value higher than 0.5), and 3 tyrosine are phosphorylation sites (potential value higher than 0.5) in the urinary prokallikrein.
Protein-protein interaction characteristics of urinary prokallikrein is predicted via String online system, and the results is shown in the Fig.4. The results show that there are 11 nodes in the protein-protein interaction network, and there are 29 interaction edges with the average node degree 5.27, PPI enrichment p-value: 0.000146.
The structural characteristics of urinary prokallikrein have not attracted many scientists, so, there is very few related works. In our study, some important characteristics of urinary prokallikrein are predicted via some famous prediction tools, and all of these tools are all widely used in studying the structure of proteins.
4. Conclusion
Acknowledgments
References