Abstract
Seryl-histidine dipeptide (Ser-His) has been recognized as the shortest peptide with hydrolysis cleavage activity; however, its protein cleavage spectrum has not yet been fully explored. Here, four differently folded proteins were treated with Ser-His, and the digestion products were evaluated with high-resolution mass spectrometry. The cleavage efficiency and cleavage propensity of Ser-His against these protein substrates were calculated at both the primary and secondary sequence levels. The above experiments show that Ser-His cleaves a broad spectrum of substrate proteins of varying secondary structures. Moreover, Ser-His could cleave at all 20 amino acids with different efficiencies according to the protein, which means that Ser-His has the original digestion function of serine proteases. Furthermore, we collected and compared the catalytic sites and cleavage sites of 340 extant serine proteases derived from 17 representative organisms. A consensus motif Ser-[X]-His was identified as the major pattern at the catalytic sites of serine proteases from all of the organisms represented except Danio rerio, which uses Ser-Lys instead. This finding indicates that Ser-His is the core component of the serine protease catalytic site. Moreover, our analysis revealed that the cleavage sites of modern serine proteases have become more specific over the evolutionary history of this family. Based on the above analysis results, it could be found that Ser-His is likely the original serine protease and maybe the evolutionary core of modern serine proteases.
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Acknowledgements
The authors acknowledge the National Basic Research Program of China (2013CB910700), the Chinese National Science Foundation (No. 21232005, No. 21375113, and No. 31271405) and the Fundamental Research Funds for the Central Universities (No. 20720150049). We also thank Prof. Zhongzhou Chen in China Agricultural University for his helpful manuscript modification.
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Yan Liu designed the experiment, performed the MS analysis of CyPA and GFP, and wrote the manuscript. Yin-bo Li performed the related data analysis and calculation. Yan Liu and Yin-bo Li contributed equally to this work. Xiang Gao performed the MS analysis of BSA and Mb. Yong-fei Yu performed one part of the mass data analysis. Zhiliang Ji designed the calculation experiments, contributed to data interpretation and provided critical. Yuan Ma and Yan-mei Li contributed to the overall concept and experiment preparation. Yu-fen Zhao designed experiments and contributed to data analysis and interpretation as well as manuscript writing.
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Liu, Y., Li, Yb., Gao, X. et al. Evolutionary relationships between seryl-histidine dipeptide and modern serine proteases from the analysis based on mass spectrometry and bioinformatics. Amino Acids 50, 69–77 (2018). https://doi.org/10.1007/s00726-017-2487-1
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DOI: https://doi.org/10.1007/s00726-017-2487-1