A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold
| Autor: | Renu Minda, Basuthkar J. Rao, Manish Shukla, Félix M. Goñi, Sandeep Chakraborty, Bjarni Ásgeirsson, Abhaya M. Dandekar, Masataka Oda, Adela Rendón-Ramírez |
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| Přispěvatelé: | Uversky, Vladimir N |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular Proteomics BIOCHEMISTRY AND MOLECULAR BIOLOGY medicine.medical_treatment Amino Acid Motifs lcsh:Medicine Biochemistry Biophysics Simulations Computer Applications pseudomonas aeruginosa chemistry.chemical_compound Computational Chemistry Phosphoinositide Phospholipase C Models AEBSF Catalytic Domain lcsh:Science Multidisciplinary biology Proteomic Databases bacterial phospholipases Serine Endopeptidases Proteolytic enzymes Software Engineering Enzymes Chemistry Networking and Information Technology R&D Infectious Diseases AGRICULTURAL AND BIOLOGICAL SCIENCES Biophysic Al Simulations Prolyl Oligopeptidases alkaline phosphatase MASP1 Algorithms outer membrane vesicles Research Article Proteases crystal structure sphingomyelinase activities General Science & Technology Biophysics cysteine proteases Bacillus cereus Bacterial Proteins medicine Computer Simulation convergent evolution Biology Serine protease Protease Edman degradation MEDICINE lcsh:R phospholipase-C Proteins Computational Biology Molecular perfringens alpha toxin Protein superfamily Semi-Empirical Methods Computing Methods chemistry Computer Science biology.protein Programming Languages lcsh:Q Generic health relevance |
| Zdroj: | PloS one, vol 8, iss 8 PLoS ONE, Vol 8, Iss 8, p e70923 (2013) Addi. Archivo Digital para la Docencia y la Investigación instname PLoS ONE |
| Popis: | Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues. BJR would like to thank the Tata Institute of Fundamental Research (Department of Atomic Energy) for financial support. MO was supported in part by a Grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan; (grant No. 21790431). FMG thanks the Spanish Ministerio de Ciencia e Innovacion for grant No. BFU 2007/62062, and the University of the Basque Country for grant No. IT 461-07. BA extends gratitude to the Icelandic National Research Council and the University of Iceland Research Found for supporting the project financially. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. |
| Databáze: | OpenAIRE |
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