Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase
| Autor: | Lipika Salaye, Swapan K. Bhattacharjee, Renu Minda, Basuthkar J. Rao, Sandeep Chakraborty |
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| Rok vydání: | 2011 |
| Předmět: |
Models
Molecular Proteomics Proteases medicine.medical_treatment Phosphatase Amino Acid Motifs Static Electricity Biophysics lcsh:Medicine Biochemistry Biophysics Simulations Serine Protein structure Catalytic Domain Decapoda medicine Animals lcsh:Science Biology Computerized Simulations chemistry.chemical_classification Multidisciplinary Protease biology Enzyme Classes Proteomic Databases Software Tools Physics lcsh:R Active site Computational Biology Software Engineering Alkaline Phosphatase Enzymes Enzyme chemistry Proteolysis Enzyme Structure Computer Science biology.protein Biocatalysis lcsh:Q Biophysic Al Simulations Protons Serine Proteases Function (biology) Algorithms Research Article |
| Zdroj: | PLoS ONE PLoS ONE, Vol 6, Iss 12, p e28470 (2011) |
| ISSN: | 1932-6203 |
| Popis: | Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - C ata L ytic A ctive S ite P rediction (CLASP). In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD) between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP), one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP), where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in vitro. |
| Databáze: | OpenAIRE |
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