Abstract
L-asparagine is essential for the correct function of some neoplastic cells; in lymphoblasts, L-asparagine is converted to aspartic acid by L-asparaginase. By conversion of L-asparagine to aspartic acid through the L-asparaginase activity in the plasma, L-asparagine was depleted and resulted in inhibiting DNA synthesis and consequently cell apoptosis. Considering the special properties of this enzyme in cancer treatment, L-asparaginase has been introduced as an anti-cancer drug in chemotherapy. The molecular cloning of a new type of L-asparaginase from E. coli was reported, previously. Here, we analyze some features of this enzyme such as CUP (codon usage preference) and rare codon cluster (RCC). By modeling of L-asparaginase 3D (three-dimensional) structure, some rare codons were detected that may have an important role in the structural and functional properties of the enzyme. In the following, the properties of the substrate binding sites were studied by molecular docking technique. Their substrate binding sites were conducted by the AutoDock Vina. This analysis recognized some amino acids that had a similar structural situation with the substrate binding site of Erwinia carotovora L-asparaginase (2jk0). In this study, five rare codons of Lys195, Leu30, Lys184, Lys160, and Lys174 were identified and studied in the structure of L-asparaginase. The substrate binding site studies showed that the Asp6, Asp77, and Thr78 incorporate in the active site of the enzyme. The results of this study can improve the understanding of L-asparaginase folding and expression challenges and help in the rational design of novel drugs.
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Abbreviations
- SPDBV:
-
Swiss-PdbViewer
- E. coli :
-
Escherichia coli
- 3D:
-
three-dimensional
- CUP:
-
codon usage preference
- I-TASSER:
-
Iterative Threading ASSEmbly Refinement
- PyMOL:
-
Python-enhanced molecular graphics tool
- AutoDock:
-
automated docking
- RCC:
-
rare codon clusters
- NCBI:
-
National Center for Biotechnology Information
- BLAST:
-
Basic Local Alignment Search Tool
- GCUA:
-
Graphical Codon Usage Analyser
- ANSI:
-
American National Standards Institute
- Pfam:
-
Protein family
- MSS:
-
Maximal Scoring Subsequences
- LOMETS:
-
Local Meta-Threading Server
- ProtParam:
-
protein parameters
- PIC:
-
Protein Interactions Calculator
- PDBQT:
-
protein Data Bank Q (partial charges) T (atom types)
- MGL:
-
Molecular Graphics Laboratory
- SDF:
-
Structure Data File
- C-score:
-
Confidence score
- TM score:
-
Template modeling score
- RMSD:
-
The root-mean-square deviation
- SDM:
-
site directed mutagenesis
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The authors wish to thank Shiraz University of Medical Sciences for supporting the conduct of this research.
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Mortazavi, M., Torkzadeh-Mahani, M., Kargar, F. et al. In silico analysis of codon usage and rare codon clusters in the halophilic bacteria L-asparaginase. Biologia 75, 151–160 (2020). https://doi.org/10.2478/s11756-019-00324-w
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DOI: https://doi.org/10.2478/s11756-019-00324-w