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Computational optimization of DEK1 calpain domain solubility through integrated structural modelling and data-driven
Mohammad Dabiri1, Zdenko Levarski2,3, Eva Struhárňanská4
1Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovak Republic. dabiri2@uniba.sk.
Scientific Reports
|February 8, 2026
Summary
Researchers improved the solubility of the DEFECTIVE KERNEL 1 (DEK1) protein
Area of Science:
- Plant Biology
- Structural Biology
- Biochemistry
Background:
- The DEFECTIVE KERNEL 1 (DEK1) protein is crucial for plant development.
- DEK1 is a large, multidomain protein with an unsolved 3D structure.
- Understanding DEK1's structure is key for functional studies.
Purpose of the Study:
- To enhance the solubility of the DEK1 calpain protease core domain (CysPc) for recombinant production.
- To develop a data-driven method for improving protein solubility without high-resolution structural data.
Main Methods:
- Integrated structural modeling and topology prediction pipeline.
- Molecular Dynamics (MD) simulations to evaluate native and mutant structures.
- Targeted single, double, and triple amino acid mutagenesis based on solubility parameters.
Main Results:
- A precise pipeline for predicting CysPc domain topology was established.
- Mutagenesis strategies successfully reduced aggregation-prone traits.
- Variants with improved solubility and preserved structural integrity were identified.
Conclusions:
- A data-driven framework effectively improves protein solubility for structural and functional studies.
- This approach is valuable when high-resolution structural data is unavailable.
- Optimized DEK1 CysPc variants facilitate further research into DEK1 function.
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