In-silico molecular designs to treat neurologic and ophthalmologic diseases caused by sorbitol excess: engineering the Agrobacterium vitis protein
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13104_2023_Article_6367.pdf
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Author(s)
Sharma, Shonit N.
Hojati, Ashkhan
Gnanasambandam, Bhargavee
Yerrabelli, Rahul S.
Brozek, Joshua
Date Issued
July 3, 2023
Publisher
BioMed Central
Citation
BMC Research Notes. 2023 Jul 03;16(1):129
Version
Final published version
Abstract
Abstract
This work presents the design of a new protein based on the adenosine triphosphate-binding cassette (ABC) transporter solute binding protein (SBP) derived from Agrobacterium vitis, a gram-negative plant pathogen. The Protein Data Bank in Europe’s dictionary of chemical components was utilized to identify sorbitol and D-allitol. Allitol bound to an ABC transporter SBP was identified in the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB). Wizard Pair Fitting and Sculpting tools in PyMOL were used to replace bound allitol with sorbitol. PackMover Python code was used to induce mutations in the ABC transporter SBP’s binding pocket, and changes in free energy for each protein-sorbitol complex were identified. The results indicate that adding charged side chains forms polar bonds with sorbitol in the binding pocket, thus increasing its stabilization. In theory, the novel protein can be used as a molecular sponge to remove sorbitol from tissue and therefore treat conditions affected by sorbitol dehydrogenase deficiency.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s13104-023-06367-2
