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Protein Silencing Using Self-Peptides
CC BY 4.0 · Indian J Med Paediatr Oncol 2024; 45(S 01): S1-S16
DOI: DOI: 10.1055/s-0044-1788223
*Corresponding author: (e-mail: maiti@tifr.res.in).
Abstract
Background: Selective silencing of proteins is usually achieved at the DNA or mRNA level, where sequence-specific hybridization provides a well-defined mode of specific interaction. It is challenging to achieve such sequence-specific interaction at the level of the proteins. Here we use the concept of a “xenonucleus” to accomplish this target.
Material and Methods: The xenonucleus is a “self-peptide,” i.e., a fragment of the protein itself, which is separately stabilized during SPPS that gets introduced to GuHCl-induced unfolded protein. Here, enhanced green fluorescent protein (EGFP) was selected as a model protein to study the self-peptide induced structural disruption kinetics due to its inherent fluorescence.
Results: EGFP’s fluorescence can easily report its state of folding. The binding of the self-peptides to the folding EGFP can perturb the EGFP chromophore environment and affect its fluorescence properties while enhancing the folding rates. The self-peptides of EGFP showed no effect on the fluorescence activity of folded EGFP, whereas the presence of self-peptides during the folding process of EGFP abolished its fluorescence. The fluorescence quenching was less in the case of randomization of the amino acid sequence of the self-peptide, demonstrating its specificity.
Conclusion: All proteins are unfolded intracellularly at the time of their synthesis in the ribosome, and our design strategy can lead to specific interactor self-peptides which will co-fold with the protein, and inhibit its activity. This demonstrates a general design principle for silencing the activity of nascent beta-barrel proteins.
Publication History
Article published online:
08 July 2024
© 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)
Thieme Medical and Scientific Publishers Pvt. Ltd.
A-12, 2nd Floor, Sector 2, Noida-201301 UP, India
*Corresponding author: (e-mail: maiti@tifr.res.in).
Abstract
Background: Selective silencing of proteins is usually achieved at the DNA or mRNA level, where sequence-specific hybridization provides a well-defined mode of specific interaction. It is challenging to achieve such sequence-specific interaction at the level of the proteins. Here we use the concept of a “xenonucleus” to accomplish this target.
Material and Methods: The xenonucleus is a “self-peptide,” i.e., a fragment of the protein itself, which is separately stabilized during SPPS that gets introduced to GuHCl-induced unfolded protein. Here, enhanced green fluorescent protein (EGFP) was selected as a model protein to study the self-peptide induced structural disruption kinetics due to its inherent fluorescence.
Results: EGFP’s fluorescence can easily report its state of folding. The binding of the self-peptides to the folding EGFP can perturb the EGFP chromophore environment and affect its fluorescence properties while enhancing the folding rates. The self-peptides of EGFP showed no effect on the fluorescence activity of folded EGFP, whereas the presence of self-peptides during the folding process of EGFP abolished its fluorescence. The fluorescence quenching was less in the case of randomization of the amino acid sequence of the self-peptide, demonstrating its specificity.
Conclusion: All proteins are unfolded intracellularly at the time of their synthesis in the ribosome, and our design strategy can lead to specific interactor self-peptides which will co-fold with the protein, and inhibit its activity. This demonstrates a general design principle for silencing the activity of nascent beta-barrel proteins.
No conflict of interest has been declared by the author(s).
Publication History
Article published online:
08 July 2024
© 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)
Thieme Medical and Scientific Publishers Pvt. Ltd.
A-12, 2nd Floor, Sector 2, Noida-201301 UP, India