Related Experiment Video
Updated: Mar 14, 2026
06:50
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
2.7K
Computational Prediction of New Intein Split Sites.
Yi-Zong Lee1, Wei-Cheng Lo2,3, Shih-Che Sue4,5
1Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, 30013, Hsinchu, Taiwan.
Methods in Molecular Biology (Clifton, N.J.)
|October 8, 2016
Summary
We developed a computational method to predict split sites for split inteins, enabling the design of novel protein ligation tools. This approach uses circular permutation prediction to identify permissive sites for creating new split inteins.
Area of Science:
- Protein Engineering
- Computational Biology
- Biochemistry
Background:
- Split inteins are valuable tools for protein engineering and biotechnology.
- Designing novel split inteins requires identifying specific sites for backbone cleavage and rejoining.
- Existing methods for split intein design can be labor-intensive and may lack predictability.
Purpose of the Study:
- To develop and validate a reliable in silico method for predicting viable split sites for novel split intein design.
- To leverage computational circular permutation (CP) prediction to identify permissive internal sites for creating split inteins.
- To integrate an accessible online CP prediction tool (CPred) into the workflow for discovering new split intein sites.
Main Methods:
- Utilized a computational circular permutation (CP) prediction method to identify internal permissive sites within protein structures.
- Developed a strategy to connect original protein termini and create new termini, simulating potential split sites.
- Integrated the CPred online tool to facilitate the search and prediction of suitable split sites for split intein engineering.
Main Results:
- Successfully identified promising candidate sites for generating new split inteins.
- Demonstrated that the identified sites are likely to tolerate backbone opening due to the structural scaffold.
- Showcased the practical application of the CPred tool in a streamlined split intein design process.
Conclusions:
- The described in silico method provides a reliable approach for predicting split sites, advancing the design of split inteins.
- Computational prediction of circular permutation sites is an effective strategy for discovering new split intein functionalities.
- The integration of CPred facilitates efficient and accessible exploration of split intein engineering possibilities.
More Related Videos
Related Concept Videos
02:53Conservative Site-specific Recombination and Phase Variation
7.3K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
7.3K
01:49Conserved Binding Sites
5.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.3K
02:32Exon Recombination
4.3K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...
Exon shuffling follows “splice frame rules.” Each exon...
4.3K