Modular Repressor Compatibility via Coevolutionary Modeling
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Solution Overview
Problem
The construction of genetic circuits is constrained by the lack of modular components, as natural biological systems respond rigidly to unique molecular signals, limiting the implementation of diverse circuit designs due to incompatibility between DNA-binding modules (DBMs) and ligand-binding modules (LBMs) from different proteins, which results in poor performance of hybrid repressors.
Innovation Solution
A novel module swapping strategy (MSS) that uses coevolutionary modeling to predict mutations that restore native-like interactions between DBMs and LBMs, enhancing the compatibility score and functionality of hybrid repressors by identifying inter-modular residue pairs that coevolve, thereby rescuing their activities.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If DBMs and LBMs are hybridized from distinct transcriptional repressors to create genetic sensors with unique combinations, then diverse circuit designs can be implemented, but incompatibility between modules occurs due to loss of critical module-module interactions
Solution Approach 1:
The patent applies parameter changes by systematically mutating amino acid residues at specific positions in the LBMs to optimize their interaction with DBMs. By changing sequence parameters at coevolutionarily coupled positions, the patent restores compatible module-module interactions while maintaining the desired diversity in circuit designs.
Solution Approach 2:
The patent employs feedback mechanisms through coevolutionary modeling that analyzes multiple sequence alignments to identify residue pairs that coevolve. This feedback loop allows the system to predict and select mutations that restore functional interactions between modules, ensuring reliable hybrid repressor performance.
2Adaptability or versatility
If module swapping is performed to create hybrid repressors, then new biosensor functions can be achieved, but the activity of hybrid repressors deteriorates due to incompatibility
Solution Approach 1:
The patent uses parameter changes by targeting specific amino acid positions in LBMs that are coevolutionarily coupled with DBM positions. By mutating residues at these optimized positions, the patent restores productive module interactions and significantly improves hybrid repressor activity, achieving up to 500-fold increased induction.
Solution Approach 2:
The patent applies preliminary action through computational coevolutionary modeling performed before creating hybrid repressors. By pre-identifying compatible residue pairs and predicting optimal mutations, the patent ensures that subsequent hybrid repressor construction achieves high activity levels from the outset.
3Reliability
If natural biological systems respond rigidly to unique molecular signals, then specific gene expression control is achieved, but implementation of diverse circuit designs is limited
Solution Approach 1:
The patent applies segmentation by dividing transcriptional repressors into independent, interchangeable modules: DNA-binding modules (DBMs) and ligand-binding modules (LBMs). This modular segmentation allows specific gene expression control through individual module function while enabling diverse circuit designs through combinatorial assembly of different modules.
Solution Approach 2:
The patent implements universality by creating a standardized modular framework where DBMs and LBMs can be universally combined to form functional hybrid repressors. The coevolutionary design ensures that modules from different proteins can be universally integrated while maintaining specific control functions, thereby achieving both reliability and versatility.
Data Source
AI summary
A method can include receiving a protein sequence (S) of a hybrid repressor, determining an original compatibility score C(S), where the compatibility score C is a function of the protein sequence (S) and predicting, based on the compatibility score C, a performance of the hybrid repressor. The hybrid protein sequence includes a plurality of DNA-binding modules (DBMs) and a plurality of ligand-binding modules (LBMs).