mRNA Codon Optimization for Co-translational Protein Folding
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for heterologous protein production in systems like E. coli often prioritize quantity over quality and function, failing to optimize folding and functionality due to inadequate consideration of translation dynamics and co-translational protein behavior.
Innovation Solution
Determine optimal mRNA sequences by analyzing translation rates and folding kinetics using experimental methods like ribosome profiling and FRET analysis, allowing for the design of optimized codon sequences that enhance co-translational folding and protein quality, irrespective of the protein's original organism.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If codon usage is optimized to maximize protein quantity production, then productivity increases, but manufacturing precision of properly folded proteins deteriorates
Solution Approach 1:
The patent applies local quality by implementing position-specific codon optimization where different codons are selected for different positions in the coding sequence based on their impact on translation rate and protein folding. Rather than uniform codon usage, the method identifies critical positions where synonymous codon choices affect co-translational folding outcomes, allowing local customization of codon selection to balance production quantity and folding accuracy.
Solution Approach 2:
The patent utilizes parameter changes by systematically varying codon selection parameters at different positions in the mRNA sequence. By changing codon identity (a nucleotide sequence parameter) while maintaining the same amino acid sequence, the method modulates translation kinetics parameters to optimize both protein yield and folding accuracy simultaneously.
2Productivity
If translation rate is increased at critical codon positions, then productivity improves, but manufacturing precision of co-translational folding deteriorates
Solution Approach 1:
The patent applies dynamics by creating a dynamic codon optimization strategy where translation rate is modulated along the coding sequence rather than maintained at a constant high rate. The method identifies regions where slower translation facilitates proper folding intermediates to form, and regions where faster translation is acceptable, creating a spatially dynamic translation rate profile that balances speed and folding accuracy.
Solution Approach 2:
The patent implements periodic action through alternating patterns of fast and slow codons at strategically positioned intervals within the coding sequence. This periodic modulation of translation rate allows periodic formation of folding-competent intermediates while maintaining overall high productivity, creating a rhythm of translation that facilitates co-translational folding at critical stages.
Data Source
AI summary
This invention relates to optimized heterologous production of properly folded and functional proteins. The present invention provides systems and methods involving determination of the optimal mRNA sequence, based on the underlying rates at which codons are translated and folding kinetic of nascent-protein, that maximizes co-translational protein folding of domains in order to maximize the proper folding and quality of the protein produced. The codon translation rates can be determined in a number of ways, including theoretical estimation and, preferably, through experimental data, such as ribosome profiling. The determination of an optimal mRNA sequence through the utilization of codon translation rates under a particular set of conditions allows for application of the method irrespective of the organism from which the protein in question was originally derived.