Modeling ribosome dynamics to optimize heterologous protein production

A method for predicting protein yield for translation of a gene, the method comprising:

• (a) determining ribosome wait time at each codon in a coding region of an mRNA encoding the protein, comprising determining a number of cycles at each codon, wherein the number of cycles is a function of tRNA abundance, ribosome displacement magnitude, and force from binding between the mRNA and a 3′ terminal rRNA tail of the ribosome;
• (b) plotting a translation bottleneck plot, wherein the plot comprises values comprising a sum of cycles within a sliding window of size N codons;
• and
• (c) determining a maximum sum in the translation bottleneck plot;
• wherein the maximum sum in the translation bottleneck plot is correlated with protein yield.

A method for predicting protein aggregation, the method comprising:

• (a) determining ribosome wait time at each codon in a coding region of an mRNA encoding the protein, comprising determining a number of cycles at each codon, wherein the number of cycles is a function of tRNA abundance, ribosome displacement magnitude, and force from binding between the mRNA and a 3′ terminal rRNA tail of the ribosome;
• and
• (b) determining a total cycle count across codons throughout the coding region;
• wherein the total cycle count across codons throughout the coding region is correlated with protein aggregation.