Designer mRNAs: A Radically New Approach to Optimizing Active Protein Yield
Protein molecules carry out an incredible array of biological functions. Almost every cellular process, from genome regulation to energy metabolism, requires a unique set of proteins.
The complexity of the proteome is coded for in the genome. Each gene in the genome codes for a unique protein. Genes are translated to a protein via a messenger RNA, also called mRNA. This flow of genetic information, from DNA to mRNA to protein, is termed the “central dogma” of biology.
First proposed in 1956, this multistep process was originally thought be to relatively linear, with coding information flowing in a straightforward manner. Today, this process is known to be incredibly complex, with each step subject to both active and passive regulation.
Assistant Professor of Chemistry Ed O’Brien, and postdoctoral scholar Ajeet Sharma sought to better understand the process from passive mRNA to protein regulation through the development of computational tools that utilized knowledge from the fields of chemistry, physics, and computer science. What they created was intellectual property (IP) that can be used in the biomedicine and biotechnology industries to optimize the yield of biologically active protein, creating high-efficiency or high-efficacy biologics.
Tuning Translation and Protein Folding
Translation is the process by which mRNAs are read and converted into proteins. mRNA sequence is “translated” by ribosomes, which match mRNA sequence code to the correct amino acids, the subunit of proteins. As they are synthesized, newly formed proteins start to fold into a specific three-dimensional structure. Known as co-translational folding, this process is crucial for accurate protein function.
Synonymous codon substitutions alter the mRNA sequence but do not cause a change in the downstream amino acid sequence. Interestingly, synonymous substitutions have been found to alter translation rate, thereby affecting protein co-translational folding.
Considering this, O’Brien and Sharma hypothesized that they could rationally introduce synonymous substitutions at strategic locations along an mRNA sequence, thereby changing the rate of translation. Theoretically, these precisely tuned translation rates could then be used to maximize the efficiency of co-translational folding and maximize protein-specific activity.
Designing mRNAs to Control Co-Translational Folding
In the validation of their hypothesis, O’Brien and Sharma invented a method and computational platform that allows users to precisely control the co-translational folding of a protein. This novel IP determines the type and position of synonymous substitutions needed to create an optimal mRNA sequence, allowing the resulting protein to fold in a user-prescribed manner. Protein folding can be designed to match a user-specified profile of protein quality or activity.
Operators begin the process by defining the desired co-translational profile. mRNA sequences are then iteratively mutated in silico until a best match is found.
Compared to current strategies, O’Brien and Sharma’s invention provides a number of demonstrable benefits. First, the inventors’ method is unlikely to miss an optimal mRNA sequence. The platform is capable of comparing co-translational folding for a large number of mRNA sequences. Secondly, it is first in field to construct mRNA sequences for optimal folding behavior. Lastly, this is the only framework available that uses protein folding kinetics to maximize protein activity. Thus, the present invention represents a considerable advance in the field of biologics.
O’Brien and Sharma seek to further enhance this proof of concept method and computational platform by collaborating with an industry or academic partner. If interested in learning more about this emerging technology, please contact Ed O’Brien at epo2@psu.edu.