The RBS Library Calculator
The RBS Calculator is an excellent tool for controlling translation initiation rate and protein production levels. When constructing single and multi protein genetic systems, it is also important that the system contain optimal enzyme expression levels for maximum pathway productivity. Rather than conducting time consuming experiments to characterize the pathway variants, researchers can use the RBS Library Calculator, another creation of Howard Salis and the Salis lab. The RBS Library Calculator catalogues the relationship between RBS sequence, enzyme expression level, and pathway productivity. From this information, users have a map to have as a knowledge base for how enzyme expression controls protein productivity for a given system. Then, when designing another similar system, there is no need to start from scratch.
The RBS Library Calculator makes the search for the ideal RBS sequence significantly more efficient. The RBS Library Calculator algorithm uses the biophysical model also utilized by the RBS Calculator. The algorithm, which has been validated with many different parameters, optimizes a degenerate RBS sequence with a small number of degeneracies that provides a large variation in translation rates across a very large scale. A primary function of the RBS Library Calculator is to use the smallest number of RBS variants that give the largest coverage of translation rate space. For example, just six RBS sequences can vary translation across a 100,000 fold scale.
The RBS Library Calculator assists users in achieving the three things needed for systematic metabolic pathway optimization. The first is the ability to quantitatively predict and control enzyme expression, which is accomplished using the original RBS Calculator. The second two necessities, an efficient way to search for optimal enzyme expression levels and a systematic mapping of the expression-activity relationship, are accomplished with the RBS Library Calculator.
Furthermore, the RBS Library Calculator simplifies the process of finding the optimal enzyme expression level for a system by cataloguing the information in an easy to navigate model. As Professor Salis states, the tool allows users to “clone less and know more” about their genetic systems.