Computational redesign of a thermostable T7 RNA polymerase

Abstract

T7 RNA polymerase (T7 RNAP) is a foundational enzyme for biotechnology, but its utility for many potential applications is limited by low thermal stability of 43-44{degrees}C. While stabilized variants exist, the most stable commercial version has a proprietary sequence. In this work we developed a highly stable T7 RNAP using structure-based computational design. We combined mutations from previous stabilized variants (M5, M8, V7abcd) with new mutations identified by PROSS. These mutations were filtered using data-driven heuristics to preserve function. Our final design, T7T+, contains 30 point mutations from the original T7 RNAP and demonstrates a functional stability (T50) of 54.9{degrees}C in a thermal challenge assay, which is 2.4{degrees}C higher than the most stable, published open-source variant to date. Circular dichroism spectroscopy showed an apparent melting temperature of 53.8{degrees}C. T7T+ retains 59% of wild-type activity at 37{degrees}C. 16 of the 18 tested protein designs had higher stability against thermal challenge compared with the genetic background, attesting to the high success rates of existing non deep learning computational methods for the design of stable, functional proteins. A plasmid encoding T7T+ has been deposited in AddGene and is freely available for non-commercial use.