De novo binders overcome the MMLV RT stability-activity trade-off

Moloney murine leukemia virus reverse transcriptase (MMLV RT) is an RNA-dependent DNA polymerase widely used in molecular diagnostics and gene editing. Its application is limited by poor thermal stability and inactivation induced by long-term storage. We combined multi-site mutagenesis with de novo-designed negatively charged protein binders targeting the nucleic acid-binding pocket to enhance stability without compromising catalysis. The engineered MMLV RT-SV variant showed improved reaction thermostability, and the addition of electrostatically complementary binders further increased intrinsic and storage stability. The resulting enzyme-binder complexes maintained full polymerase activity, exhibited a 9°C higher melting temperature, and showed minimal activity loss after accelerated aging. This study shows that de novo-designed binders can overcome the classical stability activity trade-off in enzymes, providing a generalizable strategy to improve biocatalysts for molecular biology and biotechnology.