Exploring the Thermostability of CRISPR Cas12b using Molecular Dynamics Simulations

Abstract

CRISPR (clustered regularly interspaced short palindromic repeat)- based diagnostics are at the forefront of rapid detection platforms of infectious diseases. The integration of reverse transcription-loop-mediated isothermal amplification (RT-LAMP) with CRISPR-Cas protein systems has led to the creation of advanced one-pot assays. The sensitivity of these assays has been bolstered by the utilization of a thermophilic Cas12 protein, BrCas12b, and its engineered variant, which exhibits enhanced thermal stability and allows for broader operation temperatures of the assay. Here, we perform all-atom molecular dynamics (MD) simulations on wild-type and mutant BrCas12b to reveal the mechanism of stabilization conferred by the mutation. High-temperature simulations reveal a small structural change along with greater flexibility in the PAM-interacting domain of the mutant BrCas12b, with marginal structural and flexibility changes in the other mutated domains. Comparative essential dynamics analysis between the wild-type and mutant BrCas12b at both ambient and elevated temperatures provides insights into the stabilizing effects of the mutations. Our findings not only offer a comprehensive insight into the dynamic alterations induced by mutations but reveal important motions in BrCas12b, important for the rational design of diagnostic and therapeutic platforms of Cas12 proteins.