A Structural Landscape Description of DSCLSs in Protein Thermostability Engineering

Engineering protein thermostability is a key aspect of rational protein design, aiming to broaden the applicability of enzymes and enhance their industrial utility. In this study, we introduce a strategy for identifying and reinforcing dynamic stability centers of local structure (DSCLSs) to improve protein thermostability. A DSCLS comprises key structural residues and their interactions, representing the structural basis of protein stability. Molecular dynamics, cross-correlation amino acid networks, and other analytical techniques were integrated into the method. This approach was initially inspired by thermostability engineering of exodiol dioxygenases (EDOs). The method was validated through mutational analyses of mesophilic EDO MT-2, CpKR (ketoreductase from <i>Candida parapsilosis</i>), and CaPETase (polyethylene terephthalate hydrolase from <i>Cryptosporangium aurantiacum</i>). Subsequently, we applied the approach to engineer thermostability in xp-EctC (ectoine synthase) from <i>Rhodococcus</i> and mesophilic EDO L1 from <i>Bacillus</i>, with the best-performing mutants showing <i>T</i> _m increases of ~15 °C. Notably, the catalytic efficiency of the optimal mesophilic EDO L1 mutant (T70Y) was 1.6-fold higher than that of the wild type at 60 °C, while the xp-EctC mutant (I2R) exhibited a 2.1-fold increase over the wild type. By characterizing and enhancing DSCLSs, this work presents a practical and generalizable strategy for thermostability engineering that also reduces mutational screening efforts, offering important potential for industrial applications.