Porous protein crystals as scaffolds for enzyme immobilization.

Porous protein crystals provide a template for binding and organizing guest macromolecules. Peroxidase, oxidase, and reductase enzymes immobilized in protein crystals retained activity in single-crystal and bulk assay formats. Several binding strategies, including metal affinity and physical entrapment, were employed to encourage enzyme adsorption into the protein crystals and to retain the enzymes for multiple recycles. Immobilized enzymes had lower activity compared to free enzyme in solution, in part due to diffusion limitations of substrate within the crystal pores. However, the immobilized enzymes were long-term stable and showed increased thermal tolerance. The potential applications of enzyme-laden crystals as sensing devices, delivery capsules, and microreactors motivate future development of this technology.

Discriminating between stabilizing and destabilizing protein design mutations via recombination and simulation.

Accuracy of current computational protein design (CPD) methods is limited by inherent approximations in energy potentials and sampling. These limitations are often used to qualitatively explain design failures; however, relatively few studies provide specific examples or quantitative details that can be used to improve future CPD methods. Expanding the design method to include a library of sequences provides data that is well suited for discriminating between stabilizing and destabilizing design elements. Using thermophilic endoglucanase E1 from Acidothermus cellulolyticus as a model enzyme, we computationally designed a sequence with 60 mutations. The design sequence was rationally divided into structural blocks and recombined with the wild-type sequence. Resulting chimeras were assessed for activity and thermostability. Surprisingly, unlike previous chimera libraries, regression analysis based on one- and two-body effects was not sufficient for predicting chimera stability. Analysis of molecular dynamics simulations proved helpful in distinguishing stabilizing and destabilizing mutations. Reverting to the wild-type amino acid at destabilized sites partially regained design stability, and introducing predicted stabilizing mutations in wild-type E1 significantly enhanced thermostability. The ability to isolate stabilizing and destabilizing elements in computational design offers an opportunity to interpret previous design failures and improve future CPD methods.