Designing evolvable libraries using multi-body potentials

Recent advances in rational approaches for enzyme engineering

Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks. To meet the requirements of industrial biotechnology and to introduce new functionalities, the enzymes need to be optimized by protein engineering. This article specifically reviews rational approaches for enzyme engineering and de novo enzyme design involving structure-based approaches developed in recent years for improvement of the enzymes’ performance, broadened substrate range, and creation of novel functionalities to obtain products with high added value for industrial applications.

Generation of atomic four-body statistical potentials derived from the delaunay tessellation of protein structures

Delaunay tessellation of the atomic coordinates for a crystallographic protein structure yields an aggregate of non-overlapping and space-filling irregular tetrahedral simplices. The vertices of each simplex objectively identify a quadruplet of nearest neighbor atoms in the protein. Here we apply Delaunay tessellation to 1417 high-resolution structures of single chains that share low sequence identity, for the purpose of determining the relative frequencies of occurrence for all possible nearest neighbor atomic quadruplet types. Alternative distributions are explored by varying two fundamental parameters: atomic alphabet selection and cutoff length for admissible simplex edges. The distributions are then converted to four-body potential functions by implementing the inverted Boltzmann principle, which requires calculating the distribution of the reference state. Two alternative definitions for the reference state are presented, which introduces a third parameter, and we derive and compare an array of such potential functions. These knowledge-based statistical potentials based on higher-order interactions complement and generalize the more commonly encountered atom-pair potentials, for which a number of approaches are described in the literature.

Engineering enzyme specificity using computational design of a defined-sequence library

Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.