Enzyme-like proteins by computational design

Abstract

We report the development and initial experimental validation of a computational design procedure aimed at generating enzymelike protein catalysts called ''protozymes.'' Our design approach utilizes a ''compute and build'' strategy that is based on the physical͞chemical principles governing protein stability and catalytic mechanism. By using the catalytically inert 108-residue Escherichia coli thioredoxin as a scaffold, the histidine-mediated nucleophilic hydrolysis of p-nitrophenyl acetate as a model reaction, and the ORBIT protein design software to compute sequences, an active site scan identified two promising catalytic positions and surrounding active-site mutations required for substrate binding. Experimentally, both candidate protozymes demonstrated catalytic activity significantly above background. One of the proteins, PZD2, displayed ''burst'' phase kinetics at high substrate concentrations, consistent with the formation of a stable enzyme intermediate. The kinetic parameters of PZD2 are comparable to early catalytic Abs. But, unlike catalytic Ab design, our design procedure is independent of fold, suggesting a possible mechanism for examining the relationships between protein fold and the evolvability of protein function.A prominent goal of protein design is the generation of proteins with novel functions, including the catalytic rate enhancement of chemical reactions. The ability to design an enzyme to perform a given chemical reaction has considerable practical application for industry and medicine, particularly for the synthesis of pharmaceuticals (1). Significant progress has been made at enhancing the catalytic properties of existing enzymes through directed evolution (2). In contrast, the design of proteins with novel catalytic properties has met with relatively limited success (3-5). We present a general computational approach for the design of enzyme-like proteins with novel catalytic activities.The use of transition-state analogs as haptens to elicit catalytic Abs has been the most successful technique to date for generating novel protein catalysts (6). Natural enzymes combine transition-state stabilization with precisely oriented catalytic side chains. Although a reactive hapten has been used in the generation of an Ab with a powerful nucleophile at the active site (7), current catalytic Ab technology does not efficiently select for both catalytic side chains and tight noncovalent affinity in the same molecule. The relationship between the general backbone fold of an enzyme and its catalytic properties is not well understood. This observation is particularly relevant to catalytic Abs that are currently constrained to the Ab fold and which have yet to show catalytic activity on par with natural enzymes.Rational design efforts have recently succeeded at altering the catalytic reactions of two different enzymes (8, 9). Cyclophilin, a cis-trans isomerase of X-Pro peptide bonds, was engineered into an endopeptidase by grafting a triad of catalytic residues commonly found in serine proteases at the...

Using multi-objective computational design to extend protein promiscuity

“…It is a small (108 residues) general disulphide oxidoreductase found in all the kingdoms of living organisms; it is a common model for protein design studies because of its high stability and good expression properties [19]. We aim at introducing an esterase activity [the nucleophilic hydrolysis of the p-nitrophenyl acetate (PNPA) into p-nitrophenol (PNP) and acetate] in E. coli thioredoxin, following an approach similar to that used in ref [20]. Unlike these previous studies [20], however, we intend to preserve the natural thioredoxin activity (see below for details).…”

“…We aim at introducing an esterase activity [the nucleophilic hydrolysis of the p-nitrophenyl acetate (PNPA) into p-nitrophenol (PNP) and acetate] in E. coli thioredoxin, following an approach similar to that used in ref [20]. Unlike these previous studies [20], however, we intend to preserve the natural thioredoxin activity (see below for details).…”

“…The general approach we use is similar to that described in ref. [20]; i.e., we choose a histidine residue as a nuclophile for the reaction and we model the tetrahedral transition state for the reaction as PNPA-histidine structure constructed as a generalized rotamer of the histidine. An initial exploration of the available positions to place the anchor nucleophile, and their different energies lead us to fix our search to position 39.…”

“…The rotamer of the combined histidine (Nδ as nucleophile) and tetrahedral intermediate was modeled with the same initial dihedral angles as in [20]: χ 1 and χ 2 from the histidine in the library, χ 3 (±30,±90,±150), χ 4 (±−60,±180), and χ 5 (±90). To provide a better docking of the ligand to thioredoxin, we have added a refined version of the standard library following the protocol described in [30].…”

“…This is an important point, since the original (native) active-site would be one obvious target for stabilizing mutations (active-site residues are optimized for function, not for stability) and, in this case, we aim at preserving the original activity. Indeed, in a previous work [20], the catalytic D26 residue was mutated to isoleucine, a change which enhances stability but which will impair the natural thioredoxin oxido-reductase activity. Secondly and most important, since our designed active-site is spatially close to the original one, the low-stability-cost strategy guarantees the minimal perturbation required for maintaining the original activity .…”