Structure-Based Rational Design

With the determination of high-resolution crystal structures of enzymes came the expectation that one could make rational changes to the shape of the enzyme to make desired changes in the enzyme’s activity. This expectation went largely unfulfilled because the resolution of the crystal structures was too low to allow sufficient precision in changes in the enzyme to allow the changes to achieve the desired results (Arnold, 2001). This is because small changes in relative orientation of substrate with respect to the active site cause large changes in catalytic efficiency. While the techniques of enzyme engineering via various shuffling technologies are becoming mature, other technologies such as computational rational design with powerful computer algorithms are emerging and reinvigorating the early excitement for rational design (Dahiyat and Mayo, 1997; Fox et al., 2003). A particularly efficient approach to combinatorial analysis using chimeric enzymes involves identifying shemas, or fragments of proteins that can be recombined with minimal three-dimensional perturbation to structure (Meyer et al., 2003; Voigt et al., 2002). This approach is currently being successfully applied to versatile enzymes such as cytochrome P450s (Otey et al., 2004). It seems likely that there will be a lot of interesting opportunities created by combining computational with combinatorial genetic methods.