TRITON: graphic software for rational engineering of enzymes
Damborsky, J., Prokop, M., Koca, J.
TRENDS IN BIOCHEMICAL SCIENCES 26: 71-73 (2001)
The engineering of enzymes for improving their catalytic properties is one of the present-day challenges of biochemistry and molecular biology. The rational engineering of a given enzyme requires an understanding of the structural features determining its catalytic efficiency. In particular, a protein engineer has to know which amino acid residues of the protein are involved in the catalysis and how to modify them to achieve an increased activity. The availability of the three-dimensional structure of the protein, preferably in the complex with the substrate, makes a significant step forward in the understanding the protein-ligand interactions. However, this is just an initial step in understanding how these interactions influence the conversion of the subs t rate to the product. The catalytic efficiency of enzymes is usually determined by their ability to stabilise the transition state of their reactions. Consequently, an examination of the enzyme-substrate complex, i.e. the educt structure, may not give a re a listic picture about the importance of particular residues for the catalysis. Computer modelling, namely quantum mechanic calculations, which enables the modelling of biochemical reactions and the localisation of the transition state structure, may bring substantially deeper insight to the problem.