COMPUTERAIDED PROTEIN DESIGN: METHODS AND APPLICATIONS

Abstract

Since the first reports on the use ofsite directed mutagenesis in 1982! protein engineering or - when rationally aimed - protein design has been Tecognized as a promising and fascinating field of research in many countries. In Japan (PERI) and the U.S.A. (CARB)researchinstitutes have been founded with the focus on protein design. More and more researchinstitutes in the United States, Canada, Japan and Europe have been Starting broad research projects on protein design (UK: SERC, W. Germany: GBF, EMBL). Possible prospects for applications of designed proteins with modified activities or other new properties are very high,in the areas of pharmacology, enzyme applications in food industry’, waste treatment and chemical synthesis, vaccine design, biosensors etc.*". This conception wasvery clearly lined out in an excellent article by Kevin Ulmerin 19835, Encouraging results have so far been obtained only for a small number ofcases including insulin, proteases and peptidic protease inhibitors, and some others®’. On the other hand many unpredicted andsurprising results of site directed mutagenesis experiments are reported onscientific meetings and in the literature*’, That demonstrates that our methods andtools in thatarea arestill rather crude and urgently require improvement!", Simplecalculations show that the random approach to protein-engineeringis a very slow one. There are 10°* ways to arrange aminoacids in a medium sized protein chain of 250 amino acids. Ca. 10” molecules would form the whole estimated mass ofour universe. But even whenthe information about the seven most important aminoacids is available and only five changes should be tested for each of the positions, about 80,000 different protein-mutants have to be prepared andtested. This implies that a knowledge of the 3D-protein-structure and a good understandingofthe functionactivity relationship is absolutely essential in order to do rational protein-design. Research projects in protein-design require a close cooperation between groupsspecialising in protein-isolation and purification, in fermentation techniques, in genetic-engineering, in DNAsynthesis and protein-crystallography (protein-NMR techniques are being established). This interdisciplinary connection between protein chemists, molecular biologists and stereo-chemists is essential for the protein-design cycle (Fig. 1) consisting of design, cloning, expression andtesting new proteins starting from known ones.