| Complete understanding of protein folding and structure would imply that we can design both the folding mechanism and three-dimensional structure of a protein molecule. This dissertation details the work that was done to achieve these goals, in particular using two model proteins of very similar three-dimensional structures, the Peptostreptococcal protein L and G. First, we investigated the asymmetry in the folding mechanism of protein L. We found that partial structures are formed very early during the folding of protein L and they are also present in the denatured state ensemble.; Secondly, using a computer-based strategy, we switched the folding pathway of protein G to that of protein L. This result confirms our hypothesis based on our studies of the folding kinetics of these two proteins that specific interactions that are intrinsic to the substructures of each protein determine the folding pathways of protein L and protein G and thus also give rise to the asymmetry in their folding mechanisms.; Thirdly, we test the validity of our structural prediction of the redesigned protein G variants by solving the crystal structures of these variant proteins. We found that in one variant, the predicted structure matches the real structure very closely. In addition, the structures also point to the improvements we can make in our design algorithm, namely by allowing the protein backbone to move during our design simulation. |
