title: Designing cooperativity into the designed protein Top7.
abstract: The topology of the designed protein Top7 is not found in natural proteins. Top7 shows signatures of non-cooperative folding in both experimental studies and computer simulations. In particular, molecular dynamics of coarse-grained structure-based models of Top7 show a well-populated C-terminal folding-intermediate. Since most similarly sized globular proteins are cooperative folders, the non-natural topology of Top7 has been suggested as a reason for its non-cooperative folding. Here, we computationally examine the folding of Top7 with the intent of making it cooperative. We find that its folding cooperativity can be increased in two ways: (a) Optimization of packing interactions in the N-terminal half of the protein enables further folding of the C-terminal intermediate. (b) Reduction in the packing density of the C-terminal region destabilizes the intermediate. In practice, these strategies are implemented in our Top7 model through modifications to the contact-map. These modifications do not alter the topology of Top7 but result in cooperative folding. Amino-acid mutations that mimic these modifications also lead to a significant increase in folding cooperativity. Finally, we devise a method to randomize the sizes of amino-acids within the same topology, and confirm that the structure of Top7 makes its folding sensitive to packing interactions. In contrast, the ribosomal protein S6, which has secondary structure similar to Top7, has folding which is much less sensitive to packing perturbations. Thus, it should be possible to make a sequence fold cooperatively to the structure of Top7, but to do so its side-chain packing needs to be carefully designed.
authors: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India; Manipal University, Madhav Nagar, Manipal, 576104, India.
authors: Shilpa
authors: S
authors: Yadahalli
authors: Shachi
authors: S
authors: Gosavi
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D009154:Mutation; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: Top7; computational protein folding; folding cooperativity; side-chain packing; structure-based models