Protein Folding Kinetics

Framework Model Folding

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Click the structures and reaction black arrows in sequence to view the 3D models and animations respectively

The first step of Framework Model is the rapid formation of native secondary structural elements, such as beta sheets and alpha helices. The example (PDB ID: 1CRN) above, calculated using the Yale Morph Server and Spartan08 Fixer to produce viable pdb files, shows only one intermediate but there can be several intermediates. The second step is relatively slow and is the formation of tertiary structure by diffusion and collision and also, if there is more than one stand in the protein, the quaternary structure forms.

The coordination diagram is shown below. The unfolded protein disappears rapidly and sometimes cannot be observed experimentally. During this process, a significant amount of intermediate is formed leading to a lag period of the appearance of folded protein. Also, in this process, the sum of the concentration of unfolded protein and that of folded protein cannot be 1.

Click the diagram below to visualize the whole process of folding.

Framework folding | Hairpin folding | Myoglobin helix formation