Free Essay About Protein Folding
Type of paper: Essay
Topic: Barrier, Energy, Protein, Literature, Downhill, Stability, Atomic Bomb, Denaturant
1. Free-energy barrier needs to be crossed in folding. Downhill folding is a process of protein folding without encountering a free energy barrier. The barrier-free reactions are rapid because the reaction rate is close to state of the barrier crossing process (the energy barrier ΔG≈0). The picture of the energy landscape is presented on Figure 1.
Figure 1. Energy landscape for downhill folding
2. Longer and more stable proteins fold slower because of the increased ruggedness of the energy landscape. The ß-sheet proteins fold slower due to the ruggedness of the energy landscape increases in this proteins, and the fast folding rate is because of simpler topology that requires only "zipper-up" of the helical-proteins.
3. The authors chose GCN4 protein because of its folding speed and stability.
The difference between the native GCN4 protein and the one used in the paper (GCN4p2C) is that the second one has Gly-Gly-Cy's tether located at the C terminus. The GCN4 is a coiled-coil protein, while GCN4p2C is expected to have the faster folding rate due to simpler topology.
4. The authors applied equilibrium and stop-flow measurements (with a spectropolarimeter), hydrogen exchange theory, and NMR spectroscopy.
Equilibrium and stop-flow measurements allow calculation of the equilibrium and kinetic parameters. Hydrogen exchange theory and NMR spectroscopy allow assessing the ultra-fast kinetics in the absence of denaturant.
5. The pH measurements allow calculation of the kinetic constants that were supposed to prove the barrier-free nature of protein folding. After the experiments, the authors came to conclusion that even in the absence of denaturant (folding rates approach predicted for downhill behavior) folding remains barrier-limited.
6. Hydrogen-exchange theory experiment data are depicted on Figure 2A. Namely, the stability of amide protons in the centre of GCN4p2C compared to global stability. In the low denaturant area a global stability is depicted by a denaturation profile; in high denaturation area, the global stability of protein is extrapolated.
The slopes of the lines on the right and on the left are similar, indicating that all proteins are characterized with similar sensitivity to denaturing agent. In the lection, at cytochrome studies different groups unfold with different rates.
7. The proteins folding is two-state, because they have only two observable states: the native fold and the denatured coil.
8. The authors calculated the constants values from the Figure 3. The parameter was calculated with the following equation, provided that they are pH-independent:
9. Using kf and ku values, the ∆GH2O0 was calculated by formula:
The m0 value was calculated as:
10. The authors explain that folding is not downhill even at 0 denaturant concentration using equilibrium and kinetic perspective. The exchange of the centrally located amide protons occurs in the cooperative global unfolding process (equilibrium). The closing and opening rates indicate that the most stable hydrogen bonds are broken and reformed in a single kinetic event representing the transition from N to U and back. The constants kf and ku agree with the extrapolated barrier-limited rates.
11. No, the downhill folding is the theoretical prediction, although the experiments for its detection have been performed previously. The current research resulted in a conclusion that the folding behavior is barrier-limited even for the studied protein.