1. Max Shokhirev BIOC585 December 2007
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
Margaret S. Cheung, Angel E. Garcı´a,
and Jose´ N. Onuchic
Department of Physics, University of California at San Diego
Received 11/26/2001
Max Shokhirev
BIOC585
December 2007

2. Energy Landscape/Funnel Theory
Levinthal paradox1:
Statistically, it would take 1030 seconds for proteins to sample all possible 3D conformations in a random manner.
In reality the number of allowed conformations is considerably smaller since folding follows the path of least energetic frustration.
1) C. Levinthal, J. Chem. Phys. 65, 44 (1968)

3. Energy Landscape/Funnel Theory
Traditionally we can apply this model to protein folding if the energy funnel for the protein is relatively smooth.
Fast folding
Simple folding mechanism
Independent folders

4. A concern… What about solvent effects?
Solvent effects are incorporated implicitly in previous energetically unrestricted models
This means that (de)solvation effects of the hydrophobic core are not taken into consideration in the potentials.

5. Protein (De)solvation
Hilson et al. showed that forcing water into the hydrophobic core of ß-protein leads to increased folding times1,2.
Hummer et al. calculated the effect of solvation on free-energy of simple alkane molecules, and that the PMF between two methane-like particles exhibits two minima3:
Van der Waals distance between the particles
Solvent separated minimum distance
1) Hillson, N., Onuchic, J. N. & Garcı´a, A. E. (1999) Proc. Natl. Acad. Sci. USA 96, 14848–14853.
2) Garcı´a, A. E., Hillson, N. & Onuchic, J. N. (2000) Prog. Theor. Phys. Suppl. 138, 282–291.
3) Hummer, G., Garde, S., Garcı´a, A. E., Paulaitis, M. E. & Pratt, L. R. (1998) Proc. Natl. Acad. Sci. USA 95, 1552–1555.

6. Can we incorporate desolvation?

7. A Minimalist Model for Water-Mediated Interaction
Native Contacts
Pseudo Contact
No Contact

8. A Minimalist Model for Water-Mediated Interaction
Gō-like potential was used
only attractive interactions are assigned to the native contacts (bond, angle, dihedral, LJ, electrostatic, and etc.)
repulsive interactions are assigned to the nonnative contacts (desolvation potential)
Two possible contacts for non-local interactions

9. Multicanonical Sampling
Adding non-native interaction perturbs the energy funnel.
No longer energetically unfrustrated since desolvation barrier is relatively high.
Cononical sampling rarely samples energies high enough to cross local energy barriers since energy comes from normal distribution.
Instead use a uniform energy distribution function that allows for frequent high energies, and then simply “fix” the data at the end (Multicanonical).

10. Q and “pseudo” Q Q Pseudo Q Normalized
Folding parameter used to quantify native contacts (How close are we to the “native” form?)
Pseudo Q
Folding parameter used to quantify solvation contacts (What is the degree of solvation?)
Normalized

11. Applying the model to the SH3 family of proteins

12. Free Energy vs Q and pseudo Q
High Free Energy
Low Free Energy
Figure 2B

13. Figure B,E
High Free Energy
Low Free Energy
Red = native
Blue =
Water contact

14. Figure 2B-E

15. Two step folding process…
First step involves a structural collapse toward a nearly native ensemble (τ1).
Mediated by the expulsion of 23 water molecules from the diverging turn and distal loop.

16. Two step folding process…
Second step involves water expulsion from the hydrophobic core (τ2).
Mediated by the cooperative expulsion of 17 water molecules

17. Cooperative Water Expulsion from Hydrophobic Core
Figure 2C
Cooperative Water Expulsion from Hydrophobic Core

18. Specific Heat Comparison

19. Conclusions… Folding process of SH3 protein has two steps
structure-search collapse to a nearly-native ensemble
Corresponds well to experimental data1,2
Insights into general folding mechanism
“desolvation” step
This can be achieved using a minimalist model
Gō-like model with a“desolvation” feature in the tertiary contacts pair potential
multicanonical sampling required.
1) Zhang, O. & Forman-Kay, J. D. (1997) Biochemistry 36, 3959–3970.
2) Mok, Y.-K., Kay, C. M., Kay, L. E. & Forman-Kay, J. (1999) J. Mol. Biol. 289, 619–638.

20. Thank you… “Protein folding mediated by solvation: water expulsion and
formation of the hydrophobic core occur after the structural collapse.”
Cheung MS, García AE, Onuchic JN. Proc Natl Acad Sci U S A.
2002;99(2):