Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural

1. Protein folding mediated by solvation: Waterexpulsion and formation of the hydrophobiccore 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. http://www.lsbu.ac.uk/water/images/wetsurf.gif 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 Pseudo Contact Native Contacts 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 • 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 http://www.answers.com/topic/1shg-sh3-domain-png

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. 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):685-90.