1. Entropic and Enthalpic Barriers in Cooperative Protein Folding Hue Sun C HAN Departments of Biochemistry, and of Molecular Genetics University of Toronto, Ontario M5S 1A8 Canada http://biochemistry.utoronto.ca/chan/bch.html IMA, January 17, 2008

2. What do we know from experiments? Cooperative Folding:

3. How does the calorimetric criterion work? bimodal cooperative folding unimodal noncooperative folding

4. Kinetic manifestation of folding cooperativity: linear chevron plots Linear folding and unfolding arms imply a linear relationship between log(folding/unfolding rate) and equilibrium stability Data from Jackson et al., Biochemistry 32:11270 (1993) chevron rollover is indicative of less cooperative or noncooperative folding

5. Do we understand the Physics of Generic Protein Properties? Most current coarse-grained protein chain models do not satisfy experimental cooperativity criteria Chan et al., Methods Enzymol (2004)

6. Clementi et al., JMB (2000); Koga & Takada, JMB (2001); Kaya & Chan, JMB (2003) Continuum C  Go Models Native-centric local and non-bonded interactions Langevin dynamics Thermodynamically quite cooperative CI2

7. Go-model chevron plots have significant chevron rollovers, implying that in many cases Go models are less cooperative than the real proteins they aim to mimick Jackson & Fersht, Biochemistry (1991)Kaya & Chan, JMB (2003) Theory Experiment

8. Even with native biases, pairwise additive coarse-grained interactions do not account for cooperative folding Better Mesoscopic Principles?

9. (local-nonlocal coupling) Kaya & Chan, Proteins (2003) ‘Many-body’ interactions needed to account for folding cooperativity A hypothesized cooperative interplay between favorable nonlocal interactions and local conformational preferences

10. Testing the local-nonlocal coupling idea by lattice models a < 1, attentuation factor Kaya & Chan, Proteins (2003)

11. Native Topology (Contact Pattern) Dependent Folding Rates Plaxco, Simons & Baker, JMB (1998) Plot from Plaxco et al. Biochemistry (2000) Can protein chain models capture this trend?

12. Kaya & Chan, Proteins (2003); Chan et al., Methods Enzymol (2004) Many-body interactions in the form of local-nonlocal coupling rationalize topology-dependent folding rates

13. Top7, 1qys (93aa) Kuhlman et al., Science (2003) Scalley-Kim & Baker, JMB (2004); Watters et al., Cell (2007) Kaya & Chan, Proteins (2003) Our theoretical perspective was corroborated by experiments: Cooperativity is likely an evolutionarily selected trait; cooperativity is not a corollary of a protein’s ability to fold theory experiment

14. Kaya & Chan, Proteins (2003)

15. Folding Barriers entropic & enthalpic components

16. Entropic Barriers: Role of conformational entropic barriers in native topology-dependent folding rates Wallin & Chan, J Phys Condens Matt (2006)

17. Transition-state ensembles: 1div 1pgb 1imq 1wit ‘Transition state’ as conformations around the Q barrier Q = fractional number of native contacts

18. Wallin & Chan, J Phys Condens Matt (2006); cf. Koga & Takada, JMB (2001) … found some correlation between model and experimental folding rates, suggesting that the model captures part of the physics

19. Wallin & Chan, J Phys Condens Matt (2006) Entropic barriers: The topology- folding rate relationship is likely dominated by conformational entropy effect

20. lower temperature Enthalpic barriers: non-Arrhenius folding rates, positive unfoled-to-transition state enthalpy changes at some temperatures Does this mean that the folding landscape is not funnel-like?

21. HH SS CpCp Thermodynamic Signatures of Protein Folding Kinetics CI2 “reaction profiles” 25 °C enthalpic barrier

22. Desolvation is a likely origin of robust enthalpic barriers to protein folding Liu & Chan, JMB (2005)

23. Liu & Chan, JMB (2005); Phys Biol (2005); cf. Cheung et al., PNAS (2002); Kaya & Chan, JMB (2003) Desolvation barriers enhance folding/unfolding cooperativity increasing height of pairwise desolvation barrier leads to … Higher overall free energy barrier more linear chevron plots CI2 less native fluctuation

24. A. Ferguson, Z. Liu & H.S. Chan (2007) Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins simulated folding rates span ~4.5 orders of magnitude simulated folding rates span ~1.5 orders of magnitude

25. …but pairwise desolvation barriers alone are insufficient to account for the thermodynamic signatures of cooperative folding

26. Typically, Unfolded-to-Transition-State heat capacity change is negative for protein folding, but … for the association of small nonpolar solutes in water, heat capacity change is positive around the desolvation free energy barrier. Length-scale dependence provides a possible probe for cooperativity? from  G at 8 temperatures Shimizu & Chan, JACS (2001) TIP4P water model   C P highly non-monotonic  Not well predicted by surface areas 

27. r  nm  r CH 4 Xe 3-body 2-body Paschek, J Chem Phys 120:6674 (2004)Moghaddam, Shimizu & Chan, JACS (2005) Hydrophobic interactions among small hydrophobic solutes: Robust  C P > 0 at the desolvation free energy barrier

28. Moghaddam, Shimizu & Chan, JACS (2005); Liu & Chan, JMB (2005) Enthalpic barrier can be significantly higher than the desolvation free energy barrier temperature dependence of the potential of mean force (PMF) Enthalpy-Entropy Compensation at Desolvation

29. MacCallum, Moghaddam, Chan & Tieleman, PNAS (2007)  Helix association in water as a model for rate-limiting events in protein folding A pair of 20-residue poly-alanine or poly-leucine helices ~3,800 water molecules Simulated constant- pressure free energy of association (potential of mean force, PMF) at five temperatures

30. MacCallum, Moghaddam, Chan & Tieleman, PNAS (2007) Enthalpic desolvation barriers of ~ 50 kJ/mol comparable to that of protein folding Dramatic enthalpy-entropy compensation at the desolvation step leading to low or non-existent free energy barriers At 25 deg C, Enthalpic folding barrier height for CI2 is ~ 30kJ/mol (Oliveberg et al., 1995) CspB is ~ 32kJ/mol (Schindler & Schmid, 1996)

31. MacCallum, Moghaddam, Chan & Tieleman, PNAS (2007) Enthalpic barriers caused by steric dewetting

32. Recap.: Folding cooperativity implies ‘near- Levinthal’ funnels Enthalpic barriers can be consistent with funnel- like folding landscapes ?

33. Artem Badasyan Allison Ferguson Mikael Borg Huseyin Kaya Michael Knott Zhirong Liu Maria Sabaye Moghaddam Seishi Shimizu Stefan Wallin Co-workers University of Toronto Prof. D. Peter Tieleman Justin MacCallum University of Muenster Prof. Erich Bornberg-Bauer David Vernazobres Richard Wroe University of Calgary Prof. Julie D. Forman-Kay Prof. Regis Pomes