Downhill Folding: evolution meets physics

Martin Gruebele Departments of Chemistry and Physics, and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Illinois 61801, USA

Proteins evolve not to fold rapidly into beautiful structures (although they often do that), but to fulfill a function. Even the (partial) unfoldedness of “natively-unfolded” proteins is directly related to function, such as enhanced binding or signal transduction. The sometimes conflicting interplay between folding and function explains much about why proteins fold the way they do. The same sequence encodes the information necessary for and function, and the two can conflict with one another. This raises the question: how much of a protein’s free barrier for folding is obligatory, and how much arises from energetic frustration caused by conflicts with function, or avoidance of aggregation? [1] I present several cases of proteins re-engineered to fold nearly or completely downhill. [2],[3] Such proteins demonstrate that the physics of folding is perfectly compatible with protein folding having no significant activation barrier. Where does the barrier in most natural proteins come from, then? It has biological sources: evolution for function, and evolution against aggregation. Experiments ranging from fast kinetics to X-ray crystallography, and computational results including replica exchange will be discussed. [4] The kinetic signature of downhill folding is not simply fast or nonexponential folding, but rather a smooth transition from single-exponential kinetics, to fast non-exponential and probe-dependent kinetics, and back to simpler but even faster kinetics, as the stability of the is increased. [2][5][6] This transition can be explained by Langevin simulations [7], which show that metastable intermediates (barriers >

3 kBT) would require careful fine-tuning to produce a similar result.

References: [1] M. Gruebele, “Fast protein folding: evolution meets physics,” Comptes Rendus Biologies 328, 701-712 (2005).

[2] F. Liu and M. Gruebele, “Tuning λ6-85 towards downhill folding near the unfolding transition midpoint,” J. Mol. Biol. available on the web (2007). [3] H. Nguyen, M. Jäger, J. Kelly and M. Gruebele, “Engineering a β-sheet protein towards the folding speed limit,” J. Phys. Chem. B 109, 15182-15186 (2005). [4] M. Jäger, Y. Zhang, J. Bieschke, H. Nguyen, M. Dendle, M. E. Bowman, J. P. Noel, M. Gruebele, and J. W. Kelly “The structure-function-folding relationship in a WW domain,” Proc. Nat. Acad. Sci. USA 108, 10648-10653 (2006). [5] J. Sabelko, J. Ervin and M. Gruebele, "Observation of strange kinetics in protein folding," Proc. Nat. Acad. Sci. USA 96, 6031-6036 (1999). [6] W. Yang and M. Gruebele, “Folding λ at its speed limit,” Biophys. J. 87, 596-608 (2004). [7] H. Ma and M. Gruebele, “Low barrier kinetics: dependence on observables and free energy surface,” J. Comput. Chem. 27, 125-134 (2006).