Understanding the mechanism by which proteins fold to their native structure is a central problem in protein science. Clearly, interactions between residues that are in contact in the folded state (native interactions) are likely to be important for folding, but, in principle, nonnative interactions may play a role. We used recently published microsecond to millisecond all-atom molecular dynamics simulations of proteins folding and unfolding to show, remarkably, that nonnative contacts are irrelevant to the mechanism of folding in most cases. This statistical analysis would be very difficult to perform by experiment. Although this is a limited set of proteins, the results nonetheless strongly support coarse-grained theoretical and simulation models of folding in which only native contacts are energetically favorable. A major challenge to advancing our understanding of how proteins fold is the development of an analytical theoretical model capable of calculating the quantities directly measured in both equilibrium and kinetic experiments. That is, we require a partition function to predict thermodynamic properties and a master equation to predict kinetic properties. To this end we have been developing an Ising-like model, with the major input being the contact map of the native structure. This model has been remarkably successful in quantitatively accounting for a wide range of data for the 35-residue subdomain from the villin headpiece, the smallest naturally occurring protein that autonomously folds into a globular structure (see Kubelka et al., PNAS 2008;Cellmer et al., PNAS 2008, Cellmer et al., PNAS 2011). These data include, heat capacity, tryptophan fluorescence quantum yield (QY), and natural circular dichroism spectrum (CD) as a function of temperature in both denaturants and viscogens, while the kinetic data consist of time courses of the QY from nanosecond laser temperature jump experiments as a function of temperature, denaturant concentration, and viscosity. Anticipating the next generation of folding experiments, consisting of measurements of transition paths in single molecule FRET experiments (see annual report on single molecule experiments), we have carried out stochastic kinetic to make closer connections to molecular dynamics simulations. We show that recent simulations by the Shaw group are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter is remarkably similar to the distribution in the molecular-dynamics trajectories.
| Henry, Eric R; Best, Robert B; Eaton, William A (2013) Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations. Proc Natl Acad Sci U S A 110:17880-5 |
| Best, Robert B; Hummer, Gerhard; Eaton, William A (2013) Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A 110:17874-9 |
| Cellmer, Troy; Buscaglia, Marco; Henry, Eric R et al. (2011) Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Proc Natl Acad Sci U S A 108:6103-8 |
| Cellmer, Troy; Henry, Eric R; Hofrichter, James et al. (2008) Measuring internal friction of an ultrafast-folding protein. Proc Natl Acad Sci U S A 105:18320-5 |
| Kubelka, Jan; Henry, Eric R; Cellmer, Troy et al. (2008) Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci U S A 105:18655-62 |
