Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

Constraining local structure can speed up folding by promoting structural polarization of the folding pathway

The pathway which proteins take to fold can be influenced from the earliest events of structure formation. In this light, it was both predicted and confirmed that increasing the stiffness of a beta hairpin turn decreased the size of the transition state ensemble (TSE), while increasing the folding rate. Thus, there appears to be a relationship between conformationally restricting the TSE and increasing the folding rate, at least for beta hairpin turns. In this study, we hypothesize that the enormous sampling necessary to fold even two-state folding proteins in silico could be reduced if local structure constraints were used to restrict structural heterogeneity by polarizing folding pathways or forcing folding into preferred routes. Using a Gō model, we fold Chymotrypsin Inhibitor 2 (CI-2) and the src SH3 domain after constraining local sequence windows to their native structure by rigid body dynamics (RBD). Trajectories were monitored for any changes to the folding pathway and differences in the kinetics compared with unconstrained simulations. Constraining local structure decreases folding time two-fold for 41% of src SH3 windows and 45% of CI-2 windows. For both proteins, folding times are never significantly increased after constraining any window. Structural polarization of the folding pathway appears to explain these rate increases. Folding rate enhancements are consistent with the goal to reduce sampling time necessary to reach native structures during folding simulations. As anticipated, not all constrained windows showed an equal decrease in folding time. We conclude by analyzing these differences and explain why RBD may be the preferred way to constrain structure.

Minimalist models for proteins: a comparative analysis

The last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex. In this paper, the CG models are reviewed and their features, applications and performances compared. This analysis, restricted to proteins, focuses on the minimalist models, namely those reducing at minimum the number of degrees of freedom without losing the possibility of explicitly describing the secondary structures. This class includes models using a single or a few interacting centers (beads) for each amino acid. From this analysis several issues emerge. The difficulty in building these models resides in the need for combining transferability/predictive power with the capability of accurately reproducing the structures. It is shown that these aspects could be optimized by accurately choosing the force field (FF) terms and functional forms, and combining different parameterization procedures. In addition, in spite of the variety of the minimalist models, regularities can be found in the parameters values and in FF terms. These are outlined and schematically presented with the aid of a generic phase diagram of the polypeptide in the parameter space and, hopefully, could serve as guidelines for the development of minimalist models incorporating the maximum possible level of predictive power and structural accuracy.

Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping: the phone cord effect in protein folding

The remarkable predominance of right-handedness in beta-alpha-beta helical crossovers has been previously explained in terms of thermodynamic stability and kinetic accessibility, but a different kinetic trapping mechanism may also play a role. If the beta-sheet contacts are made before the crossover helix is fully formed, and if the backbone angles of the folding helix follows the energetic pathway of least resistance, then the helix would impart a torque on the ends of the two strands. Such a torque would tear apart a left-handed conformation but hold together a right-handed one. Right-handed helical crossovers predominate even in all-alpha proteins, where previous explanations based on the preferred twist of the beta sheet do not apply. Using simple molecular simulations, we can reproduce the right-handed preference in beta-alpha-beta units, without imposing specific beta-strand geometry. The new kinetic trapping mechanism is dubbed the "phone cord effect" because it is reminiscent of the way a helical phone cord forms superhelices to relieve torsional stress. Kinetic trapping explains the presence of a right-handed superhelical preference in alpha helical crossovers and provides a possible folding mechanism for knotted proteins.