Exploring the folding free energy surface of a three-helix bundle protein

Abstract

The multidimensional free energy surface for a small fast folding helical protein is explored based on first-principle calculations. The model represents the 46-residue segment from fragment B of staphylococcal protein A. The relationship between collapse and tertiary structure formation, and the order of collapse and secondary structure formation, are investigated. We find that the initial collapse process gives rise to a transition state with about 30% of the native tertiary structure and 50-70% of the native helix content. We also observe two distinct distributions of native helix in this collapsed state (R g Ϸ 12 Å), one with about 20% of the native helical hydrogen bonds, the other with near 70%. The former corresponds to a local minimum. The barrier from this metastable state to the native state is about 2 k B T. In the latter case, folding is essentially a downhill process involving topological assembly. In addition, the order of formation of secondary structure among the three helices is examined. We observe cooperative formation of the secondary structure in helix I and helix II. Secondary structure in helix III starts to form following the formation of certain secondary structure in both helix I and helix II. Comparisons of our results with those from theory and experiment are made.The process of protein organization from the random coil manifold of states to a specific native structure remains an intriguing problem in molecular biology. Because of the vast conformational space available to the protein chain, the time it would require to locate its unique structure by a random search would be astronomical. Different ways of overcoming this search problem have been proposed. Some models such as the framework model (1) and the diffusion-collision model (2) focus on the formation of secondary structural elements followed by their assembly. Others such as the hydrophobic collapse model (3) emphasize the formation of tertiary structure accompanying secondary structure formation. More recently, a theoretical model based on a statistical landscape analysis has been proposed (4). According to this theory, folding can be described by the descent of the folding chain down a folding funnel, with local roughness reflecting the potential for transient trapping in local minima and the overall slope of the funnel representing the thermodynamic drive to the native state. The bottleneck to folding in this funnel picture is the confluence of multiple delocalized ''nuclei'' at a transition point (the transition state). While the folding funnel model incorporates many aspects of the other folding models, a fully unified view of protein folding has yet to be developed. For example, it is unclear from these models how much secondary structure, resembling that in the native state, is present in the unfolded state. Nor is the degree of similarity between the transition state and the native state well understood. Further, the order of collapse and secondary structure formation is still under debate. Because of the very...

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

“…2). The overall features of this surface are similar to that calculated previously with a different force field (9). At low T the free energy surface, ⌬G(Q,rmsd), shows a large folding basin containing two minima weakly separated; one corresponding to the native state (folded unsolvated with Q Ͼ 0.8) and the other a nearly folded state with a hydrated core (folded solvated with 0.30 Ͻ Q Ͻ 0.8).…”

“…For our studies, a natural choice is the 10-55 helical fragment B of protein A from Staphylococcus aureus, using the replica exchange molecular dynamics (REMD) algorithm described by Sugita and Okamoto (5). Protein A folds into a simple three-helix bundle (6) whose folding has been widely studied by using minimalist and all-atom simulations (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) as well as experiments (18,19). All of these different studies provided some information about the folding mechanism and the nature of the transition-state ensemble (TSE).…”

Molecular dynamics simulations of hydrophobic collapse of ubiquitin

“…Nevertheless, simulations starting from unfolded structures may provide insight into the forces driving collapse and/or secondary structure formation. Recently, using a different, but complementary approach, Bozcko and Brooks (1995) and Guo et al (1997) have investigated the energetics of this process and outlined the general folding in terms of thermodynamic coordinates.…”

A statistical mechanical model for β-hairpin kinetics

“…The theoretical advances include analytical approaches (2)(3)(4), simulations of simplified representations of proteins (2,(5)(6)(7)(8), and all-atom molecular dynamics calculations (9)(10)(11). This work has painted a comprehensive picture of possible general mechanisms and has provided a framework for experimentalists to think more clearly about the problem.…”