Kinetic Studies of Folding of the B-domain of Staphylococcal Protein A with Molecular Dynamics and a United-residue (UNRES) Model of Polypeptide Chains

Abstract

Langevin dynamics is used with our physics-based united-residue (UNRES) force field to study the folding pathways of the B-domain of staphylococcal protein A (1BDD (alpha; 46 residues)). With 400 trajectories of protein A started from the extended state (to gather meaningful statistics), and simulated for more than 35 ns each, 380 of them folded to the native structure. The simulations were carried out at the optimal folding temperature of protein A with this force field. To the best of our knowledge, this is the first simulation study of protein-folding kinetics with a physics-based force field in which reliable statistics can be gathered. In all the simulations, the C-terminal alpha-helix forms first. The ensemble of the native basin has an average RMSD value of 4 A from the native structure. There is a stable intermediate along the folding pathway, in which the N-terminal alpha-helix is unfolded; this intermediate appears on the way to the native structure in less than one-fourth of the folding pathways, while the remaining ones proceed directly to the native state. Non-native structures persist until the end of the simulations, but the native-like structures dominate. To express the kinetics of protein A folding quantitatively, two observables were used: (i) the average alpha-helix content (averaged over all trajectories within a given time window); and (ii) the fraction of conformations (averaged over all trajectories within a given time window) with Calpha RMSD values from the native structure less than 5 A (fraction of completely folded structures). The alpha-helix content grows quickly with time, and its variation fits well to a single-exponential term, suggesting fast two-state kinetics. On the other hand, the fraction of folded structures changes more slowly with time and fits to a sum of two exponentials, in agreement with the appearance of the intermediate, found when analyzing the folding pathways. This observation demonstrates that different qualitative and quantitative conclusions about folding kinetics can be drawn depending on which observable is monitored.