Folding Free Energy Surface of a Three-Stranded β-Sheet Protein

Abstract

We present a molecular dynamics (MD) simulation study of the folding thermodynamics of the three-stranded β-sheet protein Betanova. The protein and solvent are explicitly described by employing all atom models. An umbrella sampling technique was employed to probe thermodynamically relevant states at different stages of folding. A database for the sampling was generated by conducting four high-temperature simulations. The initial conditions for the umbrella sampling were selected from this database of structures by employing hierarchical clustering. Sampling of conformational space was then carried out at 275 K and the generated data were combined with the weighted histogram method to produce the two-dimensional folding free energy landscape. We found that the folding of the protein Betanova occurs in two collapse stages. The first collapse brings the protein into a basin that contains various structures differing in their size and elements of secondary structure. At the transition state from this basin of collapsed states to the native basin, the protein adopts a native-like fold and size and forms ≈60% of native contacts. Thus the formation of native-like structure is concurrent with the secondary collapse. The overall stability of protein Betanova is found to be about 1 kcal/mol, in agreement with the experimental estimate. We found that the native side chain contacts are the primary factor in driving Betanova folding and stabilizing its native three-stranded β-sheet conformation. By contrast, hydrogen bonding is found to play a minor role in the folding of Betanova. Solvent is observed to be present in the protein core until late in folding.