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Journal of Physical Chemistry B, Vol.104, No.51, 12378-12383, 2000
Comparative study of the folding free energy landscape of a three-stranded beta-sheet protein with explicit and implicit solvent models
We present a molecular dynamics (MD) simulation study of the folding thermodynamics for the three-stranded beta -sheet protein Betanova. The protein was explicitly described by employing an all-atom model. The solvation was accounted for by two different solvent models: explicit TIP3P water and implicit Generalized Born (GB) with an exterior dielectric of 80. An umbrella sampling technique was utilized to probe thermodynamically relevant states at different stages of folding. The generated data were combined with the weighted histogram method to produce the two-dimensional folding free energy landscape. Sampling of conformational space was carried out in explicit solvent at 275 K and in implicit solvent at 275, 350, and 400 K. The folding free energy surface of Betanova at 275 K was found to be consistent with that in explicit solvent. In particular, the two models agree with regard to the location of the global minimum, the absence of a significant barrier for folding on the folding free energy surface, and the minor role of hydrogen bonding in the folding of Betanova. On the other hand the GB solvent model overestimated the stability of the protein and the folding transition temperature. It also yielded a slightly different shape for the folding free energy surface, compared to the calculations with explicit solvent. Exploration of the temperature dependence of the folding landscape in the GB solvent model yielded a similar overall shape with a shift in the global minimum toward smaller values of the folding reaction coordinate. The inclusion of an explicit surface-area-based treatment of hydrophobic interactions did not qualitatively change the results obtained with the GB model. We conclude that the GB solvent model is sufficient for studying the folding thermodynamics of small polypeptides.