Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation

  • Ulmschneider J
  • Jorgensen W
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Abstract

An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations is applied to fold three polypeptides, U(117)T9D, 1, and trpzip2, which exhibit native -hairpin and -helix folds. The method includes flexible bond and dihedral angles, and a Gaussian bias is applied with driver bond and dihedral angles to optimize the sampling efficiency. Solvation in water is implemented with the generalized Born (GBSA) model. The computed lowest-energy manifolds for the folded structures of the two -hairpins agree closely with the corresponding NMR structures. In the case of the 1 peptide, the folded -helical state, which is observed as oligomers in concentrated solution and crystals, is not stable in isolation. The computed preference for random coil structures is in agreement with NMR experiments at low concentration. The fact that native states can be located on high dimensional energy surfaces starting from extended conformations shows that the present methodology samples all relevant parts of the conformational space. The OPLS-AA force field with the GBSA solvent model was also found to perform well in leading to clear energetic separation of the correctly folded structures from misfolded structures for the two peptides that form -turns. An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations is applied to fold three polypeptides, U(117)T9D, 1, and trpzip2, which exhibit native -hairpin and -helix folds. The method includes flexible bond and dihedral angles, and a Gaussian bias is applied with driver bond and dihedral angles to optimize the sampling efficiency. Solvation in water is implemented with the generalized Born (GBSA) model. The computed lowest-energy manifolds for the folded structures of the two -hairpins agree closely with the corresponding NMR structures. In the case of the 1 peptide, the folded -helical state, which is observed as oligomers in concentrated solution and crystals, is not stable in isolation. The computed preference for random coil structures is in agreement with NMR experiments at low concentration. The fact that native states can be located on high dimensional energy surfaces starting from extended conformations shows that the present methodology samples all relevant parts of the conformational space. The OPLS-AA force field with the GBSA solvent model was also found to perform well in leading to clear energetic separation of the correctly folded structures from misfolded structures for the two peptides that form -turns.

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