Removing Lattice Constraints from Lattice Protein Models: A Wang-Landau Study

We apply Wang-Landau sampling [1] to the continuum analogue of the hydrophobic-polar (HP) lattice protein model [2] to study the effects of lattice constraints on generic folding behavior in coarse-grained protein models. The continuum version is inspired by the AB polymer model [3], but incorporates potentials chosen specifically to mimic those of the lattice protein case. In this study, we compare and contrast thermodynamics during the folding process of the continuum model to the original HP lattice protein model for sequences mapped from Crambin, a 46 amino acid plant protein. We find that the folding processes for both of these coarse-grained models are quite similar, with major structural transitions occurring at almost the same temperatures. The continuum model hints at a small, additional structural transition not seen in the lattice case; the exact nature of this rearrangement is currently under investigation.

[1] F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)
[2] K. A. Dill, Biochemistry 24, 1501 - 9 (1985)
[3] F. H. Stillinger, T. Head-Gordon, and C. L. Hirshfeld, Phys. Rev. E 48, 1469 (1993)