Abstract
Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein ("H-P") model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the "Jagla-philic" monomers to the solvent, while maintaining a "hydrophobic" core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.
Original language | English (US) |
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Article number | 1841 |
Journal | Scientific reports |
Volume | 3 |
DOIs | |
State | Published - 2013 |
All Science Journal Classification (ASJC) codes
- General