Unknown

Dataset Information

0

A coarse-grained protein model in a water-like solvent.


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.

SUBMITTER: Sharma S 

PROVIDER: S-EPMC3653448 | biostudies-other | 2013

REPOSITORIES: biostudies-other

Similar Datasets

| S-EPMC3983376 | biostudies-other
| S-EPMC5816953 | biostudies-other
| S-EPMC2928645 | biostudies-literature
| S-EPMC2883601 | biostudies-literature
| S-EPMC3910140 | biostudies-literature
| S-EPMC7382508 | biostudies-literature
| S-EPMC6342926 | biostudies-literature
| S-EPMC4196741 | biostudies-literature
| S-EPMC2535944 | biostudies-literature
| S-EPMC3019136 | biostudies-literature