A coarse-grained protein model in a water-like solvent
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Published version
Date
2013-05-14
Authors
Sharma, Sumit
Kumar, Sanat K.
Buldyrev, Sergey V.
Debenedetti, Pablo G.
Rossky, Peter J.
Stanley, Harry Eugene
Version
Published version
OA Version
Citation
Sumit Sharma, Sanat K Kumar, Sergey V Buldyrev, Pablo G Debenedetti, Peter J Rossky, H Eugene Stanley. 2013. "A Coarse-Grained Protein Model in a Water-like Solvent." SCIENTIFIC REPORTS, Volume 3, 6 pp. https://doi.org/10.1038/srep01841
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.
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Attribution 4.0 International