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

Sumit Sharma, Sanat K. Kumar, Sergey V. Buldyrev, Pablo G. Debenedetti, Peter J. Rossky, H. Eugene Stanley

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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 languageEnglish (US)
Article number1841
JournalScientific reports
Volume3
DOIs
StatePublished - 2013

All Science Journal Classification (ASJC) codes

  • General

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    Sharma, S., Kumar, S. K., Buldyrev, S. V., Debenedetti, P. G., Rossky, P. J., & Stanley, H. E. (2013). A coarse-grained protein model in a water-like solvent. Scientific reports, 3, [1841]. https://doi.org/10.1038/srep01841