title: 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.
authors.affiliation: Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
authors.forename: Sumit
authors.initials: S
authors.lastname: Sharma
authors.forename: Sanat K
authors.initials: SK
authors.lastname: Kumar
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Buldyrev
authors.forename: Pablo G
authors.initials: PG
authors.lastname: Debenedetti
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Rossky
authors.forename: H Eugene
authors.initials: HE
authors.lastname: Stanley
mesh_terms: D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D012997:Solvents; D014867:Water