title: A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition.
abstract: One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.
authors.affiliation: College of Engineering, Koç University, 34450 Istanbul, Turkey.
authors.forename: Cahit
authors.initials: C
authors.lastname: Dalgicdir
authors.affiliation: College of Engineering, Koç University, 34450 Istanbul, Turkey.
authors.forename: Ozge
authors.initials: O
authors.lastname: Sensoy
authors.affiliation: Max Planck Institute for Polymer Research, 55128 Mainz, Germany.
authors.forename: Christine
authors.initials: C
authors.lastname: Peter
authors.affiliation: College of Engineering, Koç University, 34450 Istanbul, Turkey.
authors.forename: Mehmet
authors.initials: M
authors.lastname: Sayar
mesh_terms: D004151:Dipeptides; D008956:Models, Chemical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D010649:Phenylalanine / Q000031:analogs & derivatives* / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D010455:Peptides; D014867:Water; C026650:phenylalanylphenylalanine; D010649:Phenylalanine