79
Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session I
26-POS
Board 26
A Transferable Coarse-Grained Model for Diphenylalanine: How to Represent an
Environment Driven Conformational Transition
Cahit Dalgicdir
1,2
, Ozge Sensoy
1,3
, Christine Peter
2
, Mehmet Sayar
1
.
1
Koc University, Istanbul, Turkey,
2
University of Konstanz, Konstanz, Germany,
3
Weill Cornell
Medical College, New York, NY, USA.
Coarse-grained (CG) simulation models allow longer simulation times and larger systems due to
their reduced degrees of freedom compared to the all-atomistic (AA) models. However standard
CG methods yield state-dependent potentials whereas biological processes such as
folding/unfolding upon interaction with an interface or upon aggregation, involve multiple states.
The present study investigates the challenge of transferability for CG models and aims to
generate a CG model that is able to represent such processes.
Diphenylalanine is a zwitterionic dipeptide that 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. The nonbonded interactions are obtained by mimicking solvation
free energies of structurally relevant counterparts where each solvent molecule is represented
with a single bead and the peptide with a total of four beads. 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.
We show that one can construct a coarse-grained model that is able to reproduce the bulk and
interface conformational behavior and the segregation between the bulk and
hydrophobic/hydrophilic medium. We found that the cyclohexane/water interaction potential, an
interaction that does not involve the peptide can influence the conformation of the peptide as
well as 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.
1
1
Dalgicdir, C., Sensoy, O., Peter, C., & Sayar, M. (2013). A transferable coarse-grained model
for diphenylalanine: How to represent an environment driven conformational transition.
The
Journal of chemical physics
, 139(23), 234115.
