ELNEDYN: Keep your proteins stable
- Created: Sunday, 31 May 2009 23:00
- Last Updated: Monday, 19 August 2013 14:42
Combine your Martini protein model with an elastic network ...
In the mean time, read the paper in which the method is explained:
X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition. J. Chem. Th. Comp., 5:2531-2543, 2009.
Abstract: Structure-based and physics-based coarse-grained molecular force fields have
become attractive approaches to gain mechanistic insight into the function of large biomolecular
assemblies. Here, we study how both approaches can be combined into a single representation,
that we term ELNEDYN. In this representation an elastic network is used as a structural scaffold
to describe and maintain the overall shape of a protein and a physics-based coarse-grained
model (MARTINI-2.1) is used to describe both inter- and intramolecular interactions in the system.
The results show that when used in molecular dynamics simulations ELNEDYN models can be
built so that the resulting structural and dynamical properties of a protein, including its collective
motions, are comparable to those obtained using atomistic protein models. We then evaluate
the behavior of such models in (1) long, microsecond time-scale, simulations, (2) the modeling
of very large macromolecular assemblies, a viral capsid, and (3) the study of a protein-protein
association process, the reassembly of the ROP homodimer. The results for this series of tests
indicate that ELNEDYN models allow microsecond time-scale molecular dynamics simulations
to be carried out readily, that large biological entities such as the viral capsid of the cowpea
mosaic virus can be stably modeled as assemblies of independent ELNEDYN models, and that
ELNEDYN models show significant promise for modeling protein-protein association processes.