Critical testing of Martini
- Created: Wednesday, 08 February 2012 23:00
- Last Updated: Thursday, 22 August 2013 14:08
Dimerization of Martini amino acids comparable to atomistic force fields
Abstract: The interactions between amino acid side chains govern protein secondary, tertiary as well as quaternary structure formation. For molecular modeling approaches to be able to realistically describe these phenomena, the underlying forcefields have to represent these interactions as accurately as possible. Here we compare the side chain-side chain interactions for a number of commonly used forcefields, namely the all-atom OPLS, the united-hydrogen GROMOS, and the coarse-grained MARTINI forcefield. We do so by calculating the dimerization free energies between selected pairs of side chains and structural characterization of their binding modes. To mimic both polar and non-polar environments, the simulations are performed in water, n-octanol, and decane. In general, reasonable correlations are found between all three forcefields, with deviations of the order of 1 kT in aqueous solvent. In apolar solvent, however, significantly larger differences are found, especially for charged amino acid pairs between the OPLS and GROMOS forcefields, and for polar interactions in the MARTINI forcefield in comparison to the higher resolution models. Interestingly, even in cases were the dimerization free energies are similar, the binding mode may differ substantially between the forcefields. This was found to be especially the case for aromatic residues. In addition to the inter forcefield comparison, we compared the various forcefields to a knowledge based potential. The two independent approaches show good correlation in aqueous solvent with an exception of aromatic residues for which the interaction strength is lower in the knowledge based potentials.