Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling.
A hybrid coarse-grained (CG) and atomistic (AT) model for protein simulations and rapid searching and refinement of peptide-protein complexes has been developed. In contrast to other hybrid models that typically represent spatially separate parts of a protein by either a CG or an AT force field model, the present approach simultaneously represents the protein by an AT (united atom) and a CG model. The interactions of the protein main chain are described based on the united atom force field allowing a realistic representation of protein secondary structures. In addition, the AT description of all other bonded interactions keeps the protein compatible with a realistic bonded geometry. Nonbonded interactions between side chains and side chains and main chain are calculated at the level of a CG model using a knowledge-based potential. Unrestrained molecular dynamics simulations on several test proteins resulted in trajectories in reasonable agreement with the corresponding experimental structures. Applications to the refinement of docked peptide-protein complexes resulted in improved complex structures. Application to the rapid refinement of docked protein-protein complex is also possible but requires further optimization of force field parameters.
Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748 Garching, Germany. martin.zacharias@ph.tum.de
Martin
M
Zacharias
D001665:Binding Sites; D062105:Molecular Docking Simulation / Q000379:methods*; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D010455:Peptides; D011506:Proteins