Effective simulations of proteins, their complexes, and other amino-acid polymers such as peptides or peptoids are critically dependent on the performance of the simulation methods and their ability to map the conformational space of the molecule in question. The most important step in this process is the choice of the coordinates in which the conformational sampling will be executed and their uniqueness regarding the capability to unambiguously determine the energy minimum on the free-energy hypersurface. In the presented study, we show that metadynamics and chosen collective coordinates-the principal moments of the tensors of gyration and inertia, the principal radii of gyration around the principal axes, asphericity, acylindricity, and anisotropy-can be used as a powerful combination to map the conformational space of peptides and proteins. We show that the combination of these coordinates with metadynamics produces a powerful tool for the study of biologically relevant molecules.

Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague Czech Republic

References provided by Crossref.org

The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization