Paper Citing NAMD - Abstract
Oliveira, Leandro C.; Schug, Alexander; Onuchic, Jose N.
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: A detailed investigation of several reduced models
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6131-6136, MAY 15 2008
The concept of a funneled energy landscape and the principle of minimal frustration are the theoretical foundation justifying the applicability of structure-based models. In simulations, a protein is commonly reduced to a C-alpha-bead representation. These simulations are sufficient to predict the geometrical features of the folding mechanism observed experimentally utilizing a concise formulation of the Hamiltonian with low computational costs. Toward a better understanding of the interplay between energetic and geometrical features in folding, the side chain is now explicitly included in the simulations. The simplest choice is the addition of C-beta-beads at the center-of-mass position of the side chains. While one varies the energetic parameters of the model, the geometric aspects of the folding mechanism remain robust for a broad range of parameters. Energetic properties like folding barriers and protein stability are sensitive to the details of simulations. This robustness to geometry and sensitivity to energetic properties provide flexibility in choosing different parameters to represent changes in sequences, environments, stability or folding rate effects. Therefore, minimal frustration and the funnel concept guarantee that the geometrical features are robust properties of the folding landscape, while mutations and/or changes in the environment easily influence energy-dependent properties like folding rates or stability.
