The potential energy hyper-surface of a protein relates the potential energy of the protein to its conformational space. This surface
is useful in determining the native conformation of a protein or in examining a statistical-mechanical ensemble of structures (canonical
ensemble). In determining the potential energy hyper-surface of a protein three aspects must be considered; reducing the degrees of
freedom, a method to determine the energy of each conformation and a method to sample the conformational space. For reducing the degrees
of freedom the choice of solvent, coarse graining, constraining degrees of freedom and periodic boundary conditions are discussed.
The use of quantum mechanics versus molecular mechanics and the choice of force fields are also discussed, as well as the sampling of
the conformational space through deterministic and heuristic approaches. Deterministic methods include knowledge-based statistical
methods, rotamer libraries, homology modeling, the build-up method, self-consistent electrostatic field, deformation methods, tree-based
elimination and eigenvector following routines. The heuristic methods include Monte Carlo chain growing, energy minimizations, metropolis
monte carlo and molecular dynamics. In addition, various methods to enhance the conformational search including the deformation
or smoothing of the surface, scaling of system parameters, and multi copy searching are also discussed.
Keywords: Protein, potential energy surface, native state, lowest energy state, conformational sampling, structure determination, molecular
Rights & PermissionsPrintExport