Local minimum energy conformations

Mechanisms of Chemical and Physical Degradation of Proteins A folded native protein exists in a local minimum-energy conformation. Typically 5 to 15 kcaPmol of energy is needed to rapidly (in mhli-... 

Explain the significance of the terms global and local minimum energy conformations. 

Recently, MD simulation has been applied as a tool in the refinement of three-dimensional biomolecular structures from X-ray diffraction and two-dimensional NMR data. In the refinement process, MD trajectories are run at elevated temperatures (perhaps several thousand degrees Kelvin) to enhance conformational sampling. The molecular systems are cooled periodically to permit the trajectories to settle into local minimum energy conformations. Constraint terms based on X-ray structure factors or NMR NOE distances are added to the standard potential energy functions, so that the MD trajectories relax to conformations that satisfy the experimental data as the systems are cooled. Thus, the complete potential function in a refinement simulation has the form... 

The problem of finding all local minimum energy conformations can also be formulated as a single global optimization problem, which can be deterministically solved using the aBB algorithm [23]. This method stems from the idea that all stationary points (i.e., minima, maxima, and transition states) of the energy hypersurface satisfy the constraint V (0) = 0. This can be written as ... 

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