24 - Protein folding and structure dynamics

Abstract

This chapter discusses protein folding and structure dynamics. The general structure of macromolecule is influenced by the incessant motion at the lowest, microscopic level. The segments of the macromolecule change rather rapidly but get trapped in local free-energy minima, states surrounded by barriers. The molecule segments can move and lead out from such a state by some escape rate, where the Boltzmann factor always enter as a slowing factor. It is found that the native state is not reached for most prescribed interaction energies, but it is reached for a not too small proportion of all possibilities. Some proteins may attain a long-lived structure by their production pathways. A protein can be produced in ribosome complexes at the membrane and directly inserted in the membrane in a way that stabilizes a certain structure with important interaction energy to the membrane. That structure should be important for the function of the protein in the membrane, but it may not be the most favorable structure, nor has there been any possibility in the production process to provide another folding. There are observations of molecular correlation functions that show a stretched behavior for a large system of molecules, while observations of single molecules show a more conventional, exponentially decaying correlation.