Structural Hierarchy and Degrees of Mobility

The dynamics of protein molecules have been studied intensively using various experimental19-U) and theoretical112 approaches. Luminescence methods are widely applied in these investigations.12 18) Modem concepts about the structure of proteins and their dynamics which have evolved from these investigations are presented briefly in this section. 

The polypeptide chain in the native protein is folded into a compact structure, which strongly limits the freedom of molecular movement. The arrangement in space of each atom in the protein molecule is fixed and does not change with time in the absence of thermal collisions with other atoms in a protein and solvent molecules. From the thermodynamic point of view, the 

The spatial macrostructure of the native protein (the equilibrium location of the polypeptide main chain backbone and bulky side groups) is strictly determined. Individual protein molecules having the same sequence of amino acid residues do not differ in their three-dimensional structure, which is the equilibrium one and averaged in time. The activation energy of conformational transitions may be as high as several hundreds of kilojoules per mole. Therefore, the extended fluctuations which are associated with the unfolding of the native macro structure and transitions between conformations occur rather rarely. 

However, the identicalness of protein molecules possessing the same macroconformation is not absolute. Within each structurally determined conformational macrostructure, there exists a microdisordering which is similar to that observed in amorphous solids and glasses.(U,14) It is associated with the presence of multiple relative minima of the free energy depending on small shifts and variations in orientation of certain groups within the limits of available space. 

Oscillations of atoms and their groups, typically occurring on a time scale of 10 12-10 14 s, are much faster motions. However, there is evidently no sharp distinction between these motions and other slower motions. When damping and anharmonicity arise, the oscillations become diffusive and have the properties of transitions between microstates. It is natural to suppose (as 

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