Protein rotation changes after

Since PCA filters out the vibrational motions with frequencies higher than 2n/t Equation 5.14 means that the rotational velocity of the moving normal mode coordinates is determined entirely by the fastest motions recorded in the trajectory. In other words, the rotation is so quick that the same pattern of motion never appears after one cycle of vibration, or the protein continuously changes its pattern of motion by rotating the mode space. 

Heat and alkaline treatments have been known since the early part of the century to raoemize amino acid residues in proteins (1,2,). Dakin and Dudley (3) also studied digestibility of casein in vitro and in vivo after hydroxide treatment. Heating casein with 0.5 N NaOH at 37° for about 30 days completely prevented enzymatic hydrolysis and intestinal absorption when the treated casein was fed to a dog. The kinetics of base-catalyzed racemization of proteins was investigated by Levene and Bass (4-6). In these early studies, the extent of racemization was measured by changes in optical rotation. 

Assuming a spherical shape for the fluorescent molecule, the degree of change in the rotational Brownian motion is given by Eq. (3.25), where v is the volume of the spherical molecule, r)0 is the solvent viscosity, r is the fluorescence lifetime of the chromophore, and T is the temperature. The values of r0 and r/v can be obtained from a plot of Mr versus T/rj0. Thus, if the fluorescence lifetime of the chromophore is known, it is possible to determine the hydrodynamic volume of the rotating molecule and its rotational diffusion constant D,. This data treatment is known as the Perrin-Weber approximation,25 after the two scientists who first derived the equations in the case of protein chromophores. 

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