Backbone rotation, comparison between

COMPARISON BETWEEN BACKBONE DYNAMICS AND SUBSTITUENT GROUP ROTATION... 

In the past, comparisons between NMR relaxation and MD simulations have concentrated on internal motions, since these often involve sub-nanosecond time scales that could be examined with limited computer resources. In this approach, overall rotational motion is removed by an rms fitting procedure (for example, on backbone atoms in regular secondary structure), and computing time-correlation functions from the result. Typical results are shown in the upper panel of Figure 8.1 similar plots have been presented many times before [4,12,10,11]. Many backbone vectors are like Thr 49, and decay in less than 0.1 ns to a plateau value which can be identified as the order parameter for that vector. Most regions of regular secondary structure resemble this, although there can be exceptions, and there is potentially important information in the decay rates and plateau values that are obtained. 

Table 1 - A comparison between the values of the internal rotation angles and the bond angle on the CH2 of the backbone corresponding to the minima of potential energy. The comparison is between the data obtained without a-ny previous assumption and under.the restriction that exp exp they are known). The unrepor-...

The hydration dependence studies of the internal protein dynamics of hen egg white lysozyme by and H NMR relaxation have been presented. The relaxation times were quantitatively analysed by the well-established correlation function formalism and model-free approach. The obtained data was described by a model based on three types of motion having correlation times around 10 , 10 and 10 s. The slowest process was shown to originate from correlated conformational transitions between different energy minima. The intermediate process was attributed to librations within one energy minimum, and the fastest one was identified as a fast rotation of methyl protons around the symmetry axis of methyl groups. A comparison of the dynamic behaviour of lysozyme and polylysine obtained from a previous study revealed that in the dry state both biopolymers are rigid on both fast and slow time scales. Upon hydration, lysozyme and polylysine showed a considerable enhancement of the internal mobility. The side chain fragments of polylysine were more mobile than those of lysozyme, whereas the backbone of lysozyme was found to be more mobile than that of polylysine. 

Both the hindered rotation around the amide bond and the thermal cis-trans isomerization of azobenzene residues are characterized by high energy barriers in the neighborhood of 20 kcal/ mole. Some years ago, Malkin and Fischer studied the photochemical isomerization of azobenzene and found that the quantum yield is temperature-dependent they interpreted their data as reflecting an energy barrier of 2-3 kcal/mole between the excited cis and trans species. A comparison of the quantum yields for the photoisomerization of azobenzene residues in the backbone of polymer chains and in low molecular weight analogs should, therefore, indicate whether conformational transitions characterized by low activation... 

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