Region of disorder

The success rate of every prediction set was greater than the value of 50% expected by chance. Specifically, the various sets of predictions differed from the 50% value by about 3 standard deviations (for the lowest success rate, which was for the merged data) to about 12 standard deviations (for the highest success rates, which were for the medium and long regions of disorder). Overall, these data provided very strong support for our hypothesis that disorder is encoded by the amino acid sequence (Romero et al., 1997b). 

To obtain statistically significant comparisons of ordered and disordered sequences, much larger datasets were needed. To this end, disordered regions of proteins or wholly disordered proteins were identified by literature searches to find examples with structural characterizations that employed one or more of the following methods (1) X-ray crystallography, where absence of coordinates indicates a region of disorder (2) nuclear magnetic resonance (NMR), where several different features of the NMR spectra have been used to identify disorder and (3) circular dichroism (CD) spectroscopy, where whole-protein disorder is identified by a random coil-type CD spectrum. 

Three groups of disordered proteins have been assembled, with the groups defined by the experimental method used to characterize the lack of ordered structure. Because the focus has been on long regions of disorder, an identified disordered protein or region was not included in these groups if it failed to contain 40 or more consecutive residues. Disordered regions from otherwise ordered proteins as well as wholly disordered proteins were identified. Table I summarizes the collection of sequences in this database. 

Different protein folding classes can be identified by differences in their amino acid compositions (Nakashima et al., 1986) thus, we reasoned that, if disorder were encoded by the sequence, then regions of disorder would be analogous to a new folding class and hence should... 

Section II,B, this may be an overestimate of the false positive error rate because many of the apparent consecutive errors correspond to regions of disorder that are ordered in the crystal due to ligand binding or crystal contacts. Also, because disordered regions of length >40 residues are often missed due to false negative predictions of order, the data in... 

These experimental results demonstrate that the specific adsorption of anions leads to a significant decrease in junction stability, as illustrated in particular in the potential regions of disordered anion adsorption, as well as in the fluctuations in the plateau currents at potentials of the 2D-ordered anion adlayers. The instability of the conductance plateaus were statistically analyzed, by determining the standard... 

DNA unwinding in the above diagram occurs initially in the AT-rich regions of the DNA duplex (indicated as a above), and these local regions of disorder (shown in c and d ) require some twisting motions (shown in d ). As these areas grow ( e ), one reaches the point of nearly complete loss of local order ( f ), followed by formation of a large loop ( g )- As would be expected. 

The theory of Frank and Wen (54) for ion hydration involves the notion that some water molecules intimately contact the ion under consideration and subject to the strong centrosymmetric force field, are highly ordered. Beyond this area is a region of disorder, beyond which, in dilute solutions, unaffected water prevails. Typical literature values for primary hydration numbers range from 2-8 water molecules. For divalent ions, primary hydration numbers range from 10-20 water molecules while some authors have suggested hydration numbers for trivalent ions (based on compressibility data) between 20 and 30 water molecules per ion. Many attempts have been made to extend theories of this type to account better for the hydration of ions. Thus, Azzam (7, 8) and Horne and Birkett (80) have proposed a multilayer model of ion hydration. 

As mentioned earlier, regions of disorder in the spatial ensemble of calculated NMR structures can, in principle, be due to internal motions but can also reflect a relative lack of NOEs in such regions. A recent analysis83 suggests that ill-defined regions in structural ensembles often do reflect slow, large-amplitude motions, and so it is not always necessary to resort to relaxation time measurements if only a general idea of molecular motions is required for a particular protein. Even if relaxation measurements are done, it is often not necessary to undertake and extensive analysis to derive correlation... 

Fig. 8.9. Schematic of the change in backscattering yield as a function of depth through a region of disorder that gives rise to both dechanneling and direct scattering. The aligned fraction, %D, is greater than the random fraction, in the depth region of the disorder...

During ion implantation, each ion produces a region of disorder around the ion track. As the implantation dose increases, the disorder increases until all the atoms have been displaced and an amorphous layer is produced over a depth Rp. The buildup and saturation of disorder are shown in Fig. 10.1 for 40 keV phosphorus ions incident on Si. In this example, about 4 x 1014 phosphorus ions cnT2 are required to form an amorphous layer. Except for low doses or implantation with light ions, we can anticipate that an amorphous layer is formed during the implantation process. This assumes that no recovery of lattice order occurs around the ion track. 

Figure 1.3 (a) Schematic of a polycrystalline sample. A polycrystal is made up of many grains separated from one another by regions of disorder known as grain boundaries. (h) typical microstructure as seen through an optical microscope. 

S (J ). A fraction of faster relaxing intensity, comparable to that at C4, is also visible in the other resonances at Cl and C2,3,5. If one assumes that most of this faster relaxation is occurring at the crystalline surface and in 3"dimensional regions of disorder, then, by spin exchange, crystalline carbons about 1 nm from the surface will also relax more efficiently. 

Self-similar ordered regions with well-defined satellite orbits are periodically separated by regions of disorder. Should the analogy with microscopic systems hold, periodic variation of this type must also be evident, for instance, in the structure of atoms. 

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