Functional sites detection

The majority of prosite documentation refers to motifs rather than profiles. The motifs are less sensitive than profiles and do not provide statistical scores. The motifs correspond to active sites and other important functional sites in proteins. The motifs are expressed as regular expressions that can be used to detect matching proteins in the database. An example of a motif from Prosite would be the /V-glycosylation motif,... 

A method for detecting conserved residues, called evolutionary tracing (ET), was developed by lichtarge et al. [45], Several groups have embarked on developing methods for detecting functional sites based on ET and related methods (see... 

If the number of (I, k) sites detected in the sequence meets the condition T > T0, they can be considered as potential functional signals with the significance level q. 

Closely related are the 1-benzylamino-l-deoxylactitol dithiocarbamate salts developed by Eybl and co-workers316 317 for the same purpose. However, the most important application of 175 is, probably, its use as a nontoxic, water-soluble nitric oxide probe in vivo. In view of the central importance that this gaseous free-radical species plays in regulating a broad range of important biological functions, its detection and quantification near its site of production and action is of prime importance. For this purpose, the ferrous salt of MGD, which forms a stable water-soluble mononitrosyl iron-dithiocarbamate complex (176) with a characteristic electron spin resonance (ESR) spectrum at room temperature, is currently used.318-323... 

Ward et al. (65, 71) reported on the NaHY and MgHY systems. The 2 systems behave as a mixture of the 2 components. Sodium hydrogen Y was studied as a function of the sodium content from 100 to 0% exchanged (71). For the calcination conditions used (480°C), the series of samples were all in the Bronsted acid form. The concentration of acid sites detected by pyridine chemisorption increased linearly as the sodium was removed until only about 16 sodium ions were left. This corresponds to the number of easily removed sodium ions which can be exchanged with ammonium ions and subsequently form hydroxyl groups of the 3650 cm 1 type. Further exchange yields hydroxyl groups in the small-pore structure which are not accessible and/or not sufficiently acidic to react with pyridine. 

An important aspect in the sequence analysis of proteins is the detection of functional sites such as the active site, ligand binding site, signal sequence/cleavage site and post-translational modification sites. Generally, a prior knowledge concerning the chemical nature of these sites is available. For example, the active triad (Ser-His-Asp/Glu) of serine... 

Though this multistage modification on polymer is performed with improved homogeneity compared to the first one, whose functional heterogeneity had been only very roughly estimated, both of the examples demonstrate that the finally modified support will under no circumstances exhibit functional uniformity. The possibilities of handling a cross-linked polymer like a conventional chemical in a projected pathway of synthetic operations are limited, since each deviation like side reactions and incomplete conversions remains fixed to the insoluble support. In addition, small quantities of functional sites (< 10%) are scarcely detectable by IR spectroscopy and are hard to analyze by conventional methods of organic chemistry. 

To date, there does not exist a direct and accurate but nondestructive method to determine quantitatively the formation of peptide bonds on polymer. Without regard to the principal discussion of the problems of chemical analyses on heterogeneous phase (see p. 42), the detection of remaining uncoupled amino groups on polymer does not necessarily allow one to deduce the yield of support-bound peptide. Additional side reactions might have blocked a certain amount of functions fission reactions might have cleaved parts of the peptide, or new functional sites might have been introduced, which positively interfere... 

The evidence that we have presented indicates that the allele (in the absence of L-arabinose as the inducer) does produce two functionally different products the activator and the repressor. The activator function is detected by the stimulatory effect of the aUele on the ara operon cis to deletion 719 and to certain r mutants in strains containing deletion 719. The repressor function is indicated by the epistatic effect of the allele on the constitutive expression of the ara operon cis to I" A766 and by the dominance of to O as indicated previously. That one function is transformed into another is evidenced by the inducibility of the pertinent merodiploid invoked by L-arabinose. Thus it appears that L-arabinose removes the repressor from the operator site and shifts the equilibrium to the activator, which then reacts at aral and stimulates the expression of the operon (Fig. 3). 

The major conclusion that was deduced from the spectra shown in Figs. 4 and 5 is that the two sites detected for the nitroxides in the heterophasic systems studied can serve as a basis not only for describing the morphology of the system, but also to trace the evolution of the nittoxide signal as a function of treatment time, and the time dependence of the degradation process, in the morphologically different domains in the butadiene-rich and SAN-rich domains in ABS, and in the amorphous PP-rich and EPR-rich domains in HPEC. 

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