Specialized Structures or Features

Just as the position of a-helices and j8-sheets can be predicted with a relatively high degree of confidence, the presence of certain specialized structures or features, such as coiled coils and transmembrane regions, can be predicted. There are not as many methods for making such predictions as there are for secondary structures, primarily because the rules of folding that induce these structures are not completely understood. Despite this, when query sequences are searched against databases of known structures, the accuracy of prediction can be quite high. 

A slightly easier to interpret output comes from MacStripe, a Macintosh-based application that uses the Lupas COILS method to make its predictions (Knight, 

The columns, from left to right, represent the residue number (shown twice), the amino acid, the heptad frame, the position of the residue within the heptad (a-b-c-d-e-f-g), the Lupas score, and the Lupas probability. In this case, from the fifth column, we can easily discern a heptad repeat pattern. Examination of the results for the entire GCN4 sequence shows that the heptad pattern is fairly well maintained but falls apart in certain areas. The statistics should not be ignored however, the results are easier to interpret if the heptad pattern information is clearly presented. It is possible to get a similar type of output from COILS but not through the COILS Web server instead, a C-based program must be installed on an appropriate Uiux machine, a step that may be untenable for many users. 

The TMpred Web interface is very simple. The sequence, in one-letter code, is pasted into the query sequence box, and the user can specify the minimum and maximum lengths of the hydrophobic part of the transmembrane helix to be used in the analysis. The output has four sections a list of possible transmembrane helices, a table of correspondences, suggested models for transmembrane topology, and a graphic representation of the same results. When the sequence of the G-protein-coupled receptor (P51684) served as the query, the following models were generated  

2 possible models considered, only significant TM-segments used 

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Alfuzosin (91) is a prazosin-like hypotensive adrenergic a-1 receptor blocker with the special structural feature that two carbons have been excised conceptually from the piperazine ring normally present in this series. Following the usual sequence for this series, reaction of 4-amino-2-chloro-7-dimethoxyquinazoline (89) with the tetrahydro-2-furyl amide of 3-methylaminopropyla-mine (90) gives alfuzosin (91) [25], Alfuzosin is claimed to cause less orthostatic hypotention (dizziness or fainting upon sudden rising) than prazosin. 

Aldehydes and ketones are similar in their response to hydrogenation catalysis, and an ordering of catalyst activities usually applies to both functions. But the difference between aliphatic and aromatic carbonyls is marked, and preferred catalysts differ. In hydrogenation of aliphatic carbonyls, hydrogenolysis seldom occurs, unless special structural features are present, but with aryl carbonyls either reduction to the alcohol or loss of the hydroxy group can be achieved at will. 

Incorporation into a Polymer Layer In recent years a new electrode type is investigated which represents a layer of conducting polymer (such as polyaniline) into which a metal catalyst is incorporated by chemical or electrochemical deposition. In some cases the specific catalytic activity of the platinum crystallites incorporated into the polymer layer was found to be higher than that of ordinary dispersed platinum, probably because of special structural features of the platinum crystallites produced within the polymer matrix. A variant of this approach is that of incorporating the disperse catalyst directly into the surface layer of a solid polymer electrolyte. 

Either because of potential interference with other functional groups present in the molecule or because of special structural features, the following reactions require careful selection of reagents and reaction conditions. Identify the special requirements in each reactant and suggest appropriate reagents and reaction conditions for each transformation. 

The main interest of biophysical analysis is to get information about function and mechanism of interactions between biomolecules. This is reflected by the typical way of presenting models for biological systems. Individual molecules bind to each other, catalyze an enzymatic reaction, or exhibit special structural features. The idea about the system is presented on a microscopic level. 

Little attention has been paid to systematic studies of spectral properties, X-ray structure, or thermodynamic aspects for these systems. Thus, little space is devoted to these subjects unless some feature warrants special note. On the contrary, synthesis and chemical reactivity of pyrrolo[l,2,4]triazines will be methodologically reviewed. 

One special feature in the interpretation of the quantitative results seems not to have been exploited in practical analysis, and it certainly deserves attention. The result of the methylation analysis is sometimes complex, and can reveal the occurrence of 10 to 20 different methylated sugars. In this situation, it is not easy to decide, by simple inspection of the analytical data, whether the result could be caused by one complex, carbohydrate chain, or by a structure containing several saccharide chains bound to a common aglycon. In addition, it is not always easy to decide whether the result could fit any natural structure, or mixture of structures, or whether the complex result is attributable to undermethylation. 

The inherent hydrophobicity once thought to be typical of sulphides (Ravitz and Porter, 1933) is now thought to be restricted to sulphides such as molybdenite (Chander et al., 1975) and other minerals or compound with special structural feature (Gaudin et al, 1957b). Common commercial sulphide minerals, which are needed to recover in flotation, are normally composed of anion (S ) and heavy metal ions such as Cu, Cu, Pb, Zn, Hg, Sb, Bi transitive metal ion such as Fe, Co, Ni and noble and rare metal ions such as Ag, Au, Mo. On the basis of structural pattern or mode of linkage of the atoms or polyhedral imits in space, Povarennyk (1972) introduced a crystallochemical classification of sulphide minerals, which have six major patterns as shown in Table 1.1. 

Heyes and Trahar (1984) leached pyrite with cyclohexane and compared the extract with a sulphur-containing solution of cyclohexane in a UV spectra photometer as shown in Fig. 1.4, indicating that sulphur was present at the mineral surface. Therefore, the inherent hydrophobicity and natural floatability once thought to be typical of sulphides is now thought to be restricted to sulphides such as molybdenite and other minerals or compound with special structural features. The collectorless floatability that most sulphide minerals showed came from the self-induced or sulphur-induced flotation at certain pulp potential range and certain conditions. 

Because the immediate product of the polyene cyclization is a carbocation, the reaction often yields a mixture of closely related compounds resulting from the competing modes of reaction of the carbocation. The products result from capture of the carbocation by solvent or other nucleophile or by deprotonation to form an alkene. Polyene cyclization can be carried out on reactants which have special structural features that facilitate transformation of the carbocation to a stable product. Allylic silanes, for example, are... 

Specific DNA-protein interactions which either promote or inhibit CT processes through the protein-DNA interface would be the most crucial part of a biological system sensing DNA damage. Recent experiments have shown clearly that DNA-mediated CT processes are modulated both negatively and positively by DNA-binding proteins. Most importantly, each of the observed influences of the proteins can be explained by special structural features of the corresponding DNA-protein complexes. Thus, special DNA-protein interactions result in a characteristic modulation of the DNA-mediated CT. 

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