Sequencing variables

Hoehe, M. R., Kopke, K, Wendel, B., et al. (2000) Sequence variability and candidate gene analysis in complex disease association of mu opioid receptor gene variation with substance dependence. Hum. Mol. Genet. 9, 2895-2908. 

Despite the different assumptions in the two schemes described here, the properties of the calculated currents share the expected semiconducting features. This is basically due to the fact that they are formally acting on the r-stack in a similar way. Only further experimental investigation could shed more light on the discrimination of the gap-opening mechanism. Such an effort would eventually help in quantifying the influence of other insulating effects, which are possibly present in other DNA-based devices. They include (i) electron correlations and Coulomb blockade, (ii) localization effects due to the sequence variability, and (iii) local defects. 

In the process of viral assembly, HIV PR specifically cleaves nine cleavage sites on GAG and GAG-POL polypeptides [21]. Examination of the amino acid composition of the recognized substrate sites (Table 1) indicates their hydrophobic character and significant sequence variability. The loose specificity of HIV PR most likely reflects its functions in a world of reduced complexity within the confines of the budding virion. The length of the viral protein precursors (approximately 1500 amino acids) reduces the number of potential sequences the protease must discriminate from in selecting its nine cleavage sites. Therefore,... 

Burstein, Y. Schechter, I. (1977). Glutamine as a precursor to N-terminal pyrrolid-2-one-5-carboxylic acid in mouse immunoglobulin X-type light chains. Amino acid-sequence variability at the N-terminal extra piece of X-type light-chain precursors. Biochem. J. 165, 347-354. 

The genomic DNA is of necessity without design. All of the information contained within the strand in form of sequence variability comes to light through the code. One could state that the nearly limitless potential information hidden in the tons of nucleic acid of the DNA or RNA type, regardless of which code would be adapted, would inevitably lead to all the life forms on earth. The total variety of life forms on a particular planet under proper biogenesis conditions becomes a function of the total amount and variability of nucleic acids available. That gives us a biopotential theorem worthy of the new millennium. 

The sequence variability in the sample contains phylogenetic signal adequate to resolve the problem of interest. 

Subtilases comprise the second largest family of serine proteases characterized to date with members in Archaebacteria, eukaryotes, and even viruses. Surprisingly, the catalytic domains of subtilases display a high degree of sequence variability with... 

Fig. 7. Primary sequences and disulfide bond connectivities of endothelin isoforms ET-1, ET-2 and ET-3. Shading is used to indicate regions of sequence variability relative to ET-1.

The retroviruses associated with AIDS (autoimmune deficiency syndrome), namely, human immunodeficiency virus types 1 and 2 (HIV-1, -2), display considerable genome sequence variability not only between isolates from different individuals but also between isolates from the same... 

The sequence variability in transmembrane /1-barrels is higher than in water-soluble proteins and exceptionally high in the external loops. 

Ambler, R. P., 1991, Sequence variability in bacterial cytochromes c, Biochim. Biophys. Acta 1058 42n47. 

Figure 33.7. Immunoglobulin Sequence Diversity. A plot of sequence variability as a function of position along the sequence of the amino-terminal immunglobulin domain of the H chain of human IgG molecules. Three regions (in red) show remarkably high levels of variability. These hypervariable regions correspond to three loops in the immunoglobulin domain structure. [After R. A. Goldsby, T. J. Kindt, and B. A. Osborne, Kuby Immunology, 4th ed. (W. H. Freeman and Company, 2000), p. 91.]...

The location of the domain-binding site was determined by multiple sequence alignment, estimation of the sequence pattern variability, and properties of residues for particular portions of tiie structural surface template. The template prepared for the bovine yB- and pB2-crystallins was described above (Fig. 1). The sequences of mouse PA3- and PB2-aystallins were aligned with bovine yB-and PB2-crystallins, and corresponding residues were placed within the structural template. The sequence variability score was calculated for each residue in the surface template as described in the caption to Fig. 2. The location of the common domain-binding site for the bovine yB- and PB2-ciystallins and mouse PA3- and PB2-ciystallins, was determined by considering the residue positions with a positive sequence variability score (> 0) and the residues with consoved properties in corresponding portions of yB- and PB2-crystallins. 

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