Homologous from different species

Hybridization measurements have been used in many studies of homology of nucleic acids from different species. A nucleic acid is cut (e.g., by sonic oscillation) into pieces of moderate length ( 1000 nucleotides) and is denatured. The denatured DNA fragments are mixed with denatured DNA of another species. Nucleotide sequences that are closely similar between species tend to hybridize, whereas sequences that are... 

Cross-reactivity of milk proteins from different species is the main cause of similar immunoreactivity. Cross-reactivity indicates the homology in amino acid sequences and similar capacity of binding specific IgE antibodies. Weak crossreactivity is usually observed between cow milk proteins and proteins from mares and donkeys. 

Comparison of the amino acid sequences of hemoglobin and myoglobin chains from different species of animals shows that the chains from related species are similar. The number of differences increases with phylogenetically more separated species. On the assumption that proteins evolve at a constant rate, the number of differences between two homologous proteins will be proportional to the time of divergence in evolution of the species. 

Based on the above discussion it was thought that the trifluoro-methyl ketones would be more polarized and thus create a great electrophilicity on the carbonyl carbon which facilitates -OH attack by the serine residue. Yet there is no carbon-oxygen bond to be cleaved In the ketone moiety, and therefore the enzyme-trifluoromethyl ketone transition state complex does not undergo catalytic conversion. The above rationale seems reasonable as trifluoromethyl ketones were found to be extraordinary selective and potent inhibitors of cholinesterases (56) of JHE from T. ni (57) and of meperidine carboxylesterases from mouse and human livers (58). Since JH homologs are alpha-beta unsaturated esters, a sulfide bond was placed beta to the carbonyl in hopes that it would mimic the 2,3-olefln of JHs and yield more powerful inhibitors (54). This empirical approach was extremely successful since it resulted in compounds that were extremely potent inhibitors of JHEs from different species (51,54,59). 

The most valuable confirmation of this view to date is, without doubt, to be found in the known structures of homologous proteins and peptide hormones, that is compounds of identical biological function isolated from different species. As is well known, the primary structures of the homologous insulins, corticotropins, hypertensins, posterior pituitary hormones, and heme peptide sequences from cytochromes c are closely similar and differ only at certain definite sites in the peptide chains. These can, in particular, serve as a useful point of departure in a search for more general principles governing protein structure, and in the comparison of different proteins. 

Molecular replacement (see Rossmann, 1972) has another very useful application, one that has for the most part superseded that described above for directly deducing phase information from noncrystallographic relationships. It derives from the tendency of macromolecules to fall into classes with shared structural motifs, in that they are homologous and often evolutionarily related. Macromolecules of similar function from different species often share structural features and are frequently almost identical. Viruses of the same or similar families do as well. Protein domains of common occurrence may serve as modules to be assembled in different combinations to make a variety of proteins having redundant structural features. 

Figure 4.6 (a) Amino acid sequence homology (% human receptor) between the DNA- and ligand-binding domains of PXR from different species [8]. (b) Amino acid differences in the ligand-binding domain of rat, mouse, and human PXR [48]. Circles designate positions where major shifts in the physical-chemical properties occur. 

Structural comparisons of PXR from different species demonstrated that there is more than 95% sequence homology in the DBD regions, but only 75% to 80% amino acid homology in the LBD (Figure 4.6a). This striking difference in the LBD sequence across species is unusual compared to the classic nuclear receptors, such as GR, which show nearly 90% sequence identity in the LBD... 

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