Sequence locals

Primary, secondary, tertiary, and quaternary structure are familiar concepts for proteins and refer to the amino acid sequence, local folding arrangement, three-dimensional organization, and subunit interactions of polypeptide chains, respectively. Here, tertiary and quaternary structure shall be considered in the most general way, to include also the small molecules or ions that are essential for the conformational stability of the polypeptide chains. This is especially relevant for halophilic proteins, which have extensive interactions with solvent components (water molecules and salt ions). The known structure of a protein (at any level) always results from experiment, and as such is known only within appropriate error limits. 

In addition to externally inserted trapping sites, hole trapping occurs at sites of successive guanines, i.e. at GG and GGG sequences. Local oxidation potentials depend on the local environment including the bases that enclose the G-based hole carriers. GG and GGG thus have lower oxidation potentials than G isolated between A-, C- or T-bases. 

For DNA sequences, (local) sequence similarity can be calculated at the nucleotide level, at the peptide level and at both levels with the mixed-alignment option as previously explained. If the peptide-level or mixed-alignment option is used, it is possible to translate sequence segments only at the forward strand or to have the program look at both, the forward strand and the reverse complement. 

Ovcharenko, I., Loots, G. G., Giardine, B. M., et al. (2005) Mulan multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15, 184-194. 

While the original definition of a protein domain is based on the structure, it is also possible to detect re-usable modules in protein sequences. Local regions of... 

The poly(A) tracts contained in these presumptive mRNA molecules are generally 150-200 nucleotides in length and have a base composition of greater than 85 adenine. Evidence has also been presented for the occurrence of an adenylate-rich sequence in 10 S rabbit reticulocyte globin mRNA (Lim and Canellakis, 1970). RNA transcribed from vaccinia virus DNA has also been shown to contain a large poly( A) sequence localized at the 3 end of the molecule (Kates, 1970). Poly (A) tracts... 

Quite recently emerged the antitumor strategy based on the use of small molecules that specifically target telomeres and telomerase [1 ]. Telomeres are gua-nine-rich DNA sequences localized at the ends of the chromosomes. They protect chromosomal DNA from degradation, prevent end-to-end fusion and other forms of aberrant recombination, and allow it to be completely replicated without loss of genetic material. The length of the telomeres correlates with the ability of a cell to... 

Global Z scores reported in Tables XI and XII are converged using 1000 shuffled sequences. Local Z scores are, however, computed using only 50 shuffled sequences. The constraint here is of computational resources. Global Z scores are computed only for 10 energy-best structures and can be done... 

Figure 5.9 (a) Shift register in a While loop (b) Sequence local in a stacked sequence structure. 

The structure of a protein is generally understood in terms of an organizational hierarchy that consists of protein sequence, local secondary structure, tertiary stmcture, and finally quaternary structure. The study of protein structure in these terms has led to a greater understanding of... 

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