Internal repeats

Levitskaya J, Coram m, Levitsky V, Imreh S, Stegerwald-Mullen PM, Klein G, Kurilla MG, and Masucci MG (1995) Inhibition of antigen processing by the internal repeat region of the Epstein-Barr Virus nuclear antigen-1. Nature (London) 375 685-688. 

This program is used to find regions of homology. It will find internal repeats or common sequences between two sequences by displaying the two sequences in the form of a matrix and marking any regions of identity. One sequence is written along the x axis... 

Since the different domains often have quite different types of tertiary structure, they need to be described and classified separately and, if possible, should be predicted separately. Multiple domains should be considered for any sequence that suggests an internal repeat or that is longer than about 200 residues (250 for a/P structures or 100 for a disulfide-rich sequence). 

Saaf, A., Baars, L., and von Heijne, G. (2001). The internal repeats in the Na+/Ca2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. /. Biol. Chem. 276, 18905-18907. 

The large size of transferrins (670-700 residues), with the consequent difficulties of chemical sequencing, meant that it was not until 1982 that the first amino acid sequences, those of human serum transferrin 10) and chicken ovotransferrin 34,35), were established. These were closely followed by that of human lactoferrin 11). The twofold internal repeat in each sequence (see below) was immediately apparent, and comparison of all three sequences then identified conserved tyrosines and histidines that were potential ligands for iron (11). 

Two other isomeric libraries of self-assembling AB2 monodendrons based on 3,4- and 3,5-disubstituted benzyl ether internal repeat units containing four first generation monodendrons, i.e., 3,4,5-tris( -dodecan-l-... 

Amino acid sequences can be searchedfor the presence of internal repeats. Such internal repeats can reveal information about the history of an individual protein itself Many proteins apparently have arisen by duplication of a primordial gene followed by its diversification. For example, calmodulin, a ubiquitous calcium sensor in eukaryotes, contains four similar calcium-binding modules that arose by gene duplication (Figure 4.28). 

Figure 7.15. A Self-Diagonal Plot For the TATA-Box-Binding Protein From the YXant Arabidopsis. Self-diagonal plots are used to search for amino acid sequence repeats within a protein. The central diagonal is the sequence aligned with itself Red dots indicating a correspondence of amino acids appear where two or more amino acids in a row match. Lines of dots, highlighted in pink, parallel to the central diagonal suggest an internal repeat.

Figure 7.16. Sequence Alignment of Internal Repeats. (A) An alignment of the sequences of the two repeats of the TATA-hox-binding protein. The amino-terminal repeat is shown in green and the carboxyl-terminal repeat in blue. (B) Structure of the TATA-hox-binding protein. The amino-terminal domain is shown in green and the carboxyl-terminal domain in blue.

There are clusters of 6 alanine residues in positions 6—11. Preliminary experiments with carboxypeptidase A digestion indicate the presence also of a cluster of alanine at the C terminus. In contrast to the antifreeze glycoprotein, an internal repeating sequence was not found, except possibly for the sequence of Leu Thr Ala Ala Asn Asx Lys (positions 12-18) and Leu Thr Ala Asp Asn Lys (positions 23-28). 

Amino acid sequences can be searched for the presence of internal repeats. Such internal repeats can reveal the history of an individual protein itself. 

Dot plots are a powerful method of comparing two sequences. They do not predispose the analysis in any way such that they constitute the ideal first-pass analysis method. Based on the dot plot the user can decide whether he deals with a case of global, i.e., beginning-to-end similarity, or local similarity. Local similarity denotes the existence of similar regions between two sequences that are embedded in the overall sequences which lack similarity. Sequences may contain regions of self-similarity which are frequently termed internal repeats. A dot plot comparison of the sequence itself will reveal internal repeats by displaying several parallel diagonals. 

Fig. 4. Structure of GPI-anchored T-cadherin. The extracellular domain contains four internal repeats EI-E4, an extra domain E5 and a lipid anchor for integration into cell membranes.

In contrast, the apo BlOO sequence contains many internally repeated sequences that bear little resemblance to the sequences of the exchangeable apolipoproteins (L. Chan,... 

More than 10% of all proteins contain sets of two or more domains that are similar to one another. The afore-described sequence search methods can often detect internally repeated sequences that have been characterized in other proteins. Where repeated units do not correspond to previously identified domains, their presence can be detected by attempting to align a given sequence with itself. 

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