Distantly related proteins

M Grihskov, AD McLachlan, D Eisenherg. Profile analysis Detection of distantly related proteins. Proc Natl Acad Sci USA 84 4355-4358, 1987. 

R Abagyan, D Erishman, P Argos. Recognition of distantly related proteins through energy calculations. Proteins Struct Eunct Genet 19 132-140, 1994. 

Pasture, A., et al. Stmctural alignment and analysis of two distantly related proteins Aplysia limacina myoglobin and sea lamprey globin. Proteins 4 240-250, 1988. 

For these reasons, it is important to focus on the most divergent set of superfamily members that can be identified. Although a variety of new methods have recently been developed for identification of distantly related protein sequences [see, for example, Psi-Blast (Altschul et al, 1997), methods based on Hidden Markov Models such as SAMT98 (Kar-plus et al., 1998), the Intermediate Sequence Search algorithm of Park et al., (Park et al., 1997), or the simple congruence method, Shotgun (Pegg and Babbitt, 1999)], confirmation of these relationships can be technically difficult. In some cases, three-dimensional structural information or experimental structure-function analysis will be required to pro-... 

Ku CJ, Yona G (2005) The distance-profile representation and its application to detection of distantly related protein families. BMC Bioinfonnadcs 6 282. 

Gribskov, M., McLachian, A. D., Eisenberg, D. (1987) Profile Analysis Detection of distantly related proteins, Proc. Natl. Acad. Sci. USA 84 455-4358. 

Threading allows, given a query sequence, to search for sequences with a similar fold but without apparent sequence similarity. Therefore, threading has three major objectives first, provide orthogonal evidence of possible homology for distantly related protein sequences, second, detect possible homology in cases where sequence methods fail, and third, to improve structural models for the query sequence via structurally more accurate alignments. 

Kann, M. and R. A. Goldstein, Optimizing for success A new score function for distantly related protein sequence comparison, in RECOMB2000. 2000. Tokyo ACM Press. 

Improving Pairwise Sequence Alignment between Distantly Related Proteins... 

Inhibition of EGF-R tyrosine kinase by hypericin 1 was shown to be irreversible, non-competitive and time as well as temperature dependent. The IC50 increased from 0.75 pM in the dark to 44 nM with light illumination for 30 min. This effect was presumably due to a type I photosensitization mechanism since exclusion of oxygen did not alter the inhibition curve. Some Ser/Thr protein kinases (e.g., protein kinase A, casein kinase 1 and 2) and the enzyme 5 -nucleotidase were not inhibited even at concentrations > 100 pM [144]. However, the same authors recently reported that hypericin 1 in addition to protein kinase C also caused the light-dependent inhibition of certain other Ser/Thr kinases (e.g. protein kinase CK-2, mitogen-activated kinase) and the insulin receptor tyrosine kinase, while it was ineffective towards the cytosolic tyrosine kinases Lyn, Fgr, TPK-IIB and CSK. These results suggest that distantly related protein kinases could still share common reactive domains for the interaction with hypericin 1 [156]. In contrast to the above mentioned studies, Richter and Davies [157] observed no inhibition of EGF-induced tyrosine phosphorylation of the EGF-R in HN5 squamous carcinoma... 

Gribskov M, A D McLachlan and D Eisenberg 1987. Profile Analysis Detection of Distantly Related Proteins, Proceedings of the National Academy of Sciences USA 84-4335-4358. 

Lesk, A. M., Levitt, M., and Chothia, C. (1986). Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Prof. Eng. 1, 77-78. 

Currendy available crystal structures of TPR arrays show a highly homologous picture for three tandem repeats among unrelated TPR proteins and significant structural similarity to a distantly related protein family, the 14-3-3 helical repeat proteins (Das et al., 1998 Scheufler et al., 2000). Although structures of a TPR protein in both the free and ligand-bound... 

There is little question as to the scientific value of aligning amino acid sequences, especially distantly related ones. If the sequence of a protein with unknown tertiary structure can be related to one with known architecture, the main-chain folding for the latter provides a strong base for structural modeling. Aligning many distantly related proteins can point to the two or three never-substituted residues essential for function and available for site-directed mutagenesis [e.g., (38,39)]. If one of the... 

Figure 5 Structures of closely and distantly related proteins. Protein images created with UCSF Chimera. ...

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