Motif structure

This structural similarity is also reflected in the amino acid sequences of the domains, which show 40% identity. They are thus clearly homologous to each other. The motif structures within the domains superpose equally well but their sequence homology is less, being around 30% between motifs 1 and 2 and 20 Xi between 3 and 4. This study, however, clearly shows that the topological description in terms of four Greek key motifs is also valid at the structural and amino acid sequence levels. 

Murre, C., and Baltimore, D. (1992). The helix-loop-helix motif structure and function. In Transcriptional Regulation (McKnight, S. L and Yamamoto, K. R., eds.), pp. 861-879. Cold Spring Harbor Laboratory, Plainview, NY. 

Nalefski, E.A., and FaUce, J.J., 1996, The C2 domain calcium-binding motif structural and functional diversity. Protein Sci. 5 2375-2390. 

Analysis of Privileged Structural Motifs Structure Dissection Rules... 

Orengo CA, Thornton JM. Alpha plus beta fold revisited some favoured motifs. Structure 1993 1 105-120. 

Many examples of recurring domain or motif structures are available, and these reveal that protein tertiary structure is more reliably conserved than primary sequence. The comparison of protein structures can thus provide much information about evolution. Proteins with significant primary sequence similarity, and/or with demonstrably similar structure and function, are said to be in the same protein family. A strong evolutionary relationship is usually evident within a protein family. For example, the globin family has many different proteins with both structural and sequence similarity to myoglobin (as seen in the proteins used as examples in Box 4-4 and again in the next chapter). Two or more families with little primary sequence similarity sometimes make use of the same major structural... 

Main, E. R., Xiong, Y., Cocco, M. J., D Andrea, L., and Regan, L. (2003). Design of stable a-helical arrays from an idealized TPR motif. Structure 11, 497-508. 

Choi, H. J., Park-Snyder, S., Pascoe, L. T., Green, K. J., and Weis, W. I. (2002). Structures of two intermediate filament-binding fragments of desmoplakin reveal a unique repeat motif structure. Nat. Struct. Biol. 9, 612-620. 

Lectin arrays Lectin binding pmol-nmol Structural motifs Structural analysis in tissue context, living cells can be screened, no fractionation required Limited by availability and specificity of characterized lectins, quantification is challengi ng... 

CHAPTER 36, FIGURE 5 Motif structures within coagulation proteins. Common motifs are found in the amino terminal regions of the proteinase precursor molecules. Shown are the kringle motifs and EGF-like motifs found in the vitamin K-dependent proteins and in plasminogen. Fibronectin (types I and II) motifs and apple motifs (named from their two-dimensional representations) are also present but not shown. Some epidermal growth factor-like domains contain P-hydroxylated Asp residues. The cartoon structures for the motifs are derived from three-dimensional structures determined by x-ray crystallography or by two-dimensional NMR spectroscopy. 

Taylor, S. S., and E. Radzio-Andzelm. 1994. Three protein kinase structures define a common motif. Structure 2 345-355. 

Orengo, C. A., and Thornton, J. M. (1993). Alpha plus beta folds revisited Some favoured motifs. Structure 1, 105—120. 

LNA has been used in a variety of other biological applications. LNA, and its 2 -amino analogue, has been incorporated into aptamers (see section 2) for enhanced binding affinity." LNA has been substituted into i-motif structures, where it can have a significant effect on the structural stability. The presence of LNA in the structure alters the stability of the hemiprotonated cytosine base pairs, and as there is a sequence effect it is possible to tune the stability of the i-motif." Substituting LNA into quadruplex structures also has a sequence-dependent effect on stability, where in only certain positions are well-defined structures obtained." More recently the use of LNA nucleotides as polymerase substrates has been examined." KOD DNA polymerase has been shown to be a useful polymerase for the incorporation of LNA triphosphates into DNA, including its use as the polymerase in PCR reactions with LNA modifications." ... 

Small Molecules that Bind and Modulate A-motif Structures... 

Small Molecules Induce and Promote the Stability of i-Motif Structure... 

Figure 3.17 Proposed mechanism of the stabilization and induction of the i-motif structure by GQDs. Folded i-motif structure is generated from the PDB file (PDB id 1EL2). Reprinted with permission from ref. 167. Copyright 2012 American Chemical Society.

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