Classic sequence-specific binding

For a poly- or oligonucleotide catalyst-substrate interaction the problem of binding-specificity is in principle solved simply by using the complementary sequence, and chemistry based on classical... 

The detailed analysis of DNA structure in the region of contact with the binding protein often displays distinct divergence from the parameters of classical B-DNA structure. The specific sequence-determined conformation of the DNA is often a prerequisite for a specific recognition. This recognition mechanism is, for example, realized with the Trp-repressor, where the sequence determines a certain spatial arrangement of the... 

Vallely et al., 2002 Ikura and Ames, 2006). The C-terminal EF-hand contains the classical Ca2+-binding motif, common to all EF-hand proteins (see above). This Ca2+-binding motif has a typical sequence signature of 12 amino acids and is flanked by helices Hin and HIV. The N-terminal EF-hand is different from the classical EF-hand motif and is characteristic of the S100 proteins. Therefore, this EF-hand, with a 14 amino acid consensus sequence motif, is flanked by helices H, and Hn and is called the SlOO-specific or pseudo EF-hand. 

Classically, E2 binds to the ER, thus leading to conformational changes that result in dimerization of E2-ER complexes, with subsequent binding to specific EREs located within the promoter area of genes responsive to estrogen (Fig. 3). The classical ERE is an inverted hexanucleotide repeat sequence separated by three nucleotides (Beato et al., 1996). Such binding of the dimerized ER-E2 complex to ERE results in activation of transcription. 

Since PTB domains adopt the same fold as PH domains, J. Schlessinger has suggested that the PTB domain may be another class of PH domain, a relationship that was overlooked because of the absence of sequence homologies.52 This classification is supported by differences between PTB domains and classical SH2 domains. The crystal structure of the phosphotyrosine-binding domain (PTB) of a human, neuron-specific peptide (XI1) that contains a C-terminal PTB domain, provides relevant information.53 With its PTB domain, this peptide binds to the cytoplasmic domain of the p-amyloid precursor protein (P-APP), found in the brain of patients with Alzheimer s disease. The domain with which the peptide interacts is an internalization motif of P-APP (Fig. 3.4). 

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