Structure and Sequence

the true knights-errant, measure the whole earth with our own feet, exposed to the sim, to the cold, to the air, to the inclemencies of heaven, by day and night, on foot and on horseback nor do we only know enemies in pictures, but in their own real shapes and at all risks and on all occasions we attack them. 

Treatment of glycoproteins with 50 mM NaOH, 1 M NaBH, releases the O-glycosidically bound oligosaccharides. These stay intact, except for the terminal sugar unit. The latter is reduced to the corresponding alcohol (Muir and Lee 1969 Rehm et al. 1989). 

and Lee, Y. (1969). Structures of the D-galactose Oligo Saccharides From Earthworm Cuticle CoUagen, Biol Chem. 244 2343-2349. 

(1993). Use of Hydrazine to Release in Intact and Unreduced Form Both N- and O-linked Oligosaccharides from Glycoproteins, Biochemistry 32 679-693. 

(1986). Molecular Characterization of Synaptophysin, a Major Calcium Binding Protein of the Synaptic Vesicle Membrane, iiAffiO./ 5 535 541. 

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Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

As such, the magainins provide a useful initial target for peptoid-based peptido-mimetic efforts. Since the helical structure and sequence patterning of these peptides seem primarily responsible for their antibacterial activity and specificity, it is conceivable that an appropriately designed, non-peptide helix should be capable of these same activities. As previously described (Section 1.6.2), peptoids have been shown to form remarkably stable hehces, with physical characterishcs similar to those of peptide polyprohne type-I hehces (e.g. cis-amide bonds, three residues per helical turn, and 6A pitch). A faciaUy amphipathic peptoid helix design, based on the magainin structural motif, would therefore incorporate cationic residues, hydrophobic aromatic residues, and hydrophobic aliphathic residues with threefold sequence periodicity. 

It is worth noting that the past few years have witnessed tremendous development of web-based information resources. Notably, the PubMed search tool [4] has made the investigation of any life sciences topic much easier. It offers keyword and author (as well as structure and sequence) searches and covers a wide range of medicinal chemistry-related journals. This resource, coupled with e-journals, affords the medicinal chemist the tools to keep up with any research topics of interest. Because of the public nature of the Web, now a chemist can sometimes find critical journal articles on the Web that do not show up until much later in traditional literature sources. It is not uncommon that scientific meeting presentations can be found on the Web. Indeed, the Internet tools we have all become familiar with also have made the professional life of the medicinal chemist much easier. 

Tandem mass spectrometry (MS-MS) uses more than one mass analyzer for structural and sequencing studies that have been found very useful for anthocyanin characterization. These mass analyzers may be of the same type (triple or quadru-poie)85,86 Qj. such as ion trap quadrupole, - and quadrupole-time-of-flight... 

This assay system developed by Chaires [136] is a new, powerful and effective tool based on the fundamental thermodynamic principle of equilibrium dialysis for the discovery of ligands that bind to nucleic acids with structural and sequence selectivity. Here, identical concentrations of various nucleic acid samples are dialysed in dispodialysers against a common ligand solution. At equilibrium, the contents of the ligand bound to each nucleic acid are determined and this is correlated directly to the ligand s specificity to a particular sequence. 

The structure and sequence of the catalytic moiety have been determined (06, V6, W6). The enzyme consists of 362 amino acids and 40,638 daltons of the protein predicted by the cDNA sequence. The ADA gene spans 32 kb and consists of 12 exons. The apparent promoter region of the gene lacks the TATA and CAAT sequences often found in eukaryotic promoters and is extremely G/C rich. The location of the ADA gene is on chromosome 20ql2-ql3.11 (Jl). 

Cheng X, Collins RE, Zhang X (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Annu Rev Biophys Biomolec Struct 34 267-294... 

Figure 5.3 The deduced evolutionary tree for selected members of the transferrin superfamily, based on comparisons of structures and sequences. The tree combines the transferrins with a number of prokaryotic periplasmic transport proteins. From Bruns et al., 1997. Reproduced by permission of Nature Publishing Group.

The structural and sequence studies have highlighted two interesting prerequisites to fiber formation. First, the animal must control the size and... 

Fig. 3. Structure and sequence of repeats present in the fibrous proteins discussed in this chapter. (A) The adenovirus triple -spiral. A single repeat of one of the chains is shown as a stick model colored by atom, the other two as a secondary structure cartoon in yellow and orange. Amino acids contributing to the hydrophobic core are labeled, as is the glycine in the turn. (B) Triple -spiral sequence repeats. Conserved hydrophobic residues are indicated by a hash sign, the conserved glycine or proline by an asterisk. (C) The T4-hber fold. A single repeat of one of the chains is shown as a stick model colored by atom, the other two as a secondary structure cartoon in yellow and orange. Several of the conserved amino acids are labeled. (D) Repeating sequences present in bacteriophage T4 fiber proteins (Cerritelli et al., 1996). Conserved amino acids are indicated by a small letter conserved hydrophobic residues by a hash sign, and conserved small amino acids by a dot.

Nucleic acid structures and sequences primary and secondary structure of DNA fragments, translocation of genes between two chromosomes, detection of nucleic acid hybridization, formation of hairpin structures (see Box 9.4), interaction with drugs, DNA triple helix, DNA-protein interaction, automated DNA sequencing, etc. 

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