Functional motif

The term homology domain or functional domain should be used only for those protein regions that either are known to be domains in the structural sense or that are at least predicted to fulfil that condition. Conserved sequence regions that are too short to fold independently of the rest of the protein should rather be referred to as motifs . A considerable number of those functional motifs have important roles, e.g. by being responsible for specific domain- or protein-recognition events. 

As shown in Fig. 1.1, bioinformatics approaches in pharmacogenomics are conducted systematically. The lowest level in the system is at the molecular level. At this level, it is necessary to understand the detailed features of a gene and the relationship between genetic structure and function (see Subheading 1.2.1). These detailed features include sequence analytic information such as sequence retrieval and comparison, sequence variation information such as about single-nucleotide polymorphisms (SNPs), and sequence patterns that can correlate sequence structure to functional motifs. 

More recently, the Pam amino acid chimera has also been incorporated into a small j0j0a-motif peptide scaffold [28]. The family of BBA peptides was developed in our laboratory as structured platforms for the design of functional motifs. These motifs are attractive because they are small enough (23 residues) to be easily synthesized by standard solid phase synthesis methods. Additionally, the motifs appear to possess sufficient structural complexity to influence coenzyme properties while still being amenable to structural characterization by standard spectroscopic techniques [3, 29, 30]. The BBA peptides include a -hairpin domain with a type IT turn connected by a loop region to an a-heli-cal domain (Fig. 10). Packing of the sheet and helix against one another is accomplished by hydrophobic contacts created by a hydrophobic core of residues. 

Bustin, M. (1999) Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol. Cell. Biol. 19, 5237-5246. 

In sum, then, although fascinating reports of conductivity in DNA structures have been published, and some general structure/function motifs have become clear, difficulties with reproducibility of experimental data and with appropriate interfaces between nanoscale DNA structures and macroscopic electrodes have limited the accuracy with which DNA charge transport can be measured, and the depth in which it can be understood. This remains an active area, and (especially given DNA s very powerful presence as the synthetic component of nanostructures) it is one that will almost certainly be more clearly elucidated in the near future. 

Putative functional motifs are commonly reported in ITS1 sequences of neodermatans. In processing motifs such as chi-like sites (possible hot spots for recombination), the ITS1 resembles the IGS. Chi-like sites were first noted by Kane et al. (1996) in ITS1 of... 

A sequence repeat found in both fibrous and globular proteins is one in which a functional motif occurs, possibly several times in the sequence but often noncontiguously. This Type E repeat is exemplified by the Ca2+ EF hand, which is a length of sequence specifying a pair of a-helices that... 

Sequence repeats in proteins make use of structural and functional motifs that nature has found to work well in vivo. Large numbers of these motifs have now been characterized, and any newly determined amino acid sequence is generally run through computer databases to assess the number and type of repeats present, their possible conformations, and their likely functions in vivo. The characteristics of the sequence motifs... 

Neural network applications for protein sequence analysis are summarized in Table 11.1. Like the DNA coding region recognition problem, signal peptide prediction (11.2) involves both search for content and search for signal tasks. An effective means for protein sequence analysis is reverse database searching to detect functional motifs or sites (11.3) and identify protein families (11.4). Most of the functional motifs are also... 

It is not yet known whether other conserved functional motifs characteristic of class A GPCRs are involved in C5a receptor activation. The E/DRY motif, actually DRF in this receptor (Fig. 6), has not yet been investigated. Similarly, the conserved Pro of the TXP motif, ALP in this receptor (Fig. 6), could be involved in receptor activation but this possibility has not been examined. More generally, while some conserved Pro residues may play a role in activation, they have long been proposed to be important for normal receptor folding and membrane insertion (Kolakowski et al., 1995). 

The emplo5unent of robust aromatic ligand architectures able to introduce the same kind of reactivity in a reversible manner is of course much more desirable. For this purpose, biological redox cofactors such as quinones, porphyrins, flavins, and their functional analogues in biomimetic chemistry contain a built-in butadiene-t5rpe moiety as part of their n-electron system, which can be considered as a minimum functional motif for assisting the reversible uptake of two electrons and two protons. This... 

Figure 6.9. Functional motifs of drugs used to build pharmacophore points.

Modifications at the single amino acid level are possible, and various functional motifs can be added to promote neiuite outgrowth. 

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