Linker domain

Fig. 3.17 Activation of gene transcription by artificial transcription factors. (Top) The artificial activator is composed of three separate functional domains. The DNA binding domain consists of the pyrrole/imidazole polyamides (shown as connected arrows). A tethered linker domain (shown as a coil) connects the DNA binding domain to the peptide activation domain (AD, shown as an oval).

Upon binding, the artificial transcription factor recruits the necessary transcriptional machinery for gene activation. (Bottom, left) Ball-and-stick model for a polyamide conjugated to the VP2 activation domain. Symbols are as in Fig. 3.4. (Bottom, right) Structure of the polyamide-VP2 conjugate with the polyproline linker domain in brackets... 

Type and number of linker domains do not affect activity 55... 

Poly(3HB) depolymerase with cadherin-like linker domain 57... 

Singh, M., Berger, B., Kim, P. S., Berger, J. M., and Cochran, A. G. (1998). Computational learning reveals coiled-coil like motifs in histidine kinase linker domains. Proc. Natl. Acad. Sci. 95, 2738-2743. 

Leung, C. L., Zheng, M., Prater, S. M., and Liem, R. K. (2001b). The BPAG1 locus Alternative splicing produces multiple isoforms with distinct cytoskeletal linker domains, including predominant isoforms in neurons and muscles. /. Cell Biol. 154, 691-698. 

The final steps in fusion are only incompletely understood. For instance, it is controversial whether the non-bilayer transition states in fusion are initiated primarily by force, transmitted from the pull of the assembling SNARE motifs via the linkers onto the membrane, as suggested by mutagenesis of the linker domain. Alternatively, the function of the SNARE motifs may be confined to close apposition of the membranes, with the final steps being catalyzed by other factors such as a... 

These transformations indicated that the starch binding domain of Rhizopus sp. glucoamylase was located at the N-terminus, and attached to the catalytic domain by a small linker domain (Figure 7.10). This is in contrast with the A. niger glucoamy-lases that have an opposite structure, with the catalytic domain at the N-terminus and the starch binding domain at the C-terminus. 

In addition to site-directed mutations, deletion mutants that eliminated some, or all, of the linker domain have been produced for A. niger glucoamylase.173 Deletions of up to 30 amino acids from the C-terminus of the linker domain had no effect on the activity of either glucoamylase-I or glucoamylase-II.173... 

As discussed above, glucoamylases consist of three domains a catalytic domain a linker domain and a starch-binding domain. These domains can be in different orders in which the catalytic domain is located at the N-terminus or the C-terminus and conversely the starch-binding domain is at the C-terminus or the N-terminus, with the linker domain between the two. 

Figure 5 Artificial transcription factors, (a) Protein-based ATFs can consist of a DNA binding domain (DBD) that recognizes DNA and an activation domain (AD) that interacts with and recruits the transcriptional machinery, (b) Protein-DNA dimerizers do not interact directly with the transcriptional machinery but can bind and recruit other DNA binding molecules, which in turn interact with the transcriptional machinery, (c) Examples of molecules that act as functional domains used in ATFs. A DNA binding domain is connected, via a linker domain, to either an activation domain or a repression domain.

A detailed sequence analysis revealed that coronin 1 (coronin 1 A) is made up of three distinct domains (see Fig. lA) The first, N terminal domain that also contains the 5 WD repeats is rich in p-sheet and is referred to as p-propeller (residues 1-355). The second domain is comprised of a region with little regular secondary structure and is referred to as linker domain (residues 356-429). Finally, the third domain is a coiled coil containing segment which is rich in a-helices (residues 430-461). ... 

Fig. 1 Topography of the sweet taste receptor. The sweet taste receptor is an integral membrane protein complex composed of two subunits, T1R2 (red) and T1R3 (blue). Each subunit has three main domains a large, extracellular Venus-flytrap domain (VFD) at the amino end of the protein a seven-transmembrane helical domain typical of G-protein-coupled receptors on the carboxyl end and a cysteine-rich linker domain that connects the other two domains...

Many cells secrete at least one of the three immature forms of TGF-P, and essentially all cells have receptors that respond to the presence of mature TGF-P in the stroma. In the periodontium, TGF-P stimulates fibroblast and osteoblast proliferation during connective tissue or bone remodeling (Sect. 10.1.3), and maintains the proliferation of dentally attached epithelial cells (Sect. 5.2.3). The linker domains that connect calcium binding domains in fibrillin are identical to the sequence of protein receptors that bind to TGF-P (Sect. 6.1.1). 

The highest interfacial electron transfer rate constant yet reported (about 14,000 s ) is for a c-type cytochrome from Aquifex aolicus This protein has a 62-amino acid linker domain by which it is usually anchored to the periplasmic side of the inner membrane this linker has a cysteine as the terminal residue before the signal region, and the sulfur atom provides an anchor point. The cytochrome adsorbs strongly onto a Au electrode that is already modified with a hexane-thiol SAM (note this requires that the molecules in the SAM move or vacate to allow this). The results are striking. 

Fig. 11.8 A) Domain structure of STATs. STATs bind to receptors and dimerize via bivalent SH2-phosphotyrosine interactions. Phosphorylation ofthe conserved tyrosine is required for STATs dimerization. The N-terminal region mediates oligomerization of STAT dimers. B) Dimer of Stat2 bound to DNA. Dimerization is mediated by reciprocal SH2-Tyr-phosphate interactions ofthe monomers. The view is along the DNA helix. The DNA binding domain is in red, the linker domain in orange and the SH2 domain in light green. The C-termini ofthe two Stat2 molecules are shown in yellow and magenta.

Figure 13 Cartoon representation of Salmonella typhimurlum IgPurL (1T3T). The N-terminal domain (1-140) is colored green, the linker domain (141-214) is colored yellow, the FGAM synthetase domain (215-979) is colored blue, and the glutaminase domain (980-1295) is colored red. Image rendered in PYMOL.

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