Domains of proteins

Figure 17.10 Construction of a two helix truncated Z domain, (a) Diagram of the three-helix bundle Z domain of protein A (blue) bound to the Fc fragment of IgG (green). The third helix stabilizes the two Fc-binding helices, (b) Three phage-display libraries of the truncated Z-domaln peptide were selected for binding to the Fc. First, four residues at the former helix 3 interface ("exoface") were sorted the consensus sequence from this library was used as the template for an "intrafece" library, in which residues between helices 1 and 2 were randomized. The most active sequence from this library was used as a template for five libraries in which residues on the Fc-binding face ("interface") were randomized. Colored residues were randomized blue residues were conserved as the wild-type amino acid while yellow residues reached a nonwild-type consensus, [(b) Adapted from A.C. Braisted and J.A. Wells,...

Natural products from the Euphorbiaccae family of plants that mimic the effects of diacylglycerol by binding the Cl domain of proteins such as PKC. 

The partial backbone assignment of the catalytic domain of protein kinase A (PKA) using a combination of NMR techniques was reported in 2004 [51]. This represented the first reported NMR assignment of any protein kinase catalytic domain. Backbone resonance assignment of the 42kDa protein was achieved using a combination of triple-labelled ( H, N)... 

Benes CH, Wu N, Elia AE, Dharia T, Cantley LC, Soltoff SP. The C2 domain of protein kinase C-delta is a phosphotyrosine binding domain. Cell 2005 121 (2) 271-280. 

The second mode of toxicity is postulated to involve the direct interaction of the epidithiodiketopiperazine motif with target proteins, forming mixed disulfides with cysteine residues in various proteins. Gliotoxin, for example, has been demonstrated to form a 1 1 covalent complex with alcohol dehydrogenase [13b, 17]. Epidithiodi-ketopiperazines can also catalyze the formation of disulfide bonds between proxi-mally located cysteine residues in proteins such as in creatine kinase [18]. Recently, epidithiodiketopiperazines have also been implicated in a zinc ejection mechanism, whereby the epidisulfide can shuffle disulfide bonds in the CHI domain of proteins, coordinate to the zinc atoms that are essential to the tertiary structure of that domain, and remove the metal cation [12d, 19],... 

Modified E2 protein, now containing the IgG binding domain of Protein A... 

Verdaguer, N., Corbalan-Garcia, S., Ochoa, W.E., Eita, 1., and Gomez-Eemandez, J.C., 1999, bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine. EMBO J. 18 6329-6338. 

Acs P, Wang QJ, Bogi K, Marquez AM, Lorenzo PS, Biro T, Szallasi Z, Mushinski JF, Blumberg PM (1997) Both the catalytic and regulatory domains of protein kinase C chimeras modulate the proliferative properties of NIH 3T3 cells. J Biol Chem 272 28793-28799... 

The catalytic domain of protein kinase A has a two lobe structure, composed of a smaller lobe with a large portion of P-sheet structures and a larger lobe that is mostly a-helical. All Ser/Thr- and Tyr-specific protein kinases structurally characterized to date show a similar domain structure. 

Fig. 7.5. Functional domains of protein kinase A. The functional domains of the catalytic (C) and regulatory (R) subunits of protein kinase A (bovine) are shown in a hnear configuration. M myristoylation.

Fig. 7.8. Functional domains of protein kinase C. The functional domains of protein kinase Ca and C8 are shown as a linear representation. The binding site for TPA lies in domain Cl. Domain C2 contains the Ca binding site. Protein kinase C8 lacks the C2 elements and thus regulation by Ca. According to Azzi et ah, (1992). Pseudosubstrate autoinhibitory sequence with pseudosubstrate character.

Zang, G., Kazanietz, M.G., Blumberg, EM. and Hurley, J.H. Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester (1995) Cell 81, 917-924... 

The catalytic center of the protein tyrosine phosphatases includes ca. 230 amino acids and contains the conserved sequence motif HA -C-(X)5-R-S/T-G/A/P (X is any amino acid) which is involved in phosphate binding and in catalysis and is part of a loop known as the P loop. The available structural data on the catalytic domains of protein tyrosine phosphatases indicate that the mechanism shown schematically in Fig. 8.17 is likely (see Tainer and Russell, 1994). The invariant Cys and Arg residues of the P loop have a central function in binding and cleavage of the phosphate residue. 

RNA is the only macromolecule known to have a role both in the storage and transmission of information and in catalysis, which has led to much speculation about its possible role as an essential chemical intermediate in the development of life on this planet. The discovery of catalytic RNAs, or ribozymes, has changed the very definition of an enzyme, extending it beyond the domain of proteins. Proteins nevertheless remain essential to RNA and its functions. In the modem cell, all nucleic acids, including RNAs, are complexed with proteins. Some of these complexes are quite elaborate, and... 

Structural domains of proteins are sometimes encoded by a single coding segment of DNA i.e., by a single exon in a split gene. Domains of this type may have served as evolutionarily mobile modules that have spread to new proteins and multiplied during evolution. For example, the immunoglobulin structural domain is found not only in antibodies but also in a variety of cell surface proteins.229 252... 

Usually, owing to insolubility or unacceptable buffers, large protein fragments are not beneficially analyzed by ESI-MS. However, the identity of stable domains of protein molecules can still be inferred from the accurate mass measurements of the smaller polypeptide fragments obtained from limited proteolysis. This provides a basis for resolving the compact domains for proteins in situations where matrix-assisted laser desorption ionization (MALDI) data are ambiguous and ESI-MS of the large protein may be precluded. 

Transcription factors that increase the rate of transcription usually have at least two domains of protein structure, a DNA-binding domain that recognizes the specific DNA control element to bind to, and an activation domain that interacts with other transcription factors or the RNA polymerase. Many transcription factors operate as dimers (homodimers or heterodimers) held together via dimerization domains. Some transcription factors interact with small ligands via a ligand-binding domain. 

Specific domains of proteins (for example, those mentioned in the section Organic Phase ) adsorbed to biomaterial surfaces interact with select cell membrane receptors (Fig. 8) accessibility of adhesive domains (such as specific amino acid sequences) of select adsorbed proteins may either enhance or inhibit subsequent cell (such as osteoblast) attachment (Schakenraad, 1996). Several studies have provided evidence that properties (such as chemistry, charge, and topography) of biomaterial surfaces dictate select interactions (such as type, concentration, and conformation or bioactivity) of plasma proteins (Sinha and Tuan, 1996 Horbett, 1993 Horbett, 1996 Brunette, 1988 Davies, 1988 Luck et al., 1998 Curtis and Wilkinson, 1997). Albumin has been the protein of choice in protein-adsorption investigations because of availability, low cost (compared to other proteins contained in serum), and, most importantly, well-documented conformation or bioactive structure (Horbett, 1993) recently, however, a number of research groups have started to examine protein (such as fibronectin and vitronectin) interactions with material surfaces that are more pertinent to subsequent cell adhesion (Luck et al., 1998 Degasne et al., 1999 Dalton et al., 1995 Lopes et al., 1999). 

What is meant by a domain of protein structure Give an example of a domain in a real protein. 

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