Multidomain

Fig. 12. Total energy vs particle diameter for single- and multidomain particles.

In Figure 13 the relation between the intrinsic coercivity and the particle diameter dis given. The figure is based on a described model (35). The maximum is found around the critical particle diameter. In general the particle diameter and size is not very well defined. For the multidomain particles (d > ) the is smaller than the intrinsic anisotropy field of the particle. Nucleation effects cause a decrease in as the increases. This behavior is... 

All known eight-stranded a/p-barrel domains have enzymatic functions that include isomerization of small sugar molecules, oxidation by flavin coenzymes, phosphate transfer, and degradation of sugar polymers. In some of these enzymes the barrel domain comprises the whole subunit of the protein in others the polypeptide chain is longer and forms several additional domains. An enzymatic function in these multidomain subunits, however, is always associated with the barrel domain. 

Peptidases have been classified by the MEROPS system since 1993 [2], which has been available viatheMEROPS database since 1996 [3]. The classification is based on sequence and structural similarities. Because peptidases are often multidomain proteins, only the domain directly involved in catalysis, and which beais the active site residues, is used in comparisons. This domain is known as the peptidase unit. Peptidases with statistically significant peptidase unit sequence similarities are included in the same family. To date 186 families of peptidase have been detected. Examples from 86 of these families are known in humans. A family is named from a letter representing the catalytic type ( A for aspartic, G for glutamic, M for metallo, C for cysteine, S for serine and T for threonine) plus a number. Examples of family names are shown in Table 1. There are 53 families of metallopeptidases (24 in human), 14 of aspartic peptidases (three of which are found in human), 62 of cysteine peptidases (19 in human), 42 of serine peptidases (17 in human), four of threonine peptidases (three in human), one of ghitamicpeptidases and nine families for which the catalytic type is unknown (one in human). It should be noted that within a family not all of the members will be peptidases. Usually non-peptidase homologues are a minority and can be easily detected because not all of the active site residues are conserved. 

Coacervation occurs in tropoelastin solutions and is a precursor event in the assembly of elastin nanofibrils [42]. This phenomenon is thought to be mainly due to the interaction between hydro-phobic domains of tropoelastin. In scanning electron microscopy (SEM) picmres, nanofibril stmc-tures are visible in coacervate solutions of elastin-based peptides [37,43]. Indeed, Wright et al. [44] describe the self-association characteristics of multidomain proteins containing near-identical peptide repeat motifs. They suggest that this form of self-assembly occurs via specific intermolecular association, based on the repetition of identical or near-identical amino acid sequences. This specificity is consistent with the principle that ordered molecular assembhes are usually more stable than disordered ones, and with the idea that native-like interactions may be generally more favorable than nonnative ones in protein aggregates. 

The previous ELP fusions all are examples of protein purification in which the ELP is covalently connected to the protein of choice. This approach is suitable for the purification of recombinant proteins that are expressed to high levels, but at very low concentrations of ELP the recovery becomes limited. Therefore this approach is not applicable for proteins expressed at micrograms per liter of bacterial culture, such as toxic proteins and complex multidomain proteins. An adjusted variant of ITC was designed to solve this problem. This variant makes use of coaggregation of free ELPs with ELP fusion proteins. In this coaggregation process, an excess of free ELP is added to a cell lysate to induce the phase transition at low concentrations of... 

Aulisa L, Dong H, Hartgerink ID (2009) Self-assembly of multidomain peptides sequence variation allows control over cross-linking and viscoelasticity. Biomacromolecules 10 2694-2698... 

These methods will also be useful in tackling longer-term projects that may involve carving out individual modules from large, multidomain assemblies and using dehydrogenase active sites to catalyze other types of carbonyl additions. 

Figure 1. Schematic diagram of a hysteresis curve for a typical ferromagnet showing magnetization (a) as a function of the applied magnetic field (H) Saturation magnetization Is Indicated by Os- Inset shows the multidomain structure and subdomain superparamagnetlc clusters.

It is equally important to work with full-length versions of enzymes whenever this is feasible. Some enzymes are expressed naturally as multidomain proteins in which the catalytic machinery is localized to a single, discrete protein domain. In... 

A major problem in unfolding studies of large proteins is irreversibility. In a study of elastase temperature-induced denaturation, second-derivative FTIR show a distinct loss of several sharp amide V features (dominant /3-sheet components and growth in broadened bands at 1645 and 1668 cm-1 (Byler et al., 2000). These features persisted on cooling, indicating lack of reversibility, a feature common to longer multidomain proteins. A graphic example of this is seen in the triosephosphate... 

Fischer L., Muhlen E.Z., Brummer G.W., Niehus H. Atomic force microscopy investigations of the surface topography of a multidomain porous goethite. European J Soil Sci 1996 47 329-334. 

Approximately 90% of CF patients carry a loss-of-function CFTR mutation on at least one allele that results in deletion of phenylalanine 508 (F508del) in the first CFTR nucleotide-binding domain [7]. The F508del prevents the proper domain folding and assembly of the multidomain CFTR protein during its biogenesis in the endoplasmic... 

Kolb, V. A., Makeyev, E. V., and Spirin, A. S. (2000). Co-translational folding of a eukaryotic multidomain protein in a prokaryotic translation system. J. Biol. Chem. 275, 16597-16601. 

Usually, TS /1-solenoids represent only parts of larger multidomain proteins. Other trimeric motifs found in these proteins include a-helical coiled coils, TS /1-spirals, trimeric bundles of single-stranded /1-solenoids, and irregular globular structures. Some of these domains may be needed for correct folding of the TS /1-solenoid. 

Several /i-solenoid domains appear to promote the oligomerization of multidomain proteins. There are at least three types of /i-solenoid association. First, oligomers (dimers or trimers) are formed by lateral interaction of the solenoids. For example, the C-terminal domain of the bacterial cell division inhibitor MinC is a short right-handed T-type solenoid with an apolar lateral face that mediates homodimerization (Cordell et al., 2001). Trimers of several bacterial transferases are formed by lateral, in-register, interaction of left-handed T-type /1-solenoids (Fig. 5). Second, dimers may form via interactions of the open terminal coils of /1-solenoids as in the dimeric structure of iron transporter stabilizer SufD (Badger et al., 2005). Finally, dimerization may be mediated by swapping of /1-strands of the terminal coils, as in the CAP (Dodatko et al., 2004) (Fig. S). 

ABC transporters are multidomain systems that translocate substrates across membranes. A common characteristic is the well-conserved ATP binding cassette (ABC) domain that couples ATP hydrolysis to transport. Members of this group of proteins constitute the largest superfamily of transport components, and they are found in all organisms from Archaea to humans. According to the work of Dassa, who developed a classification based on the ATPase components, the ABC systems can be divided into a number of subfamilies (for details see http //www.pasteur.fr/recherche/unites/pmtg/abc/) [136]. 

The dependence of the residual dipolar coupling on the angle that the vector forms with a reference axis explains why the use of dipolar couplings makes possible the determination of the relative orientation of different domains in a multidomain protein and facilitates nucleic acid structure determination. Dipolar couplings can constitute up to 50% of the total structural data available for nucleic acids, while this number drops to 10-15% in proteins. Thus, the impact of the use of dipolar couplings on the structure determination of nucleic acids is generally more substantial than in the case of proteins. Furthermore, the presence or absence of tertiary structure in a protein or nucleic acid does not have a major influence on the number of dipolar couplings that can be measured, in contrast to the case of the NOE. 

In a multidomain protein whose domains have fixed orientations relative to each other, a unique alignment tensor will represent the preferred orientation of all the domains in the anisotropic environment. Therefore, structure refinement with dipolar couplings is performed as in one-domain proteins (Sect. 8.4). Several examples are reported in the literature of cases with conformational ambiguity due to the lack of NOE contacts between the domains. One example is the determination of subdomain orientation of the riboso-mal protein S4 z)41 [97]. In this work the lack of NOE contacts between the domains produces an ambiguity in interdomain orientation. The authors use two different anisotropic media to obtain dipolar couplings (DMPC/DHPC bicelles and Pfl filamentous bacteriophages). They conclude that subdomain orientation in solution is similar to the one present in the crystal structure. 

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