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Isolated Domains (isolated + domain)
Selected AbstractsNucleotide-binding domain 1 of cystic fibrosis transmembrane conductance regulatorFEBS JOURNAL, Issue 17 2000Production of a suitable protein for structural studies Cystic fibrosis is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). This protein belongs to the large ATP-binding cassette (ABC) family of transporters. Most patients with cystic fibrosis bear a mutation in the nucleotide-binding domain 1 (NBD1) of CFTR, which plays a key role in the activation of the channel function of CFTR. Determination of the three dimensional structure of NBD1 is essential to better understand its structure,function relationship, and relate it to the biological features of CFTR. In this paper, we report the first preparation of recombinant His-tagged NBD1, as a soluble, stable and isolated domain. The method avoids the use of renaturing processes or fusion constructs. ATPase activity assays show that the recombinant domain is functional. Using tryptophan intrinsic fluorescence, we point out that the local conformation, in the region of the most frequent mutation ,F508, could differ from that of the nucleotide-binding subunit of histidine permease, the only available ABC structure. We have undertaken three dimensional structure determination of NBD1, and the first two dimensional 15N- 1H NMR spectra demonstrate that the domain is folded. The method should be applicable to the structural studies of NBD2 or of other NBDs from different ABC proteins of major biological interest, such as multidrug resistance protein 1 or multidrug resistance associated protein 1. [source] Combined use of selective inhibitors and fluorogenic substrates to study the specificity of somatic wild-type angiotensin-converting enzymeFEBS JOURNAL, Issue 8 2006Nicolas D. Jullien Somatic angiotensin-converting enzyme (ACE) contains two homologous domains, each bearing a functional active site. Studies on the selectivity of these ACE domains towards either substrates or inhibitors have mostly relied on the use of mutants or isolated domains of ACE. To determine directly the selectivity properties of each ACE domain, working with wild-type enzyme, we developed an approach based on the combined use of N-domain-selective and C-domain-selective ACE inhibitors and fluorogenic substrates. With this approach, marked differences in substrate selectivity were revealed between rat, mouse and human somatic ACE. In particular, the fluorogenic substrate Mca-Ala-Ser-Asp-Lys-DpaOH was shown to be a strict N-domain-selective substrate of mouse ACE, whereas with rat ACE it displayed marked C-domain selectivity. Similar differences in selectivity between these ACE species were also observed with a new fluorogenic substrate of ACE, Mca-Arg-Pro-Pro-Gly-Phe-Ser-Pro-DpaOH. In support of these results, changes in amino-acid composition in the binding site of these three ACE species were pinpointed. Together these data demonstrate that the substrate selectivity of the N-domain and C-domain depends on the ACE species. These results raise concerns about the interpretation of functional studies performed in animals using N-domain and C-domain substrate selectivity data derived only from human ACE. [source] Groundwater fluctuations and footslope ferricrete soils in the humid tropical zone of southern CameroonHYDROLOGICAL PROCESSES, Issue 16 2005Emile Temgoua Abstract This paper discusses the relationship between the differentiation of ferruginous accumulations and the variable water saturation of footslope soil patterns. An analysis of the slope morphology of a typical hill in the forest zone of southern Cameroon and a seasonal survey of the levels of groundwaters, springs and rivers were considered in relation to the petrology of different soil patterns. The study site is a tabular hillock whose slopes present a progressive development from steep to gentle slopes. The variable residence time of water within the soil, creating an alternation of reducing and oxidizing conditions, affects soil chemistry, structure and lateral extension of the soil patterns. The ferruginous soil patterns, being formed on the footslopes, gradually increase in extent with decreasing slope angle and the relative rise of the groundwater level. The steep footslopes, where groundwater has a shorter residence time, show a soft mottled clay pattern, restricted to the bottom part of the slope. The moderate footslopes exhibit a deep permanent and a temporary perched groundwater table. The latter, with its regular capillary fringe, contributes to more reducing conditions within isolated domains in the soil patterns, and thus to the alternation with oxidizing conditions, generating a continuous hard soil pattern (massive carapace). The more gently dipping footslopes exhibit groundwater levels near the surface and also a significant amplitude of groundwater fluctuation. Iron, previously accumulated in moderate footslope patterns, is reduced, remobilized, and leached. The soil patterns formed develop into a variegated carapace, more extended along the slope, containing less iron, but nevertheless more hardened, due to the important fluctuations of the groundwater table. These patterns are limited to the zone of groundwater fluctuation and deteriorate as the water fluctuation zone recedes. Copyright © 2005 John Wiley & Sons, Ltd. [source] Fabrication of Continuous and Segmented Polymer/Metal Oxide Nanowires Using Cylindrical Micelles and Block Comicelles as TemplatesADVANCED MATERIALS, Issue 18 2009Hai Wang Cylindrical micelles were added as templates to sol,gel reaction mixtures to yield highly elongated polymer/inorganic nanostructures with smooth nanothin surface coatings of silica, zirconia, or alumina. Differences in the templating activity of neutral or cationic coronas can be exploited by using triblock comicelles to produce discrete nanocylinders with spatially isolated domains of titania surface deposition. [source] Prediction of structures of multidomain proteins from structures of the individual domainsPROTEIN SCIENCE, Issue 2 2007Andrew M. Wollacott Abstract We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high-resolution search in which all atoms are treated explicitly and backbone and side chain degrees of freedom are simultaneously optimized. The method recapitulates, often with very high accuracy, the structures of existing multidomain proteins. [source] Slicing a protease: Structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domainsPROTEIN SCIENCE, Issue 8 2006Tatyana V. Rotanova Abstract ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA+ superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure,function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA+ domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases. [source] Direct evidence by H/D exchange and ESI-MS for transient unproductive domain interaction in the refolding of an antibody scFv fragmentPROTEIN SCIENCE, Issue 3 2000Marcus Jäger Abstract The refolding kinetics of a single-chain Fv (scFv) fragment, derived from a stabilized mutant of the phosphorylcholine binding antibody McPC603, was investigated by H/D exchange and ESI-MS and compared with the folding kinetics of its constituting domains VH and VL. Both VH and VL adopt essentially native-like exchange protection within the dead time of the manual-mixing H/D exchange experiment (10 s) and in the case of VL, which contains two cis -prolines in the native conformation, this fast protection is independent of proline cis/trans isomerization. At the earliest time point resolvable by manual mixing, fewer deuterons are protected in the scFv fragment than in the two isolated domains together, despite the fact that the scFv fragment is significantly more stable than VL and VH. Full H/D exchange protection in the scFv fragment is gained on a time scale of minutes. This means that the domains in the scFv fragment do not refold independently. Rather, they associate prematurely and in nonnative form, a kinetic trap. Unproductive domain association is observed both after equilibrium- and short-term denaturation. For the equilibrium-denatured scFv fragment, whose native structure formation is dependent on a cis conformation of an interface proline in VL, this cis/trans isomerization reaction proceeds about one order in magnitude more slowly than the escape from the trap to a conformation where full H/D exchange protection is already achieved. We interpret these data in terms of a general kinetic scheme involving intermediates with and without domain association. [source] | ||||||||||