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PubMed2005

TEM study of the influence of antisite defects on magnetic domain structures in double perovskite Ba2FeMoO6.

Magnetic domain structures and crystal structures of double perovskite Ba(2)FeMoO(6) were studied using Lorentz transmission electron microscopy (TEM), dark-field imaging and high-resolution TEM. Two types of magnetic domain structure were observed below the Curie temperature: an ordinary 180 degrees ferromagnetic domain structure and a typical maze-pattern structure. In regions where maze-pattern structures were observed, antiphase boundaries were found by dark-field imaging and high-resolution TEM and develop densely in Fe/Mo-ordering domains, suggesting that Fe/Mo antisite defects affect magnetic domain structures.

Journal Article↗

PubMed1983

Lipid domain structures in biological membranes.

Phase separation represents a possibility for segregation of lipidic membrane components into structurally distinct domains. Freeze-fracture electronmicroscopy is a useful method for detection of lipid domains. Indications of a possible domain-nature of structures are a regular pattern within a separated area, a regular outline of such an area and a local modulation of curvature (evagination or invagination). Candidates for domain structures in biological membranes are smooth particle-free areas and arrays of regularly arranged particles. The interpretation of the particle-free areas is more reliable than that of the arrays with regularly arranged particles. Phase separation in biological membranes can be induced experimentally by lowering the temperature, but physiologically the isothermically induced domains are more important. Factors in control of isothermic domain formation are divalent cations, proteins, cholesterol etc. Suggestions on the biological relevance of domain formation concern mainly their role in the mechanism of membrane fusion, but domains in form of transient or stable membrane structures seem to occur also otherwise and disturbances in domain formation or artificially induced domains can be suitable for pathological alterations.

Animals↗

PubMed2005

Domain structure in a superconducting ferromagnet.

The domain structure is inherent to all ferromagnets and the recent discovery of the superconducting ferromagnets raises the question of the modification of this domain structure by superconductivity. In the framework of the general London theory, applicable to both singlet and triplet superconductors, we demonstrate that superconductivity leads to a dramatic shrinkage of the domain width. The presence of this dense domain structure has to be taken into account for all magnetic measurements on superconducting ferromagnets, and the study of the domain structure evolution could provide important information on the mechanisms of superconductivity and magnetism interplay.

Journal Article↗

PubMed1984

The structural basis of ankyrin function. I. Identification of two structural domains.

The structure of ankyrin, a major linking protein between spectrin and the erythrocyte membrane, was analyzed after restricted proteolytic digestion at 0 degree C. By the use of two-dimensional peptide mapping, we found that tryptic digestion of ankyrin (1 h, 0 degree C) resulted in the production of two nonoverlapping peptides of molecular weights 82,000 and 55,000. The 82,000-dalton peptide had a basic isoelectric point (7.9) and was remarkably sensitive to further proteolytic digestion; after 24 h at 0 degree C, trypsin completely digested this peptide into fragments too small to detect by gel electrophoresis. The 55,000-dalton peptide was neutral (isoelectric point = 6.9-7.2) and more resistant to further proteolytic cleavage. After a 24-h digestion with trypsin at 0 degrees C, the 55,000-dalton peptide was cleaved into two complementary fragments of molecular weight 32,000 and 15,000. Analysis of phosphorylated ankyrin indicated that the phosphates were exclusively found in these two complementary peptides. By comparison with larger fragments, we were able to align the constituent peptides of ankyrin and propose a low resolution model. Ankyrin appears to be a bipolar molecule containing a basic domain of 82,000 daltons and a neutral phosphorylated domain of 55,000 daltons.

Ankyrins↗

PubMed2002

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.

Animals↗

PubMed2002

Ferroelectric domain structure of SrBi2Nb2O9 epitaxial thin films.

The domain structure in a ferroelectric with well-defined crystallography and negligible ferroelastic distortion (<0.002%) is reported. In contrast to prototypical ferroelectrics in which long-range elastic strain dictates the domain structure, in SrBi2Nb2O9 the elastic term is insignificant, allowing dipole-dipole interactions and domain wall energies to dominate in determining the domain structure. Electron microscopy reveals ferroelectric domains that are irregularly shaped and highly curved. Out-of-phase boundary defects are shown to be weakly correlated with 90 degrees ferroelectric domain structure.

Journal Article↗

PubMed2006

Solution structure of p53 core domain: structural basis for its instability.

The 25-kDa core domain of the tumor suppressor p53 is inherently unstable and melts at just above body temperature, which makes it susceptible to oncogenic mutations that inactivate it by lowering its stability. We determined its structure in solution using state-of-the-art isotopic labeling techniques and NMR spectroscopy to complement its crystal structure. The structure was very similar to that in the crystal but far more mobile than expected. Importantly, we were able to analyze by NMR the structural environment of several buried polar groups, which indicated structural reasons for the instability. NMR spectroscopy, with its ability to detect protons, located buried hydroxyl and sulfhydryl groups that form suboptimal hydrogen-bond networks. We mutated one such buried pair, Tyr-236 and Thr-253 to Phe-236 and Ile-253 (as found in the paralogs p63 and p73), and stabilized p53 by 1.6 kcal/mol. We also detected differences in the conformation of a mobile loop that might reflect the existence of physiologically relevant alternative conformations. The effects of temperature on the dynamics of aromatic residues indicated that the protein also experiences several dynamic processes that might be related to the presence of alternative hydrogen-bond patterns in the protein interior. p53 appears to have evolved to be dynamic and unstable.

Crystallography↗

PubMed1992

6-Deoxyerythronolide-B synthase 2 from Saccharopolyspora erythraea. Cloning of the structural gene, sequence analysis and inferred domain structure of the multifunctional enzyme.

Sequencing of the eryA region of the erythromycin biosynthetic gene cluster from Saccharopolyspora erythraea has revealed another structural gene (ORF B), in addition to the previously characterised ORF A, which appears to encode a component of 6-deoxyerythronolide-B synthase, the enzyme that catalyses the first stage in the biosynthesis of the polyketide antibiotic erythromycin A. The nucleotide sequence of ORF B, which lies immediately adjacent to ORF A, has been determined. The predicted gene product of ORF B is a polypeptide of 374417 Da (3568 amino acids), which is highly similar to the product of ORF A and which likewise contains a number of separate domains, each with substantial amino acid sequence similarity to components of known fatty-acid synthases and polyketide synthases. The order of the predicted active sites along the chain from the N-terminus is 3-oxoacyl-synthase--acyltransferase--acyl-carrier-protein-- 3-oxoacyl-synthase--acyltransferase--dehydratase--enoylreductase-- oxoreductase--acyl-carrier-protein. The position of the dehydratase active site has been pinpointed for the first time for any polyketide synthase or vertebrate fatty-acid synthase. The predicted domain structure of 6-deoxyerythronolide-B synthase is strikingly similar to that previously established for vertebrate fatty-acid synthases. This analysis of the sequence supports the view that the erythromycin-producing polyketide synthase contains three multienzyme polypeptides, each of which accomplishes two successive cycles of polyketide chain extension. In this scheme, the role of the ORF B gene product is to accomplish extension cycles 3 and 4.

Amino Acid Sequence↗

PubMed2004

Toward consistent assignment of structural domains in proteins.

The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function, yet little quality assurance has been performed. Here, the differences in the assignment of structural domains are evaluated using six common assignment methods. Three human expert methods (AUTHORS (authors' annotation), CATH and SCOP) and three fully automated methods (DALI, DomainParser and PDP) are investigated by analysis of individual methods against the author's assignment as well as analysis based on the consensus among groups of methods (only expert, only automatic, combined). The results demonstrate that caution is recommended in using current domain assignments, and indicates where additional work is needed. Specifically, the major factors responsible for conflicting domain assignments between methods, both experts and automatic, are: (1) the definition of very small domains; (2) splitting secondary structures between domains; (3) the size and number of discontinuous domains; (4) closely packed or convoluted domain-domain interfaces; (5) structures with large and complex architectures; and (6) the level of significance placed upon structural, functional and evolutionary concepts in considering structural domain definitions. A web-based resource that focuses on the results of benchmarking and the analysis of domain assignments is available at

Algorithms↗

PubMed1995

A reference of the GOLD classification of monoclonal antibodies against carcinoembryonic antigen to the domain structure of the carcinoembryonic antigen molecule.

The epitopes of 42 well-characterized monoclonal antibodies (MAbs) against carcinoembryonic antigen (CEA) from 10 different research groups were mapped in terms of domain structure (domains N, A1-B1, A2-B2, and A3-B3) of the CEA molecule on the basis of the reactivities with recombinant CEA proteins expressed in Chinese hamster ovary cells. Thirty-six of the 42 MAbs tested have previously been classified into 5 essentially nonoverlapping epitope groups (GOLD 1-5) by cross-competition assays among MAbs for CEA binding (Hammarström S, et al.: Cancer Res. 1989; 49:4852-4858). The epitopes recognized by GOLD 2 MAbs were all present on domain A2-B2, those for GOLD 5 MAbs were all on domain N, and those for GOLD 4 were mapped around domains A1-B1 and A2-B2. On the other hand, the epitopes for GOLD 1 MAbs were distributed into domains N, A2-B2, and A3-B3, and those for GOLD 3 MAbs were separated into domains N and A3-B3. Although the exact reasons for the dispersed patterns of GOLD 1 and 3 MAbs on the domain structure of the CEA molecule are unclear at present, several factors, such as a spatial relation or a close proximity of epitopes, conformation dependency, and repetitivity of epitopes, may be considered as possible explanations. The epitope mapping reported here helps form the basis for understanding the relation between the chemical structure and antigenic activities of the CEA molecule and may be useful to study the functions of the CEA molecule, especially those of the respective domains.

Animals↗

PubMed1995

Domain structure, stability and domain-domain interactions in recombinant factor XIII.

The process of heat denaturation of recombinant factor XIII (rFXIII), as well as its C-terminal 24 kDA and 12 kDa elastase-produced fragments starting at Ser514 and Thr628, respectively, was investigated in a wide range of conditions by fluorescence, CD and differential scanning calorimetry (DSC). It was found that the intact protein melts in two distinct temperature regions reflecting unfolding of different parts of the molecule with different stability. The less stable structures unfold in a low temperature transition with a tm of 69 degrees C or lower depending on conditions. Unfolding of the more stable structures was observed at extremely high temperatures, tm > 110 degrees C at acidic pH < 3.5 and tm = 90 degrees C at pH 8.6 with 2 M GdmCL. Thermodynamic analysis of the low and high temperature DSC-obtained heat absorption peaks indicated unambiguously that the first represents melting of three thermolabile independently folded domains while two thermostable domains melt in the second one giving a total of five domains in each a subunit of rFXIII. Both 24 kDa and 12 kDa fragments exhibited a sigmoidal spectral transition at comparatively high temperature where the thermolabile structures are already denatured, indicating that two thermostable domains are formed by the C-terminal portion of rFXIII and correspond to the two beta-barrels revealed by crystallography. The remaining 56 kDa portion forms three thermolabile domains, one of which corresponds to the N-terminal beta-sandwich and the other two to the catalytic core. Fast accessible surface calculations of the X-ray model of rFXIII confirmed the presence of two structural subdomains in the core region with the boundary at residue 332. The thermolabile domains appear to interact with each other intra- and/or intermolecularly resulting in dimerization the a subunits. At acidic pH, where all domains became destabilized but still remained folded, interdomainial interactions seemed to be abolished, resulting in the reversible dissociation of the dimer as revealed by ultracentrifugation analysis.

Calorimetry, Differential Scanning↗

PubMed2004

Demonstration of the involvement of outer surface protein E coiled coil structural domains and higher order structural elements in the binding of infection-induced antibody and the complement-regulatory protein, factor H.

Factor H (fH) is an important regulator of the alternative complement cascade. Several human pathogens have been shown to bind fH to their surface, a process that facilitates immune evasion or cell to cell interaction. Among the pathogens that bind fH are some Borrelia species associated with Lyme disease and relapsing fever. The fH-binding proteins of the Lyme spirochetes form two classes (I and II). In Borrelia burgdorferi B31MI, class I includes the outer surface protein E (OspE) paralogs, L39, N38, and P38, whereas the class II group includes A68 and additional proteins that have not yet been identified. To identify the OspE determinants involved in fH and OspE-targeting infection-induced Ab (iAb) binding, deletion, random, and site-directed mutagenesis of L39 were performed. Mutations in several different regions of L39 abolished fH and or iAb binding, indicating that separable domains and residues of OspE are required for ligand binding. Some of the mutants that lost the ability to bind fH, iAb, or both had only a single amino acid change. Site-directed mutagenesis of three putative coiled coil motifs of OspE revealed that these higher order structures are required for fH binding but not for iAb binding. The data presented within demonstrate that the binding of fH and iAb to the OspE protein is mediated by higher order structures and protein conformation. These studies advance our understanding of fH binding as a virulence mechanism and facilitate ongoing efforts to use fH-binding proteins in the development of microbial vaccines.

Amino Acid Motifs↗

PubMed2000

Voltage dependent activation of potassium channels is coupled to T1 domain structure.

The T1 domain, a highly conserved cytoplasmic portion at the N-terminus of the voltage-dependent K+ channel (Kv) alpha-subunit, is responsible for driving and regulating the tetramerization of the alpha-subunits. Here we report the identification of a set of mutations in the T1 domain that alter the gating properties of the Kv channel. Two mutants produce a leftward shift in the activation curve and slow the channel closing rate while a third mutation produces a rightward shift in the activation curve and speeds the channel closing rate. We have determined the crystal structures of T1 domains containing these mutations. Both of the leftward shifting mutants produce similar conformational changes in the putative membrane facing surface of the T1 domain. These results suggest that the structure of the T1 domain in this region is tightly coupled to the channel's gating states.

Amino Acid Substitution↗

PubMedDate not supplied

Membrane switch hypothesis. 1. Cell density influences lateral domain structure of tumor cell membranes.

The domain structure of human cancer cells membranes was investigated by electron paramagnetic resonance (EPR) in different phases of cell growth, and the results were compared to those obtained for nonmalignant cells. On the basis of computer simulation of the EPR spectra using a newly developed GHOST condensation routine it was suggested that plasma membranes of cancer cells have less lateral lipid domain types at confluent conditions than in the exponential growing phase, while in nonmalignant cells the domain structure does not change significantly during cell growth. In accordance to our experimental data we propose a membrane switch hypothesis: disappearance of certain membrane domain types might act as a switch promoting the clustering of membrane constituents into the active units in a common lipid membrane domain and thus influencing the physiology of cells.

Cell Count↗

PubMed1996

A database of globular protein structural domains: clustering of representative family members into similar folds.

BACKGROUND: A database of globular domains, derived from a non-redundant set of proteins, is useful for the sequence analysis of aligned domains, for structural comparisons, for understanding domain stability and flexibility and for fold recognition procedures. Domains are defined by the program DIAL and classified structurally using the procedure SEA. RESULTS: The DIAL-derived domain database (DDBASE) consists of 436 protein chains involving 695 protein domains. Of these, 206 are alpha-class, 191 are beta-class and 294 alpha and beta class. The domains, 63% from multidomain proteins and 73% less than 150 residues in length, were clustered automatically using both single-link cluster analysis and hierarchical clustering to give a quantitative estimate of similarity in the domain-fold space. CONCLUSIONS: Highly populated and well described folds (doubly wound alpha/beta, singly wound alpha/beta barrels, globins alpha, large Greek-key beta and flavin-binding alpha/beta) are recognized at a SEA cut-off score of 0.55 in single-link clustering and at 0.65 in hierarchical clustering, although functionally related families are usually clearly distinguished at more stringent values.

Cluster Analysis↗

PubMed1983

Differences in domain structure between pericellular matrix and plasma fibronectins as revealed by domain-specific antibodies combined with limited proteolysis and S-cyanylation: a preliminary note.

Differences in domain structure between human fibronectins obtained from pericellular matrix and plasma have been revealed by limited proteolysis and S-cyanylation, followed by identification of each domain with domain-specific antibodies. Although the overall domain structure is similar between pericellular and plasma fibronectins, the fragments derived from the COOH-terminal region of these fibronectins, which were defined by specific antibodies, exhibited clear differences in their molecular weights and protease susceptibility, suggesting that the structure near the COOH-terminal region is significantly different between these two proteins.

Antibodies↗

PubMedDate not supplied

[Domain structure of CAF1M protein from Yersinia pestis. Structure and the role of various domains].

The cooperative structure of Caf1M from Yersinia pestis was studied using scanning microcalorimetry, fluorescence, and limited proteolysis. It was shown that, in Caf1M-Hg (a derivative in which the disulfide bond is replaced by an S-Hg-S bond), the first to melt is the N-domain. Then the C-domain melts. After renaturation in a buffer with a low NaCl concentration, only the C-domain is in the native state, and it can be obtained by limited proteolysis. After renaturation in a buffer with a high NaCl concentration, only the N-domain is in the native state, and it can be obtained by limited proteolysis. Both domains have native structure; however, only the N-domain interacts with Cafl (natural substrate for Caf1M).

Bacterial Proteins↗

PubMed2003

Enzymatic activity of protein kinase LOSK: possible regulatory role of the structural domain.

LOSK (LOng Ste20-like Kinase) protein kinases of mammals belong to a recently identified family of GCK kinases which are involved in the induction of apoptosis. LOSK have an N-terminal acidic catalytic domain and a long C-terminal basic structural domain which is cleaved off in cells by caspases during apoptosis. To study the LOSK enzymatic activity and its dependence on the structural domain, two preparations of this protein kinase were prepared: a natural full-length protein immunoprecipitated from CHO-K1 cultured cells and a recombinant N-terminal catalytic fragment synthesized in E. coli. Both preparations displayed the ability for autophosphorylation and the ability for phosphorylation of MBP and of H1 histone, and their activities were comparable. H1 histone was a better substrate for LOSK than casein and ATP was a better substrate than other nucleotides. The pH dependence of the activity of the immunoprecipitated protein was more pronounced than the pH dependence of its recombinant fragment deprived of the C-terminal domain. The catalytic and the structural domains of LOSK can interact through electrostatic forces; therefore, effects were studied of various polyions at the concentration of 0.1 mg/ml on the activity. Heparin, protamine sulfate, and poly(L-Lys) decreased tenfold the ability of the full-length kinase to phosphorylate H1 histone. Heparin did not affect the activity of the recombinant fragment, whereas protamine sulfate and poly(L-Lys) had a slight effect. Moreover, protamine increased fourfold the autophosphorylation of the immunoprecipitated protein kinase. These data suggest that the structural C-terminal domain of LOSK should be involved in the regulation of its protein kinase activity: the LOSK protein kinase with C-terminal domain cleaved off could significantly less depend on conditions in the cell than the full-size enzyme.

Adenosine Triphosphate↗