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Domain Interaction (domain + interaction)
Selected AbstractsDomain,Domain Interactions in the Iterative Type I Polyketide Synthase ATX from Aspergillus terreusCHEMBIOCHEM, Issue 8 2008Tomomi Moriguchi Analyzing ATX mutants: ATX, a 6-methylsalicylic acid synthase from Aspergillus terreus, has five catalytic domains in its monomer and forms a homotetramer. Coexpression of inactive ATX catalytic domain mutants in yeast showed that ATX activity was reconstituted by all combinations of the domain mutants, suggesting that the five catalytic domains could interact with each other with substantial flexibility to carry out 6-methylsalicylic acid synthesis. [source] Prion domain interaction responsible for species discrimination in yeast [PSI+] transmissionGENES TO CELLS, Issue 12 2003Hideyuki Hara Background:, The yeast [PSI+] factor is transmitted by a prion mechanism involving self-propagating Sup35 aggregates. As with mammalian prions, a species barrier prevents prion transmission between yeast species. The N-terminal of Sup35 of Saccharomyces cerevisiae, necessary for [PSI+], contains two species-signature elements,a Gln/Asn-rich region (residues 1,41; designated NQ) that is followed by oligopeptide repeats (designated NR). Results:, In this study, we show that S. cerevisiae[PSI+] is transmissible through plasmid shuffling and cytoplasmic transfer to heterotypic Sup35s whose NQ is replaced with the S. cerevisiae NQ. In addition to homology, the N-terminal location is essential for NQ mediated susceptibility to [PSI+] transmission amongst heterotypic Sup35s. In vitro, a swap of NQ of S. cerevisiae Sup35 led to cross seeding of amyloid formation. Conclusions:, These findings suggest that NQ discriminates self from non-self, and is sufficient to initiate [PSI+] transmission irrespective of whether NR is heterotypic. NR as well as NQ alone coalesces into existing [PSI+] aggregates, showing their independent potentials to interact with the identical sequence in the [PSI+] conformer. The role of NQ and NR in [PSI+] prion formation is discussed. [source] The von Willebrand factor self-association is modulated by a multiple domain interactionJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 3 2005H. ULRICHTS Summary.,Background:,Platelet adhesion and aggregation at sites of vascular injury exposed to rapid blood flow require von Willebrand factor (VWF). VWF becomes immobilized by binding to subendothelial components or by a self-association at the interface of soluble and surface-bound VWF. Objectives:,As this self-association has been demonstrated only under shear conditions, our first goal was to determine whether the same interaction could be observed under static conditions. Furthermore, we wanted to identify VWF domain(s) important for this self-association. Results:,Biotinylated VWF (b-VWF) interacted dose-dependently and specifically with immobilized VWF in an enzyme-linked immunosorbent assay (ELISA) assay, showing that shear is not necessary to induce the VWF self-association. Whereas anti-VWF monoclonal antibodies (mAbs) had no effect on the self-association, the proteolytic VWF-fragments SpII(1366,2050) and SpIII(1,1365) inhibited the b-VWF,VWF interaction by 70 and 80%, respectively. Moreover, a specific binding of b-VWF to immobilized Sp-fragments was demonstrated. Finally, both biotinylated SpII and SpIII were able to bind specifically to both immobilized SpII and SpIII. Similar results were observed under flow conditions, which confirmed the functional relevance of our ELISA system. Conclusion:,We have developed an ELISA binding assay in which a specific VWF self-association under static conditions can be demonstrated. Our results suggest a multiple domain interaction between immobilized and soluble VWF. [source] Dimensions of human-work domain interaction: A preliminary analysis for the design of a corporate digital libraryPROCEEDINGS OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE & TECHNOLOGY (ELECTRONIC), Issue 1 2003Hong (Iris) Xie The author applies the cognitive system engineering approach to investigate human-work interaction at a corporate setting. This study reports the preliminary analysis of data collected from diary analysis and interview of 20 subjects. The results present the identification of three dimensions for each of four interactive activities involved in human-work interaction and their relationships. An enhanced model and its implications for the development of a corporate digital library are further discussed. [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] Structure of Stenotrophomonas maltophilia FeoA complexed with zinc: a unique prokaryotic SH3-domain protein that possibly acts as a bacterial ferrous iron-transport activating factorACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Yi-Che Su Iron is vital to the majority of prokaryotes, with ferrous iron believed to be the preferred form for iron uptake owing to its much better solubility. The major route for bacterial ferrous iron uptake is found to be via an Feo (ferrous iron-transport) system comprising the three proteins FeoA, FeoB and FeoC. Although the structure and function of FeoB have received much attention recently, the roles played by FeoA and FeoC have been little investigated to date. Here, the tertiary structure of FeoA from Stenotrophomonas maltophilia (Sm), a vital opportunistic pathogen in immunodepressed hosts, is reported. The crystal structure of SmFeoA has been determined to a resolution of 1.7,Å using an Se single-wavelength anomalous dispersion (Se-SAD) approach. Although SmFeoA bears low sequence identity to eukaryotic proteins, its structure is found to adopt a eukaryotic SH3-domain-like fold. It also bears weak similarity to the C-terminal SH3 domain of bacterial DtxR (diphtheria toxin regulator), with some unique characteristics. Intriguingly, SmFeoA is found to adopt a unique dimer cross-linked by two zinc ions and six anions (chloride ions). Since FeoB has been found to contain a G-protein-like domain with low GTPase activity, FeoA may interact with FeoB through the SH3,G-protein domain interaction to act as a ferrous iron-transport activating factor. [source] Solution structure and proposed domain,domain recognition interface of an acyl carrier protein domain from a modular polyketide synthasePROTEIN SCIENCE, Issue 10 2007Viktor Y. Alekseyev Abstract Polyketides are a medicinally important class of natural products. The architecture of modular polyketide synthases (PKSs), composed of multiple covalently linked domains grouped into modules, provides an attractive framework for engineering novel polyketide-producing assemblies. However, impaired domain,domain interactions can compromise the efficiency of engineered polyketide biosynthesis. To facilitate the study of these domain,domain interactions, we have used nuclear magnetic resonance (NMR) spectroscopy to determine the first solution structure of an acyl carrier protein (ACP) domain from a modular PKS, 6-deoxyerythronolide B synthase (DEBS). The tertiary fold of this 10-kD domain is a three-helical bundle; an additional short helix in the second loop also contributes to the core helical packing. Superposition of residues 14,94 of the ensemble on the mean structure yields an average atomic RMSD of 0.64 ± 0.09 Å for the backbone atoms (1.21 ± 0.13 Å for all non-hydrogen atoms). The three major helices superimpose with a backbone RMSD of 0.48 ± 0.10 Å (0.99 ± 0.11 Å for non-hydrogen atoms). Based on this solution structure, homology models were constructed for five other DEBS ACP domains. Comparison of their steric and electrostatic surfaces at the putative interaction interface (centered on helix II) suggests a model for protein,protein recognition of ACP domains, consistent with the previously observed specificity. Site-directed mutagenesis experiments indicate that two of the identified residues influence the specificity of ACP recognition. [source] Arm,domain interactions can provide high binding cooperativityPROTEIN SCIENCE, Issue 10 2004Robert Schleif Abstract Peptidyl arms extending from one protein domain to another protein domain mediate many important interactions in biology. A well-studied example of this type of protein,protein interaction occurs between the yeast homeodomain proteins, MAT ,2 and MAT a1, which form a high-affinity heterodimer on DNA. The carboxyl-terminal arm extending from MAT ,2 to MAT a1 has been proposed to produce an allosteric conformational change in the a1 protein that generates a very large increase in the DNA binding affinity of a1. Although early studies lent some support to this model, a more recent crystal structure determination of the free a1 protein argues against any allosteric change. This note presents a thermodynamic argument that accounts for the proteins' binding behavior, so that allosteric conformational changes are not required to explain the large affinity increase. The analysis presented here should be useful in analyzing binding behavior in other systems involving arm interactions. [source] Structure of full-length ubiquitin-conjugating enzyme E2-25K (huntingtin-interacting protein 2)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Randall C. Wilson The ubiquitin-conjugating enzyme E2-25K has been identified as a huntingtin (the key protein in Huntington's disease) interacting protein and has been shown to play a role in mediating the toxicity of A,, the principal protein involved in Alzheimer's disease pathogenesis. E2-25K is a dual-domain protein with an ubiquitin-associated (UBA) domain as well as a conserved ubiquitin-conjugating (UBC) domain which catalyzes the formation of a covalent bond between the C-terminal glycine of an ubiquitin molecule and the ,-amine of a lysine residue on the acceptor protein as part of the ubiquitin-proteasome pathway. The crystal structures of E2-25K M172A mutant protein at pH 6.5 and pH 8.5 were determined to 1.9 and 2.2,Å resolution, respectively. Examination of the structures revealed domain,domain interactions between the UBC and UBA domains which have not previously been reported. [source] Bayesian Methods for Predicting Interacting Protein Pairs Using Domain InformationBIOMETRICS, Issue 3 2007Inyoung Kim Summary Protein,protein interactions (PPIs) play important roles in most fundamental cellular processes including cell cycle, metabolism, and cell proliferation. Therefore, the development of effective statistical approaches to predicting protein interactions based on recently available large-scale experimental data is very important. Because protein domains are the functional units of proteins and PPIs are mostly achieved through domain,domain interactions (DDIs), the modeling and analysis of protein interactions at the domain level may be more informative and insightful. However, due to the large number of domains, the number of parameters to be estimated is very large, yet the amount of information for statistical inference is quite limited. In this article we propose a full Bayesian method and a semi-Bayesian method for simultaneously estimating DDI probabilities, the false positive rate, and the false negative rate of high-throughput data through integrating data from several organisms. We also propose a model to associate protein interaction probabilities with domain interaction probabilities that reflects the number of domains in each protein. Our Bayesian methods are compared with the likelihood-based approach (Deng et al., 2002, Genome Research12, 1504,1508; Liu, Liu, and Zhao, 2005, Bioinformatics21, 3279,3285) developed using the expectation maximization algorithm. We show that the full Bayesian method has the smallest mean square error through both simulations and theoretical justification under a special scenario. The large-scale PPI data obtained from high-throughput yeast two-hybrid experiments are used to demonstrate the advantages of the Bayesian approaches. [source] Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: A new tool to resolve protein structure and dynamicsBIOPOLYMERS, Issue 1-2 2004C. Vigano Abstract As more and more high-resolution structures of proteins become available, the new challenge is the understanding of these small conformational changes that are responsible for protein activity. Specialized difference Fourier transform infrared (FTIR) techniques allow the recording of side-chain modifications or minute secondary structure changes. Yet, large domain movements remain usually unnoticed. FTIR spectroscopy provides a unique opportunity to record 1H/2H exchange kinetics at the level of the amide proton. This approach is extremely sensitive to tertiary structure changes and yields quantitative data on domain/domain interactions. An experimental setup designed for attenuated total reflection and a specific approach for the analysis of the results is described. The study of one membrane protein, the gastric H+,K+ -ATPase, demonstrates the usefulness of 1H/2H exchange kinetics for the understanding of the molecular movement related to the catalytic activity. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] | ||||||||||