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Different Specificities (different + specificity)
Selected AbstractsSite-directed mutagenesis and footprinting analysis of the interaction of the sunflower KNOX protein HAKN1 with DNAFEBS JOURNAL, Issue 1 2005Mariana F. Tioni The interaction of the homeodomain of the sunflower KNOX protein HAKN1 with DNA was studied by site-directed mutagenesis, hydroxyl radical footprinting and missing nucleoside experiments. Binding of HAKN1 to different oligonucleotides indicated that HAKN1 prefers the sequence TGACA (TGTCA), with changes within the GAC core more profoundly affecting the interaction. Footprinting and missing nucleoside experiments using hydroxyl radical cleavage of DNA showed that HAKN1 interacts with a 6-bp region of the strand carrying the GAC core, covering the core and nucleotides towards the 3, end. On the other strand, protection was observed along an 8-bp region, comprising two additional nucleotides complementary to those preceding the core. Changes in the residue present at position 50 produced proteins with different specificities. An I50S mutant showed a preference for TGACT, while the presence of lysine shifted the preference to TGACC, suggesting that residue 50 interacts with nucleotide(s) 3, to GAC. Mutation of Lys54,Val produced a protein with reduced affinity and relaxed specificity, able to recognize the sequence TGAAA, while the conservative change of Arg55,Lys completely abolished binding to DNA. Based on these results, we propose a model for the interaction of HAKN1 with DNA in which helix III of the homeodomain accommodates along the major groove with Arg55, Asn51, Lys54 and Ile50, establishing specific contacts with bases of the GACA sequence or their complements. This model can be extended to other KNOX proteins given the conservation of these amino acids in all members of the family. [source] Production of Monoclonal Antibodies to Sugarcane Yellow Leaf Virus Using Recombinant Readthrough ProteinJOURNAL OF PHYTOPATHOLOGY, Issue 8-9 2002J. Korimbocus Abstract Yellow leaf syndrome (YLS) of sugarcane is associated with sugarcane yellow leaf virus (SCYLV), a member of the family Luteoviridae. A fragment of the coat protein and readthrough domain of SCYLV wasexpressed in a bacterial expression system. The resulting protein was purified and used to immunize mice for monoclonal antibody (MAb) production. Two MAbs, 3A2E3 and 2F7H5, were selected following the screening of hybridoma cells using both plate-trapped antigen enzyme-linked immunosorbent assay (PTA-ELISA) and tissue blot immunoassay (TBIA). These MAbs can be incorporated into the TBIA assay currently used for the routine detection of SCYLV but could not be used in triple antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA). The two antibodies selected have slightly different specificities. Antibody 3A2E3 gave equivalent results to a polyclonal antiserum (raised to purified virus) in comparative testing using TBIA. The MAbs produced should provide a widely available, uniform reagent for SCYLV diagnosis with the potential to help manage YLS. [source] Exploring functional roles of multibinding protein interfacesPROTEIN SCIENCE, Issue 8 2009Manoj Tyagi Abstract Cellular processes are highly interconnected and many proteins are shared in different pathways. Some of these shared proteins or protein families may interact with diverse partners using the same interface regions; such multibinding proteins are the subject of our study. The main goal of our study is to attempt to decipher the mechanisms of specific molecular recognition of multiple diverse partners by promiscuous protein regions. To address this, we attempt to analyze the physicochemical properties of multibinding interfaces and highlight the major mechanisms of functional switches realized through multibinding. We find that only 5% of protein families in the structure database have multibinding interfaces, and multibinding interfaces do not show any higher sequence conservation compared with the background interface sites. We highlight several important functional mechanisms utilized by multibinding families. (a) Overlap between different functional pathways can be prevented by the switches involving nearby residues of the same interfacial region. (b) Interfaces can be reused in pathways where the substrate should be passed from one protein to another sequentially. (c) The same protein family can develop different specificities toward different binding partners reusing the same interface; and finally, (d) inhibitors can attach to substrate binding sites as substrate mimicry and thereby prevent substrate binding. [source] Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidasesPROTEIN SCIENCE, Issue 4 2004Matthias Bochtler Abstract Specific peptidases exist for nearly every amide linkage in peptidoglycan. In several cases, families of peptidoglycan hydrolases with different specificities turned out to be related. Here we show that lysostaphin-type peptidases and D-Ala-D-Ala metallopeptidases have similar active sites and share a core folding motif in otherwise highly divergent folds. The central Zn2+ is tetrahedrally coordinated by two histidines, an aspartate, and a water molecule. The Zn2+ chelating residues occur in the order histidine, aspartate, histidine in all sequences and contact the metal via the N,, the O,, and the N,, respectively. The identity of the other active-site residues varies, but in all enzymes of known structure except for VanX, a conserved histidine is present two residues upstream of the second histidine ligand to the Zn2+. As the same arrangement of active-site residues is also found in the N-terminal, cryptic peptidase domain of sonic hedgehog, we propose that this arrangement of active-site residues be called the "LAS" arrangement, because it is present in lysostaphin-type enzymes, D-Ala-D-Ala metallopeptidases, and in the cryptic peptidase in the N-domain of sonic hedgehog. [source] Motor foundations of higher cognition: similarities and differences in processing regular and violated perceptual sequences of different specificityEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 12 2009Andreja Bubic Abstract Processing perceptual sequences relies on the motor system, which is able to simulate the dynamics of the environment by developing internal representations of external events and using them to predict the incoming stimuli. Although it has previously been demonstrated that such models may incorporate predictions based on exact stimulus properties and single stimulus dimensions, it is not known whether they can also support abstract predictions pertaining to the level of stimulus categories. This issue was investigated within the present event-related functional magnetic resonance imaging study, which compared the processing of perceptual sequences of different specificity, namely those in which the sequential structure was based on the order of presentation of individual stimuli (token), and those in which such structure was defined by stimulus categories (type). The results obtained indicate a comparable engagement of the basic premotor,parietal network in processing both specific and categorical perceptual sequences. However, type sequences additionally elicited activations within the lateral prefrontal, occipital and posterior temporal regions that supported categorization in this task context. Introducing sequential deviants into token sequences activated parietotemporal and ventrolateral frontal cortices, whereas a less pronounced overall response, dominated by lateral prefrontal activation, was elicited by violations introduced into type sequences. Overall, the findings obtained suggest that, although forward models in perception may be able to incorporate expectations of lower specificity when compared to the motor domain, such processing is crucially dependent on additional contributions from lateral prefrontal as well as inferior occipital and temporal cortices that support categorization occurring in such a dynamic context. [source] Inactivation of Escherichia coli and Shigella in acidic fruit and vegetable juices by peroxidase systemsJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2006I. Van Opstal Abstract Aims:, To study the bactericidal properties of the lactoperoxidase (LPER)-thiocyanate and soybean peroxidase (SBP)-thiocyanate systems at low pH, their efficiency for inactivation of Escherichia coli and Shigella in acidic fruit and vegetable juices, their effect on colour stability of the juices and interaction with ascorbic acid. Methods and Results:, Three-strain cocktails of E. coli and Shigella spp. in selected juices were supplemented with the LPER or SBP system. Within 24 h at 20°C, the LPER system inactivated both cocktails by ,5 log10 units in apple, 2,5 log10 units in orange and ,1 log10 unit in tomato juices. In the presence of SBP, browning was significant in apple juice and white grape juice, slight in pink grape juice and absent in orange or tomato juice. Ascorbic acid protected E. coli and Shigella against inactivation by the LPER system, and peroxidase systems significantly reduced the ascorbic acid content of juices. Conclusions:, Our results suggest a different specificity of LPER and SBP for SCN,, phenolic substrates of browning and ascorbic acid in acidic juices. The LPER system appeared a more appropriate candidate than the SBP system for biopreservation of juices. Significance and Impact of the Study:, This work may open perspectives towards the development of LPER or other peroxidases as biopreservatives in acidic foods. [source] | |||||||||||||