The structural and functional determinants of the Axin and Dishevelled DIX domains.

BACKGROUND: The dishevelled and axin genes encode multi-domain proteins that play key roles in WNT signalling. Dishevelled prevents beta-catenin degradation by interfering with the interaction of beta-catenin with the degradation-mediating Axin-APC-GSK3beta complex. This interference leads to an accumulation of cytoplasmic beta-catenin, which enters the nucleus and interacts with transcription factors that induce expression of Wnt-target genes. Axin, as a component of the degradation-mediating complex, is a potent negative regulator of Wnt signalling, whereas Dishevelled is a potent activator. Both Dishevelled and Axin possess a DIX (Dishevelled/Axin) domain, which mediates protein-protein interactions, specifically homodimerization. RESULTS: An evolutionary trace analysis of DIX domains identified conserved residues which, when mapped onto the crystal structure of the Axin DIX domain and a comparative model of the Dishevelled DIX domain, allow their categorization as residues of either structural or functional importance. We identify residues that are structural and functional determinants of the DIX domain fold, as well as those that are specific to homodimerization of Axin and Dishevelled. CONCLUSION: This report provides the first explanation of the mutant phenotypes caused by non-synonymous substitutions in the Dishevelled and Axin DIX domain by correlating their presumed functional significance with molecular structure.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Putative extrinsic blood coagulation pathway inhibitors from the tick Ornithodoros savignyi

Commercial (high-grade) BaS04 selectively adsorbs two proteins from crude 0. savignyi salivary gland extracts. They co-purify during reversed-phase HPLC, but can be separated by hydrophobic-interaction chromatography. Both proteins have been characterized in terms of their molecular mass, amino acid composition and one partial internal amino acid sequence was determined. Their molecular masses were established through electro-spray mass spectrometry as 9333 Da and 9173 Da, respectively. The 9.3 kDa protein was designated BSAP1 and the 9.1 kDa protein BSAP2. Their amino acid compositions shows significant differences, in particular the presence of 6-7 and 8 cysteine residues in BSAP1 and BSAP2, respectively. It is therefore unlikely that these proteins are isoforms. All of the cysteine residues are involved in the formation of disulphide bonds, the only possible exception being one residue in BSAP1. Both proteins appear to be N-terminally blocked. An internal amino acid sequence Asp/Ser-Gly-Gly-Xxx-Xxx-Ile-Leu-Gly was obtained by sequencing a fragment of the cyanogen bromide cleaved BSAP2. It was suspected that these proteins might exhibit anticoagulant activity. The prothrombin time (PT) and activated partial thromboplastin time (aPPT) in the presence of the presumptive inhibitors were therefore evaluated. The aPPT was not significantly prolonged. The PT however did indicate a slight delay in the clotting time. This delay is not due to inhibition of factor VII, one of only two unique coagulation factors in the extrinsic pathway. The other factor is thromboplastin, also known as tissue factor. The nature of the protein adsorption to BaS04 was examined. From literature it is known that ϒ-carboxyglutamic acid-containing proteins, as well as some hydroxyproline and hydroxylysine-rich glycoproteins adsorb selectively to BaS04. The BSAPs were analysed for the presence of these modified amino acids, but all tests proved negative. The absence of Gla residues was determined using a Gla-specific stain on a polyacrylamide gel and was confirmed by performing mass spectrometry on native and decarboxylated protein samples. The absence of hydroxyproline and hydroxylysine was demonstrated by amino acid analysis. Both BSAPI and BSAP2 bind to neutral and negative membranes. BSAPI binds neutral and negative membranes more strongly than BSAP2. Its affinity for negative membranes is however much lower than its affinity for neutral membranes. In contrast, BSAP2 binds both membranes equally strongly. The binding of the proteins to the membranes was significantly lowered upon pre-incubation with Ca2+.Dissertation (MSc (Biochemistry))--University of Pretoria, 2006.Biochemistryunrestricte

JNK mediates differentiation, cell polarity and apoptosis during amphioxus development by regulating actin cytoskeleton dynamics and ERK signalling

c-Jun terminal kinase (JNK) is a multi-functional protein involved in a diverse array of context-dependent processes, including apoptosis, cell cycle regulation, adhesion and differentiation. It is integral to a number of signalling cascades, notably downstream of non-canonical Wnt and MAPK signalling pathways. As such, it is a key regulator of cellular behaviour and patterning during embryonic development across the animal kingdom. The cephalochordate amphioxus is an invertebrate chordate model system straddling the invertebrate to vertebrate transition and is thus ideally suited for comparative studies of morphogenesis. However, next to nothing is known about JNK signalling or cellular processes in this lineage. Pharmacological inhibition of JNK signalling using SP600125 during embryonic development arrests gastrula invagination and causes convergence extension-like defects in axial elongation, particularly of the notochord. Pharynx formation and anterior oral mesoderm derivatives like the preoral pit are also affected. This is accompanied by tissue-specific transcriptional changes, including reduced expression of six3/6 and wnt2 in the notochord, and ectopic wnt11 in neurulating embryos treated at late gastrula stages. Cellular delamination results in accumulation of cells in the gut cavity and a dorsal fin-like protrusion, followed by secondary Caspase3-mediated apoptosis of polarity-deficient cells, a phenotype only partly rescued by co-culture with the pan-caspase inhibitor Z-VAD-fmk. Ectopic activation of ERK signalling in the neighbours of extruded notochord and neural cells, possibly due to altered adhesive and tensile properties

The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors

Background: A deep understanding of what causes the phenotypic variation arising from biological patterning processes, cannot be claimed before we are able to recreate this variation by mathematical models capable of generating genotype-phenotype maps in a causally cohesive way. However, the concept of pattern in a multicellular context implies that what matters is not the state of every single cell, but certain emergent qualities of the total cell aggregate. Thus, in order to set up a genotype-phenotype map in such a spatiotemporal pattern setting one is actually forced to establish new pattern descriptors and derive their relations to parameters of the original model. A pattern descriptor is a variable that describes and quantifies a certain qualitative feature of the pattern, for example the degree to which certain macroscopic structures are present. There is today no general procedure for how to relate a set of patterns and their characteristic features to the functional relationships, parameter values and initial values of an original pattern-generating model. Here we present a new, generic approach for explorative analysis of complex patterning models which focuses on the essential pattern features and their relations to the model parameters. The approach is illustrated on an existing model for Delta-Notch lateral inhibition over a two-dimensional lattice. Results: By combining computer simulations according to a succession of statistical experimental designs, computer graphics, automatic image analysis, human sensory descriptive analysis and multivariate data modelling, we derive a pattern descriptor model of those macroscopic, emergent aspects of the patterns that we consider of interest. The pattern descriptor model relates the values of the new, dedicated pattern descriptors to the parameter values of the original model, for example by predicting the parameter values leading to particular patterns, and provides insights that would have been hard to obtain by traditional methods. Conclusion: The results suggest that our approach may qualify as a general procedure for how to discover and relate relevant features and characteristics of emergent patterns to the functional relationships, parameter values and initial values of an underlying pattern-generating mathematical model

ATP half-sites in RadA and RAD51 recombinases bind nucleotides.

Homologous recombination is essential for repair of DNA double-strand breaks. Central to this process is a family of recombinases, including archeal RadA and human RAD51, which form nucleoprotein filaments on damaged single-stranded DNA ends and facilitate their ATP-dependent repair. ATP binding and hydrolysis are dependent on the formation of a nucleoprotein filament comprising RadA/RAD51 and single-stranded DNA, with ATP bound between adjacent protomers. We demonstrate that truncated, monomeric Pyrococcus furiosus RadA and monomerised human RAD51 retain the ability to bind ATP and other nucleotides with high affinity. We present crystal structures of both apo and nucleotide-bound forms of monomeric RadA. These structures reveal that while phosphate groups are tightly bound, RadA presents a shallow, poorly defined binding surface for the nitrogenous bases of nucleotides. We suggest that RadA monomers would be constitutively bound to nucleotides in the cell and that the bound nucleotide might play a structural role in filament assembly.We would like to thank Dr Timothy Sharpe for help with MALS analysis of the monomeric RadA protein and Dr Tara Pukala for the mass spectrometric analysis of the same protein. We would like to thank X-ray crystallographic and Biophysics facilities at the Department of Biochemistry for access to their instrumentation. We thank Diamond Light Source for access to beamline I04 (proposal MX315), European Synchrotron Radiation Facility for access to beamline ID23-1 (proposal MX-705 17 and MX-857) and Swiss Light Source for access to beamline PXIII that contributed to the results presented here. This work was funded by Translational Award from the Wellcome Trust (080083/Z/06/Z).This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by Wiley

Understanding signaling cascades in melanoma

Understanding regulatory pathways involved in melanoma development and progression has advanced significantly in recent years. It is now appreciated that melanoma is the result of complex changes in multiple signaling pathways that affect growth control, metabolism, motility and the ability to escape cell death programs. Here we review the major signaling pathways currently known to be deregulated in melanoma with an implication to its development and progression. Among these pathways are Ras, B-Raf, MEK, PTEN, phosphatidylinositol-3 kinase (PI3Ks) and Akt which are constitutively activated in a significant number of melanoma tumors, in most cases due to genomic change. Other pathways discussed in this review include the [Janus kinase/signal transducer and activator of transcription (JAK/STAT), transforming growth factor-beta pathways which are also activated in melanoma, although the underlying mechanism is not yet clear. As a paradigm for remodeled signaling pathways, melanoma also offers a unique opportunity for targeted drug development.Fil: Lopez Bergami, Pablo Roberto. Sanford-burnham Medical Research Institute; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Fitchmann, B. Sanford-burnham Medical Research Institute; Estados UnidosFil: Ronai, Ze´ev. Sanford-burnham Medical Research Institute; Estados Unido

Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment

Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells

Improved mycobacterial protein production using a Mycobacterium smegmatis groEL1ΔC expression strain

<p>Abstract</p> <p>Background</p> <p>The non-pathogenic bacterium <it>Mycobacterium smegmatis </it>is widely used as a near-native expression host for the purification of <it>Mycobacterium tuberculosis </it>proteins. Unfortunately, the Hsp60 chaperone GroEL1, which is relatively highly expressed, is often co-purified with polyhistidine-tagged recombinant proteins as a major contaminant when using this expression system. This is likely due to a histidine-rich C-terminus in GroEL1.</p> <p>Results</p> <p>In order to improve purification efficiency and yield of polyhistidine-tagged mycobacterial target proteins, we created a mutant version of GroEL1 by removing the coding sequence for the histidine-rich C-terminus, termed GroEL1ΔC. GroEL1ΔC, which is a functional protein, is no longer able to bind nickel affinity beads. Using a selection of challenging test proteins, we show that GroEL1ΔC is no longer present in protein samples purified from the <it>groEL1ΔC </it>expression strain and demonstrate the feasibility and advantages of purifying and characterising proteins produced using this strain.</p> <p>Conclusions</p> <p>This novel <it>Mycobacterium smegmatis </it>expression strain allows efficient expression and purification of mycobacterial proteins while concomitantly removing the troublesome contaminant GroEL1 and consequently increasing the speed and efficiency of protein purification.</p

Evasion of anti-growth signaling: a key step in tumorigenesis and potential target for treatment and prophylaxis by natural compounds

The evasion of anti-growth signaling is an important characteristic of cancer cells. In order to continue to proliferate, cancer cells must somehow uncouple themselves from the many signals that exist to slow down cell growth. Here, we define the anti-growth signaling process, and review several important pathways involved in growth signaling: p53, phosphatase and tensin homolog (PTEN), retinoblastoma protein (Rb), Hippo, growth differentiation factor 15 (GDF15), AT-rich interactive domain 1A (ARID1A), Notch, insulin-like growth factor (IGF), and Krüppel-like factor 5 (KLF5) pathways. Aberrations in these processes in cancer cells involve mutations and thus the suppression of genes that prevent growth, as well as mutation and activation of genes involved in driving cell growth. Using these pathways as examples, we prioritize molecular targets that might be leveraged to promote anti-growth signaling in cancer cells. Interestingly, naturally-occurring phytochemicals found in human diets (either singly or as mixtures) may promote anti-growth signaling, and do so without the potentially adverse effects associated with synthetic chemicals. We review examples of naturally-occurring phytochemicals that may be applied to prevent cancer by antagonizing growth signaling, and propose one phytochemical for each pathway. These are: epigallocatechin-3-gallate (EGCG) for the Rb pathway, luteolin for p53, curcumin for PTEN, porphyrins for Hippo, genistein for GDF15, resveratrol for ARID1A, withaferin A for Notch and diguelin for the IGF1-receptor pathway. The coordination of anti-growth signaling and natural compound studies will provide insight into the future application of these compounds in the clinical setting

Diversity of fate outcomes in cell pairs under lateral inhibition

Cell fate determination by lateral inhibition via Notch/Delta signalling has been extensively studied. Most formalised models consider Notch/Delta interactions in fields of cells, with parameters that typically lead to symmetry breaking of signalling states between neighbouring cells, commonly resulting in salt-and-pepper fate patterns. Here we consider the case of signalling between isolated cell pairs, and find that the bifurcation properties of a standard mathematical model of lateral inhibition can lead to stable symmetric signalling states. We apply this model to the adult intestinal stem cell (ISC) of Drosophila, whose fate is stochastic but dependent on the Notch/Delta pathway. We observe a correlation between signalling state in cell pairs and their contact area. We interpret this behaviour in terms of the properties of our model in the presence of population variability in contact areas, which affects the effective signalling threshold of individual cells. Our results suggest that the dynamics of Notch/Delta signalling can contribute to explain stochasticity in stem cell fate decisions, and that the standard model for lateral inhibition can account for a wider range of developmental outcomes than previously considered