The kinetics of PDZ domain-ligand interactions and implications for the binding mechanism

PDZ domains are protein adapter modules present in a few hundred human proteins. They play important roles in scaffolding and signal transduction. PDZ domains usually bind to the C termini of their target proteins. To assess the binding mechanism of this interaction we have performed the first in-solution kinetic study for PDZ domains and peptides corresponding to target ligands. Both PDZ3 from postsynaptic density protein 95 and PDZ2 from protein tyrosine phosphatase L1 bind their respective target peptides through an apparent A + B --> A.B mechanism without rate-limiting conformational changes. But a mutant with a fluorescent probe (Trp) outside of the binding pocket suggests that slight changes in the structure take place upon binding in protein tyrosine phosphatase-L1 PDZ2. For PDZ3 from postsynaptic density protein 95 the pH dependence of the binding reaction is consistent with a one-step mechanism with one titratable group. The salt dependence of the interaction shows that the formation of electrostatic interactions is rate-limiting for the association reaction but not for dissociation of the complex.

Rate constants and branching ratios for the dissociative recombination of C3D7+ and C4D9+

Product branching ratios and thermal rate coefficients for the dissociative recombination of C3D(+)7 and C4D(+)9 have been measured in the ion storage ring CRYRING. The results for C3D(+)7 are believed to be slightly more accurate than those obtained earlier for C3H(+)7. Only the C-C bond breaking channels could be measured for C4D(+)9 and were found to be in excellent agreement with earlier data.

First observation of four-body breakup in electron recombination: C2D+5

We report the first observation of four-body breakup in electron dissociative recombination of a molecular ion: C2D+5. In an ion storage ring experiment, the branching ratio for the process C2D+5 + e(-)-->C2D2 + D + D + D was determined to be 13%. This means that three covalent chemical bonds are broken as a result of the action of a single electron. This is the first time a four-body breakup of chemical bonds has been observed in a low-energy binary reaction.

Dissociative recombination cross section and branching ratios of protonated dimethyl disulfide and N-methylacetamide

Dimethyl disulfide (DMDS) and N-methylacetamide are two first choice model systems that represent the disulfide bridge bonding and the peptide bonding in proteins. These molecules are therefore suitable for investigation of the mechanisms involved when proteins fragment under electron capture dissociation (ECD). The dissociative recombination cross sections for both protonated DMDS and protonated N-methylacetamide were determined at electron energies ranging from 0.001 to 0.3 eV. Also, the branching ratios at 0 eV center-of-mass collision energy were determined. The present results give support for the indirect mechanism of ECD, where free hydrogen atoms produced in the initial fragmentation step induce further decomposition. We suggest that both indirect and direct dissociations play a role in ECD.

Structural basis of actin sequestration by thymosin-beta4: implications for WH2 proteins

The WH2 (Wiscott-Aldridge syndrome protein homology domain 2) repeat is an actin interacting motif found in monomer sequestering and filament assembly proteins. We have stabilized the prototypical WH2 family member, thymosin-beta4 (Tbeta4), with respect to actin, by creating a hybrid between gelsolin domain 1 and the C-terminal half of Tbeta4 (G1-Tbeta4). This hybrid protein sequesters actin monomers, severs actin filaments and acts as a leaky barbed end cap. Here, we present the structure of the G1-Tbeta4:actin complex at 2 A resolution. The structure reveals that Tbeta4 sequesters by capping both ends of the actin monomer, and that exchange of actin between Tbeta4 and profilin is mediated by a minor overlap in binding sites. The structure implies that multiple WH2 motif-containing proteins will associate longitudinally with actin filaments. Finally, we discuss the role of the WH2 motif in arp2/3 activation.

Involvement of protein kinase C-alpha and -epsilon in extracellular Ca2+ signalling mediated by the calcium sensing receptor

The sensing of extracellular Ca(2+) concentration ([Ca(2+)](o)) and modulation of cellular processes associated with acute or sustained changes in [Ca(2+)](o) are cell-type specific and mediated by the calcium sensing receptor (CaR). [Ca(2+)](o) signalling requires protein kinase C (PKC), but the identity and role of PKC isoforms in CaR-mediated responses remain unclear. Here we show that high [Ca(2+)](o) activated PKC-alpha and PKC- in parathyroid cells and in human embryonic kidney (HEK293) cells overexpressing the CaR (HEK-CaR) and that this response correlated with the CaR-dependent activation of mitogen-activated protein kinases ERK1/2. Activation of ERK1/2 by acute high [Ca(2+)](o) required influx of Ca(2+)through Ni(2+)-sensitive Ca(2+)channels and phosphatidylinositol-dependent phospholipase C-beta activity. Inhibition of PKC by co-expression of dominant-negative (DN) mutants of PKC-alpha or - with the CaR attenuated sustained ERK1/2 activation. Overexpression of a PKC phosphorylation site (T888A) mutant CaR in HEK293 cells showed that this site was important for ERK1/2 activation at high [Ca(2+)](o). Activation of ERK1/2 by high [Ca(2+)](o) was not necessary for the [Ca(2+)](o)-regulated secretion of parathyroid hormone (PTH) in dispersed bovine parathyroid cells. These data suggest that the CaR-mediated [Ca(2+)](o) signal leading to regulated PTH secretion that requires diacylglycerol-responsive PKC isoforms is not mediated via the ERK pathway.

Dissociative recombination of NH4+ and ND4+ ions: Storage ring experiments andab initiomolecular dynamics

The dissociative recombination (DR) process of NH4+ and ND4+ molecular ions with free electrons has been studied at the heavy-ion storage ring CRYRING (Manne Siegbahn Laboratory, Stockholm University). The absolute cross sections for DR of NH4+ and ND4+ in the collision energy range 0.001-1 eV are reported, and thermal rate coefficients for the temperature interval from 10 to 2000 K are calculated from the experimental data. The absolute cross section for NH4+ agrees well with earlier work and is about a factor of 2 larger than the cross section for ND4+. The dissociative recombination of NH4+ is dominated by the product channels NH3+H (0.85+/-0.04) and NH2+2H (0.13+/-0.01), while the DR of ND4+ mainly results in ND3+D (0.94+/-0.03). Ab initio direct dynamics simulations, based on the assumption that the dissociation dynamics is governed by the neutral ground-state potential energy surface, suggest that the primary product formed in the DR process is NH3+H. The ejection of the H atom is direct and leaves the NH3 molecule highly vibrationally excited. A fraction of the excited ammonia molecules may subsequently undergo secondary fragmentation forming NH2+H. It is concluded that the model results are consistent with gross features of the experimental results, including the sensitivity of the branching ratio for the three-body channel NH2+2H to isotopic exchange.

Measure of Processes of Care (MPOC) applied to measure parent's perception of the habilitation process in Sweden

AIM

To evaluate the instrument Measure of Processes of Care (MPOC) in a Swedish context.

METHODS

The MPOC consists of 56 questions in the five scales: enabling and partnership; providing general information; providing specific information about the child; co-ordinated and comprehensive care; and respectful and supportive care. The questionnaire was translated into Swedish and distributed to 850 families, served by four habilitation centres. After two reminders, a response rate of 74.9% was obtained, and about 60% of the questionnaires qualified for further statistical analysis. Reliability, calculated as Cronbach's alpha, was high for four of the five scales and acceptable for the fifth (scale no. 3).

RESULTS

Significant differences were shown between centres as well as between age groups. These differences were reasonable as judged through background knowledge, indicating that the instrument was able to discriminate between actual differences in services. Commenting on the practical use of the questionaire, staff, as well as responding parents, found the questionnaire rather long and some parents reported difficulties in giving answers as specific as the questionnaire asked them to.

CONCLUSION

The MPOC shows sufficient sensitivity to be used as an evaluation tool for services at a centre or program level, and can be recommended for research and practical use.

Modelling diffuse nutrient flow in eutrophication control scenarios

The Swedish Water Management Research Programme (VASTRA) focuses on the development and demonstration of tools for more efficient eutrophication control when implementing the EU water framework directive in Sweden. During the first half of the programme, models for nitrogen flow were developed, and at present, similar models for phosphorus are under construction (e.g. HBV-P). The programme is interdisciplinary, and scientists are collaborating in actor-games and focus group evaluations including scenario analysis. The scenarios modelled in VASTRA phase I, show that (i) changed agricultural practices can be the most effective and least expensive way to reduce nitrogen transport from land to the sea; (ii) constructed agricultural wetlands may only have small impact on riverine nitrogen transport in some regions, due to natural hydrometeorological dynamics; (iii) removing planktivorous fish may be an efficient way of reducing the algal concentrations in lakes without the undesired side-effect of increased nutrient load to the down-stream river system. In VASTRA phase II, one of the highlights will be interdisciplinary scenario-modelling of different measure strategies in a pilot catchment of southern Sweden (Rönne å).

Cognitive functions in depressive disorders: evidence from a population-based study

BACKGROUND

Most of the available evidence on the effects of depression is based on in- and out-patient samples focusing on individuals suffering from major depression. The aims of this study were to examine cognitive functioning in population-based samples and to determine whether cognitive performance varies as a function of depression subgroup.

METHOD

Population-based samples (aged 20-64 years) with major depression (N = 68), dysthymia (N = 28), mixed anxiety-depressive disorder (N = 25) and minor depression (N = 66) were examined on a variety of cognitive tasks (i.e. episodic memory, verbal fluency, perceptual-motor speed and mental flexibility). One hundred and seventy-five non-depressed individuals served as controls.

RESULTS

The total group of depressed individuals showed impairments in tasks tapping episodic memory and mental flexibility. Of more interest, however, was the observation that the pattern of impairments varied as a function of depression subgroup: the major depression and mixed anxiety-depressive disorder groups exhibited significant memory dysfunction, whereas individuals with dysthymia showed pronounced difficulties in mental flexibility. Minor depression did not affect cognitive performance. Verbal fluency and perceptual-motor speed were not affected by depression.

CONCLUSIONS

These results indicate that persons with depressive disorders in the population exhibit cognitive impairments in tasks tapping episodic memory and mental flexibility and that cognitive impairment varies as a function of depressive disorder.

A model for chronic quantitative studies of colorectal sensitivity using balloon distension in conscious mice -- effects of opioid receptor agonists

In the current study, colorectal distension (CRD) was performed in conscious mice, in order to study visceral (colon) sensitivity. Electrodes were chronically implanted into the external oblique muscle to obtain the electromyographic (EMG) response to CRD. CRD was performed using a computerized system, which inflated the balloon with air to the desired pressures. An increasing (10-80 mmHg) and a repeated (12 x 55 mmHg) phasic paradigm with distensions lasting 10 s and with 5-min intervals were used. The EMG recordings were linearly correlated to intracolonic pressures between 10 and 80 mmHg, which are characteristic of the visceromotor response (VMR). Repeated phasic distensions at 55 mmHg resulted in a stable VMR in female mice, but an increasing VMR in male mice. Interestingly, the duration of the VMR was about 5 s, which is shorter than the actual duration of the distension. U-69593 and fentanyl (selective kappa and mu opioid receptor agonists) significantly reduced the VMR at subcutaneous doses of 0.5 and 0.05 mg x kg-1, respectively. In conclusion, a CRD model for repetitive quantitative studies of colorectal sensitivity and evaluation of pharmacological modulation of visceral sensitivity in conscious mice is presented.

Selective interaction of megalin with postsynaptic density-95 (PSD-95)-like membrane-associated guanylate kinase (MAGUK) proteins

Megalin is an integral membrane receptor belonging to the low-density lipoprotein receptor family. In addition to its role as an endocytotic receptor, megalin has also been proposed to have signalling functions. Using interaction cloning in yeast, we identified the membrane-associated guanylate kinase family member postsynaptic density-95 (PSD-95) as an interaction partner for megalin. PSD-95 and a truncated version of megalin were co-immunoprecipitated from HEK-293 cell lysates overexpressing the two proteins, which confirmed the interaction. The two proteins were found to be co-localized in these cells by confocal microscopy. Immunocytochemical studies showed that cells in the parathyroid, proximal tubuli of the kidney and placenta express both megalin and PSD-95. We found that the interaction between the two proteins is mediated by the binding of the C-terminus of megalin, which has a type I PSD-95/ Drosophila discs-large/zona occludens 1 (PDZ)-binding motif, to the PDZ2 domain of PSD-95. The PSD-95-like membrane-associated guanylate kinase ('MAGUK') family contains three additional members: PSD-93, synapse-associated protein 97 (SAP97) and SAP102. We detected these proteins, apart from SAP102, in parathyroid chief cells, a cell type having a marked expression of megalin. The PDZ2 domains of PSD-93 and SAP102 were also shown to interact with megalin, whereas no interaction was detected for SAP97. The SAP97 PDZ2 domain differed at four positions from the other members of the PSD-95 subfamily. One of these residues was Thr(389), located in the alphaB-helix and part of the hydrophobic pocket of the PDZ2 domain. Surface plasmon resonance experiments revealed that mutation of SAP97 Thr(389) to alanine, as with the other PSD-95-like membrane-associated guanylate kinases, induced binding to megalin.

Cross-presentation of cell-associated antigens by dendritic cells

There is a strict requirement for professional antigen-presenting cells (APCs) in the generation of immunity toward most viruses. Exogenous pathways of MHC class I-restricted antigen presentation play an important role in the generation of antiviral immunity, particularly in the immune surveillance of virus-infected tissues of nonhematopoietic origin, and to bypass the detrimental effects of direct virus infection on professional APCs. The mechanisms underlying generation of antiviral immunity under these circumstances are discussed.

An enhanced cosmic-ray flux towards zeta Persei inferred from a laboratory study of the H3+-e- recombination rate

The H3+ molecular ion plays a fundamental role in interstellar chemistry, as it initiates a network of chemical reactions that produce many molecules. In dense interstellar clouds, the H3+ abundance is understood using a simple chemical model, from which observations of H3+ yield valuable estimates of cloud path length, density and temperature. But observations of diffuse clouds have suggested that H3+ is considerably more abundant than expected from the chemical models. Models of diffuse clouds have, however, been hampered by the uncertain values of three key parameters: the rate of H3+ destruction by electrons (e-), the electron fraction, and the cosmic-ray ionization rate. Here we report a direct experimental measurement of the H3+ destruction rate under nearly interstellar conditions. We also report the observation of H3+ in a diffuse cloud (towards Persei) where the electron fraction is already known. From these, we find that the cosmic-ray ionization rate along this line of sight is 40 times faster than previously assumed. If such a high cosmic-ray flux is ubiquitous in diffuse clouds, the discrepancy between chemical models and the previous observations of H3+ can be resolved.

Novel candidate genes for atherosclerosis are identified by representational difference analysis-based transcript profiling of cholesterol-loaded macrophages

OBJECTIVES

To analyze the early gene expression in macrophages accompanying the phenotypic changes into foam cells upon exposure to oxidized low-density lipoprotein. To identify candidate genes and markers for further studies into the pathogenesis of atherosclerosis.

METHODS

Cells of the monocytic cell line THP-1 were activated by PMA and exposed to oxidized low-density lipoprotein. Gene expression profiles were investigated after 24 h, using a solid phase cDNA representational difference analysis (RDA) method and shotgun sequencing. Results were verified by microarray hybridization, and analyzed in the virtual chip display of a novel software tool for transcript profile exploration.

RESULTS

By comparing transcript profiles of exposed/unexposed cells, 1,984 transcript sequences, representing a total of 921 genes with altered expression levels in response to oxidized low-density lipoprotein exposure, were identified. Genes that are central to cell cycle control and proliferation, inflammatory response, and of pathways not previously implicated in atherosclerosis were identified. The data obtained is also made available on-line at http:// biobase.biotech.kth.se/thp1a for further exploration.

CONCLUSION

The identification of new candidate genes for atherosclerotic disease through RDA-based transcript profiling facilitates further functional genomic studies in coronary artery disease. Candidate genetic polymorphism markers of potential clinical relevance can be identified by filtering information in genome variation databases through the virtual chip analysis of the transcript profiles and subsequently tested in association studies.

Chondrodysplasia punctata (CDP) with features of the tibia-metacarpal type and maternal phenytoin treatment during pregnancy

We describe a 2-year-old boy with chondrodysplasia punctata (CDP). The boy was exposed to phenytoin, in combination with carbamazepine, during pregnancy. There has been previous evidence for a connection between phenytoin exposure during pregnancy and chondrodysplasia punctata. The boy had clinical and some radiological characteristic features of CDP, of the tibia-metacarpal type. We know of no other report on a child exposed to phenytoin during pregnancy who developed CDP of this type.

Hepatocyte growth factor may accelerate healing in chronic leg ulcers: a pilot study

BACKGROUND

Hepatocyte growth factor (HGF) is a heparin-binding protein with mitogenic, motogenic and morphogenic activities for various cell types. The regenerative properties of HGF have been the object of several animal and in vitro studies in recent years.

OBJECTIVE

To investigate the physiological and therapeutic effects of HGF on chronic leg ulcers.

METHODS

HGF in gel form was locally applied, once daily for 7 days, to 15 of 19 chronic leg ulcers in 11 elderly patients. All patients had previously been treated by conventional methods and their leg ulcers had been in stable conditions for between 1 and 14 years. Any signs of allergy, discomfort or pain were reported daily. Microcirculation perfusion in the ulcers, compared to the intact contiguous skin, was determined by laser Doppler at the beginning of the study, after 1 week and again after 3 months (in seven patients). Ulcer size and characteristics were also documented.

RESULTS

It was observed that microcirculatory perfusion, which might reflect the angiogenic effect of HGF, was statistically significantly correlated (r = 0.94, p < 0.002) to ulcer area reduction in the treated ulcers. Excellent (84-100% area reduction) or partial healing (58-59%) was seen in eight out of 11 patients. No control group was included in this pilot study, which must be completed by proper control studies.

CONCLUSION

This study suggests that HGF may heal chronic leg ulcers, possibly by improving the microcirculation. Proper control studies need to be performed.