Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

Understanding the structural mechanisms of protein–ligand binding and their dependence on protein sequence and conformation is of fundamental importance for biomedical research. Here we investigate the interplay of conformational change and ligand-binding kinetics for the serine protease Trypsin and its competitive inhibitor Benzamidine with an extensive set of 150 μs molecular dynamics simulation data, analysed using a Markov state model. Seven metastable conformations with different binding pocket structures are found that interconvert at timescales of tens of microseconds. These conformations differ in their substrate-binding affinities and binding/dissociation rates. For each metastable state, corresponding solved structures of Trypsin mutants or similar serine proteases are contained in the protein data bank. Thus, our wild-type simulations explore a space of conformations that can be individually stabilized by adding ligands or making suitable changes in protein sequence. These findings provide direct evidence of conformational plasticity in receptors

CO2 and non-CO2 radiative forcings in climate projections for twenty-first century mitigation scenarios

Climate is simulated for reference and mitigation emissions scenarios from Integrated Assessment Models using the Bern2.5CC carbon cycle-climate model. Mitigation options encompass all major radiative forcing agents. Temperature change is attributed to forcings using an impulse-response substitute of Bern2.5CC. The contribution of CO2 to global warming increases over the century in all scenarios. Non-CO2 mitigation measures add to the abatement of global warming. The share of mitigation carried by CO2, however, increases when radiative forcing targets are lowered, and increases after 2000 in all mitigation scenarios. Thus, non-CO2 mitigation is limited and net CO2 emissions must eventually subside. Mitigation rapidly reduces the sulfate aerosol loading and associated cooling, partly masking Greenhouse Gas mitigation over the coming decades. A profound effect of mitigation on CO2 concentration, radiative forcing, temperatures and the rate of climate change emerges in the second half of the centur

On the complexity of IgE: The role of structural flexibility and glycosylation for binding its receptors.

It is well established that immunoglobulin E (IgE) plays a crucial role in atopy by binding to two types of Fcε receptors (FcεRI and FcεRII, also known as CD23). The cross-linking of FcεRI-bound IgE on effector cells, such as basophils and mast cells, initiates the allergic response. Conversely, the binding of IgE to CD23 modulates IgE serum levels and antigen presentation. In addition to binding to FcεRs, IgE can also interact with other receptors, such as certain galectins and, in mice, some FcγRs. The binding strength of IgE to its receptors is affected by its valency and glycosylation. While FcεRI shows reduced binding to IgE immune complexes (IgE-ICs), the binding to CD23 is enhanced. There is no evidence that galectins bind IgE-ICs. On the other hand, IgE glycosylation plays a crucial role in the binding to FcεRI and galectins, whereas the binding to CD23 seems to be independent of glycosylation. In this review, we will focus on receptors that bind to IgE and examine how the glycosylation and complexation of IgE impact their binding

Biochemical analysis of genetically-modified mice with learning and memory phenotypes.

Recent advances in molecular genetics have enabled generation of sophisticated genetically-modified mouse models to study specific molecules and their biological function in vivo. Here, I investigated biochemical changes in two different genetically-modified mouse lines with previously described learning and memory phenotypes. Firstly, I analysed biochemical changes in a mouse line carrying a threonine to alanine point mutation at Thr286 of alpha Ca2+/calmoduline-dependent kinase II (aCaMKII), which disenables this phosphorylation site. Autophosphorylation at Thr286 switches aCaMKII into an autonomous activity mode. The T286A mutant mice displayed changes in basal phosphorylation levels. In order to study biochemical changes after activity-dependent synaptic potentiation, an in vivo long-term potentiation (LTP) approach was established and validated by assessing activity-dependent changes in phosphorylation levels of well-characterised marker molecules including synapsin I and NR2B. Both aCaMKII and pCaMKII exhibited elevated levels of autophosphorylation after LTP stimulation in hippocampal area CA1 and dentate gyrus (DG). This finding indicates that pCaMKII may compensate for the loss of autonomous aCaMKII activity in T286A mutants. Furthermore, induction of LTP triggered phosphorylation of glycogen synthase kinase 3 (GSK3) at its inhibitory site suggesting a role for GSK3 in synaptic plasticity. Secondly, I investigated a transgenic (TG) mouse line expressing the cyclin-dependent kinase (Cdk5) activator protein, p25, a protein previously linked to some aspects of Alzheimer's disease (AD). The forebrain restricted expression of p25 started postnatally and stayed constant throughout the life-span of the TG mice. The expression of p25 triggered constitutive over-activation of Cdk5 in the TG mice. The p25 TG mice displayed age-dependent hyperphosphorylation of the microtubule-associated protein tail and age-dependent alterations in the processing of amyloid precursor protein (APP). Furthermore, p25-induced over-activation of Cdk5 led to inhibition of GSK3. This negative regulation of GSK3 was lost in aged p25 TG mice and correlated with the increased tau hyperphosphorylation. The levels of tau phosphorylation in aged p25 mice were reduced after treatment with lithium, an inhibitor of GSK3. These results indicate that GSK3 directly mediates tau hyperphosphorylation, whereas Cdk5 acts indirectly via inhibitory control of GSK3

Revision of the global carbon budget due to changing air-sea oxygen fluxes

Carbon budgets inferred from measurements of the atmospheric oxygen to nitrogen ratio (O2/N2) are revised considering sea-to-air fluxes of O2 and N2 in response to global warming and volcanic eruptions. Observational estimates of changes in ocean heat content are combined with a model-derived relationship between changes in atmospheric O2/N2 due to oceanic outgassing and heat fluxes to estimate ocean O2 outgassing. The inferred terrestrial carbon sink for the 1990s is reduced by a factor of two compared with the most recent estimate by the Intergovernmental Panel on Climate Change (IPCC). This also improves the agreement between calculated ocean carbon uptake rates and estimates from global carbon cycle models, which indicate a higher ocean carbon uptake during the 1990s than the 1980s. The simulated decrease in oceanic O2 concentrations is in qualitative agreement with observed trends in oceanic O2 concentrations

Probabilistic climate change projections using neural networks

Anticipated future warming of the climate system increases the need for accurate climate projections. A central problem are the large uncertainties associated with these model projections, and that uncertainty estimates are often based on expert judgment rather than objective quantitative methods. Further, important climate model parameters are still given as poorly constrained ranges that are partly inconsistent with the observed warming during the industrial period. Here we present a neural network based climate model substitute that increases the efficiency of large climate model ensembles by at least an order of magnitude. Using the observed surface warming over the industrial period and estimates of global ocean heat uptake as constraints for the ensemble, this method estimates ranges for climate sensitivity and radiative forcing that are consistent with observations. In particular, negative values for the uncertain indirect aerosol forcing exceeding -1.2Wm-2 can be excluded with high confidence. A parameterization to account for the uncertainty in the future carbon cycle is introduced, derived separately from a carbon cycle model. This allows us to quantify the effect of the feedback between oceanic and terrestrial carbon uptake and global warming on global temperature projections. Finally, probability density functions for the surface warming until year 2100 for two illustrative emission scenarios are calculated, taking into account uncertainties in the carbon cycle, radiative forcing, climate sensitivity, model parameters and the observed temperature records. We find that warming exceeds the surface warming range projected by IPCC for almost half of the ensemble members. Projection uncertainties are only consistent with IPCC if a model-derived upper limit of about 5K is assumed for climate sensitivit

Trends in marine dissolved oxygen: Implications for ocean circulation changes and the carbon budget

Recent measurements and model studies have consistently identified a decreasing trend in the concentration of dissolved O2 in the ocean over the last several decades. This trend has important implications for our understanding of anthropogenic climate change. First, the observed oceanic oxygen changes may be a signal of the beginning of a reorganization of large-scale ocean circulation in response to anthropogenic radiative forcing. Second, the repartitioning of oxygen between the ocean and the atmosphere requires a revision of the current atmospheric carbon budget and the estimates of the terrestrial and oceanic carbon sinks as calculated by the Intergovernmental Panel on Climate Change (IPCC) from measurements of atmospheric O2/N2

Verhaltenstherapeutische Behandlung eines Patienten mit beginnender Alzheimer-Demenz

The following case report shows a behavioral treatment of a 53-year-old Patient with Alzheimer's Disease (AD), The treatment includes procedures described in the Behavioral Competency Training (VKT) for patients with early-stage AD developed by Ehrhardt and associates. The program consists of about 20 weekly treatment sessions in which the patient's resources are activated and patient's coping is supported. The therapy and the intervention are debated in the light of the ongoing discussion about a state-of-the-art therapy for AD