Efficient Segmental Isotope Labeling of Integral Membrane Proteins for High-Resolution NMR Studies.

High-resolution structural NMR analyses of membrane proteins are challenging due to their large size, resulting in broad resonances and strong signal overlap. Among the isotope labeling methods that can remedy this situation, segmental isotope labeling is a suitable strategy to simplify NMR spectra and retain high-resolution structural information. However, protein ligation within integral membrane proteins is complicated since the hydrophobic protein fragments are insoluble, and the removal of ligation side-products is elaborate. Here, we show that a stabilized split-intein system can be used for rapid and high-yield protein trans-splicing of integral membrane proteins under denaturing conditions. This setup enables segmental isotope labeling experiments within folded protein domains for NMR studies. We show that high-quality NMR spectra of markedly reduced complexity can be obtained in detergent micelles and lipid nanodiscs. Of note, the nanodisc insertion step specifically selects for the ligated and correctly folded membrane protein and simultaneously removes ligation byproducts. Using this tailored workflow, we show that high-resolution NMR structure determination is strongly facilitated with just two segmentally isotope-labeled membrane protein samples. The presented method will be broadly applicable to structural and dynamical investigations of (membrane-) proteins and their complexes by solution and solid-state NMR but also other structural methods where segmental labeling is beneficial.

Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21.

Triose phosphates (TPs) are the primary products of photosynthetic CO2 fixation in chloroplasts, which need to be exported into the cytosol across the chloroplast inner envelope (IE) and outer envelope (OE) membranes to sustain plant growth. While transport across the IE is well understood, the mode of action of the transporters in the OE remains unclear. Here we present the high-resolution nuclear magnetic resonance (NMR) structure of the outer envelope protein 21 (OEP21) from garden pea, the main exit pore for TPs in C3 plants. OEP21 is a cone-shaped ß-barrel pore with a highly positively charged interior that enables binding and translocation of negatively charged metabolites in a competitive manner, up to a size of ~1 kDa. ATP stabilizes the channel and keeps it in an open state. Despite the broad substrate selectivity of OEP21, these results suggest that control of metabolite transport across the OE might be possible.

Slow motion bias: Exploring the relation between time overestimation and increased perceived intentionality.

Recent research on time perception has revealed that actions which are replayed in slow motion are perceived to take longer and rated to be more intentional (e.g., foul plays). Interestingly, the bias on duration estimations seems to disappear when information on the slow motion factor (i.e., the degree the video was slowed down) was provided. Here, we scrutinize the question whether also the intentionality bias disappears when explicit information about the slow motion factor is provided. To this end, two groups watched the same video clips, all displaying foul situations in a basketball match, in different video speeds. While the uninformed group saw the videos without further information, the informed group received additional information about the current slow motion factor. This study replicated the overestimation of original duration with increasing slow motion and indicated that this effect might be reduced when information about the slow motion factor is provided. However, despite generally lower intentionality ratings in the informed group, video speed information was not able to reduce the rise in intentionality ratings with increasing slow motion. Potential reasons and open questions regarding the nature and mechanisms behind these perceptual temporal biases (e.g., different time processing systems) are discussed.

The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labelling for NMR spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy can be used to determine the structure, dynamics and interactions of proteins. However, protein NMR requires stable isotope labelling for signal detection. The cells used for the production of recombinant proteins must therefore be grown in medium containing isotopically labelled substrates. Stable isotope labelling is well established in Escherichia coli, but bacteria are only suitable for the production of simple proteins without post-translational modifications. More complex proteins require eukaryotic production hosts, but their growth can be impaired by labelled media, thus reducing product yields and increasing costs. To address this limitation, we used media supplemented with isotope-labelled substrates to cultivate the tobacco-derived cell line BY-2, which was then cast into plant cell packs (PCPs) for the transient expression of a labelled version of the model protein GB1. Mass spectrometry confirmed the feasibility of isotope labelling with 15 N and 2 H using this approach. The resulting NMR spectrum featured a signal dispersion comparable to recombinant GB1 produced in E. coli. PCPs therefore offer a rapid and cost-efficient alternative for the production of isotope-labelled proteins for NMR analysis, especially suitable for complex proteins that cannot be produced in microbial systems.

High-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane.

Permeabilization of the outer mitochondrial membrane by pore-forming Bcl2 proteins is a crucial step for the induction of apoptosis. Despite a large set of data suggesting global conformational changes within pro-apoptotic Bak during pore formation, high-resolution structural details in a membrane environment remain sparse. Here, we used NMR and HDX-MS (Hydrogen deuterium exchange mass spectrometry) in lipid nanodiscs to gain important high-resolution structural insights into the conformational changes of Bak at the membrane that are dependent on a direct activation by BH3-only proteins. Furthermore, we determined the first high-resolution structure of the Bak transmembrane helix. Upon activation, α-helix 1 in the soluble domain of Bak dissociates from the protein and adopts an unfolded and dynamic potentially membrane-bound state. In line with this finding, comparative protein folding experiments with Bak and anti-apoptotic BclxL suggest that α-helix 1 in Bak is a metastable structural element contributing to its pro-apoptotic features. Consequently, mutagenesis experiments aimed at stabilizing α-helix 1 yielded Bak variants with delayed pore-forming activity. These insights will contribute to a better mechanistic understanding of Bak-mediated membrane permeabilization.

NMR Structural and Biophysical Analysis of the Disease-Linked Inner Mitochondrial Membrane Protein MPV17.

MPV17 is an integral inner mitochondrial membrane protein, whose loss-of-function is linked to the hepatocerebral form of the mitochondrial-DNA-depletion syndrome, leading to a tissue-specific reduction of mitochondrial DNA and organ failure in infants. Several disease-causing mutations in MPV17 have been identified and earlier studies with reconstituted protein suggest that MPV17 forms a high conductivity channel in the membrane. However, the molecular and structural basis of the MPV17 functionality remain only poorly understood. In order to make MPV17 accessible to high-resolution structural studies, we here present an efficient protocol for its high-level production in E. coli and refolding into detergent micelles. Using biophysical and NMR methods, we show that refolded MPV17 in detergent micelles adopts a compact structure consisting of six membrane-embedded α-helices. Furthermore, we demonstrate that MPV17 forms oligomers in a lipid bilayer that are further stabilized by disulfide-bridges. In line with these findings, MPV17 could only be inserted into lipid nanodiscs of 8-12 nm in diameter if intrinsic cysteines were either removed by mutagenesis or blocked by chemical modification. Using this nanodisc reconstitution approach, we could show that disease-linked mutations in MPV17 abolish its oligomerization properties in the membrane. These data suggest that, induced by oxidative stress, MPV17 can alter its oligomeric state from a properly folded monomer to a disulfide-stabilized oligomeric pore which might be required for the transport of metabolic DNA precursors into the mitochondrial matrix to compensate for the damage caused by reactive oxygen species.

On the role of different subdimensions of inhibition for successful motor skill change.

Modifying already automatized movement skills often causes proactive interference resulting in initial performance decrements. Dealing with interference is closely linked to inhibitory functions, since inhibition is needed to suppress automatic, but undesired behavior. The aim of this study was to investigate the role of three different inhibition dimensions for interference control in motor skill change. To this end, 42 participants performed three tests each measuring a different dimension of inhibition: resistance to distractor interference (Eriksen-Flanker Task), resistance to proactive interference (Brown-Peterson Variant) and prepotent response inhibition (Stop-Signal Task). To examine the amount of proactive interference in a motor skill change task, participants were then asked to type a short paragraph as fast and accurately as possible on a regular computer keyboard. After this baseline measure, in order to induce proactive interference, they were confronted with a manipulated keyboard on which the letters S and L were switched. This change led to an immediate performance decline, observable in increased typing times and errors. Results also showed that larger performance decrements were significantly associated with better baseline performance, lower scores on prepotent response inhibition and higher scores on resistance to distractor interference. Besides supporting the idea of inhibition as a multidimensional construct, these findings replicate and confirm recent research indicating that the success in motor skill change is predicted by the ability to suppress prepotent response tendencies.

Why Do Actions in Slow Motion Appear to Last Longer? On the Effect of Video Speed Information.

When displayed in slow motion, actions are often perceived longer compared with original speed. However, it remains to be determined why this bias exists. Is it possible that the bias emerges because participants underestimate the factor by which a video was slowed down and hence arrive at erroneous conclusions about the original duration? If true, providing explicit information about the respective video speed should eliminate this slow motion effect. To scrutinize the nature of this bias, participants rated the original duration of sports actions displayed at original speed or slow motion. Results revealed the expected overestimation bias consisting in longer ratings with increasing slow motion. However, the bias disappeared when information about the current video speed was provided. The observations suggest an influence of knowledge about video playback speed on cognitive-evaluative processes which may hold important implications for future research and practice.

Reduced mitochondrial resilience enables non-canonical induction of apoptosis after TNF receptor signaling in virus-infected hepatocytes.

BACKGROUND & AIMS: Selective elimination of virus-infected hepatocytes occurs through virus-specific CD8 T cells recognizing peptide-loaded MHC molecules. Herein, we report that virus-infected hepatocytes are also selectively eliminated through a cell-autonomous mechanism. METHODS: We generated recombinant adenoviruses and genetically modified mouse models to identify the molecular mechanisms determining TNF-induced hepatocyte apoptosis in vivo and used in vivo bioluminescence imaging, immunohistochemistry, immunoblot analysis, RNAseq/proteome/phosphoproteome analyses, bioinformatic analyses, mitochondrial function tests. RESULTS: We found that TNF precisely eliminated only virus-infected hepatocytes independently of local inflammation and activation of immune sensory receptors. TNF receptor I was equally relevant for NF-kB activation in healthy and infected hepatocytes, but selectively mediated apoptosis in infected hepatocytes. Caspase 8 activation downstream of TNF receptor signaling was dispensable for apoptosis in virus-infected hepatocytes, indicating an unknown non-canonical cell-intrinsic pathway promoting apoptosis in hepatocytes. We identified a unique state of mitochondrial vulnerability in virus-infected hepatocytes as the cause for this non-canonical induction of apoptosis through TNF. Mitochondria from virus-infected hepatocytes showed normal biophysical and bioenergetic functions but were characterized by reduced resilience to calcium challenge. In the presence of unchanged TNF-induced signaling, reactive oxygen species-mediated calcium release from the endoplasmic reticulum caused mitochondrial permeability transition and apoptosis, which identified a link between extrinsic death receptor signaling and cell-intrinsic mitochondrial-mediated caspase activation. CONCLUSION: Our findings reveal a novel concept in immune surveillance by identifying a cell-autonomous defense mechanism that selectively eliminates virus-infected hepatocytes through mitochondrial permeability transition. LAY SUMMARY: The liver is known for its unique immune functions. Herein, we identify a novel mechanism by which virus-infected hepatocytes can selectively eliminate themselves through reduced mitochondrial resilience to calcium challenge.

Interindividual differences in the capability to change automatized movement patterns.

When modifying established, automatized skills, performers often experience proactive interference resulting in initial performance decrements. Notably, individuals seem to differ quite largely with respect to their interference susceptibility. The aim of the present study was to scrutinize the roots of these interindividual differences by examining the role of executive functions, age, baseline performance and gaze behavior applying a motor skill change task. As the ability to deal with proactive interference seems to be particularly linked to inhibitory mechanisms, we also assessed whether the application of a motor restriction which prevents unwanted movements may facilitate inhibition and hence result in less proactive interference. To this end, skilled touch-typists were confronted with a rule change that prohibited the left index finger for subsequent typing which immediately disrupted participants' automatized typing fluency. Regression analyses revealed that the amount of interference was significantly related to age and that the application of a motor restriction tended to predict less proactive interference. Additional correlation analyses revealed that a higher amount of proactive interference was also associated with higher baseline performance and lower prepotent response inhibition abilities. However, none of the remaining executive functions could explain the amount of interference. It follows that individual factors such as age, baseline performance and prepotent response inhibition as well as the physical option to execute a certain movement may play important roles in overcoming proactive interference when changing automatized skills.

Quantifying the insertion of membrane proteins into lipid bilayer nanodiscs using a fusion protein strategy.

A membrane protein's oligomeric state modulates its functionality in various cellular processes. Since membrane proteins have to be solubilized in an appropriate membrane mimetic, the use of classical biophysical methods to analyze protein oligomers is challenging. We here present a method to determine the number of membrane proteins inserted into lipid nanodiscs. It is based on the ability to selectively quantify the amount of a small and robust fusion protein that can be proteolytically cleaved off from a membrane protein after incorporation into lipid nanodiscs. A detailed knowledge of the number of membrane proteins per nanodisc at defined assembly conditions is essential to estimate the tendency for oligomerization, but also for guiding sample optimization for structural investigations that require the presence of a homogenous oligomeric state. We show that this method can efficiently be used to determine the number of VDAC1 channels in nanodiscs at various assembly conditions, as confirmed by negative stain EM. The presented method is suitable in particular for membrane proteins that cannot be probed easily by other methods such as single span transmembrane helices. This assay can be applied to any membrane protein that can be incorporated into a nanodisc without the requirement for special instrumentation and will thus be widely applicable and complementary to other methods that quantify membrane protein insertion in lipid nanodiscs.

Reducing Proactive Interference in Motor Tasks.

Changing automatized movement patterns often leads to initial performance decrements caused by proactive interference. In this study, we scrutinized whether proactive interference could be reduced by inhibiting the to-be-changed movement pattern by means of a physical movement constraint and verbal inhibition instructions, and whether any of the two interventions may be superior. Skilled typists typed short texts as fast and accurately as possible on a regular QWERTZ keyboard. After baseline measures, a new rule prohibiting the use of the left index finger was introduced. Subsequently, participants took part in either a verbal instruction or an additional motor restriction intervention phase. Results revealed that the original rule change was successful in inducing proactive interference in skilled typists. Most importantly, the two interventions similarly reduced proactive interference both immediately following the rule change and after ten practice sessions. We conclude that reducing proactive interference by means of physical motor restrictions and verbal instructions may be equally effective.

Crosstalk of Cellulose and Mannan Perception Pathways Leads to Inhibition of Cellulase Production in Several Filamentous Fungi.

It is essential for microbes to acquire information about their environment. Fungi use soluble degradation products of plant cell wall components to understand the substrate composition they grow on. Individual perception pathways have been well described. However, the interconnections between pathways remain poorly understood. In the present work, we provide evidence of crosstalk between the perception pathways for cellulose and the hemicellulose mannan being conserved in several filamentous fungi and leading to the inhibition of cellulase expression. We used the functional genomics tools available for Neurospora crassa to investigate this overlap at the molecular level. Crosstalk and competitive inhibition could be identified both during uptake by cellodextrin transporters and intracellularly. Importantly, the overlap is independent of CRE-1-mediated catabolite repression. These results provide novel insights into the regulatory networks of lignocellulolytic fungi and will contribute to the rational optimization of fungal enzyme production for efficient plant biomass depolymerization and utilization.IMPORTANCE In fungi, the production of enzymes for polysaccharide degradation is controlled by complex signaling networks. Previously, these networks were studied in response to simple sugars or single polysaccharides. Here, we tackled for the first time the molecular interplay between two seemingly unrelated perception pathways: those for cellulose and the hemicellulose (gluco)mannan. We identified a so far unknown competitive inhibition between the respective degradation products acting as signaling molecules. Competition was detected both at the level of the uptake and intracellularly, upstream of the main transcriptional regulator CLR-2. Our findings provide novel insights into the molecular communication between perception pathways. Also, they present possible targets for the improvement of industrial strains for higher cellulase production through the engineering of mannan insensitivity.

Embracing the Diversity of Halogen Bonding Motifs in Fragment-Based Drug Discovery-Construction of a Diversity-Optimized Halogen-Enriched Fragment Library.

Halogen bonds have recently gained attention in life sciences and drug discovery. However, it can be difficult to harness their full potential, when newly introducing them into an established hit or lead structure by molecular design. A possible solution to overcome this problem is the use of halogen-enriched fragment libraries (HEFLibs), which consist of chemical probes that provide the opportunity to identify halogen bonds as one of the main features of the binding mode. Initially, we have suggested the HEFLibs concept when constructing a focused library for finding p53 mutant stabilizers. Herein, we broaden and extent this concept aiming for a general HEFLib comprising a huge diversity of binding motifs and, thus, increasing the applicability to various targets. Using the construction principle of feature trees, we represent each halogenated fragment by treating all simple to complex substituents as modifiers of the central (hetero)arylhalide. This approach allows us to focus on the proximal binding interface around the halogen bond and, thus, its integration into a network of interactions based on the fragment's binding motif. As a first illustrative example, we generated a library of 198 fragments that unifies a two-fold strategy: Besides achieving a diversity-optimized basis of the library, we have extended this "core" by structurally similar "satellite compounds" that exhibit quite different halogen bonding interfaces. Tuning effects, i.e., increasing the magnitude of the σ-hole, can have an essential influence on the strength of the halogen bond. We were able to implement this key feature into the diversity selection, based on the rapid and efficient prediction of the highest positive electrostatic potential on the electron isodensity surface, representing the σ-hole, by VmaxPred.