Respiratory complex I: 'steam engine' of the cell?

Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine.     

Respiratory Health – Exposure Measurements and Modeling in the Fragrance and Flavour Industry

Although the flavor and fragrance industry is about 150 years old, the use of synthetic materials started more than 100 years ago, and the awareness of the respiratory hazard presented by some flavoring substances emerged only recently. In 2001, the US National Institute of Occupational Safety and Health (NIOSH) identified for the first time inhalation exposure to flavoring substances in the workplace as a possible occupational hazard. As a consequence, manufacturers must comply with a variety of workplace safety requirements, and management has to ensure the improvement of health and safety of the employees exposed to hazardous volatile organic compounds. In this sensitive context, MANE opened its facilities to an intensive measuring campaign with the objective to better estimate the real level of hazardous respiratory exposure of workers. In this study, exposure to 27 hazardous volatile substances were measured during several types of handling operations (weighing-mixing, packaging, reconditioning-transferring), 430 measurement results were generated, and were exploited to propose an improved model derived from the well-known ECETOC-TRA model. The quantification of volatile substances in the working atmosphere involved three main steps: adsorption of the chemicals on a solid support, thermal desorption, followed by analysis by gas chromatography-mass spectrometry. Our approach was to examine experimental measures done in various manufacturing workplaces and to define correction factors to reflect more accurately working conditions and habits. Four correction factors were adjusted in the ECETOC-TRA to integrate important exposure variation factors: exposure duration, percentage of the substance in the composition, presence of collective protective equipment and wearing of personal protective equipment. Verification of the validity of the model is based on the comparison of the values obtained after adaptation of the ECETOC-TRA model, according to various exposure scenarios, with the experimental values measured under real conditions. After examination of the predicted results, 98% of the values obtained with the proposed new model were above the experimental values measured in real conditions. This must be compared with the results of the classical ECETOC-TRA system, which generates only 37% of overestimated values. As the values generated by the new model intended to help decision-makers of the industry to implement adapted protective action and information, and considering the high variability of the working environments, it was of the utmost importance to us not to underestimate the exposure level. The proposed correction factors have been designed to achieve this goal. We wish to propose the present method as an improved monitoring tool to improve respiratory health and safety in the flavor and fragrance manufacturing facilities.     

Respiratory reactions on microinjections of GABA and baclofen into the Bötzinger complex and the pre-Bötzinger complex in rats

In adult anaesthetized rats the respiratory reactions to microinjections of GABA (10(-5) M) and baclofen (10(-6) M) into Botzinger complex (BC) and pre-Botzinger complex (PBC) were investigated. It was shown, that GABA microinjections into BC shortened inspiratory time and extended expiratory time while respiratory rate was not changed essentially, under this conditions the tidal volume and ventilation were increased. GABA microinjections into PBC significantly inhibited respiratory rhythm due to inspiratory and expiratory time prolongations and reduced tidal volume. The microinjections of baclofen into BC reduced expiration time and ventilation, and increased respiratory frequency whereas microinjections into PBC increased tidal volume without respiratory rate and expiratory time changes. It is suggested that the reactions observed demonstrate the various contribution of GABAergic mechanisms, including GABA(B)-receptors within BC and PBC, in control of respiratory pattern parameters.     

Computational exploration of metal–organic frameworks: examples of advances in crystal structure predictions and electronic structure tuning

The purpose of this article is to consider some recent developments in the area of the computational chemistry of metal–organic frameworks (MOFs), and more specifically on their crystal structure prediction and electronic structures. We intend here to illustrate how computational approaches might be powerful tool for the discovery of new families of hybrid frameworks, helping to understand their often complex energy landscapes. Also, MOFs have attracted a lot of attention due to their potential use for photocatalysis and optoelectronic, making it necessary to develop strategies to control their electronic structures. We will show how recent computational studies in this area have allowed a better understanding of their electronic properties and their potential tunability, highlighting when they have given successful guidelines for the discovery of novel MOFs with targeted properties.     

Solution structure of β2-microglobulin and insights into fibrillogenesis

The solution structure of human β₂-microglobulin (β₂-m) was determined by ¹H NMR spectroscopy and restrained modeling calculations. Compared to the crystal structure of type I major histocompatibility complex (MHC-I), where the protein is associated to the heavy-chain component, several differences are observed, i.e., increased separation between strands A and B, displacements of strand C′ and loop DE, shortening of strands D and E. These modifications can be considered as the prodromes of the amyloid transition. Even minor charge changes in response to pH, as is the case with H31 imidazole protonation, trigger the transition that starts with unpairing of strand A. The same mechanism accounts for the partial unfolding and fiber formation subsequent to Cu²⁺ binding which is shown to occur primarily at H31. Solvation of the protected regions in MHC-I decreases the tertiary packing by breaking the contiguity of the surface hydrophobic patches via surface charge cluster. Mutants or truncated forms of β₂-m can be designed to remove the instability from H31 titration or to enhance the instability through surface charge suppression. By monitoring the conformational evolution of wild-type protein and variants thereof, either in response or absence of external perturbation, valuable insights into intermediate structure and fibrillogenesis mechanisms are gained.     

Remote sensing for lake research and monitoring – Recent advances

Lakes are important ecosystems providing various ecosystem services. Stressors such as eutrophication or climate change, however, threaten their ecological functions. National and international legislations address these threats and claim consistent, long-term monitoring schemes. Remote sensing data and products provide synoptic, spatio-temporal views and their integration can lead to a better understanding of lake ecology and water quality. Remote sensing therefore gains increasing awareness for analysing water bodies. Various empirical and semi-analytical algorithms exist to derive remote sensing indicators as proxies for climate change or ecological response variables. Nevertheless, most monitoring networks lack an integration of remote sensing data. This review article therefore provides a comprehensive overview how remote sensing can support lake research and monitoring. We focus on remote sensing indicators of lake properties, i.e. water transparency (suspended particulate matter, coloured dissolved organic matter, Secchi disc depth, diffuse attenuation coefficient, turbidity), biota (phytoplankton, cyanobacteria, submerged and emerged aquatic vegetation), bathymetry, water temperature (surface temperature) and ice phenology (ice cover, ice-on, ice-out). After a brief background introducing principles of lake remote sensing we give a review on available sensors and methods. We categorise case studies on remote sensing indicators with respect to lake properties and processes. We discuss existing challenges and benefits of integrating remote sensing into lake monitoring and ecological research including data availability, ready-to-use tools and accuracies.     

Structural insights into the Aedes aegypti aquaporins and aquaglyceroporins – an in silico study

There has been a fair bit of understanding on the structure–function relationship of Aquaporins (AQPs) from plants and vertebrates obtained from available X-ray crystallography data. However, there is a lacuna in understanding the structure of AQPs from sanguinivorous insects like the mosquito where it plays a crucial role in survival. In this study, we have built homology models for the Aedes aegypti AQPs, identified key channel lining residues and compared the structure and sequence with orthodox AQPs. Although Ar/R filter residues of AaAQP1 were exactly similar to orthodox AQPs, AaAQP2 has a substitution at LE1position possibly making it less efficient in high capacity water transport. The huge difference in the selectivity filter region of AaAQP3 suggests a different transport property for this channel. The changes observed in the H5 position of the filter of AaAQP4 and AaAQP5 may explain the presence of a larger pore aperture to permit the passage of larger solute molecules. AaAQP6 possesses a completely hydrophobic filter like that in mammalian super aquaporins. The identified key residues are pivotal in understanding the mechanism of action and gating of these channels.     

The IκB kinase complex in NF-κB regulation and beyond

The IκB kinase (IKK) complex is the signal integration hub for NF-κB activation. Composed of two serine-threonine kinases (IKKα and IKKβ) and the regulatory subunit NEMO (also known as IKKγ), the IKK complex integrates signals from all NF-κB activating stimuli to catalyze the phosphorylation of various IκB and NF-κB proteins, as well as of other substrates. Since the discovery of the IKK complex components about 15 years ago, tremendous progress has been made in the understanding of the IKK architecture and its integration into signaling networks. In addition to the control of NF-κB, IKK subunits mediate the crosstalk with other pathways, thereby extending the complexity of their biological function. This review summarizes recent advances in IKK biology and focuses on emerging aspects of IKK structure, regulation and function.     

Recent advances in structure and function of cytosolic IMP-GMP specific 5′nucleotidase II (cN-II)

Cytosolic 5′ nucleotidase II (cN-II) catalyses both the hydrolysis of a number of nucleoside monophosphates (e.g., IMP + H₂O→ inosine + Pi), and the phosphate transfer from a nucleoside monophosphate donor to the 5′ position of a nucleoside acceptor (e.g., IMP + guanosine → inosine + GMP). The enzyme protein functions through the formation of a covalent phosphoenzyme intermediate, followed by the phosphate transfer either to water (phosphatase activity) or to a nucleoside (phosphotransferase activity). It has been proposed that cN-II regulates the intracellular concentration of IMP and GMP and the production of uric acid. The enzyme might also have a potential therapeutic importance, since it can phosphorylate some anti-tumoral and antiviral nucleoside analogues that are not substrates of known kinases. In this review we summarise our recent studies on the structure, regulation and function of cN-II. Via a site-directed mutagenesis approach, we have identified the amino acids involved in the catalytic mechanism and proposed a structural model of the active site. A series of in vitro studies suggests that cN-II might contribute to the regulation of 5-phosphoribosyl-1-pyrophosphate (PRPP) level, through the so-called oxypurine cycle, and in the production of intracellular adenosine, formed by ATP degradation.     

Prediction of proton chemical shifts in RNA – Their use in structure refinement and validation

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct., 76, 81–92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341–346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the ¹H chemical shifts revealing their physical origin. For example, a down-field shift of either H2 or H3 or both indicates a high-syn/syn -angle. In an A-helix it is essentially the 5-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed ¹H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings.     

Molecular mechanisms of cardiac pathology in diabetes – Experimental insights

Diabetic cardiomyopathy is a distinct pathology independent of co-morbidities such as coronary artery disease and hypertension. Diminished glucose uptake due to impaired insulin signaling and decreased expression of glucose transporters is associated with a shift towards increased reliance on fatty acid oxidation and reduced cardiac efficiency in diabetic hearts. The cardiac metabolic profile in diabetes is influenced by disturbances in circulating glucose, insulin and fatty acids, and alterations in cardiomyocyte signaling. In this review, we focus on recent preclinical advances in understanding the molecular mechanisms of diabetic cardiomyopathy. Genetic manipulation of cardiomyocyte insulin signaling intermediates has demonstrated that partial cardiac functional rescue can be achieved by upregulation of the insulin signaling pathway in diabetic hearts. Inconsistent findings have been reported relating to the role of cardiac AMPK and β-adrenergic signaling in diabetes, and systemic administration of agents targeting these pathways appear to elicit some cardiac benefit, but whether these effects are related to direct cardiac actions is uncertain. Overload of cardiomyocyte fuel storage is evident in the diabetic heart, with accumulation of glycogen and lipid droplets. Cardiac metabolic dysregulation in diabetes has been linked with oxidative stress and autophagy disturbance, which may lead to cell death induction, fibrotic ‘backfill’ and cardiac dysfunction. This review examines the weight of evidence relating to the molecular mechanisms of diabetic cardiomyopathy, with a particular focus on metabolic and signaling pathways. Areas of uncertainty in the field are highlighted and important knowledge gaps for further investigation are identified. This article is part of a Special issue entitled Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers.     

Structure and function of the C-terminal domain of MrpA in the Bacillus subtilis Mrp-antiporter complex – The evolutionary progenitor of the long horizontal helix in complex I

MrpA and MrpD are homologous to NuoL, NuoM and NuoN in complex I over the first 14 transmembrane helices. In this work, the C-terminal domain of MrpA, outside this conserved area, was investigated. The transmembrane orientation was found to correspond to that of NuoJ in complex I. We have previously demonstrated that the subunit NuoK is homologous to MrpC. The function of the MrpA C-terminus was tested by expression in a previously used Bacillus subtilis model system. At neutral pH, the truncated MrpA still worked, but at pH 8.4, where Mrp-complex formation is needed for function, the C-terminal domain of MrpA was absolutely required.     

Liquid-EM goes viral – visualizing structure and dynamics

Liquid-electron microscopy (EM), the room temperature correlate to cryo-EM, is an exciting new technique delivering real-time data of dynamic reactions in solution. Here, we explain how liquid-EM gained popularity in recent years by examining key experiments conducted on viral assemblies and host–pathogen interactions. We describe developing workflows for specimen preparation, data collection, and computing processes that led to the first high-resolution virus structures in a liquid environment. Equally important, we review why liquid-electron tomography may become the next big thing in biomedical research due to its ability to monitor live viruses entering cells within seconds. Taken together, we pose the idea that liquid-EM can serve as a dynamic complement to current cryo-EM methods, inspiring the “real-time revolution” in nanoscale imaging.     

Mini-review: Antimicrobial central venous catheters – recent advances and strategies

Central venous catheters (CVCs) nowadays constitute critical devices used in medical care, namely in intensive care units. However, CVCs also represent one of the indwelling medical devices with enhanced risk of nosocomial device-related infection. Catheter-related infections (CRIs) are a major cause of patient morbidity and mortality, often justifying premature catheter removal and an increase in costs and use of resources. Adhesion and subsequent biofilm formation on the surfaces of indwelling catheters is elemental to the onset of pathogenesis. Seeking the prevention of CVC colonisation and CRI, a variety of approaches have been studied, tested and, in some cases, already applied in clinical practice. This review looks at the current preventive strategies often used to decrease the risk of CRIs due to colonization and biofilm formation on catheter surfaces, as well as at the more recent approaches under investigation.     

Crystal structure determination of the β-cyclodextrin-p-aminobenzoic acid inclusion complex from powder X-ray diffraction data

The 1:1 inclusion complex of β-cyclodextrin and p-aminobenzoic acid was prepared and characterized by TG-DTA. The crystal structure of the complex was solved directly from powder X-ray diffraction data using the direct space approach and refined using Rietveld refinement techniques. The complex crystallizes in monoclinic P2₁ space group, with unit cell parameters a = 20.7890 ?, b = 10.2084 ?, c = 15.1091 ?, β = 110.825°, V = 2997 ?³. The amino group is located at the wide side of the β-cyclodextrin cavity, forming hydrogen bonds with β-cyclodextrin, and the carboxyl group is located at the narrow side. The crystallographic data obtained from powder diffraction data were compared with the single crystallographic data, and the result shows that solving crystal structure of cyclodextrins inclusion complexes of such complexity is accessible to powder diffractionists to some extent.     

Technical-Induced Hemolysis in Patients with Respiratory Failure Supported with Veno-Venous ECMO – Prevalence and Risk Factors

The aim of the study was to explore the prevalence and risk factors for technical-induced hemolysis in adults supported with veno-venous extracorporeal membrane oxygenation (vvECMO) and to analyze the effect of hemolytic episodes on outcome. This was a retrospective, single-center study that included 318 adult patients (Regensburg ECMO Registry, 2009–2014) with acute respiratory failure treated with different modern miniaturized ECMO systems. Free plasma hemoglobin (fHb) was used as indicator for hemolysis. Throughout a cumulative support duration of 4,142 days on ECMO only 1.7% of the fHb levels were above a critical value of 500 mg/l. A grave rise in fHb indicated pumphead thrombosis (n = 8), while acute oxygenator thrombosis (n = 15) did not affect fHb. Replacement of the pumphead normalized fHb within two days. Neither pump or cannula type nor duration on the first system was associated with hemolysis. Multiple trauma, need for kidney replacement therapy, increased daily red blood cell transfusion requirements, and high blood flow (3.0–4.5 L/min) through small-sized cannulas significantly resulted in augmented blood cell trauma. Survivors were characterized by lower peak levels of fHb [90 (60, 142) mg/l] in comparison to non-survivors [148 (91, 256) mg/l, p≤0.001]. In conclusion, marked hemolysis is not common in vvECMO with modern devices. Clinically obvious hemolysis often is caused by pumphead thrombosis. High flow velocity through small cannulas may also cause technical-induced hemolysis. In patients who developed lung failure due to trauma, fHb was elevated independantly of ECMO. In our cohort, the occurance of hemolysis was associated with increased mortality.