Nanodiscs: A toolkit for membrane protein science

Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self‐assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native‐like bilayer environment that maintain a target''s functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.     

Hydrogen bond and acid-base interactions in erythromycin solutions

The association and conformational structure of the molecule of erythromycin in solutions of CCl4, C2Cl4 and CHCl3 were studied by the IR spectra in the region of v OH and vC = O. The analysis of the concentration and temperature changes showed that the erythromycin association was accounted for by the hydrogen linkage of OH ... O = C to the ester group. In the monomer molecule of erythromycin, all hydroxyl groups participated in the intramolecular hydrogen linkage. Band 3513 cm-1 belonged to the OH group in the five-membered cycles of OH ... O. Components 3500, 3530 and 3560 cm-1 of the wide band vOH were assigned to the cycles with OH ... N and OH ... O linkages of a larger size. The association was due to a break in a part of the intramolecular hydrogen linkages. Addition of strong acceptors of proton-hexamethanol and trioctylphosphinoxide to the solution resulted in attenuation of these bands and appearance of a strong band vOH of the erythromycin-acceptor complexes. In the presence of monochloroacetic acid in the solution of CHCl3 stoichiometric protonization of erythromycin was observed. The total acid was in the form of anion (vaCO-2 1610 cm-1) up to a ratio of 1:1. The protonization proceeded according to the nitrogen atom since the antibiotic spectrum in the region of vC=O did not change. Propionic acid titrated erythromycin in methanol solution and in mixtures of water and methanol up to a ratio of 1:5 (v/v). However, in the solution of CHCl3 equilibrium between the neutral and ionized molecules of the acid was seen.     

Characterization of a novel and spontaneous mouse model of inflammatory arthritis

Introduction  

Mouse models of rheumatoid arthritis (RA) have proven critical for identifying genetic and cellular mechanisms of the disease. Upon discovering mice in our breeding colony that had spontaneously developed inflamed joints reminiscent of RA, we established the novel IIJ (inherited inflamed joints) strain. The purpose of this study was to characterize the histopathological, clinical, genetic and immunological properties of the disease.     

Sediments,not plants,offer the preferred refuge for Daphnia against fish predation in Mediterranean shallow lakes: an experimental demonstration

1. Different behavioural responses of planktonic animals to their main predators, fish, have been reported from shallow lakes. In north temperate lakes, large‐bodied zooplankton may seek refuge from predation among macrophytes, whereas in subtropical lakes, avoidance of macrophytes has been observed. The prevalent behaviour probably depends on the characteristics of the fish community, which in Mediterranean lakes is typically dispersed in both the open water zone and in the littoral, as in temperate lakes, and is dominated by small size classes, as in subtropical lakes. 2. We performed ‘habitat choice’ experiments to test the response of Daphnia magna to predation cues at both the horizontal and vertical level by mimicking a ‘shallow littoral’ zone with plants and a ‘deeper pelagic’ zone with sediments. 3. Initial separate response experiments showed that natural plants, artificial plants and predation cues all repelled D. magna in the absence of other stimuli, while sediments alone did not trigger any significant response by D. magna. 4. The habitat choice experiments showed that, in the presence of predation cues and absence of plants, Daphnia moved towards areas with sediment. In the presence of both plants and sediments, Daphnia moved away from the plants towards the sediments under both shallow and deep water treatment conditions. 5. Based on these results, we suggest that Daphnia in Mediterranean shallow lakes avoid submerged macrophytes and instead prefer to hide near the sediment when exposed to predation risk, as also observed in subtropical shallow lakes. This pattern is not likely to change with water level alterations, a common feature of lakes in the region, even if the effectiveness of the refuge may be reduced.     

Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes

Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm-incorporating phase information-further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s-increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides.     

Molecular basis of anticoagulant and anticomplement activity of the tick salivary protein Salp14 and its homologs

During feeding, a tick''s mouthpart penetrates the host''s skin and damages tissues and small blood vessels, triggering the extrinsic coagulation and lectin complement pathways. To elude these defense mechanisms, ticks secrete multiple anticoagulant proteins and complement system inhibitors in their saliva. Here, we characterized the inhibitory activities of the homologous tick salivary proteins tick salivary lectin pathway inhibitor, Salp14, and Salp9Pac from Ixodesscapularis in the coagulation cascade and the lectin complement pathway. All three proteins inhibited binding of mannan-binding lectin to the polysaccharide mannan, preventing the activation of the lectin complement pathway. In contrast, only Salp14 showed an appreciable effect on coagulation by prolonging the lag time of thrombin generation. We found that the anticoagulant properties of Salp14 are governed by its basic tail region, which resembles the C terminus of tissue factor pathway inhibitor alpha and blocks the assembly and/or activity of the prothrombinase complex in the same way. Moreover, the Salp14 protein tail contributes to the inhibition of the lectin complement pathway via interaction with mannan binding lectin–associated serine proteases. Furthermore, we identified BaSO₄-adsorbing protein 1 isolated from the tick Ornithodoros savignyi as a distant homolog of tick salivary lectin pathway inhibitor/Salp14 proteins and showed that it inhibits the lectin complement pathway but not coagulation. The structure of BaSO₄-adsorbing protein 1, solved here using NMR spectroscopy, indicated that this protein adopts a noncanonical epidermal growth factor domain–like structural fold, the first such report for tick salivary proteins. These data support a mechanism by which tick saliva proteins simultaneously inhibit both the host coagulation cascade and the lectin complement pathway.     

Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes – relevance for vaccine design

To properly characterize protective polyclonal antibody responses, it is necessary to examine epitope specificity. Most antibody epitopes are conformational in nature and, thus, cannot be identified using synthetic linear peptides. Cyclic peptides can function as mimetics of conformational epitopes (termed mimotopes), thereby providing targets, which can be selected by immunoaffinity purification. However, the management of large collections of random cyclic peptides is cumbersome. Filamentous bacteriophage provides a useful scaffold for the expression of random peptides (termed phage display) facilitating both the production and manipulation of complex peptide libraries. Immunoaffinity selection of phage displaying random cyclic peptides is an effective strategy for isolating mimotopes with specificity for a given antiserum. Further epitope prediction based on mimotope sequence is not trivial since mimotopes generally display only small homologies with the target protein. Large numbers of unique mimotopes are required to provide sufficient sequence coverage to elucidate the target epitope. We have developed a method based on pattern recognition theory to deal with the complexity of large collections of conformational mimotopes. The analysis consists of two phases: 1) The learning phase where a large collection of epitope-specific mimotopes is analyzed to identify epitope specific "signs" and 2) The identification phase where immunoaffinity-selected mimotopes are interrogated for the presence of the epitope specific "signs" and assigned to specific epitopes. We are currently using computational methods to define epitope "signs" without the need for prior knowledge of specific mimotopes. This technology provides an important tool for characterizing the breadth of antibody specificities within polyclonal antisera.     

Structure and homodynamia of the intersegmental connection TI-TII

The reason to consider the second thoracic cerebrospinal nerve (Th2) as one of the sources of the brachial plexus is the fact of the intersegmentary connection between Th1 and Th2 by means of a neural branch situating on the internal surface of the thorax near the vertebral column (the intrathoracic or paravertebral branch). However, not all cases of the intersegmentary connection Th1-Th2 should be regarded only as participation of Th2 in the formation of the brachial plexus, this is conditioned by certain peculiarities of its structure and by the character of interconnections with the I intercostal nerve. The macro-microscopic method demonstrates that the intersegmentary connection Th1-Th2 includes somatic and vegetative components, that to the same extent participate both in formation of the brachial plexus and in the I intercostal nerve. The intersegmentary connection Th1-Th2 is considered as a vegetative neural structure, containing somatic conductors and is considered as a homologue of superficial connective branches. It is the way, by which sympathetic fibers can reach the brachial plexus from the segment situating below, without passing through the superior thoracic nodes of the sympathetic trunk.