Structure of compstatin in complex with complement component C3c reveals a new mechanism of complement inhibition

Undesired complement activation is a major cause of tissue injury in various pathological conditions and contributes to several immune complex diseases. Compstatin, a 13-residue peptide, is an effective inhibitor of the activation of complement component C3 and thus blocks a central and crucial step in the complement cascade. The precise binding site on C3, the structure in the bound form, and the exact mode of action of compstatin are unknown. Here we present the crystal structure of compstatin in complex with C3c, a major proteolytic fragment of C3. The structure reveals that the compstatin-binding site is formed by the macroglobulin (MG) domains 4 and 5. This binding site is part of the structurally stable MG-ring formed by domains MG 1-6 and is far away from any other known binding site on C3. Compstatin does not alter the conformation of C3c, whereas compstatin itself undergoes a large conformational change upon binding. We propose a model in which compstatin sterically hinders the access of the substrate C3 to the convertase complexes, thus blocking complement activation and amplification. These insights are instrumental for further development of compstatin as a potential therapeutic.     

Chlorpyrifos immersion to eliminate third instars of Japanese beetle (Coleoptera: Scarabaeidae) in balled and burlapped trees and subsequent treatment effects on red maple

This study examined chlorpyrifos immersion of balled and burlapped (B&B) nursery trees for elimination of third instars of Japanese beetle, Popillia japonica Newman (Coleoptera: Scarabaeidae), and for phytotoxicity on red maple, Acer rubrum L. Trees were harvested as 45- and 60-cm-diameter B&B and immersed in chlorpyrifos at U.S. Domestic Japanese Beetle Harmonization Plan rate (0.24 kg active ingredient [AI/100 liters) or lower rates of 0.015, 0.03, 0.06, and 0.12 kg (AI)/100 liters. The 0.03, 0.06, and 0.24 kg (AI) rates provided 100% control of Japanese beetle grubs in both 45- and 60-cm B&B. The 0.015 and 0.12 kg (AI) chlorpyrifos rates were 100% effective in three tests. However, in another test, 0.015 and 0.12 kg (AI) chlorpyrifos treatments had four (93% control) and one (98% control) grubs recovered, respectively. Root ball soils consisted of loam, silt loam, or clay loam texture classifications. Trunk diameter and internode growth of red maple harvested as 45-cm B&B decreased linearly with increasing chlorpyrifos dip rate during the first year, but effects were unapparent in the second year. Chlorpyrifos rates had no measurable impact on growth of red maples harvested as 60-cm B&B. No visual phytotoxicity symptoms were detected for chlorpyrifos rate or root ball size treatments. In conclusion, results support lowering the U.S. Domestic Japanese Beetle Harmonization Plan chlorpyrifos dip rate for category 2 states to at least 0.03 kg (AI) for B&B diameters < or =60 cm. Chlorpyrifos rates < 0.24 kg (AI) will lower cost, reduce worker exposure, and lessen potential environmental contamination.     

Affinity chromatography: a useful tool in proteomics studies

Separation or fractionation of a biological sample in order to reduce its complexity is often a prerequisite to qualitative or quantitative proteomic approaches. Affinity chromatography is an efficient protein separation method based on the interaction between target proteins and specific immobilized ligands. The large range of available ligands allows to separate a complex biological extract in different protein classes or to isolate the low abundance species such as post-translationally modified proteins. This method plays an essential role in the isolation of protein complexes and in the identification of protein-protein interaction networks. Affinity chromatography is also required for quantification of protein expression by using isotope-coded affinity tags.     

Development and validation of a liquid chromatography/tandem mass spectrometry method for the determination of DMXAA in human and mouse plasma

A rapid, sensitive, and specific LC/MS/MS-based method was developed for determining the concentration of DMXAA in human and mouse plasma. Sample preparation involved a single protein precipitation step using acetonitrile. Separation of DMXAA and 6-isopropoxy-9-oxoxanthene-2-carboxylic acid, the internal standard, was achieved on a Waters X-Terra C(18) (50 mm x 2.1mm i.d., 3.5 microm) analytical column using a mobile phase consisting of acetonitrile/10 mM ammonium acetate (55:45, v/v) containing 0.1% formic acid and isocratic flow at 0.2 mL/min for 3 min. The analytes were monitored by tandem mass spectrometry with electrospray positive ionization. Linear calibration curves were generated over the range of 5-3000 ng/mL. The values for precision and accuracy were <9.6%, except at the LLOQ (5 ng/mL) level, which was within 16.8%. Recovery of DMXAA in mouse plasma was >65%. DMXAA was stable through 2 freeze/thaw cycles, to 2h in mouse plasma or 50% acetonitrile, and on the autosampler to 5.1h. This method was subsequently used to measure concentrations of DMXAA in mice following intraperitoneal administration.     

Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex

Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes.     

Scleractinian corals (Fungiidae,Agariciidae and Euphylliidae) of Pulau Layang-Layang,Spratly Islands,with a note on Pavona maldivensis (Gardiner, 1905)

Layang-Layang is a small island part of an oceanic atoll in the Spratly Islands off Sabah, Malaysia. As the reef coral fauna in this part of the South China Sea is poorly known, a survey was carried out in 2013 to study the species composition of the scleractinian coral families Fungiidae, Agariciidae and Euphylliidae. A total of 56 species was recorded. The addition of three previously reported coral species brings the total to 59, consisting of 32 Fungiidae, 22 Agariciidae, and five Euphylliidae. Of these, 32 species are new records for Layang-Layang, which include five rarely reported species, i.e., the fungiids Lithophyllon ranjithi, Podabacia sinai, Sandalolitha boucheti, and the agariciids Leptoseris kalayaanensis and Leptoseris troglodyta. The coral fauna of Layang-Layang is poor compared to other areas in Sabah, which may be related to its recovery from a crown-of-thorns seastar outbreak in 2010, and its low habitat diversity, which is dominated by reef slopes consisting of steep outer walls. Based on integrative molecular and morphological analyses, a Pavona variety with small and extremely thin coralla was revealed as Pavona maldivensis. Since specimens from Sabah previously identified as Pavona maldivensis were found to belong to Pavona explanulata, the affinities and distinctions of Pavona maldivensis and Pavona explanulata are discussed.     

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.     

Extent of metal ion-sulfur binding in complexes of thiouracil nucleosides and nucleotides in aqueous solution

Previously published stability constants of several metal ion (M2+) complexes formed with thiouridines and their 5'-monophosphates, together with recently obtained log K(M(U))(M) versus pK(U)(H) plots for M2+ complexes of uridinate derivatives (U-) allowed now a quantitative evaluation of the effect that the exchange of a (C)O by a (C)S group has on the stability of the corresponding complexes. For example, the stability of the Ni2+, Cu2+ and Cd2+ complexes of 2-thiouridinate is increased by about 1.6, 2.3, and 1.3 log units, respectively, by the indicated exchange of groups. Similar results were obtained for other thiouridinates, including 4-thiouridinate. The structure of these complexes and the types of chelates formed (involving (N3)- and (C)S) are discussed. A recently advanced method for the quantification of the chelate effect allows now also an evaluation of several complexes of thiouridinate 5'-monophosphates. In most instances the thiouracilate coordination dominates the systems, allowing only the formation of small amounts of phosphate-bound isomers. Among the complexes studied only the one formed by Cu2+ with 2-thiouridinate 5'-monophosphate leads to significant amounts of the macrochelated isomer, which means that in this case Cu2+ is able to force the nucleotide from the anti to the syn conformation, allowing thus metal ion binding to both potential sites and this results in the formation of about 58% of the macrochelated isomer. The remaining 42% are species in which Cu2+ is overwhelmingly coordinated to the thiouracilate residue; Cu2+ binding to the phosphate group occurs in this case only in trace amounts.     

Preexisting hypoxia is associated with a delayed but more sustained rise in T/QRS ratio during prolonged umbilical cord occlusion in near-term fetal sheep

There is limited information about whether preexisting fetal hypoxia alters hemodynamic responses and changes in T/QRS ratio and ST waveform shape during subsequent severe asphyxia. Chronically instrumented near-term sheep fetuses (124 +/- 1 days) were identified as either normoxic Pa(O(2)) > 17 mmHg (n = 9) or hypoxic Pa(O(2)) < or = 17 mmHg (n = 5); then they received complete occlusion of the umbilical cord for 15 min. Umbilical cord occlusion led to sustained bradycardia, severe acidosis, and transient hypertension followed by profound hypotension in both groups. Preexisting hypoxia did not affect changes in mean arterial blood pressure but was associated with a more rapid initial fall in femoral blood flow and vascular conductance and with transiently higher fetal heart rate at 2 min and from 9 to 11 min of occlusion compared with previously normoxic fetuses. Occlusion was associated with a significant but transient rise in T/QRS ratio; preexisting hypoxia was associated with a significant delay in this rise (maxima 3.7 +/- 0.4 vs. 6.2 +/- 0.5 min), but a slower rate of fall. There was a similar elevation in troponin-T levels 6 h after occlusion in the two groups [median (range) 0.43 (0.08, 1.32) vs. 0.55 (0.16, 2.32) microg/l, not significant]. In conclusion, mild preexisting hypoxia in normally grown singleton fetal sheep is associated with more rapid centralization of circulation after umbilical cord occlusion and delayed elevation of the ST waveform and slower fall, suggesting that chronic hypoxia alters myocardial dynamics during asphyxia.