Proton transport coupled ATP synthesis by the purified yeast H-ATP synthase in proteoliposomes

The H⁺/ATP synthase from yeast mitochondria, MF₀F₁, was purified and reconstituted into liposomes prepared from phosphatidylcholine and phosphatidic acid. Analysis by mass spectrometry revealed the presence of all subunits of the yeast enzyme with the exception of the K-subunit. The MF₀F₁ liposomes were energized by acid-base transitions (ΔpH) and a K⁺/valinomycin diffusion potential (Δφ). ATP synthesis was completely abolished by the addition of uncouplers as well as by the inhibitor oligomycin. The rate of ATP synthesis was optimized as a function of various parameters and reached a maximum value (turnover number) of 120 s^− 1 at a transmembrane pH difference of 3.2 units (at pH_in = 4.8 and pH_out = 8.0) and a Δφ of 133 mV (Nernst potential). Functional studies showed that the monomeric MF₀F₁ was fully active in ATP synthesis. The turnover increased in a sigmoidal way with increasing internal and decreasing external proton concentration. The dependence of the turnover on the phosphate concentration and the dependence of K_M on pH_out indicated that the substrate for ATP synthesis is the monoanionic phosphate species H₂PO₄⁻.     

Regulation of Sealing Ring Formation by L-plastin and Cortactin in Osteoclasts

The aim of this study is to identify the exact mechanism(s) by which cytoskeletal structures are modulated during bone resorption. In this study, we have shown the possible role of different actin-binding and signaling proteins in the regulation of sealing ring formation. Our analyses have demonstrated a significant increase in cortactin and a corresponding decrease in L-plastin protein levels in osteoclasts subjected to bone resorption for 18 h in the presence of RANKL, M-CSF, and native bone particles. Time-dependent changes in the localization of L-plastin (in actin aggregates) and cortactin (in the sealing ring) suggest that these proteins may be involved in the initial and maturation phases of sealing ring formation, respectively. siRNA to cortactin inhibits this maturation process but not the formation of actin aggregates. Osteoclasts treated as above but with TNF-α demonstrated very similar effects as observed with RANKL. Osteoclasts treated with a neutralizing antibody to TNF-α displayed podosome-like structures in the entire subsurface and at the periphery of osteoclast. It is possible that TNF-α and RANKL-mediated signaling may play a role in the early phase of sealing ring configuration (i.e. either in the disassembly of podosomes or formation of actin aggregates). Furthermore, osteoclasts treated with alendronate or αv reduced the formation of the sealing ring but not actin aggregates. The present study demonstrates a novel mechanistic link between L-plastin and cortactin in sealing ring formation. These results suggest that actin aggregates formed by L-plastin independent of integrin signaling function as a core in assembling signaling molecules (integrin αvβ3, Src, cortactin, etc.) involved in the maturation process.     

Limitations of Peptide Retro-inverso Isomerization in Molecular Mimicry

A retro-inverso peptide is made up of d-amino acids in a reversed sequence and, when extended, assumes a side chain topology similar to that of its parent molecule but with inverted amide peptide bonds. Despite their limited success as antigenic mimicry, retro-inverso isomers generally fail to emulate the protein-binding activities of their parent peptides of an α-helical nature. In studying the interaction between the tumor suppressor protein p53 and its negative regulator MDM2, Sakurai et al. (Sakurai, K., Chung, H. S., and Kahne, D. (2004) J. Am. Chem. Soc. 126, 16288–16289) made a surprising finding that the retro-inverso isomer of p53(15–29) retained the same binding activity as the wild type peptide as determined by inhibition enzyme-linked immunosorbent assay. The authors attributed the unusual outcome to the ability of the d-peptide to adopt a right-handed helical conformation upon MDM2 binding. Using a battery of biochemical and biophysical tools, we found that retro-inverso isomerization diminished p53 (15,–29) binding to MDM2 or MDMX by 3.2–3.3 kcal/mol. Similar results were replicated with the C-terminal domain of HIV-1 capsid protein (3.0 kcal/mol) and the Src homology 3 domain of Abl tyrosine kinase (3.4 kcal/mol). CD and NMR spectroscopic as well as x-ray crystallographic studies showed that d-peptide ligands of MDM2 invariably adopted left-handed helical conformations in both free and bound states. Our findings reinforce that the retro-inverso strategy works poorly in molecular mimicry of biologically active helical peptides, due to inherent differences at the secondary and tertiary structure levels between an l-peptide and its retro-inverso isomer despite their similar side chain topologies at the primary structure level.     

Effects of co-existed proteins on measurement of pesticide residues in blood by gas chromatography-mass spectrometry

Accurate measurement of pesticides in biological fluids such as blood is important for quantifying environmental exposures. Beyond sample enrichment and separation, the method presented here is focused on studies of interactions between pesticides and co-existed proteins. It was experimentally demonstrated that entrapped or adsorbed pesticide residues within the folded native structures of proteins were poorly recovered using direct solvent extraction solely. We described here an effective approach termed Enzymatic Digestion-Organic Solvent Extraction (eDOSE) that utilizes the enzymatic approach to disrupt the folded structures of proteins and release entrapped or adsorbed pesticide residues. In this approach, samples were first reduced, alkylated, tryptically digested and then diluted 10 times before the subsequent extraction using an n-hexane solution. Resultant pesticide residues were determined by capillary gas chromatography coupled with a mass spectrometer. Mean recoveries of the 5 organophosphorus pesticides pre-spiked in fish blood including diazinon, parathion-methyl, malathion, parathion-ethyl and ethion were 85%, 95%, 84%, 103%, and 43% respectively using eDOSE strategy but only 24%, 45%, 40%, 27%, and 29% respectively using direct solvent extraction approach. The eDOSE approach was effective for demonstrating the critical role of folded native structure of serum albumin in adsorption of exogenous chemicals. It provides an alterative means for denaturation of proteins when the target analytes are not stable in acidic solution or entrapped within the protein aggregates caused by organic solvents such as acetone that have been applied for protein denaturation. The eDOSE approach should be able to combine with other advanced techniques of enrichment and separation for more efficient and accurate measurement of target compounds present in the context of complex biological systems. This approach can provide wide applications to the analysis of a variety of small molecules including environmental pesticide residues and metabolites as well as other toxins present in cells, tissues and biofluids.     

Towards native-state imaging in biological context in the electron microscope

Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context.     

Earthworm invasions in the tropics

The effects and implications of invasive species in belowground terrestrial ecosystems are not well known in comparison with above-ground terrestrial and marine environments. The study of earthworm invasions in the tropics is limited by a lack of taxonomic knowledge and the potential for loss of species in native habitats due to anthropogenic land use change. Alteration of land use plays a major role in determining the abundance and community structure of earthworms and the establishment of exotic earthworms in areas previously inhabited by worms. Once an exotic species has become established into a new place, site and species characteristics seem to be key factors determining their spread. We reviewed the literature on the distribution and effects of exotic earthworms to understand the interactions of earthworm invasion and land use history in the tropics. Patterns in the abundance, effects and mechanisms of earthworm invasions on ecosystem processes in the tropics are elucidated using Pontoscolex corethrurus as a case study.     

Asymptomatic Helicobacter pylori infection and iron deficiency are not associated with decreased growth among Alaska Native children aged 7-11 years

Introduction: Alaska Native children have high Helicobacter pylori infection and iron deficiency prevalences, and their average height‐for‐age is lower than US reference populations. During a clinical trial to determine the impact of H. pylori treatment on iron deficiency, we evaluated the effects of H. pylori infection and treatment on growth. Materials and Methods: We measured height and weight for children aged 7–11 years in western Alaska using village‐based measuring devices. H. pylori infection was determined by urea breath test and iron deficiency using serum ferritin. Children with H. pylori infection and iron deficiency entered the treatment phase and received iron alone or iron plus triple therapy for H. pylori. Follow‐up evaluations occurred at 2, 8, and 14 months. We evaluated the association between baseline H. pylori infection and growth; among children in the treatment phase, we also assessed the effect of H. pylori resolution on growth. Results: At baseline, 566 (87.1%) of 650 children were infected with H. pylori. Neither height and weight, nor body mass index differed by H. pylori infection status. Of 189 children in the treatment phase, 20 (10.6%) were uninfected at all three follow‐up periods, and 54 (28.6%) were uninfected for one or two periods. Compared with continuously infected children, children in these two groups had little evidence of improvements in any of the measured growth outcomes. Conclusions: H. pylori infection is not related to growth among Alaska Native children aged 7–11 years. Growth deficiency should not be considered an indication for H. pylori therapy.     

The change of soil carbon stocks and fine root dynamics after land use change from a native pasture to a pine plantation

A published meta-analysis of worldwide data showed soil carbon decreasing following land use change from pasture to conifer plantation. A paired site (a native pasture with Themeda triandra dominant, and an adjacent Pinus radiata plantation planted onto the pasture 16 years ago) was set up as a case study to assess the soil carbon reduction and the possible reason for the reduction under pine, including the change in fine root (diameter <2 mm) dynamics (production and mortality). Soil analysis confirmed that soil carbon and nitrogen stocks to 100 cm under the plantation were significantly less than under the pasture by 20 and 15%, respectively. A 36% greater mass of fine root was found in the soil under the pasture than under the plantation and the length of fine root was about nine times greater in the pasture. Much less fine root length was produced and roots died more slowly under the plantation than under the pasture based on observations of fine root dynamics in minirhizotrons. The annual inputs of fine root litter to the top 100 cm soil, estimated from soil coring and minirhizotron observations, were 6.3 Mg dry matter ha⁻¹ year⁻¹ (containing 2.7 Mg C and 38.9 kg N) under the plantation, and 9.7 Mg ha⁻¹ year⁻¹ (containing 3.6 Mg C and 81.4 kg N) under the pasture. The reduced amount of carbon, following afforestation of the pasture, in each depth-layer of the soil profile correlated with the lower length of dead fine roots in the layer under the plantation compared with the pasture. This correlation was consistent with the hypothesis that the soil carbon reduction after land use change from pasture to conifer plantation might be related to change of fine root dynamics, at least in part.     

Folding subdomains of thioredoxin characterized by native-state hydrogen exchange

Native-state hydrogen exchange (HX) studies, used in conjunction with NMR spectroscopy, have been carried out on Escherichia coli thioredoxin (Trx) for characterizing two folding subdomains of the protein. The backbone amide protons of only the slowest-exchanging 24 amino acid residues, of a total of 108 amino acid residues, could be followed at pH 7. The free energy of the opening event that results in an amide hydrogen exchanging with solvent (DeltaG(op)) was determined at each of the 24 amide hydrogen sites. The values of DeltaG(op) for the amide hydrogens belonging to residues in the helices alpha(1), alpha(2), and alpha(4) are consistent with them exchanging with the solvent only when the fully unfolded state is sampled transiently under native conditions. The denaturant-dependences of the values of DeltaG(op) provide very little evidence that the protein samples partially unfolded forms, lower in energy than the unfolded state. The amide hydrogens belonging to the residues in the beta strands, which form the core of the protein, appear to have higher values of DeltaG(op) than amide hydrogens belonging to residues in the helices, suggesting that they might be more stable to exchange. This apparently higher stability to HX of the beta strands might be either because they exchange out their amide hydrogens in a high energy intermediate preceding the globally unfolded state, or, more likely, because they form residual structure in the globally unfolded state. In either case, the central beta strands-beta(3,) beta(2), and beta(4)-would appear to form a cooperatively folding subunit of the protein. The native-state HX methodology has made it possible to characterize the free energy landscape that Trx can sample under equilibrium native conditions.     

High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas

A total of 63 binary polymorphisms and 10 short tandem repeats (STRs) were genotyped on a sample of 2,344 Y chromosomes from 18 Native American, 28 Asian, and 5 European populations to investigate the origin(s) of Native American paternal lineages. All three of Greenberg's major linguistic divisions (including 342 Amerind speakers, 186 Na-Dene speakers, and 60 Aleut-Eskimo speakers) were represented in our sample of 588 Native Americans. Single-nucleotide polymorphism (SNP) analysis indicated that three major haplogroups, denoted as C, Q, and R, accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y chromosome lineages; however, most haplogroup R lineages present in Native Americans most likely came from recent admixture with Europeans. Although different phylogeographic and STR diversity patterns for the two major founding haplogroups previously led to the inference that they were carried from Asia to the Americas separately, the hypothesis of a single migration of a polymorphic founding population better fits our expanded database. Phylogenetic analyses of STR variation within haplogroups C and Q traced both lineages to a probable ancestral homeland in the vicinity of the Altai Mountains in Southwest Siberia. Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas.