Human Mitochondrial AAA+ ATPase SKD3/CLPB forms Nucleotide-Stabilized Dodecamers

SKD3, also known as human CLPB, belongs to the AAA+ family of ATPases associated with various activities. Mutations in the SKD3/CLPB gene cause 3-methylglutaconic aciduria type VII and congenital neutropenia. SKD3 is upregulated in acute myeloid leukemia, where it contributes to anti-cancer drug resistance. SKD3 resides in the mitochondrial intermembrane space, where it forms ATP-dependent high-molecular weight complexes, but its biological function and mechanistic links to the clinical phenotypes are currently unknown. Using sedimentation equilibrium and dynamic light scattering, we show that SKD3 is monomeric at low protein concentration in the absence of nucleotides, but it forms oligomers at higher protein concentration or in the presence of adenine nucleotides. The apparent molecular weight of the nucleotide-bound SKD3 is consistent with self-association of 12 monomers. Image-class analysis and averaging from negative-stain electron microscopy (EM) of SKD3 in the ATP-bound state visualized cylinder-shaped particles with an open central channel along the cylinder axis. The dimensions of the EM-visualized particle suggest that the SKD3 dodecamer is formed by association of two hexameric rings. While hexameric structure has been often observed among AAA+ ATPases, a double-hexamer sandwich found for SKD3 appears uncommon within this protein family. A functional significance of the non-canonical structure of SKD3 remains to be determined.

Gas Deviation Factor Calculation Made Easy and Accurate Using an IR 4.0 Tool

Gas deviation factor (z-factor) and other gas reservoir fluid properties, such as formation volume factor, density, and viscosity, are normally obtained from Pressure-Volume-Temperature (PVT) experimental analysis. This process of reservoir fluid characterization usually requires collecting pressurized fluid samples from the wellbore to conduct the experimental work. The scope of this paper will provide an alternative methodology for obtaining the z-factor. An IR 4.0 tool that heavily utilizes software coding was developed. The advanced tool uses the novel apparent molecular weight profiling concept to achieve the paper objective timely and accurately. The developed tool calculates gas properties based on downhole gradient pressure and temperature data as inputs. The methodology is applicable to dry, wet or condensate gas wells. The gas equation of state is modified to solve numerically for the z-factor using the gradient survey pressure and temperature data. The numerical solution is obtained by applying an iterative computation scheme as described below:A gas apparent molecular weight value is initialized and then gas mixture specific gravity and pseudo-critical properties are calculated.Gas mixture pseudo-reduced properties are calculated from the measured pressure and temperature values at the reservoir depth.A first z-factor value is determined as a function of the pseudo-reduced gas properties.Gas pressure gradient is obtained at the reservoir depth from the survey and used to back-calculate a second z-factor value by applying the modified gas equation of state.Relative error between the two z factor values is then calculated and compared against a low predefined tolerance.The above steps are reiterated at different assumed gas apparent molecular weight values until the predefined tolerance is achieved. This numerical approach is computerized to perform the highest possible number of iterations and then select the z-factor value corresponding to the minimum error among all iterations. The proposed workflow has been applied on literature data with known reservoir gas properties, from PVT analysis, and showed an excellent prediction performance compared to laboratory analysis with less than 5% error.

TRPC3, but not TRPC1, as a good therapeutic target for standalone or complementary treatment of DMD

Background Duchenne muscular dystrophy (DMD) is an X-linked inherited disease caused by mutations in the gene encoding dystrophin that leads to a severe and ultimately life limiting muscle-wasting condition. Recombinant adeno-associated vector (rAAV)-based gene therapy is promising, but the size of the full-length dystrophin cDNA exceeds the packaging capacity of a rAAV. Alternative or complementary strategies that could treat DMD patients are thus needed. Intracellular calcium overload due to a sarcolemma permeability to calcium (SPCa) increase is an early and critical step of the DMD pathogenesis. We assessed herein whether TRPC1 and TRPC3 calcium channels may be involved in skeletal muscle SPCa alterations and could represent therapeutic targets to treat DMD. Methods All experiments were conducted in the DMDmdx rat, an animal model that closely reproduces the human DMD disease. We measured the cytosolic calcium concentration ([Ca2+]c) and SPCa in EDL (Extensor Digitorum Longus) muscle fibers from age-matched WT and DMDmdx rats of 1.5 to 7 months old. TRPC1 and TRPC3 expressions were measured in the EDL muscles at both the mRNA and protein levels, by RT-qPCR, western blot and immunocytofluorescence analysis. Results As expected from the malignant hyperthermia like episodes observed in several DMDmdx rats, calcium homeostasis alterations were confirmed by measurements of early increases in [Ca2+]c and SPCa in muscle fibers. TRPC3 and TRPC1 protein levels were increased in DMDmdx rats. This was observed as soon as 1.5 months of age for TRPC3 but only at 7 months of age for TRPC1. A slight but reliable shift of the TRPC3 apparent molecular weight was observed in DMDmdx rat muscles. Intracellular localization of both channels was not altered. We thus focused our attention on TRPC3. Application of Pyr10, a specific inhibitor of TRPC3, abolished the differences between SPCa values measured in WT and DMDmdx. Finally, we showed that a rAAV-microdystrophin based treatment induced a high microdystrophin expression but only partial prevention of calcium homeostasis alterations, skeletal muscle force and TRPC3 protein increase. Conclusions All together our results show that correcting TRPC3 channel expression and/or activity appear to be a promising approach as a single or as a rAAV-based complementary therapy to treat DMD.

Sodium Dodecyl Sulfate–Polyacrylamide Gel Electrophoresis of Proteins

Most analytical electrophoreses of proteins are achieved by separation in polyacrylamide gels under conditions that ensure dissociation of proteins into individual polypeptide subunits and minimize aggregation. Most commonly, the anionic detergent sodium dodecyl sulfate (SDS) is used in combination with a reducing agent (β-mercaptoethanol or dithiothreitol) and with heating to dissociate proteins before loading onto the gel. SDS binding denatures the polypeptides and imparts a negative charge that masks their intrinsic charge. The amount of SDS bound is generally sequence-independent and proportional to molecular weight; at saturation, approximately one SDS molecule is bound per two amino acids, or ∼1.4 g of SDS per gram of polypeptide. Therefore, the migration of SDS–polypeptide complexes in an electric field is proportional to the relative size of the polypeptide chain, and its molecular weight can be estimated by comparison to protein markers of known molecular weight. However, hydrophobicity, highly charged sequences, and certain posttranslational modifications such as glycosylation or phosphorylation may also influence migration. Thus, the apparent molecular weight of modified proteins does not always accurately reflect the mass of the polypeptide chain. This protocol describes preparation and running of SDS-PAGE gels, followed by staining to detect proteins using Coomassie Brilliant Blue. Finally, the stained SDS-PAGE gel may be scanned to an image or preserved by drying.

Apparent Molecular Weight Distributions for Investigating Aging in Polymer-Modified Bitumen

The oxidative aging of bituminous binders affects the performance and durability of pavements. In the case of polymer-modified binders, aging involves both bitumen and polymers and has a strong impact on the whole architecture of the material. Rheology may help in understanding these structural changes, and interesting information may be obtained by analysing the evolution of apparent molecular weight distributions. This was demonstrated with a bituminous binder modified with a poly(styrene-butadiene) block copolymer and subjected to prolonged artificial aging. Isothermal frequency sweep tests were used to construct master curves of the phase angle and magnitude of the complex modulus. The master curves were then used to calculate relaxation spectra and apparent molecular weight distributions of the binders, as well as simulated temperature sweep tests. A comparison of the behaviour of the base and modified bitumen highlighted the role of the polymer in aging. Polymer degradation significantly damages the elastomeric network, yet the residual polymer chains still interact with the bitumen molecules and reduce their oxidative aging. The apparent molecular weight distributions were deconvoluted to create an aging index specifically developed for polymer-modified bitumen.

Amino Acids 785, 787 of the Na+/H+ Exchanger Cytoplasmic Tail Modulate Protein Activity and Tail Conformation

The mammalian Na+/H+ exchanger isoform 1 (NHE1) is a plasma membrane protein ubiquitously present in humans. It regulates intracellular pH by removing an intracellular proton in exchange for an extracellular sodium. It consists of a 500 amino acid membrane domain plus a 315 amino acid, regulatory cytosolic tail. Here, we investigated the effect of mutation of two amino acids of the regulatory tail, Ser785 and Ser787, that were similar in location and context to two amino acids of the Arabidopsis Na+/H+ exchanger SOS1. Mutation of these two amino acids to either Ala or phosphomimetic Glu did not affect surface targeting but led to a slight reduction in the level of protein expressed. The activity of the NHE1 protein was reduced in the phosphomimetic mutations and the effect was due to a decrease in Vmax activity. The Ser to Glu mutations also caused a change in the apparent molecular weight of both the full-length protein and of the cytosolic tail of NHE1. A conformational change in this region was indicated by differential trypsin sensitivity. We also found that a peptide containing amino acids 783–790 bound to several more proximal regions of the NHE1 tail in in vitro protein interaction experiments. The results are the first characterization of these two amino acids and show that they have significant effects on enzyme kinetics and the structure of the NHE1 protein.

Protein hydrolysates from silkworm (Bombyx mori) pupae protein treated with a novel neutral protease

Edible insects, regarded as a potential contributor to food security are currently given wide consideration due to their rich protein and other micronutrients contents. In this study, protease-assisted hydrolysis proposes an economically effective approach to hydrolyse proteins from silkworm (Bombyx mori) pupae to improve its functional properties. The proteolytic activity of a novel neutral protease (265.14 U/ml) with appreciable thermal activities, was identified using 16S rDNA as Stenotrophomonas maltophilia JW20 (SmNP20). The neutral protease with an apparent molecular weight of 28 kDa emerged active at pH 7 and maintained stability in pH range 6.0-8.0. The optimum temperature was 60 °C and stable at 55-60 °C, maintaining over 80% of its initial activity, with a half-life of 78.75, 89, 66.8 and 44 min at 50, 60, 70 and 80 °C. It was purified to 9.98-fold with a specific activity of 455.06 U/mg and 63.73% yield. The Km and Vmax values were 0.70 mg/ml and 9.48 μmol/min/mg, respectively. Enzymolysis with neutral protease enhanced the degree of hydrolysis (97.46±4.87%), increased water solubility over 50%, and a significant protein solubility of 63.44±0.65%. The Km and Vmax of the protein yield were 0.24 mg/ml and 165.63 μmol/min/mg respectively. A total of 17 amino acids have been detected in the hydrolysates obtained from the silkworm pupae protein. In comparison with neutrase and flavorzyme®, the enzyme possesses an elevated hydrolytic and catalytic efficiency. Emulsion activity and foam capacity ranged from 8-48 m2/g and 6-25% respectively. Hence, this study confirms the unique and efficient characteristics of an insect-enzyme correlation that is practically significant with potential improvement in nutritional composition and functional quality of insect proteins.

Use of Linear Viscoelastic Functions to Estimate the Aging Resistance and Internal Structure of Bituminous Binders

Rheology is the most widely used technique to evaluate the performance and aging of bituminous binders. Since there are many available rheological tests, there is also a wide range of aging indexes and it is not easy to choose the most appropriate one, because a single value may hardly be adequate for different properties or operating conditions. In order to generalize the usefulness of an index, a good starting point is deriving it from a set of data, such as the master curves of linear viscoelastic functions. Then, the problem is the quantification of aging in a single numerical value from continuous curves, covering a wide range of frequencies/temperatures. In this work, a summary of the aging indexes derived from the master curves is reported and discussed. The indexes are applied to a bituminous binder either with or without the addition of an organo-modified layered silicate. The apparent molecular weight distributions and relaxation spectra were also calculated from the master curves and used to characterize the effect of aging on the binder properties and structure. In this way, an interesting parallelism was observed between the SARA fractions and the populations derived from a deconvolution analysis of the apparent molecular weight distributions.

Quaternary Structure and Hetero-Oligomerization of Recombinant Human Small Heat Shock Protein HspB7 (cvHsp)

In this study, a reliable and simple method of untagged recombinant human HspB7 preparation was developed. Recombinant HspB7 is presented in two oligomeric forms with an apparent molecular weight of 36 kDa (probably dimers) and oligomers with an apparent molecular weight of more than 600 kDa. By using hydrophobic and size-exclusion chromatography, we succeeded in preparation of HspB7 dimers. Mild oxidation promoted the formation of large oligomers, whereas the modification of Cys 126 by iodoacetamide prevented it. The deletion of the first 13 residues or deletion of the polySer motif (residues 17–29) also prevented the formation of large oligomers of HspB7. Cys-mutants of HspB6 and HspB8 containing a single-Cys residue in the central part of the β7 strand in a position homologous to that of Cys137 in HspB1 can be crosslinked to the wild-type HspB7 through a disulfide bond. Immobilized on monoclonal antibodies, the wild-type HspB6 interacted with the wild-type HspB7. We suppose that formation of heterodimers of HspB7 with HspB6 and HspB8 may be important for the functional activity of these small heat shock proteins.