Age-related changes of aqueous protein profiles in rat fast and slow twitch skeletal muscles

Two-dimensional electrophoresis was used to generate the aqueous protein expression patterns of rat extensor digitorum longus muscle (EDL, fast twitch muscle) and solues muscle (SOL, slow twitch muscle) of different ages. Two specific protein spots, S1 and S3, were identified from EDL muscles at the ages of 12 and 18 months onward respectively. In the EDL muscles of aged rat (24 months) after intensive exercise training, S3 was still detected while S1 disappeared. In addition, diaphragm muscle (DIA, fast twitch muscle), which retains physically active throughout the life span, was used as nondisuse control. The results showed that the expressions of S1 and S3 in 24-month DIA muscle were identical with the trained aged EDL muscle. It is suggested that exercise might delay the onset of S1 expression. However, the expression of S3 over age seemed to be progressive and exercise independent. Another protein spot, S2 was identified to express only in young EDL and SOL muscles, but its expression decreased over age. Furthermore, exercise has no effect on S2 expression since S2 could not be detected in aged DIA as well as trained aged EDL and SOL muscles. These results indicated that aqueous protein expression patterns of skeletal muscle undergo changes during aging. Some of these changes such as S2 and S3 appear progressively, and some such as S1 could be delayed by exercise. S3 was identified as ubiquitin, which might play an important role in protein degradation during skeletal muscle aging process.     

Quantitative comparison of the relative cell permeability of cyclic and linear peptides

Cyclic peptides are of considerable interest as potential protein ligands. It has been postulated that cyclic molecules might be more cell permeable than their linear counterparts due to their reduced conformational flexibility. We report a study that tests this hypothesis by using a quantitative, reporter gene-based assay that measures the relative cell permeability of steroid conjugates of molecules of interest. We demonstrate that cyclic peptides are, in fact, not generally more permeable than their linear counterparts.     

Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis

Identification of unknown binding partners of a protein of interest can be a difficult process. Current strategies to determine protein binding partners result in a high amount of false-positives, requiring use of several different methods to confirm the accuracy of the apparent association. We have developed and utilized a method that is reliable and easily substantiated. Complexes are isolated from cell extract after exposure to the radiolabeled protein of interest, followed by resolution on a native polyacrylamide gel. Native conformations are preserved, allowing the complex members to maintain associations. By radiolabeling the protein of interest, the complex can be easily identified at detection levels below the threshold of Serva Blue, Coomassie, and silver stains. The visualized radioactive band is analyzed by MS to identify binding partners, which can be subsequently verified by antibody shift and immunoprecipitation of the complex. By using this method we have successfully identified binding partners of two proteins that reside in different locations of a cellular organelle.     

Recent developments in thermal analysis of polymers: Calorimetry in the limit of slow and fast heating rates

This review focuses on new insights into the crystal melting transition and the amorphous glass transition of polymers that have been gained through recent advances in thermoanalytical methods. The specific heat capacity can now be studied under two extreme limits, that is, under quasi‐isothermal conditions (limit of zero heating rate) and, at the other end of the scale, under rapid heating conditions (heating rates on the order of thousands of degrees per second), made possible through nanocalorimetry. The reversible melting, and multiple reversible melting, of semicrystalline polymers is explored using quasi‐isothermal temperature modulated differential scanning calorimetry, TMDSC. The excess reversing heat capacity, above the baseline, measured under nearly isothermal conditions is attributed to locally reversible surface melting and crystallization processes that do not require molecular nucleation. Observations of double reversible melting endotherms in isotactic polystyrene suggest existence of two distinct populations of crystals, each showing locally reversible surface melting. The second subject of the review, nanocalorimetry, is utilized to study samples of small mass under conditions of very fast heating and cooling. The glass transition properties of thin amorphous polymer films are observed under adiabatic conditions. The glass transition temperature appears to be independent of film thickness, and is observed even in ultra‐thin films. Recrystallization and reorganization during rapid heating are studied by nanocalorimetry of semicrystalline polymers. The uppermost endotherm seen under normal DSC scanning of poly(ethylene terephthalate) is caused by reorganization, and vanishes under the rapid heating conditions (3000K/s) provided by nanocalorimetry. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 629–636, 2005     

Measuring screw-sense preference in a helical oligomer by comparison of 13C NMR signal separation at slow and fast exchange

While an unequal population of rapidly interconverting left- and right-handed conformers of a helical oligomer can be detected by circular dichroism, precise quantification of a conformer ratio has not previously been achieved. We demonstrate, using a set of labeled peptide analogues, that simple analysis of peak separation in their (13)C NMR spectra at slow and fast exchange allows an accurate value for the ratio of helical conformers to be obtained. The method reports the ratio of conformers at the site of the label and can therefore be used to investigate local variations in helical conformational control.     

Quantitative analysis of immobilized proteins and protein mixtures by amino acid analysis

Biomolecular surface engineering of materials often requires precise, versatile and efficient quantification of immobilized proteins at solid surfaces. Acidic hydrolysis of surface-bound proteins and subsequent HPLC analysis of fluorescence-derivatized amino acids were adapted and critically evaluated for that purpose. Contaminations and concentration-dependent amino acid retrieval during HPLC were found to influence the accuracy of the method. In addition to the choice of adequate conditions for hydrolysis, derivatization and chromatographic separation extensions of the data evaluation were suggested to improve the accuracy of the approach when applied to single protein systems: comparing the experimentally obtained amino acid ratio to the protein constitution enabled to identify the properly separated and detected amino acids. Those amino acids were selected for a more precise calculation of the amount of immobilized protein. To further increase the accuracy of the method, the retrieval of amino acids corresponding to protein amounts in the range between 0.5 and 4.0 microg was analyzed for a variety of proteins of interest to derive protein-specific correction factors. The evaluation of amino acid data was furthermore applied to quantify binary protein mixtures at similar settings. This method was proven useful to detect the composition of protein mixtures throughout a wide range of absolute and relative concentrations.     

Quantitative analysis of sesquiterpenes and comparison of three Curcuma wenyujin herbal medicines by micro matrix solid phase dispersion coupled with MEEKC

A simple, efficient and environmental friendly method was proposed for determining five sesquiterpenoids of Curcuma wenyujin by MSPD extraction coupled with MEEKC separation. Molecular sieve was applied as a solid support for extraction of sesquiterpenoids for the first time. Various parameters affecting extraction and separation efficiency were investigated. The optimized conditions involved dispersing sample (200 mg) with 200 mg of TS‐1 for 150 s and using 1000 μL of methanol to elute five target analytes. Finally, they were well separated by using a running buffer containing 1.3% SDS, 5.0% 1‐butanol, 0.5% ethyl acetate and 10% acetonitrile in 10 mM borate buffer at pH 9.0. Consequently, the developed method was fully validated and successfully applied to determine the five sesquiterpenoids including curdine, curcumenol, germacrone, furanodiene and β‐elemene in Curcuma wenyujin origin's Chinese herbal medicines. Furthermore, hierarchical cluster analysis was performed based on the contents of target compounds for distinguishing steamed and non‐steamed drugs. The present study provided a promising method for fast investigation and discrimination of chemical difference in steam & non‐steamed Chinese medicines from Curcuma wenyujin origin.     

Semi-automated image analysis: detecting carbonylation in subcellular regions of skeletal muscle

The level of carbonylation in skeletal muscle is a marker of oxidative damage associated with disease and aging. While immunofluorescence microscopy is an elegant method to identify carbonylation sites in muscle cross-sections, imaging analysis is manual, tedious, and time consuming, especially when the goal is to characterize carbonyl contents in subcellular regions. In this paper, we present a semi-automated method for the analysis of carbonylation in subcellular regions of skeletal muscle cross-sections visualized with dual fluorescent immunohistochemistry. Carbonyls were visualized by their reaction with 2,4-dinitrophenylhydrazine (DNPH) followed by immunolabeling with an Alexa488-tagged anti-DNP antibody. Mitochondria were probed with an anti-COXI primary antibody followed by the labeling with an Alexa568-tagged secondary antibody. After imaging, muscle fibers were individually analyzed using a custom-designed, lab-written, computer-aided procedure to measure carbonylation levels in subsarcolemmal and interfibrillar mitochondrial regions, and in the cytoplasmic and extracellular regions. Using this procedure, we were able to decrease the time necessary for the analysis of a single muscle fiber from 45 min to about 1 min. The procedure was tested by four independent analysts and found to be independent on inter-person and intra-person variations. This procedure will help increase highly needed throughput in muscle studies related to ageing, disease, physical performance, and inactivity that use carbonyl levels as markers of oxidative damage.     

Quantitative determination of aceclofenac and its three major metabolites in rat plasma by HPLC-MS/MS

We developed a method for the simultaneous quantification of aceclofenac and its three major metabolites in rat plasma. After protein precipitation with acetonitrile including flufenamic acid as an internal standard (IS), aceclofenac, diclofenac, 4'-hydroxyaceclofenac, 4'-hydroxydiclofenac, and the IS were chromatographed on a reverse-phase C18 analytical column. The isocratic mobile phase of acetonitrile/0.1% formic acid (aq; 9:1 [v/v]) was eluted at 0.3 mL/min. Quantification was performed on a triple-quadrupole mass spectrometer using electrospray ionization, and the ion transitions were monitored in selective reaction-monitoring mode. The coefficient of variation in the assay precision was less than 8%, and the accuracy was 92-103%. This method was successfully used to measure the concentrations of aceclofenac and its three major metabolites in rat plasma following the oral administration of a single 20 mg/kg oral dose of aceclofenac.     

Rapid ion-exchange method for the determination of 3-methylhistidine in rat urine and skeletal muscle

A method for the determination of 3-methylhistidine using an automatic amino acid analyser has been developed. A single column system with lithium buffer (pH 3.950, 0.500 mol/l lithium and 0.067 mol/l citrate) was used for elution. The standard amino acid mixture of basic amino acids and some dipeptides usually present in physiological fluids was analysed for the development of the method. 3-Methylhistidine eluted in 46.7 +/- 0.049 min and the peak area coefficient of variation for the same sample was 1.07%. As 3-methylhistidine is completely resolved from the other basic amino acids and some dipeptides (anserine and carnosine), this method is suitable for the analysis of urine and muscle extracts as well as skeletal muscle protein hydrolysates where this amino acid is present in much lower concentrations than other amino acids.     

Quantitative analysis of inositol lipids and inositol phosphates in synaptosomes and microvessels by column chromatography: comparison of the mass analysis and the radiolabelling methods.

Chromatographic methods that measure both the mass and the radiolabelling of various inositol lipids and inositol phosphates in tissues have been developed. The mass of phosphatidylinositol (PtdIns), phosphatidylinositol-4-monophosphate [PtdIns(4)P] and phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2] was quantitated by measuring the inorganic phosphate, whereas inositol monophosphate (IP), inositol bisphosphate (IP2), inositol trisphosphate (IP3) and inositol tetrakisphosphate (IP4) were quantitated by using an enzymic method. The radiolabelling of various inositol lipids and inositol phosphates was determined by incubating the tissue samples with [3H]myo-inositol, separating individual inositol lipids and inositol phosphates, and measuring the radioactivity in each compound. Although the mass analysis method was sensitive enough to measure low levels of inositol lipids or inositol phosphates, the method was laborious and time-consuming. Compared with the enzymic method, the radiolabelling method was simple and fast, but it gave variable results. This study demonstrated differences in inositol lipid and inositol phosphate levels by radiolabelling and mass measurements, and agonist-stimulated phosphatidylinositol turnover of synaptosomes versus the blood-brain barrier as represented by microvessels. Although the mass of PtdIns, PtdIns(4)P and PtdIns(4,5)P2 was comparable in synaptosomes and microvessels, the incorporation of [3H]myo-inositol into phosphorylated PtdIns in microvessels was less than that in synaptosomes.     

Determination of methyl tert-butyl ether in gasoline: a comparison of three fast methods based on mass spectrometry

A high-speed quantitative analysis of methyl tert-butyl ether (MTBE) using three different methods with mass spectrometry detection has been performed. The first method is based on fast chromatography and required an analysis time of 5.23 min per sample, although a certain period (6 min) was necessary for the initial measurement conditions to be regained prior to analysing the next sample. The other two are non-separative methods and are based on direct injection and headspace generation. The analysis times were 1.5 and 3.5 min, respectively, although in the latter case an additional period of time was required to extract volatiles from the sample. The analytical characteristics of all three methods are highly satisfactory in terms of linearity, lack of fit, precision and accuracy. The methods were applied to the determination of MTBE in different gasoline samples. The non-separative methods afforded slightly higher concentrations than those found when fast chromatography was used; this is due to the presence of other minor components that contribute to the abundance of the ion at m/z 73, characteristic of MTBE. We propose a correction that removes this error very satisfactorily and allows the same results to be obtained with all three methodologies proposed.     

Determination of the number and relative molecular mass of subunits in an oligomeric protein by two-dimensional electrophoresis Application to the subunit structure analysis of rat liver amidophosphoribosyltransferase

To determine simultaneously the relative molecular mass (M_r) of a native oligomeric protein, and the number and M_r of its subunits, a method using two-dimensional electrophoresis was developed. To determine the M_r of a native oligomeric protein, pore gradient gel electrophoresis was performed for the first dimension. Native proteins were dissociated into their subunits by sodium dodecyl sulphate (SDS) in a gel slice, then applied to SDS polyacrylamide gel electrophoresis for the second dimension to determine the M_r of subunits. The advantage, accuracy, limitations and application of the method are discussed.     

Diabetes induces compositional, structural and functional alterations on rat skeletal soleus muscle revealed by FTIR spectroscopy: a comparative study with EDL muscle

Diabetes Mellitus (DM) is a metabolic disorder, characterized by abnormally high blood glucose levels due to decreased secretion or effectiveness in function of insulin. Having a role in carbohydrate and lipid metabolism, skeletal muscle is affected by the absence of insulin in diabetic conditions. This current study reports the application of Fourier transform infrared (FTIR) spectroscopy in the determination of macromolecular alterations in streptozotocin (STZ)-induced diabetic rat skeletal Soleus (SOL) muscles, which highlight the promise of this technique in medical research. The results revealed that DM induced several alterations in macromolecular content and structure of slow-contracting SOL muscles. In diabetic SOL muscles, a decrease in the content of lipids, proteins and nucleic acids together with an increase in lipid order was observed. The decrease in the level of unsaturation and acyl chain length of lipids demonstrated the increased lipid peroxidation in DM. There were alterations in protein secondary structure in DM with a decrease in α-helix and β-sheet content of proteins, whereas the content of aggregated β-strands increased, which is generally seen when proteins denature. Besides, the integrity of collagen molecules was found to be decreased, demonstrating the alterations in its triple helical structure in diabetic muscles. Furthermore, the same alterations mentioned above were also observed in diabetic fast-contracting Extensor Digitorum Longus (EDL) muscles. However, having a high content of mitochondria and relying on an oxidative pathway, SOL muscle was found to be more affected by DM.     

Prunus yedoensis Matsum. stimulates glucose uptake in L6 rat skeletal muscle cells by activating AMP-activated protein kinase and phosphatidylinositol 3-kinase/Akt pathways

Prunus yedoensis Matsum. is used as a medicinal plant to alleviate symptoms of diabetes; however, the molecular mechanism underlying its antihyperglycaemic activity is unknown. In this study, we investigated the antihyperglycaemic effects of P. yedoensis and its molecular mechanism. Prunus yedoensis leaf extract (PLE) increased the glucose uptake of phosphorylatinginsulin receptor substrate (IRS)-1, 3'-phosphoinositide-dependent kinase (PDK)-1 and Akt PLE, and also increased the phosphorylation of AMP-activated protein kinase (AMPK) and p38 mitogen-activated protein kinase (p38 MAPK). PLE-stimulated glucose uptake was blocked by an AMPK inhibitor (Compound C) and a p38 MAPK inhibitor (SB203580). Inhibition of AMPK activity reduced p38 MAPK phosphorylation, whereas the inhibition of p38 MAPK activity did not affect AMPK phosphorylation. Pretreatment with the phosphatidylinositol 3-kinase inhibitor LY294002 and Compound C reduced PLE-stimulated glucose uptake. Our results demonstrate that PLE stimulated glucose uptake by activating both insulin signalling and AMPK-p38 MAPK pathways. PLE shows potential as a natural antihyperglycaemic agent.     

Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy

Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure (1)H-(15)N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated (15)N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S(2) as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins.     

Mutation scanning for sequence variation in three mitochondrial DNA regions for members of the Contracaecum osculatum (Nematoda: Ascaridoidea) complex

Anisakid nematodes of seals from different geographical origins, previously identified by multilocus enzyme electrophoresis as Contracaecum osculatum A (CoA), C. osculatum B (CoB), C. osculatum C (CoC), C. osculatum D (CoD), C. osculatum E (CoE) and C. osculatum baicalensis (Cob), were characterised genetically using a mutation scanning approach, in order to define genetic markers for their specific identification and differentiation. Three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit I (COI), and the small and large subunits of rRNA (ssrRNA and IsrRNA, respectively) were amplified separately from individual nematodes by polymerase chain reaction (PCR), analysed by single-strand conformation polymorphism (SSCP), and samples displaying sequence variability were subjected to sequencing. Forty-six haplotypes were defined for 62-66 individuals (representing the six members of C. osculatum). All taxa except CoD and CoE could be identified, or delineated from one another, by nucleotide differences in the COI, ssrRNA and/or IsrRNA sequences. For all three mtDNA regions, 4 (10.5%), 7 (18.4%), 15 (39.5%) and 11 (28.9%) of 38 nucleotide positions were considered diagnostic (fixed) and could thus unequivocally delineate CoA, CoB, CoC and Cob. The lack of an unequivocal nucleotide difference in any of the three mtDNA sequences between CoD and CoE was in accordance with previous ribosomal DNA sequence data but inconsistent with multilocus enzyme electrophoretic data. Using all fixed nucleotide positions, CoA, CoD/E and CoB were genetically more similar to Cob than each was to CoC, similar to previous findings. In spite of not being able to distinguish among all six taxa of C. osculatum, the present study demonstrated clearly the usefulness and attributes of the mutation scanning approach for investigating population genetic structures of species of parasitic nematodes.