Electronic gel protein transfer and identification using matrix-assisted laser desorption/ionization-mass spectrometry

An electronic protein transfer technique is described for achieving the rapid and efficient recovery of sodium dodecyl sulfate (SDS)-protein complexes from polyacrylamide gels. This process involves the use of small-dimension capillaries in physical contact with a resolved protein band within the polyacrylamide gel, providing a large potential drop and high electric field strength at the capillary/gel interface. Several factors controlling the electronic protein transfer, including the applied electric field strength, the electrophoresis buffer concentration, and the capillary dimension, are studied to further enhance the use of field-amplification for sample stacking of extracted SDS-protein complexes. As a result of sample stacking, the extracted proteins from a 50 ng gel loading are present in a narrow ( approximately 80 nL) and highly concentrated (0.46 mg/mL or 3.3 x 10(-5) M for cytochrome c) solution plug. Three model proteins with molecular mass ranging from 14 kDa (cytochrome c) to 116 kDa (beta-galactosidase) are stained by Coomassie blue and electrophoretically extracted from gels with protein loadings as low as 50 ng. The capillary format of the electronic protein transfer technique allows direct deposition of extracted proteins onto a matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) target. Various matrices and solvent compositions are evaluated for the analysis of extracted and concentrated SDS-protein complexes using MALDI-MS. The electronic protein transfer technique, when operated under optimized conditions, is demonstrated for the effective (>70% recovery), speedy (less than 5 min), and sensitive MS identification of gel resolved proteins (as low as 50 ng).     

Characterization of plutonium contamination at the former nuclear weapons testing range,at Maralinga in South Australia

Re-suspension studies on soils contaminated with plutonium during nuclear weapons tests were performed by use of a mechanical dust-raising apparatus. Airborne dust was analyzed in terms of mass and²⁴¹Am activities for particle sizes less than 7 m. The AMAD was determined as 4.8 to 6 m, for re-suspended soil. Also, surface soil was characterized in the laboratory by means of sieving and microparticle classification, yielding mass and²⁴¹Am activity distributions with respect to size. Data indicate the granularity of plutonium contamination at both major and minor trial sites. Depth profile analyses for undisturbed, areas demonstrate that most (74% on average) of the americium and plutonium activity is found in the top 10 mm of soil. Plutonium and americium activities were found to be enhanced in the inhalable fraction over their values, in the total soil, and the enhancement factors were similar in re-suspended dust and surface soil. Observed enhancement factors ranged from 3.7 to 32.5.     

Capillary electrochromatography-applicability to the analysis of pesticides and compounds of environmental concern and the theory of electroosmosis

Summary The applicability of capillary electrochromatography to the automated analysis of pesticides and phthalate esters that are of environmental concern was assessed. Reversed phase packing materials were compared. Column to column and run to run reproducibility was established. Peak height with an internal standard gave the best reproducibility. Faster analysis than alternative HPLC methods was demonstrated for a mixture of the insecticide pirimicarb and related pyrimidines. The relationship between the concentration of an analyte in a sample and at the detector was determined by the use of radio-labelled¹⁴C-pirimicarb. The volume fraction of the liquid zone was 0.64. The possibility of electroosmosis through the pores is discussed with reference to the Rice-Whitehead model for electroosmotic flow in a capillary. A new parameter, the effective pore size is used in equations for electroosmosis through porous packings.     

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric analysis of metal-ion selected dynamic protein libraries

The application of electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to the investigation of the relative stabilities (and thus packing efficiencies) of Fe-bound trihelix peptide bundles is demonstrated. Small dynamic protein libraries are created by metal-ion assisted assembly of peptide subunits. Control of the trimeric aggregation state is coupled to stability selection by exploiting the coordination requirements of Fe(2+) in the presence of bidentate 2,2'-bipyridyl ligands covalently appended to the peptide monomers. At limiting metal-ion concentration, the most thermodynamically stable, optimally packed peptide trimers dominate the mass spectrum. The identities of optimally stable candidate trimers observed in the ESI FT-ICR mass spectra are confirmed by resynthesis of exchange-inert analogues and measurement of their folding free energies. The peptide composition of the trimers may be determined by infrared multiphoton dissociation (IRMPD) MS(3) experiments. Additional sequence information for the peptide subunits is obtained from electron capture dissociation (ECD) of peptides and metal-bound trimers. The experiments also suggest the presence of secondary structure in the gas phase, possibly due to partial retention of the solution-phase coiled coil structure.     

De novo design of a redox-active minimal rubredoxin mimic

Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment.     

2 + 2] cross coupling of benzene and tropylium ligands in reductively activated piano stool complexes of Mn,Cr, and W

We have established cation/anion coupling reactions between the tropylium ligand in [M(eta7-C7H7)(CO)3]+ (M = Cr, W) and the reductively activated eta4-benzene ligand in [Mn(eta4-C6H6)(CO)3]- (3-) to form [M(CO)3(mu2-eta6:eta5-C7H7-C6H6)Mn(CO)3]; [Cr(CO)3(mu2-eta6:eta5-C7H7-C6H6)Mn(CO)3] can be further reduced to [Cr(CO)3(mu2-eta5:eta4-C7H7-C6H6)Mn(CO)3]2-, in which the tropylium and benzene ligands have undergone a [2 + 2] cross coupling reaction.     

BOLD--a biological O-linked glycan database

Glycans can be O-linked to proteins via the hydroxyl group of serine, threonine, tyrosine, hydroxylysine or hydroxyproline. Sometimes the glycan is O-linked to the hydroxyl group via a phosphodiester bond. The core monosaccharide residue may be N-acetylgalactosamine, N-acetylglucosamine, galactose, glucose, fucose, mannose, xylose or arabinose. These O-linked glycans can remain as a monosaccharide, but often a complex structure is built up by stepwise addition of monosaccharides. Monosaccharides known to be added include galactose, N-acetylglucosamine, fucose, N-acetylneuraminic acid, N-glycolylneuraminic acid and 2-keto-3-deoxynonulosonic acid. O-linked glycans can also contain sulfate and phosphate residues. This leads to the possibility of the existence of numerous O-glycan structures. The biological O-linked database (BOLD) is a relational database that contains information on O-linked glycan structures, their biological sources (with a link to the SWISS-PROT protein database), the references in which the glycan was described (with a link to MEDLINE), and the methods used to determine the glycan structure. The database provides a valuable resource for glycobiology researchers interested in O-linked oligosaccharide structures that have been previously described on proteins from different species and tissues.     

THE MICROVASCULAR EFFECTS OF PHOTODYNAMIC THERAPY: EVIDENCE FOR A POSSIBLE ROLE OF CYCLOOXYGENASE PRODUCTS

Photodynamic therapy (PDT) of malignant tumours may involve the interruption of tumor and peritumor microcirculation. We have studied the effect of light activation of the photosensitizing drug dihematoporphyrin ether (DHE) on rat subcutaneous arterioles and the modulation of these effects by cyclooxygenase inhibitors indomethacin and acetyl salicylic acid (ASA). Animals received DHE 48 h prior to light activation and additionally either indomethacin, ASA or saline 3 h prior to treatment. Light activation (630 nm, 60 J/cm2) resulted in a significant reduction to 62 +/- 2% SEM of initial blood flow. This effect was inhibited by ASA (98 +/- 8% SEM) and indomethacin (87 +/- 8% SEM). Results from the administration of various doses of both compounds indicate that this inhibition is dose related. The data presented here show that PDT causes a significant reduction in blood flow in normal arterioles and that this effect was inhibited by ASA and indomethacin indicating that prostaglandins or thromboxane A2 may play an important role in the microvascular response to PDT.     

Fast reduction of a copper center in laccase by nitric oxide and formation of a peroxide intermediate

The rapid reduction of one of the copper atoms (type 2) of tree laccase by nitric oxide (NO) has been detected. Addition of NO to native laccase in the presence of oxygen leads to EPR changes consistent with fast reduction and slow reoxidation of this metal center. These events are paralleled by optical changes that are reminiscent of formation and decay of the peroxide intermediate in a fraction of the enzyme population. Formation of this species is only possible if the trinuclear copper cluster (type 2 plus type 3) is fully reduced. This condition can only be met if, as suggested previously, a fraction of the enzyme contains both type 3 coppers already reduced before addition of NO. Our data are consistent with this assumption. We have suggested recently that fast reduction of copper is the mechanism by which NO interacts with the oxidized dinuclear center in cytochrome c oxidase. The present experiments using laccase strongly support this view and suggest this reaction as a general mechanism by which copper proteins interact with NO. In addition, this provides an unexploited way to produce a stable peroxide intermediate in copper oxidases in which the full complement of copper atoms is present. This enables the O-O scission step in the catalytic cycle to be studied by electron addition to the peroxide derivative through the native electron entry site, type 1 copper.     

Novel perturbation expansion for the Langevin equation

We discuss the randomly driven systemdx/dt= -W(x) +f(t), wheref(t) is a Gaussian random function or stirring force withf(t)f(t)=2(t–t), andW(x) is of the formgx ¹⁺². The parameter is a measure of the nonlinearity of the equation. We show how to obtain the correlation functionsx(t)f(t)···x(t( n)) _f as a power series in. We obtain three terms in the expansion and show how to use Padé approximants to analytically continue the answer in the variable. By using scaling relations, we show how to get a uniform approximation to the equal-time correlation functions valid for allg and.