Sequencing membrane proteins by tandem mass spectrometry

Tandem mass spectrometry (MS/MS) is an attractive technique for sequencing membrane proteins because it can be applied to peptides in mixtures that are difficult to separate chromatographically. To evaluate the suitability of MS/MS sequencing for membrane proteins and to develop protocols for the preparation of the cleaved peptides, we employed the well characterized apoproteins of bacteriorhodopsin and bovine rhodopsin, i.e. bacterioopsin and opsin, respectively. Without separation, nine out of ten peptides resulting from cyanogen bromide cleavage of bacterioopsin were detected by fast atom bombardment MS, the single undetected fragment being a tetrapeptide that was presumably hidden in the low-m/z matrix background. Furthermore, MS/MS was used to confirm the sequence of all the peptides detected with m/z values below 3.5 kDa (40% of the protein). Bovine opsin was analyzed in a similar fashion. Tandem MS/MS has thus allowed the sequencing of substantial portions of two integral membrane proteins by the analysis of unseparated peptide mixtures, demonstrating for the first time that this technique can obviate some of the most serious difficulties associated with sequencing membrane proteins, namely the difficult-to-achieve separation of the ‘sticky’ peptide fragments.     

The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code

The problem of numerical accuracy in the calculation of vibrational frequencies of crystalline compounds from the hessian matrix is discussed with reference to alpha-quartz (SiO(2)) as a case study and to the specific implementation in the CRYSTAL code. The Hessian matrix is obtained by numerical differentiation of the analytical gradient of the energy with respect to the atomic positions. The process of calculating vibrational frequencies involves two steps: the determination of the equilibrium geometry, and the calculation of the frequencies themselves. The parameters controlling the truncation of the Coulomb and exchange series in Hartree-Fock, the quality of the grid used for the numerical integration of the Exchange-correlation potential in Density Functional Theory, the SCF convergence criteria, the parameters controlling the convergence of the optimization process as well as those controlling the accuracy of the numerical calculation of the Hessian matrix can influence the obtained vibrational frequencies to some extent. The effect of all these parameters is discussed and documented. It is concluded that with relatively economical computational conditions the uncertainty related to these parameters is smaller than 2-4 cm(-1). In the case of the Local Density Approximation scheme, comparison is possible with recent calculations performed with a Density Functional Perturbation Theory method and a plane-wave basis set.     

Determination of phosphate in natural water employing a monosegmented flow system with simultaneous multiple injection

A monosegmented flow system was employed for the determination of low contents of phosphate in natural water. In this approach, sample and reagents are simultaneously injected to a PTFE reaction coil where the homogenization of the mixture occurs while the monosegment is pumped forwards the photometric detector. The proposed system was evaluated by determining phosphate ion, based on the reaction of association between molybdophosphate and malachite green. It was evaluated individually the best concentration of the reagent solution in relation to blank signal (absorbance of the blank) and the sensitivity of the method. A factorial design was proposed to explain the contribution of each component on the formation of the ion association complex, evaluating the individual contributions as well as the synergistic and antagonistic effects. With the established conditions, phosphorous is determined in the concentration range of 5.0-75 μg P PO₄³⁻ l⁻¹ (r=0.9992), with a detection limit of 0.70 μg P PO₄³⁻ l⁻¹ and a relative standard deviation of 2% (20 μg P PO₄³⁻ l⁻¹, n=8). The proposed method has a sampling frequency of 72 h⁻¹.     

Coadsorption and surface forces for selective surfaces in contact with aqueous mixtures of oppositely charged surfactants and low charge density polyelectrolytes

The coadsorption of a positively charged polyelectrolyte (with 10% of the segments carrying a permanent positive charge, AM-MAPTAC-10) and an anionic surfactant (sodium dodecyl sulfate, SDS) on silica and glass surfaces has been investigated using optical reflectometry and a noninterferometric surface force technique. This is a selective coadsorption system in the sense that the polyelectrolyte does adsorb to the surface in the absence of surfactant, whereas the surfactant does not adsorb in the absence ofpolyelectrolyte. It is found that the total adsorbed amount goes through a maximum when the SDS concentration is increased. Maximum adsorption is found when the polyelectrolyte/surfactant complexes formed in bulk solution are close to the charge neutralization point. Some adsorption does occur also when SDS is present in significant excess. The force measured between AM-MAPTAC-10-coated surfaces on approach in the absence of SDS is dominated at long range by an electrostatic double-layer force. Yet, layers formed by coadsorption from solutions containing both polyelectrolyte and surfactant generate long-range forces of an electrosteric nature. On separation, adhesive interactions are found only when the adsorbed amount is low, i.e., in the absence of SDS and in a large excess of SDS. The final state of the adsorbed layer is found to be nonhysteretic, i.e., independent of the history of the system. The conditions for formation of long-lived trapped adsorption states from mixed polymer-surfactant solutions are discussed.     

Post-translational modifications of recombinant B. cinerea EPG 6

The fungus Botrytis cinerea is a ubiquitous plant pathogen that infects more than 200 different plant species and causes substantial economic losses in a wide range of agricultural crops and harvested products. Endopolygalacturonases (EPGs) are among the first array of cell-wall-degrading enzymes secreted by fungi during infection. Up to 13 EPG glycoforms have been described for B. cinerea. The presence of multiple N-linked glycosylation modifications in BcPG1-6 is predicted by their deduced amino acid sequences. In this work, the glycosylation sites and the attached oligosaccharide structures on BcPG6 were analyzed. The molecular mass of the intact glycoprotein was determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analysis. BcPG6 contains seven potential N-linked glycosylation sites. Occupancy of these glycosylation sites and the attached carbohydrate structures were analyzed by tryptic digestion followed by liquid chromatography/mass spectrometry (LC/MS) using a stepped orifice voltage approach. Five out of seven potential N-linked sites present in BcPG6 were determined to be occupied by high-mannose-type oligosaccharides. Four of them were readily determined to be at Asn58 (T3 peptide), Asn198 (T7 peptide), Asn237 (T9 peptide) and Asn256 (T11 peptide), respectively. Another was located on the T8 peptide, which contained two potential N-linked sites, Asn224 and Asn227 (SNNN224VTN227ITFK). LC/MS/MS of a sample treated with N-glycanase placed the glycan in this peptide at Asn224 rather than at Asn227. The potential glycosylation site on Asn146 (T6 peptide) was not glycosylated. In addition, two disulfide bonds were observed, linking the Cys residues within the T13 and T16 peptides.     

Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations

The nucleophilic aromatic substitution (SNAr) reaction between azide ion and 4-fluoronitrobenzene has been investigated using QM/MM and DFT/PCM calculations in protic and dipolar aprotic solvents. The effects of solvation on the transition structures, the intermediate Meisenheimer complex, and the rate of reaction are elucidated. The large rate increases in proceeding from protic to dipolar aprotic solvents are only reproduced by the QM/MM methodology.     

Short, stereoselective synthesis of C-glycosyl asparagines via an olefin cross-metathesis

The Grubbs second generation ruthenium catalyst was employed for the cross metathesis between α- and β-C-allyl glycosides and suitably protected l-vinyl glycines to furnish olefinic products in 57-94% yields. Hydrogenation afforded the C-glycosyl asparagines in high yield.     

Consequences of the nanoporosity of cellulosic fibers on their streaming potential and their interactions with cationic polyelectrolytes

Electrokinetic tests, based on the streaming potential method, were used to elucidate interactions between cationic polyelectrolytes and cellulosic fibers and to reveal aspects of fibers’ nanoporosity. The fibrillated and nanoporous nature of bleached kraft fibers gave rise to time-dependent changes in streaming potential, following treatment of the wetted fibers with poly-diallyldimethylammonium chloride. Electrokinetic test results were consistent with an expected longer time required for higher-mass polyelectrolytes to diffuse into pore spaces, compared to lower-mass polyelectrolytes. Further evidence of the relative inability of polyelectrolyte molecules to diffuse into the pores of cellulose was obtained by switching back and forth between high and low ionic strength conditions during repeated measurement of streaming potential, after the fibers had been treated with a moderate amount of cationic polymer. By changing the concentration of sodium sulfate it was possible to switch the sign of streaming potential repeatedly from positive to negative and back again. Such results imply that a continuous path for liquid flow exists either in a fibrillar layer or within the cell walls. The same concepts also helped to explain the dosages of high-charge cationic polymer needed to achieve maximum dewatering rates, as well as the results of retention experiments using positively and negatively charged microcrystalline cellulose particles.     

A multicommuted flow system for sequential spectrophotometric determination of hydrosoluble vitamins in pharmaceutical preparations

A multicommuted flow system is proposed for spectrophotometric determination of hydrosoluble vitamins (ascorbic acid, thiamine, riboflavine and pyridoxine) in pharmaceutical preparations. The flow manifold was designed with computer-controlled three-way solenoid valves for independent handling of sample and reagent solutions and a multi-channel spectrophotometer was employed for signal measurements. Periodic re-calibration as well as the standard addition method was implemented by using a single reference solution. Linear responses (r=0.999) were obtained for 0.500-10.0 mg l⁻¹ ascorbic acid, 2.00-50.0 mg l⁻¹ thiamine, 5.00-50.0 mg l⁻¹ riboflavine and 0.500-8.00 mg l⁻¹ pyridoxine. Detection limits were estimated as 0.08 mg l⁻¹ (0.5 μmol l⁻¹) ascorbic acid, 0.8 mg l⁻¹ (2 μmol l⁻¹) thiamine, 0.2 mg l⁻¹ (0.5 μmol l⁻¹) riboflavine and 0.1 mg l⁻¹ (0.9 μmol l⁻¹) pyridoxine at 99.7% confidence level. A mean sampling rate of 60 determinations per hour was achieved and coefficients of variation of 1% (n=20) were estimated for all species. The mean reagent consumption was 25-fold lower in relation to flow-based procedures with continuous reagent addition. Average recoveries between 95.6 and 100% were obtained for commercial pharmaceutical preparations. Results agreed with those obtained by reference methods at 95% confidence level. The flow system is suitable for application in quality control processes and in dissolution studies of vitamin tablets.     

Target-space duality between simple compact Lie groups and Lie algebras under the Hamiltonian formalism: I. Remnants of duality at the classical level

It has been suggested that a possible classical remnant of the phenomenon of target-space duality (T-duality) would be the equivalence of the classical string Hamiltonian systems. Given a simple compact Lie groupG with a bi-invariant metric and a generating function suggested in the physics literature, we follow the above line of thought and work out the canonical transformation generated by together with an Ad-invariant metric and a B-field on the associated Lie algebra ofG so thatG and form a string target-space dual pair at the classical level under the Hamiltonian formalism. In this article, some general features of this Hamiltonian setting are discussed. We study properties of the canonical transformation including a careful analysis of its domain and image. The geometry of the T-dual structure on is lightly touched. We leave the task of tracing back the Hamiltonian formalism at the quantum level to the sequel of this paper.