The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers

Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D₂O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D₂O. In contrast, both the rate and the extent of H/D exchange with D₂O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions.     

An abundance of nodulation factors

In this issue of Chemistry & Biology, Morón et al. [1] report that Rhizobium tropici CIAT899 produces different Nod factors in response to flavonoid induction under differing environmental conditions. This unanticipated environmental dependence has implications for altering or potentially improving the host-bacteria interaction in bean nodulation.     

Size-selected (2-10 nm) gold nanoparticles for matrix assisted laser desorption ionization of peptides

In this report, first use of size-selected gold nanoparticles (AuNPs) as matrixes for matrix assisted laser desorption/ionization (MALDI) is described for peptides and proteins. In comparison with conventional organic acid MALDI matrixes, the optimum matrix-to-analyte ratio with AuNP matrixes is reduced by 10-14 orders of magnitude. Significant differences in the relative abundances of the ions observed in positive and negative mode MALDI-time-of-flight mass spectrometry (TOFMS) are revealed as the AuNP size distribution is decreased from 10 to 2 nm, whereby 2-nm AuNPs exhibit quantum confinement effects prevalent in quantum dots. AuNP matrixes allow for selective analyte ionization, as demonstrated in the selective MALDI-TOFMS of phosphotyrosine in a background of phosphoserine and phosphothreonine peptides.     

Preparation and properties of surface modified ceramic membranes. Part III. Gas permeation of 5 nm alumina membranes modified by trichloro-octadecylsilane

Stable trichloro-octadecyl silane (ODS) derivatives of a 5 nm γ-alumina ceramic membrane were prepared. Gas permeabilities of the untreated membrane did not show Knudsen diffusion at 20°C. Gas permeabilities of the ODS membrane were three orders of magnitude lower; He, Ne, Ar, CO₂, C₃H₈ have near constant permeabilities 360 mol s⁻¹ m⁻² bar⁻¹, except methane which has the highest permeability of the group, 481 mol s⁻¹ m⁻² bar⁻¹. The mechanism of diffusion is solution/diffusion. Remarkably, permeabilities of ODS-alumina membrane were reduced by 5 X after exposure to a pressure difference of 1 atm (active layer side) against vacuum for only 10 min. The effect was metastable but could be reversed on standing for several hours, reversal of pressure difference or after washing with (hydrocarbon solvent) toluene. The mechanism was presumed to be due to movement of the octadecyl-hydrocarbon chains of the silane monolayer causing a partially blocked pore structure; perhaps a unique example of self-fouling.     

Amides as precursors of imidoyl radicals in cyclisation reactions

Amides have been successfully used as precursors of imidoyl radicals for radical cyclisation. The amides have been converted to imidoyl selanides via reaction with phosgene to yield imidoyl chlorides followed by reaction with potassium phenylselanide. Imidoyl selanides were reacted with tributyltin hydride (Bu₃SnH) as the radical mediator with triethylborane or AIBN as initiators to yield imidoyl radicals for cyclisation reactions. Imidoyl radicals have been cyclised onto alkenes to yield 2,3-substituted-indoles and -quinolines and also onto pyrroles and indoles to give bi- and tricyclic heteroarenes.     

Trypsin activity assay in substrate-specific one- and two-dimensional gels: a powerful method to separate and characterize novel proteases in active form in biological samples

To separate and identify the proteases, a substrate-specific, sensitive assay in sodium dodecyl sulfate (SDS)-polyacrylamide gels after two-dimensional (2-D) electrophoresis has been developed. This method allows simultaneous determination of protease cleavage specificity, molecular weight, isoelectric point, and if necessary, amino acid sequencing. After isoelectric focusing in immobilized pH gradient (IPG) strips (pH 6-11) (first dimension), trypsin was electrophoresed in 12% SDS polyacrylamide gels (second dimension) copolymerized with Boc-Gln-Ala-Arg-MCA (4-methyl-coumaryl-7-amide). The gels were washed in cold 2.5% Triton X-100 and water, and incubated in assay buffer (6.3 mM Bicine, 100 mM NaCl). Trypsin cleavage of the peptide-MCA generated fluorescent 7-amino-4-methyl-coumarin. In 1-D gels, as low as 500 pg trypsin could be detected and trypsin band volumes correlated linearly with the amounts of trypsin (R(2) = 0.999). In 2-D gels, the lowest amount of trypsin detected was 1 ng. The linear regression of spot volume and loading amount was still good (R(2) = 0.974). To optimize renaturation conditions, 5x5 min washes with 2.5% Triton X-100 and water, respectively, gave the strongest band volume. For fluorescence development, an assay buffer at pH 9 was the best; incubation at 37 degrees C for 30 min was sufficient. The method has application for identifying novel proteases as it does not rely on antibodies.     

Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine

DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.     

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Combined phenyl silane and immunoaffinity column cleanup with liquid chromatography for determination of ochratoxin A in roasted coffee: collaborative study

A collaborative study was conducted to evaluate a liquid chromatography (LC) method for ochratoxin A using sequential phenyl silane and immunoaffinity column cleanup. The method was tested at 3 different levels of ochratoxin A in roasted coffee, which spanned the range of possible future European regulatory limits. The test portion was extracted with methanol and sodium bicarbonate by shaking for 30 min. The extract was filtered, centrifuged, and then cleaned up on a phenyl silane column before being eluted from the washed column with methanol-water. The eluate was diluted with phosphate-buffered saline (PBS) and applied to an ochratoxin A immunoaffinity column, which was washed with water. The ochratoxin A was eluted with methanol, the solvent was evaporated, and the residue was redissolved in injection solvent. After injection of this solution onto a reversed-phase LC apparatus, ochratoxin A was measured by fluorescence detection. Eight laboratory samples of low-level naturally contaminated roasted coffee and 2 laboratory samples of blank coffee (< 0.2 ng/g ochratoxin A at the signal-to-noise ratio of 3:1), along with ampules of ochratoxin A calibrant and spiking solutions, were sent to 15 laboratories in 13 different European countries. Test portions of the laboratory samples were spiked at levels of 4 ng/g ochratoxin A, and recoveries ranged from 65 to 97%. Based on results for spiked blank material (blind duplicates) and naturally contaminated material (blind duplicates at 3 levels), the relative standard deviation for repeatability (RSDr) ranged from 2 to 22% and the relative standard deviation for reproducibility (RSDR) ranged from 14 to 26%. The method showed acceptable within- and between-laboratory precision, as evidenced by HORRAT values, at the low level of determination for ochratoxin A in roasted coffee.     

Does alpha-fluorination affect the structural trans-influence and kinetic trans-effect of an alkyl ligand? Molecular structures of Pd(TMEDA)(CH(3))(R(F)) and a kinetic study of the trans to cis isomerization of Pt(TMEDA)(CH(3))(2)I(R(F)) [R(F) = CF(2)CF(3), CFHCF(3), CH(2)CF(3)

Reaction of Pd(TMEDA)(CH(3))(2) [TMEDA = tetramethylethylenediamine] with fluoroalkyl iodides R(F)I affords a series of square planar Pd(II) complexes Pd(TMEDA)(CH(3))(R(F)) [R(F) = CF(2)CF(3) (9), CFHCF(3) (10), CH(2)CF(3) (11)], presumably by oxidative addition followed by reductive elimination of CH(3)I. The solid-state structures of each compound have been determined by single crystal X-ray diffraction studies, allowing the effect of increasing alpha-fluorination on the structural trans-influence of alkyl ligands to be examined. In these compounds there is no significant difference observed in the trans-influence of the three fluorinated alkyl ligands toward the trans-N atom, although a significant cis-influence on the neighboring methyl ligand is apparent. Oxidative addition of the same series of fluoroalkyl ligands to the corresponding Pt(TMEDA)(CH(3))(2) affords octahedral Pt(IV) complexes trans-Pt(TMEDA)(CH(3))(2)(R(F))I [R(F) = CF(2)CF(3) (12), CFHCF(3) (13), CH(2)CF(3) (14)] as the kinetic products. In each case, subsequent isomerization to the corresponding all cis-isomers is observed; in the case of 13, the stereocenter at the alpha-carbon results in two diastereomeric cis-isomers, which are formed at different rates. The molecular structures of 13 and its more stable all cis-isomer 16b have been crystallographically determined. Kinetic studies of the trans-cis isomerization reactions show the mechanism to involve a polar transition state, presumably involving iodide dissociation, followed by rearrangement of the cation, and iodide recombination. High dielectric solvents increase the rate, but solvent coordinating ability has no effect. Dissolved salts (LiI, LiOTf) show normal accelerative salt effects, with no inhibition in the case of added iodide, consistent with the formation of an intimate ion pair intermediate. The kinetic parameters show that the trans-effects of fluoroalkyl ligands in these compounds follow the order expected from the relative sigma-donor properties of the ligands, with CF(2)CF(3) < CFHCF(3) < CH(2)CF(3).