Evaluation of automated nano-electrospray mass spectrometry in the determination of non-covalent protein-ligand complexes

The use of electrospray ionization mass spectrometry (ESI-MS) for studying non-covalent interactions between macromolecules and ligands is well established. ESI-MS can be a useful tool for the determination of dissociation constants between molecules in the gas phase. We validate this method by studying the binding of the catalytic domain of cellobiohydrolase I (CBH I) from Trichoderma reesei to the disaccharide inhibitor cellobiose. The method was further applied to study two newly synthesized cellobiose derivatives (m-iodobenzyl 2-deoxy-2-azido-beta-cellobioside and p-benzyloxybenzyl beta-cellobioside). In a titration experiment, peak areas of different charge states of the free enzyme and the complex were summed in order to determine the dissociation constant. For cellobiose and m-iodobenzyl 2-deoxy-2-azido-beta-cellobioside, the calculated values are in good agreement with those reported from either displacement titration or equilibrium binding experiments in solution. Due to non-specific binding, the dissociation constant of p-benzyloxybenzyl beta-cellobioside does not correspond with the solution-based value. Our results indicate the need for careful interpretation of data sets when using nanoESI to study non-covalent interactions.     

Carbon and nitrogen isotope analysis of atrazine and desethylatrazine at sub-microgram per liter concentrations in groundwater

Environmental degradation of organic micropollutants is difficult to monitor due to their diffuse and ubiquitous input. Current approaches—concentration measurements over time, or daughter-to-parent compound ratios—may fall short, because they do not consider dilution, compound-specific sorption characteristics or alternative degradation pathways. Compound-specific isotope analysis (CSIA) offers an alternative approach based on evidence from isotope values. Until now, however, the relatively high limits for precise isotope analysis by gas chromatography—isotope ratio mass spectrometry (GC-IRMS) have impeded CSIA of sub-microgram-per-liter scale micropollutant concentrations in field samples. This study presents the first measurements of C and N isotope ratios of the herbicide atrazine and its metabolite desethylatrazine at concentrations of 100 to 1,000 ng/L in natural groundwater samples. Solid-phase extraction and preparative HPLC were tested and validated for preconcentration and cleanup of groundwater samples of up to 10 L without bias by isotope effects. Matrix interferences after solid-phase extraction could be greatly reduced by a preparative HPLC cleanup step prior to GC-IRMS analysis. Sensitivity was increased by a factor of 6 to 8 by changing the injection method from large-volume to cold-on-column injection on the GC-IRMS system. Carbon and nitrogen isotope values of field samples showed no obvious correlation with concentrations or desethylatrazine-to-atrazine ratios. Contrary to expectations, however, δ ¹³ C values of desethylatrazine were consistently less negative than those of atrazine from the same sites. Potentially, this line of evidence may contain information about further desethylatrazine degradation. In such a case, the common practice of using desethylatrazine-to-atrazine ratios would underestimate natural atrazine degradation.     

Instrumental Dependent Dissociations of n-Propyl/Isopropyl Phosphonate Isomers: Evaluation of Resonant and Non-Resonant Vibrational Activations

Structural elucidation and distinction of isomeric neurotoxic agents remain a challenge. Tandem mass spectrometry can be used for this purpose in particular if a “diagnostic” product ion is observed. Different vibrational activation methods were investigated to enhance formation of diagnostic ions through consecutive processes from O,O-dialkyl alkylphosphonates. Resonant and non-resonant collisional activation and infrared multiphoton dissociation (IRMPD) were used with different mass spectrometers: a hybrid quadrupole Fourier transform ion cyclotron resonance (Qh-FTICR) and a hybrid linear ion trap-Orbitrap (LTQ/Orbitrap). Double resonance (DR) experiments, in ion cyclotron resonance (ICR) cell, were used for unambiguous determination of direct intermediate yielding diagnostic ions. From protonated n-propyl and isopropyl O-O-dialkyl-phosphonates, a diagnostic m/z 83 ion characterizes the isopropyl isomer. This ion is produced through consecutive dissociation processes. Conditions to favor its formation and observation using different activation methods were investigated. It was shown that with the LTQ, consecutive experimental steps of isolation/activation with modified trapping conditions limiting the low mass cut off (LMCO) effect were required, whereas with FT-ICR by CID and IRMPD the diagnostic ion detection was provided only by one activation step. Among the different investigated activation methods it was shown that by using low-pressure conditions or using non-resonant methods, efficient and fast differentiation of isomeric neurotoxic agents was obtained. This work constitutes a unique comparison of different activation modes for distinction of isomers showing the instrumental dependence characteristic of the consecutive processes. New insights in the dissociation pathways were obtained based on double-resonance IRMPD experiments using a FT-ICR instrument with limitation at low mass values.

Do halogen and methyl substituents have electronic effects on the structures of simple disilanes? An experimental and theoretical study of the molecular structures of the series X3SiSiMe3 (X = H, F, Cl and Br)

The gas-phase molecular structures of a series of halogen-substituted disilanes [X₃SiSiMe₃ (X = H, F, Cl and Br)], 1,1,1-trimethyldisilane (H₃SiSiMe₃), 1,1,1-trifluoro-2,2,2-trimethyldisilane (F₃SiSiMe₃), 1,1,1-trichloro-2,2,2-trimethyldisilane (Cl₃SiSiMe₃) and 1,1,1-tribromo-2,2,2-trimethyldisilane (Br₃SiSiMe₃), have been determined in the gas phase by electron diffraction. Ab initio calculations at the HF and MP2 level were used to support the experimental investigation using the SARACEN method. All of the investigated structures were determined to adopt a staggered structure with C _3v symmetry. The effect of substitution on the Si–Si bond and the Si–Si–X bond angle was investigated and these results were compared to results obtained from a recent study of halogen-substituted disilanes [X₃SiSiXMe₂ (X = F, Cl, Br and I)] to consider the effect of the methyl groups on the substituted disilanes.     

Preparation and Characterization of Niobium Oxide Coated Cellulose Fiber

The Nb₂O₅/cellulose composite was prepared by reacting α-cellulose with NbCl_5-n(OC₂H₅)_n, in nonaqueous solvent, under nitrogen atmosphere and submitting the obtained material to hydrolysis. An increase in the crystallinity degree is observed in the composite material because the precursor reagent reacts with the amorphous phase of the cellulose fibers. Loadings between 4.5 and 16.0% of the oxide were achieved and in every case the oxide particles uniformly cover the fiber surface. Lewis and Brønsted acid sites were determined by using pyridine as the basic molecular probe.     

Biosurfactants from potato process effluents

High-solids (HS) and low-solids (LS) potato process effluents were tested as substrates for surfactin production. Tests used effluents diluted 1∶10, unamended and amended with trace minerals or corn steep liquor. Heat pretreatment was necessary for surfactin production from effluents due to indigenous bacteria, whose spores remained after autoclaving. Surfactin production from LS surpassed HS in all cases. Surfactin yields from LS were 66% lower than from a pure culture in an optimized potatostarch medium. LS could potentially be used without sterilization for surfactin production for low-value applications such as environmental remediation or oil recovery.     

Boron complexes of S-trityl- -cysteine and S-tritylglutathione

S-Trityl- -cysteine and S-tritylglutathione have been converted to 1,3,2-oxazaborolidine-5-ones by reaction with B-methoxydialkylborane derivatives. The synthesis of dicyclohexyl[S-trityl-(R)-cysteinato-O,N]boron (2), diisopinocampheyl[S-trityl-(R)-cysteinato-O,N]boron (3) and 9-borabicyclo[3.3.1]non-9-yl[S-tritylglutathionato-O,N]boron (5), dicyclohexyl[S-tritylglutathionato-O,N]boron (6) and diisopinocampheyl[S-tritylglutathionato-O,N]boron (7) from S-trityl- -cysteine and S-tritylglutathione, respectively, with potential application in boron neutron capture therapy is reported. The structure of 9-borabicyclo[3.3.1]non-9-yl[S-trityl-(R)-cysteinato-O,N]boron 1 has been determined by X-ray diffraction.     

Use of a polar ionic liquid as second column for the comprehensive two-dimensional GC separation of PCBs

The orthogonality of three columns coupled in two series was studied for the congener specific comprehensive two-dimensional GC separation of polychlorinated biphenyls (PCBs). A non-polar capillary column coated with poly(5%-phenyl–95%-methyl)siloxane was used as the first (¹D) column in both series. A polar capillary column coated with 70% cyanopropyl-polysilphenylene-siloxane or a capillary column coated with the ionic liquid 1,12-di(tripropylphosphonium)dodecane bis(trifluoromethane-sulfonyl)imide were used as the second (²D) columns. Nine multi-congener standard PCB solutions containing subsets of all native 209 PCBs, a mixture of 209 PCBs as well as Aroclor 1242 and 1260 formulations were used to study the orthogonality of both column series. Retention times of the corresponding PCB congeners on ¹D and ²D columns were used to construct retention time dependences (apex plots) for assessing orthogonality of both columns coupled in series. For a visual assessment of the peak density of PCBs congeners on a retention plane, 2D images were compared. The degree of orthogonality of both column series was, along the visual assessment of distribution of PCBs on the retention plane, evaluated also by Pearson's correlation coefficient, which was found by correlation of retention times t_R,i,2D and t_R,i,1D of corresponding PCB congeners on both column series. It was demonstrated that the apolar + ionic liquid column series is almost orthogonal both for the 2D separation of PCBs present in Aroclor 1242 and 1260 formulations as well as for the separation of all of 209 PCBs. All toxic, dioxin-like PCBs, with the exception of PCB 118 that overlaps with PCB 106, were resolved by the apolar/ionic liquid series while on the apolar/polar column series three toxic PCBs overlapped (105 + 127, 81 + 148 and 118 + 106).