Protein structure determination using long-distance constraints from double-quantum coherence ESR: study of T4 lysozyme

We report the use of a novel pulsed ESR technique for distance measurement, based on the detection of double quantum coherence (DQC), which yields high quality dipolar spectra, to significantly extend the range of measurable distances in proteins using nitroxide spin-labels. Eight T4 lysozyme (T4L) mutants, doubly labeled with methanethiosulfonate spin-label (MTSSL), have been studied using DQC-ESR at 9 and 17 GHz. The distances span the range from 20 A for the 65/76 mutant to 47 A for the 61/135 mutant. The high quality of the dipolar spectra also allows the determination of the distance distributions, the width of which can be used to set upper and lower bounds in future computational strategy. It is also demonstrated that the shape of these distributions can reveal the presence of multiple conformations of the spin-label, an issue of critical relevance to the structural interpretation of the distances. The distances and distributions found in this study are readily rationalized in terms of the known crystal structure, the characteristic conformers of the nitroxide side chains, and molecular modeling. This study sets the stage for the use of DQC-ESR for determining the tertiary structure of large proteins with just a small number of long-distance constraints.     

Photostabilizing activity of sterically hindered piperidines—II: Radical trapping ability

The abilities of both 2,2,6,6-tetramethylpiperidine (I) and its nitroxyl (II) to trap radicals involved in hydrocarbon photo-oxidations have been studied in cumene and 1,3,5-trimethylcyclohexane at 27° using AIBN, hydroperoxide and dialkylperoxide as initiators: the light was either the band 300–400 nm or 366 nm. Under conditions of photolysis of ROOH (degenerate branching), I is oxidized to II. II is capable of trapping R' radicals, the rate constant being ～50 times lower than that for RO^.₂ formation. RO^.₂ radicals react with neither I nor II. Under the condition of degenerate branching, II is capable of intercepting the radical fragments from decomposing hydroperoxide. The rate constant of this process is ～500 times higher than that for hydrogen abstraction by these fragments. A reaction mechanism is suggested: hydrogen bonded associates formed between an N-containing stabilizer and ROOH play a dominant role. The principal intermediates in this mechanism are represented by >NO^., >NOH and >NOR species.     

The immunosensors for measurement of 2,4-dichlorophenoxyacetic acid based on electrochemical impedance spectroscopy

Electrochemical impedance spectroscopy (EIS) was evaluated for the direct determination of herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). Specific antibody against 2,4-D was immobilised onto different gold electrodes. Several methods of antibody immobilisation by covalent linkage to modified surface were studied. Self-assembled monolayers formed using thiocompounds as cystamine, 4-aminothiophenol (ATPh), 3,3'-dithiopropionic acid di-(N-succinimidyl ester) (DTSP) and 11-mercaptoundecanoic acid (MUA) were chosen for the sensing surface activation. Three different sensor types were tested: screen-printed disc and finger-like structures and interdigitated array (IDA) electrodes produced by lithography. The measurements were carried out in a stationary arrangement, and the reaction between hapten and the immobilised antibody was observed online. Changes of impedance parameters were evaluated, and the best immobilisation technique (using 4-aminothiophenol) was chosen for further measurements. Impedance changes due to immunocomplex formation were evaluated, and the possibility of direct monitoring of 2,4-D binding to the antibody was demonstrated at a fixed frequency. For the strip sensor, the calibration curves were constructed in concentration range from 45 nmol l(-1) to 0.45 mmol l(-1) of 2,4-D.     

A top-down approach to protein structure studies using chemical cross-linking and Fourier transform mass spectrometry

In a preliminary communication we described a top-down approach to the determination of chemical cross-link location in proteins using Fourier transform mass spectrometry (FT-MS). We have since extended the approach to use a series of homobifunctional cross-linkers with the same reactive functional groups, but different cross-linker arm lengths. Correlating cross-linking data across a series of related linkers allows the distance constraint derived from a cross-link between two reactive side chains to be determined more accurately and increases the confidence in the assignment of the cross-links. In ubiquitin, there are seven lysines with primary amino groups and the amino terminus. Disuccinimidyl suberate (DSS, cross-linker arm length = 11.4 A), disuccinimidyl glutarate (DSG, cross-linker arm length = 7.5 A) and disuccinimidyl tartrate (DST, cross- linker arm length = 5.8 A) are homobifunctional cross-linking reagents that react specifically with primary amines. Using tandem mass spectrometry (MS/MS) on the singly, internally cross-linked precursor ion of ubiquitin, we found cross-links with DSS and DSG between the amino terminus and Lys 6, between Lys 6 and Lys 11, and between Lys 63 and Lys 48. Using disuccinimidyl tartrate (DST), the shortest cross-linker in the series, only the cross-links between the amino terminus and Lys 6, and between Lys 6 and Lys 11 were observed. The observed cross-links are consistent with the crystal structure of ubiquitin, if the lysine side chains and the amino terminus are assumed to have considerable flexibility. In a separate study, we probed the reactivity of the primary amino groups in ubiquitin using the amino acetylating reagent, N-hydroxy succinimidyl acetate (NHSAc), and a top-down approach to localize the acetylated lysine residues. The reactivity order obtained in that study (M1 approximate, equals K6 approximate, equals K48 approximate, equals K63) > K33 > K11 > (K27, K29), shows that the cross-link first formed in ubiquitin by reaction with DSS and DSG occurs between the most reactive residues.     

Rhodium(I) complexes with 1′-(diphenylphosphino)ferrocenecarboxylic acid as active and recyclable catalysts for 1-hexene hydroformylation

The rhodium complex trans-[Rh(CO)(Hdpf-κP)(dpf-κ²O,P)] (1), (Hdpf = 1′-(diphenylphosphino)ferrocenecarboxylic acid) was used as an efficient and recyclable catalyst for 1-hexene hydroformylation producing ca. 80% of aldehydes at 10 atm CO/H₂ and 80 °C. After the reaction, unchanged complex 1 was separated from the reaction mixture and used again three times with the same catalytic activity. The effect of modifying ligands, phosphines and phosphites, on the reactivity of 1 was investigated. The active catalytic systems containing 1 or trans-[Rh(CO)(L)(dpf-κ²O,P)] (2) were formed in situ from acetylacetonato rhodium(I) precursors [Rh(CO)₂(acac)] (3) or [RhL(CO)(acac)] (4) and Hdpf or Medpf (L = phosphine, Medpf = methyl ester of Hdpf).     

Surface patterns of block copolymers in thin layers after vapor treatment

A systematic study of formation of surface patterns in block copolymer thin layers after their exposure to solvent vapors was performed. The studied effect involves layers of thickness approximately equal to the ordering size of polymers - about 45 nm. Experiments were performed on three styrene - methacrylate derivative block copolymers, synthesized by living anionic polymerization: poly(4-octylstyrene)-block-poly(butyl methacrylate), poly(4-fluorostyrene)-block-poly(butyl methacrylate) and poly(p-octylstyrene)-block-poly(methyl methacrylate). The polymers were exposed to vapors of chloroform, 1,4-dioxane, hexane, acetone and tetrahydrofuran.     

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

A comparison of performance of various analytical columns in pharmaceutical analysis: conventional C18 and high throughput C18 zorbax columns

New improved types of analytical columns Zorbax Eclipse XDB-C18 (75 mm x 4.6 mm i.d., 3.5 microm) and Zorbax Eclipse XDB-C18 (50 mm x 4.6 mm i.d., 1.8 microm) have been tested for determination of estradiol (active substance), methylparaben, propylparaben (preservatives) and estrone (degradation product) and compared with the conventional C18 columns (250 mm x 3.0 mm i.d., 5.0 microm). The Zorbax columns differ with their particle size, column length and ODS (octadecylsilica) type as well. Higher flow-rates (up to about 2.5 ml min(-1)) could be applied regardless to back-pressure. The analysis - previously done at 40 degrees C - could be performed even at ambient temperature. Analytical run was shortened to 3.5 min (from 12 min used for the conventional C18 column) with the same or better retention characteristics. System suitability data for all Zorbax columns show the advantages of these columns for the practical use in routine quality control of pharmaceuticals, particularly from the point of view of speed of analysis and solvent consumption.     

Ruthenium(II) complexes with ferrocene-modified arene ligands: synthesis and electrochemistry

A series of arene-ruthenium complexes of the general formula [RuCl₂{η⁶-C₆H₅(CH₂)₂R}L] with R=OH, CH₂OH, OC(O)Fc, CH₂OC(O)Fc (Fc=ferrocenyl) and L=PPh₃, (diphenylphosphino)ferrocene, or bridging 1,1^′-bis(diphenylphosphino)ferrocene, have been synthesized. Two synthetic pathways have been used for these ferrocene-modified arene-ruthenium complexes: (a) esterification of ferrocene carboxylic acid with 2-(cyclohexa-1,4-dienyl)ethanol, followed by condensation with RuCl₃ · nH₂O to afford [RuCl₂{η⁶-C₆H₅(CH₂)₂OC(O)Fc}]₂, and (b) esterification between ferrocene carboxylic acid and [RuCl₂{η⁶-C₆H₅(CH₂)₃OH}L] to give [RuCl₂{η⁶-C₆H₅(CH₂)₃OC(O)Fc}L]. All new compounds have been characterized by NMR and IR spectroscopy as well as by mass spectrometry. The single-crystal X-ray structure analysis of [RuCl₂{η⁶-C₆H₅(CH₂)₃OH}(PPh₃)] shows that the presence of a CH₂CH₂CH₂OH side-arm allows [RuCl₂{η⁶-C₆H₅(CH₂)₃OH}(PPh₃)] to form an intramolecular hydrogen bond with a chlorine atom. The electrochemical behavior of selected representative compounds has been studied. Complexes with ferrocenylated side arms display the expected cyclic voltammograms, two independent reversible one-electron waves of the Ru(II)/Ru(III) and Fe(II)/Fe(III) redox couples. Introduction of a ferrocenylphosphine onto the ruthenium is reflected by an additonal reversible, one-electron wave due to ferrocene/ferrocenium system which is, however, coupled with the Ru(II)/Ru(III) redox system.     

Capillary ion chromatography

This review summarizes progress in capillary ion chromatography. Theoretical aspects and practical limitations of packed and open tubular capillary columns are considered. Applications of packed and open tubular capillary IC are described. Emerging technologies such chip-scale IC and the use of monolithic columns are discussed.