Impact of deglycosylation methods on two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry for proteomic analysis

Glycosylation is a common post-translational modification that can add complexity to the proteome of many cell types. We used enzymatic and chemical methods of deglycosylation to treat a heavily glycosylated exoproteome sample from the filamentous fungus Trichoderma reesei. Deglycosylated samples were resolved on one-dimensional (1-D) and two-dimensional (2-D) gels in order to determine the effect of deglycosylation on the electrophoresis patterns and on the ability to identify proteins by peptide mass matching using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis of in-gel tryptic digests. We found that deglycosylation of the protein sample resulted in different protein patterns on 1-D and 2-D gels, reduced the complexity of gel patterns, and enhanced the protein identification of some proteins via MALDI-TOF-MS. Deglycosylation with trifluoromethanesulfonic acid (TFMS) was found to be more effective than enzymatic treatments. These deglycosylation techniques may be employed in whole proteome analysis to locate glycosylated proteins and assist in their identification by MS.     

Optimal choice of dividing surface for the computation of quantum reaction rates

We consider the calculation of quantum mechanical rate constants for chemical reactions via algorithms that utilize short-time values of the symmetrized flux-flux correlation function. We argue that the dividing surface that makes optimal use of the short-time quantum information is the surface that minimizes the value at the origin of the symmetrized flux-flux correlation function. We also demonstrate that, in the classical limit, this quantum variational criterion produces the same dividing surface as Wigner's variational principle. Finally, we argue that the quantum variational criterion behaves in a nearly optimal fashion with respect to the minimization of the extent of re-crossing flux.     

The NCI Drug Information System. 3. The DIS Chemistry Module

The Chemistry Module of the Drug Information System (DIS) handles a database of 400,000 structures. New or modified records are created in this database on a daily basis and are merged into the file promptly. The Chemistry database is searchable in a wide variety of ways and provides novel methods for both input and output of chemical structures.     

Alkaloids of Glycosmis arborea—II Structure of arborine

On the basis of a critical study of the ultra-violet and the infra-red absorption spectra of arborine, dihydroarborine, 1,2-dimethylquinazol-4-one, 2-ethyl-1-methylquinazol-4-one, 2,3-dihydro-1,2-dimethylquinazol-4-one and 2,3-dihydro-2-ethyl-1-methylquinazol-4-one, it has been shown that arborine is 2-benzyl-1-methylquinazol-4-one and not the tautomeric form, 2-benzylidene-1-methylquinazol-4-one. This has been confirmed on the basis of the nuclear magnetic resonance spectrum of arborine. Incidentally, it has been shown that 'glycosine' of Chatterjee and Ghosh Majumdar is not a new alkaloid and this name should be deleted from the literature.     

Temperature dependence of particle-particle adherence forces in ice and clathrate hydrates

Particle-particle pulloff adherence forces were measured as a function of temperature in the ice/n-decane/ice and tetrahydrofuran (THF) hydrate/n-decane/THF hydrate systems using a newly developed micromechanical testing technique. Experiments using approximately 200 microm radius particles were performed at atmospheric pressure over the temperature range 263-275 K. The ice and hydrate particles displayed very similar behavior. While the measured adherence forces had significant variation, the shapes of the cumulative force distribution curves were similar among the different sets of experiments. The measured adherence forces distributions shifted to lower force values as the temperature was decreased from the solid melting temperature. The observed forces and trends were explained by the capillary cohesion of rough surfaces, with the capillary bridging liquid being stabilized below its freezing point by the negative curvature of the bridging liquid/n-decane interface.     

Design of a fraction collector for capillary array electrophoresis

This paper describes a prototype instrument for high-throughput fraction collection with capillary array electrophoresis (CAE). The design of the system was based on a comprehensive collection approach, in which fractions from all capillaries were simultaneously collected in individual collection microwells in predefined time intervals. The location of the fractions in the microwells on the collection plate was determined by monitoring the individual zone velocities close to the end of each capillary. The collection microwell plate was fabricated from buffer-saturated agarose gel, which maintained permanent electrical contact with the separation capillaries during the collection process. Since the collection gel plate consisted of over 90% water, liquid evaporation from the collection wells was minimized. A 12-capillary array instrument was built with two-point detection using a side illumination scheme. The collection performance was demonstrated by reinjection of selected fractions of a double-stranded DNA (dsDNA) separation. The identity of collected DNA fragments was confirmed by PCR and sequencing.     

Mass spectra of geometrical isomers: The isomeric 3- and 7-cyclohexyl-2-norbornanols

The mass spectra of isomeric 3- and 7-cyclohexyl-2-norbornanols have been studied. The 3-substituted norbornanols give very similar mass spectra, whereas large differences were observed between the mass spectra of 7-syn and 7-anti isomers. While the mass spectra of these bicyclic alcohols show extensive rearrangements to give rise to many odd-electron ions, the Wagner-Meerwein rearrangement of the molecular ion prior to fragmentation or during the process of dehydration is not important. The origins and the mechanisms for the formation of some major ions are discussed in terms of low voltage spectra, defocused metastables and their relative abundances, and ionization or appearance potentials of the ions of interest.     

Organoboron compounds: XXVII. A13C NMR Study of PhB(NMe2NHBut and PhB(NMe2)NHSiMe3

The rotational barriers (ΔG) about the

bond in PhB(NMe₂)NHBu^t and PhB(NMe₂)NHSiMe₃ have been determined by variable temperature ¹³C NMR.     

Chiral capillary electrophoretic analysis of the enantiomeric purity of a pharmaceutical compound using sulfated beta-cyclodextrin

A practical chiral capillary electrophoresis method using randomly sulfated beta-cyclodextrin was developed for the quantitative determination of the chiral purity of a pharmaceutical compound. A systematic method development approach was conducted by modifying selected parameters such as the concentration of the chiral selectors, buffer pH, organic modifiers, buffer concentrations and type, temperature and applied voltage. The results of the investigation permitted an improved understanding of the separation mechanism. Two facile strategies for the reversal of the enantiomer elution order are also described. The optimized method was validated in terms of variability of the chiral selector, linearity, sensitivity, accuracy, recovery, ruggedness, and precision.     

Polynuclear chromium(III) carboxylates. 1. Synthesis,structure, and magnetic properties of an octanuclear complex with a ring structure

A novel cyclic octanuclear chromium(III) complex with hydroxo and acetato bridging ligands was isolated and its structure determined by X-ray crystallography. The complex [Cr8(OH)12(OAc)12] (1) (OAc- = CH3CO2-), as found in crystals of 1.34H2O, is obtained by refluxing an aqueous solution of the trinuclear "basic" chromium acetate. 1.34H2O crystallizes in the tetragonal space group I42d with the following unit cell dimensions: a = 16.592(2) A, c = 31.557(4) A, V = 8687(1) A3, and Z = 2. A total of 2000 unique data with I > 3 sigma (I) were used to solve and refine the structure to R(Fo) = 0.066 and Rw(Fo) = 0.085. The structure consists of eight Cr(III) ions that form a ring structure and are bridged by hydroxo and acetato ligands. Each of the two neighboring metal atoms in 1 is bridged either by two OH- ligands and one OAc- ligand, with a Cr...Cr distance of 2.949(2) A, or by two OAc- ligands and one OH- ligand, with a Cr...Cr distance of 3.383(2) A in an alternating fashion. The complex resides on a crystallographic 4 center, and the overall symmetry of 1 is S4. The magnetic susceptibility of 1.34H2O was measured in the temperature range of 5-240 K. Our theoretical modeling of the susceptibility data indicates alternating antiferromagnetic exchange interactions between adjacent spin 3/2 Cr3+ ions around the ring, of magnitude J/kB = 13.7 and 8.9 K, respectively.