Homogeneous sample preparation for automated high throughput analysis with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

This work presents a simple method for obtaining homogeneous sample surfaces in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) for the automated analysis of peptides and proteins. The sample preparation method is based on applying the sample/matrix mixture onto a pre-deposited highly diluted matrix spot. The pre-deposited crystals act as seeds for the new sample containing crystals which become much smaller in size and more evenly distributed than with conventional methods. This 'seed-layer' method was developed, optimised and compared with the dried-droplet method using peptides and proteins in the 1000-20,000 Da range. The seed-layer method increases the surface homogeneity, spot to spot reproducibility and sample washability as compared with the commonly used dried-droplet method. This methodology is applicable to alpha-cyanohydroxycinnamic acid, sinapinic acid and ferulic acid, which all form homogeneous crystal surfaces. Within-spot variation and between-spot variation was investigated using statistics at a 95% confidence level (n = 36). The statistical values were generated from more than 5000 data points collected from 500 spectra. More than 90% of the sample locations results in high intensity spectra with relatively low standard deviations (RSDs). Typically obtained data showed an RSD of 19-35% within a sample spot as well as in-between spots for proteins, and an RSD of < or = 50% for peptides. Linear calibration curves were obtained within one order of magnitude using internal calibration with a point-RSD of 3% (n = 10). The sample homogeneity allows mass spectra (average of 16 laser shots) to be obtained on each individual sample within 15 sec, whereby a 100 spot target plate can be run in 25 min. High density target plates using the seed-layer method were prepared by spotting approximately 100 picoliter droplets onto the target, resulting in sample spots < or = 500 microns in diameter using a flow-through piezo-electric micro-dispenser. By using this automated sample preparation step lower standard deviations are obtained in comparison to manually prepared samples.     

Some practical aspects of free energy calculations from molecular dynamics simulation

In this work, we address two critical aspects of calculation of the free energy differences in molecular systems from molecular simulations. The first aspect involves checking whether the calculated free energy difference depends significantly on the extent of perturbation used for accomplishment of a given transformation. The second aspect of interest is to verify if the sampling errors in calculating the free energy differences between the wild-type molecule and a mutated one in its free state and in a complex are similar, or not, for a finite-length dynamic simulation. The reliability of the free energy estimates obtained from molecular simulations using thermodynamic cycles depends in part on this fact. For investigating these aspects, we use a self-transformation scheme in which a transformation of a part of a molecular system into itself is considered. We perform MD simulations of DNA fragments in which a part of a specific base is subjected to such a self-transformation. Results indicate that the estimated free energy differences do not depend significantly on the extent of perturbation used to achieve the transformation. Interestingly, the variation in the cumulative free energy difference, ΔA, with the coupling parameter, λ, depends significantly on the extent of perturbation. We examine the physical basis of the observed nature of the variation of the accumulated free energy difference, ΔA, against the λ value in the case of a self-transformation. In a thermodynamic cycle, the sampling errors due to the finite-length simulation for the molecular system are found to be similar to each other for the two perturbations (free and in a complex) justifying the use of such approach in calculating ΔΔA in molecular complexes. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 877–885, 1999     

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations

Molecular orbital calculations of the complex between DNA-ERE (estrogen response element) and ER (estrogen receptor)-DBD (DNA-binding domain) were performed using the fragment molecular orbital (FMO) method, which enables large-scale MO (molecular orbital) calculations by reducing the computational cost and by significantly increasing efficiency for parallel computation. Such a large system, which contains 3354 atoms, is impractical via conventional MO methods due to the immense computational cost. Details of the interaction between DNA-ERE and ER-DBD were revealed in this study as follows by using the FMO calculations to analyze the interfragment interaction energies (IFIEs) and the electrostatic potentials (ESPs). An area with a high positive ESP is identified on the DNA-binding side of ER-DBD and is the main driving force behind access to the DNA. The position of the ER-DBD monomer can be fixed on a phosphate group of DNA-ERE by the strong electrostatic interactions, whereas the rotation cannot be fixed. In contrast, both the position and rotation of the ER-DBD dimer can be fixed and can therefore form the stable (ER-DBD)2...DNA-ERE complex. Dimerization of the ER-DBD monomers, each of which have a charge of +5 , is mainly due to large attractive interaction energies of the second Zn fragments. The base pairs in the consensus sequence of DNA-ERE interact only with the recognition helix located in the major groove due to the large shielding effect of the phosphate groups of DNA. The recognition helix has weaker interactions with the base pairs than the electrostatic interactions with the phosphate groups. Thus, the DNA-binding machinery of the ER-DBD dimer, which can secure the recognition helix in the major groove of DNA, is crucial for interactions between the recognition helix and base pairs.     

Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS

Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. However, it was not possible to exactly pinpoint sulfate attachment residues, for protonated precursors, due to extensive fragmentation of sulfate groups using high-energy collision induced dissociation (HCD). To circumvent the well-recognized sulfate instability, we now introduced Na⁺ ions to form sodiated precursors, which protected sulfate groups from decomposition and facilitated the assignment of sulfate modifications. Sulfate groups were pinpointed to both Gal residues and to the GalNAc of the hexasaccharide structure. The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. The realization of these structural variants should be beneficial in studies aimed at investigating the importance of the CS linkage region with regards to the biosynthesis of CS and potential interactions to CS binding proteins. Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides.

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Mass,momentum and energy conservation laws in zero-pressure gas dynamics and δ-shocks: II

We study δ-shocks in a one-dimensional system of zero-pressure gas dynamics. In contrast to well-known papers (see References) this system is considered in the form of mass, momentum and energy conservation laws. In order to define such singular solutions, special integral identities are introduced which extend the concept of classical weak solutions. Using these integral identities, the Rankine–Hugoniot conditions for δ-shocks are obtained. It is proved that the mass, momentum and energy transport processes between the area outside the of one-dimensional δ-shock wave front and this front are going on such that the total mass, momentum and energy are independent of time, while the mass and energy concentration processes onto the moving δ-shock wave front are going on. At the same time the total kinetic energy transforms into total internal energy.     

Gauge Modules for the Lie Algebras of Vector Fields on Affine Varieties

Algebras and Representation Theory - For a smooth irreducible affine algebraic variety we study a class of gauge modules admitting compatible actions of both the algebra $mathcal {A}$ of functions...     

Hyperfine structure in the 6p5d configuration and isotope shifts in transitions between the 6s5d and the 6p5d configurations in Ba I

High-resolution laser fluorescence spectroscopy, using a single-mode dye laser acting on a collimated atomic beam, has been performed to determine the hyperfine-structure (hfs) constants in six states of the 6p 5d configuration of¹³⁵Ba and¹³⁷Ba. Isotope shifts (IS) for eleven transitions between the 6s 5d and the 6p 5d configurations have also been measured. From an analysis of the energy levels, intermediate angular wavefunctions have been deduced. The wavefunctions are used to evaluate experimental hyperfine parameters from the experimental hfs constants. The parameters are, for the magnetic-dipole interaction compared with theoretical values, and for the electricquadrupole interaction used to estimate the nuclear quadrupole moments for the odd isotopes. The IS in the measured transitions are analysed using a King-plot, with the first resonance line in Ba II as the reference. Specific mass and field shifts are evaluated for the measured transitions. The field shifts have been used to determine the change in mean-square radius between the natural abundant Ba-isotopes.     

A number theoretical observation about the degeneracy of the genetic code

We discuss the similarity of the degeneration structure of the genetic code with a purely number theoretic “divisors code.” The most interesting thing about our observation is not that there is a connection between number theory and the genetic code, but the simplicity of the rule. We hope that the observation and the naive model presented in this paper will spur ideas for other models of the degeneracy of the genetic code. Maybe, the ideas of this article can also be used in the area of artificial life to synthesize artificial genetic codes.     

Kinetics of the gas‐phase reactions of chlorine atoms with CH2F2, CH3CCl3, and CF3CFH2 over the temperature range 253–553 K

Relative rate techniques were used to study the title reactions in 930–1200 mbar of N₂ diluent. The reaction rate coefficients measured in the present work are summarized by the expressions k(Cl + CH₂F₂) = 1.19 × 10^?17 T² exp(?1023/T) cm³ molecule^?1 s^?1 (253–553 K), k(Cl + CH₃CCl₃) = 2.41 × 10^?12 exp(?1630/T) cm³ molecule^?1 s^?1 (253–313 K), and k(Cl + CF₃CFH₂) = 1.27 × 10^?12 exp(?2019/T) cm³ molecule^?1 s^?1 (253–313 K). Results are discussed with respect to the literature data. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 401–406, 2009