The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides

The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model -sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.     

Shipboard analysis of picomolar levels of manganese in seawater by chelating resin concentration and chemiluminescence detection

A new shipboard analytical method for determining picomolar levels of manganese in seawater has been developed. The method is based on a combination of chelating resin column extraction and improved chemiluminescence (CL) detection in a closed flow system. In this method, manganese in sample solution is selectively collected on newly-developed iminodiacetate-immobilized chelating resin, and then eluted with acidic solution containing hydrogen peroxide. The resulting eluent is mixed with luminol solution and aqueous ammonia after removal of iron ions by a chelating resin column, and then the mixture is introduced into the CL cell. The manganese concentration is obtained from the CL intensity. The detection limit (3SD) of manganese is 5 pmol L^–1 from 9 mL of seawater sample. The method was applied to seawater samples collected at the Okinawa Trough.     

Characterization of acylphosphatidylglycerols from <Emphasis Type="Italic">salmonella typhimurium</Emphasis> by tandem mass spectrometry with electrospray ionization

Acylphosphatidylglycerol (Acyl-PG), a polar lipid class containing three fatty acyl groups, was isolated from Salmonella bacteria and characterized by tandem quadrupole and quadrupole ion-trap mass spectrometric methods with electrospray ionization. The structural characterization of the acyl-PG with various acyl groups (A-B/C-PG, where A not equal B not equal C) is based on the findings that the carboxylate anions (R(x)CO(2)(-)) arising from sn-2 (R(2)CO(2)(-)) is more abundant than that arising from sn-3' (R(3')CO(2)(-)), which is much more abundant than that arising from sn-1 (R(1)CO(2)(-)). This information provides a simple method for determination of the fatty acyl moieties and their positions in the molecule. The structural identification of the molecule can also be achieved by the findings that the fragment ion reflecting the ketene loss at sn-2 is more prominent than that reflecting the acid loss (i.e., [M - H - R'(2)CH=CO](-) > [M - H - R(2)CO(2)H](-)), while the ion arising from acid loss at sn-1 or sn-3' is, respectively, more abundant than the corresponding ketene loss (i.e., [M - H - R(1)CO(2)H](-) > [M - H - R'(1)CH=CO](-); [M - H - R(3')CO(2)H](-) > [M - H -R'(3')CH=CO](-)). The identity of the acyl moiety at sn-3' can be confirmed by an acyl-glycerophosphate anion observed in the product-ion spectrum obtained with a triple-stage quadrupole (TSQ) instrument, but not in that obtained with an ion-trap mass spectrometer (ITMS). However, the MS(2)-spectrum obtained with an ITMS is featured by the ion series that abundances of [M - H - R'(2)CH=CO - R(3)CO(2)H - 74](-) > [M - H - R'(2)CH=CO - R(1)CO(2)H - 74](-) z.Gt; [M - H - R'(1(or 3'))CH=CO - R(3'(or 1))CO(2)H - 74](-). This information also facilitates structural elucidation of the acyl-PG subclass that contains various acyl substituents. Structural identifications of molecular species having two identical fatty acyl substituents at sn-1, sn-2, or sn-3' or consisting of more than one isomeric structures are also demonstrated. The identities of the minor isomeric species in the molecules can be revealed by the aforementioned structural information arising from the various ion series combined.     

Structural determination of neutral O-linked oligosaccharide alditols by negative ion LC-electrospray-MS<Superscript>n</Superscript>.

Neutral O-linked oligosaccharides released from the salivary mucin MUC5B were separated and detected by negative ion LC-MS and LC-MS(2). The resolution of the chromatography and the information obtained from collision induced dissociation of detected [M - H](-) ions were usually sufficient to identify the sequence of individual oligosaccharides, illustrated by the fact that 50 different oligosaccharides ranging from disaccharides to nonasaccharides could be assigned from the sample. Fragmentation was shown to yield mostly reducing end sequence fragments (Z(i) and Y(i)), enabling primary sequence assignment. Specific fragmentation pathways or patterns were also detected giving specific linkage information. The reducing end core (Gal/GlcNAcbeta1-3GalNAcol or Gal/GlcNAcbeta1-3(GlcNAcbeta1-6)GalNAcol) could be deduced from the pronounced glycosidic C-3 cleavage and A(i) type cleavages of the reducing end GalNAcol, together with the non reducing end fragment from the loss of a single substituted GalNAcol. Substitution patterns on GlcNAc residues were also found, indicative for C-4 substitution ((0,2)A(i) - H(2)O cleavage) and disubstitution of C-3 and C-4 (Z(i)/Z(i) cleavages). This kind of fragmentation can be used for assigning the mode of chain elongation (Galbeta1-3/4GlcNAcbeta1-) and identification of Lewis type antigens like Lewis a/x and Lewis b/y on O-linked oligosaccharides. In essence, negative ion LC-MS(2) was able to generate extensive data for understanding the overall glycosylation pattern of a sample, especially when only a limited amount of material is available.     

Investigation of sulfur release in ETV-ICP-AES and its application for the determination of sulfates

Electrothermal vaporization inductively coupled plasma atomic emission spectrometry was applied to the determination of sulfur species in aqueous solutions. The sensitivity for sulfur as sulfate was found to be depending on the cations in the sample. For understanding this phenomenon the thermal behavior of sulfuric acid, ammonium sulfate and the sulfates of sodium, zinc, magnesium and silver was studied. There were significant differences in the thermal release of sulfur from these sulfates. To explain these phenomena different reaction mechanisms were calculated using thermodynamic data. Pd(NO₃)₂ and Ge in KOH were successfully applied as modifiers for the stabilization of the sulfates during the thermal pre-treatment step and to establish a uniform thermal behavior of different sulfates. The stabilization of sulfur using Ge and Pd as modifiers is based on the reduction of the sulfates in presence of carbon, resulting in the formation of GeS and PdS, respectively. This explanation has been supported by comparing the experimental results with thermodynamic calculations considering different reactions for the thermal decomposition of the sulfates. Applying Ge (in KOH) as modifier the absolute detection limit was 300 pg sulfur (e.g. LOD 30 ng mL^–1). The significant influence of phosphates on the determination of sulfur could be essentially reduced by Pd as modifier. Received: 11 November 1997 / Revised: 14 January 1998 / Accepted: 18 January 1998     

Establishment of traceability of ammonium nitrogen determination in wastewater

A case study is presented for the establishment of traceability for ammonium nitrogen determination in wastewater in a routine laboratory in order to fulfil the requirements of ISO/IEC standard 17025. The necessary relevant information was obtained from the method validation data, the quality control data and equipment calibration certificates. The method of measurement is described together with the measurement equation, selected traceable reference standards and the associated measurement uncertainty. The major sources of uncertainty of the result of measurement were identified and the combined uncertainty was calculated. Identification of the main uncertainty sources represents the basis for target operations for reducing the measurement uncertainty of this determination.     

Photochemical reactions of metal carbonyls [M(CO)6 (M = Cr,Mo and W), Re(CO)5Br,Mn(CO)3Cp] with 2-hydroxyacetophenone methanesulfonylhydrazone (apmsh)

Five new complexes, [M(CO)₅(apmsh)] [M = Cr; (1), Mo; (2), W; (3)], [Re(CO)₄Br(apmsh)] (4) and [Mn(CO)₃(apmsh)] (5) have been synthesized by the photochemical reaction of metal carbonyls [M(CO)₆] (M = Cr, Mo and W), [Re(CO)₅Br], and [Mn(CO)₃Cp] with 2-hydroxyacetophenone methanesulfonylhydrazone (apmsh). The complexes have been characterized by elemental analysis, mass spectrometry, f.t.-i.r. and ¹H spectroscopy. Spectroscopic studies show that apmsh behaves as a monodentate ligand coordinating via the imine N donor atom in [M(CO)₅(apmsh)] (1–4) and as a tridentate ligand in (5).     

Determination of traces of bismuth by quenching of solid-substrate room-temperature phosphorescence from morin-labeled silicon dioxide nano-particles

Silicon dioxide nano-particles, diameter 50 nm, containing morin (morin–SiO₂) have been synthesized by the sol–gel method. They emit strong and stable room-temperature phosphorescence (SS-RTP) on filter paper as substrate, and bismuth can quench the intensity of the SS-RTP. On this basis a new morin–SiO₂ solid-substrate room-temperature phosphorescence-quenching method has been established for determination of traces of bismuth. Reduction of phosphorescence intensity (I_p) is directly proportional to the concentration of bismuth in the working range 0.16–14.4 ag spot^–1 (sample volume 0.40 L spot^–1, corresponding to the concentration range 0.40–36.0 fg mL^–1). The regression equation of the working curve is I_p=14.86+5.279×[Bi³⁺] (ag spot^–1) (n=6, r=0.9982). The detection limit of this method is 0.026 ag spot^–1 (corresponding to a concentration of 6.5×10^–17 g mL^–1).This sensitive, reproducible and accurate method has been used for successful analysis of real samples.     

Photophysical properties of a tetraphenoxy-substituted perylene bisimide derivative characterized by single-molecule spectroscopy.

We present a detailed study of the photophysical properties of a tetraphenoxy-substituted perylene bisimide derivative. The probe molecules were immobilized in a Shpol'skii matrix of hexadecane and investigated by single-molecule spectroscopy at cryogenic temperatures. By using single-molecule spectroscopic techniques we reveal the triplet substate kinetics and the fluorescence quantum yield, and we provide an estimate for the S1-S0 transition dipole moment.     

Structural regulation of a peptide-conjugated graft copolymer: a simple model for amyloid formation

The self-assembly of peptides and proteins into beta-sheet-rich high-order structures has attracted much attention as a result of the characteristic nanostructure of these assemblies and because of their association with neurodegenerative diseases. Here we report the structural and conformational properties of a peptide-conjugated graft copolymer, poly(gamma-methyl-L-glutamate) grafted polyallylamine (1) in a water-2,2,2-trifluoroethanol solution as a simple model for amyloid formation. Atomic force microscopy revealed that the globular peptide 1 self-assembles into nonbranching fibrils that are about 4 nm in height under certain conditions. These fibrils are rich in beta-sheets and, similar to authentic amyloid fibrils, bind the amyloidophilic dye Congo red. The secondary and quaternary structures of the peptide 1 can be controlled by manipulating the pH, solution composition, and salt concentration; this indicates that the three-dimensional packing arrangement of peptide chains is the key factor for such fibril formation. Furthermore, the addition of carboxylic acid-terminated poly(ethylene glycol), which interacts with both of amino groups of 1 and hydrophobic PMLG chains, was found to obviously inhibit the alpha-to-beta structural transition for non-assembled peptide 1 and to partially cause a beta-to-alpha structural transition against the 1-assembly in the beta-sheet form. These findings demonstrate that the amyloid fibril formation is not restricted to specific protein sequences but rather is a generic property of peptides. The ability to control the assembled structure of the peptide should provide useful information not only for understanding the amyloid fibril formation, but also for developing novel peptide-based material with well-defined nanostructures.